Biology subjects

Wang, C.

Publications and source records attributed to Wang, C..

At least 253 records · Page 14Linked to original sources

bioRxiv2025

Optic nerve regeneration requires the intracellular domain of LIFRa/CD118

Identifying cell-autonomous and non-autonomous factors that govern retinal ganglion cells (RGCs) ability to extend axons is an important step in developing therapies to achieve recovery after optic nerve injury. Here we report that the intracellular domain of the leukemia inhibitory factor receptor (LIFR/CD118) is essential for mature RGCs ability to regenerate injured axons independent of the cognate ligand (LIF) and other therapies. Overexpression of LIFR in adult RGCs induces neurite outgrowth in cultured RGCs and axon regeneration in vivo while strongly amplifying RGCs response to LIF itself and to unrelated growth factors. Conversely, in loss-of-function studies, down-regulation of LIFR eliminates the pro-regenerative effects of Pten deletion and other potent stimuli. LIFR bidirectionally regulates the constitutive activity of the MAP kinase pathway, in contrast to LIF itself, which primarily activates pSTAT3. Expression of a truncated LIFR lacking the extracellular domain is sufficient to promote axon regeneration and selectively increases the survival of particular RGC subtypes, placing the LIFR intracellular domain as an essential, cell-autonomous regulator of optic nerve regeneration.

neuroscience↗

bioRxiv2025

AEBP2-Directed H3K27me2 Defines a Specific Vulnerability in EZH2-mutant Lymphoma

The catalytic subunit of Polycomb Repressive Complex 2 (PRC2), EZH2, is recurrently mutated in 25% of diffuse large B-cell lymphomas (DLBCL), causing increased H3K27me3 and decreased H3K27me2 levels. EZH2 inhibitors provide clinical benefit, but resistance frequently develops, highlighting the need for alternative therapeutic targets. Here, we identify the PRC2 accessory protein AEBP2 as a specific genetic dependency in EZH2-mutant DLBCL. While AEBP2 acts through PRC2, its essential role is surprisingly independent of canonical H3K27me3-mediated gene silencing. Instead, AEBP2 functions within a PRC2.2 complex lacking JARID2, using its zinc-finger domains to sample intergenic chromatin to sustain H3K27me2. Notably, loss of AEBP2 or NSD2 caused contrasting changes in intergenic H3K27me2 levels, driving sensitivity or resistance to PRC2 inhibitors, respectively. Our findings identify AEBP2-PRC2.2-maintained intergenic H3K27me2 as a therapeutic vulnerability in EZH2-mutant DLBCL and highlight dysregulated H3K27me2 as an underappreciated form of PRC2 dysfunction in cancer, with important therapeutic implications.

cancer biology↗

bioRxiv2025

Quantifying Uncertainty in Polygenic Risk Scores Using Conformalized Quantile Regression

Polygenic risk scores (PRS) are widely used in post-GWAS analyses to predict complex traits across humans, animals, and plants, yet the uncertainty of these predictions is rarely quantified at the individual level. Here, we introduce a framework for individualized uncertainty quantification based on quantile regression and conformal prediction, enabling the construction of prediction intervals with guaranteed coverage under minimal assumptions. Quantile regression enables adaptive, individual-specific prediction intervals that capture asymmetry and allow interval widths to vary substantially across individuals based on genetic information alone. Applying this framework to 62 traits in the UK Biobank and the ProgeNIA/SardiNIA studies, we show that these intervals maintain valid coverage and reduce uncertainty in risk stratification compared to existing methods, driven by their adaptive construction. Prediction interval width correlates positively with age and BMI, indicating reduced genetic predictability in subsets of the population where genetic effects interact with environmental factors. Our results demonstrate that incorporating uncertainty is essential for interpreting polygenic predictions and provide a principled approach to distinguish individuals whose phenotypes are well explained by genetic predictors from those in whom non-genetic influences dominate.

bioinformatics↗

bioRxiv2025

Chronic kidney disease exacerbates hyperlipidemia and atherosclerosis via miR-148a-3p targeting SIK1/AMPKα1 in liver

BackgroundCardiovascular complications are the leading cause of death in patients with chronic kidney disease (CKD). As a major risk factor for atherosclerotic cardiovascular disease (ASCVD), hyperlipidemia is a common sequela of CKD, which is linked to increased lipid synthesis, impaired lipoprotein clearance, and maladapted reverse cholesterol transport. Because exosomes can transport miRNAs to modulate intercellular and tissue communication, we hypothesized that exosomal miRNAs can act as endocrine-like molecules to modulate the CKD-associated hyperlipidemia and ASCVD. MethodsSmall RNA-seq and qPCR were used to determine the differential plasma level of exosomal miR-148a-3p in ASCVD patients with and without CKD. RNA-seq and in silico analysis were used to establish the regulation of lipid metabolism via miR-148a-3p/salt-inducible kinase 1 (SIK1)/AMP-activated protein kinase alpha 1 subunit (AMPK1) in the liver. Inhibition of miR-148a-3p or overexpression of SIK1/AMPK1 in ApoE-/- mice with 5/6 nephrectomy was used to elucidate the role of the miR-148a-3p/SIK1/AMPK1 axis in CKD-related hyperlipidemia and atherosclerosis. ResultsThe plasma level of exosomal miR-148a-3p was significantly elevated in patients with ASCVD and CKD (ASCVD/CKD) and ApoE-/- mice with 5/6 nephrectomy. Via circulating exosomes, kidney-generated miR-148a-3p was delivered to the liver, where it targeted SIK1/AMPK1 transcripts, thereby upregulating SREBP2/PCSK9 and reciprocally downregulating LDLR. Levels of SIK1 and AMPK1 were decreased in hepatocytes transfected with miR-148a-3p or treated with plasma exosomes from ASCVD/CKD patients, with attendant SREBP2 activation and attenuated LDL-C binding. The decreased LDL-C binding was rectified by SIK1/AMPK1 or LNA-miR-148a-3p overexpression. LNA-miR-148a-3p or AAV8-SIK1/AMPK administration in 5/6 nephrectomy/ApoE-/- mice significantly ameliorated hyperlipidemia and atherosclerosis. ConclusionIn ASCVD/CKD patients and nephrectomy/ApoE-/- mice, kidney-originating miR-148a-3p targeted hepatic SIK1/AMPK1 mRNA. This exosome-mediated endocrine effect upregulated SREBP2/PCSK9 and reciprocally reduced LDLR level, which elevated plasma LDL-C level and exacerbated ASCVD. These findings underscore a kidney-liver-artery axis involved in cardiovascular-kidney-metabolic syndrome.

pathology↗

bioRxiv2025

Kinase KEY1 controls pyrenoid condensate size throughout the cell cycle by disrupting phase separation interactions

Biomolecular condensates spatially organize cellular functions, but the regulation of their size, number, dissolution, and re-condensation is poorly understood. The pyrenoid, an algal biomolecular condensate that mediates one-third of global CO2 fixation, typically exists as one large condensate per chloroplast, but during cell division it transiently dissolves and reconfigures into multiple smaller condensates. Here, we identify a kinase, KEY1, in the model alga Chlamydomonas reinhardtii that regulates pyrenoid condensate size and number dynamics throughout the cell cycle and is necessary for normal pyrenoid function and growth. Unlike wild type, key1 mutant cells have multiple smaller condensates throughout the cell cycle that fail to dissolve during cell division. We show that KEY1 localizes to the condensates and promotes their dissolution by disrupting interactions between their core constituents, the CO2-fixing enzyme Rubisco and its linker protein EPYC1, through EPYC1 phosphorylation. We develop a biophysical model that recapitulates KEY1-mediated condensate size and number regulation and suggests a mechanism for controlling condensate position. These data provide a foundation for the mechanistic understanding of the regulation of size, number, position, and dissolution in pyrenoids and other biomolecular condensates.

cell biology↗

bioRxiv2025

Transcriptional and epigenetic repression of hematopoietic stem cells underlies bone marrow failure after spinal cord injury

Spinal cord injury (SCI) triggers systemic pathology beyond the nervous system, including bone marrow failure that can worsen infection risk, anemia, and motor recovery. Here we identify a neuroendocrine mechanism that rapidly imprints long-lasting dysfunction in hematopoietic stem cells (HSCs), which sustain lifelong production of immune cells, red blood cells, and platelets. Rather than mounting a canonical stress-hematopoietic response, SCI HSCs enter a broadly repressed state marked by chromatin closure and suppression of programs required for cell-cycle entry, genome maintenance, and redox defense. This maladaptive state leads to persistent DNA damage, impaired oxidative stress resolution, pancytopenia, and loss of long-term HSC regenerative capacity. Mechanistically, SCI-induced glucocorticoid surges drive glucocorticoid receptor-dependent repression of DNA repair genes, including Lig1 and Fen1. Acute glucocorticoid receptor blockade after SCI restores durable hematopoiesis, revealing an early therapeutic window to preserve hematopoietic integrity after neurotrauma. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=136 SRC="FIGDIR/small/680535v2_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@1627bb3org.highwire.dtl.DTLVardef@a73e19org.highwire.dtl.DTLVardef@1ddf85dorg.highwire.dtl.DTLVardef@1dcd8fe_HPS_FORMAT_FIGEXP M_FIG C_FIG Key FindingsO_LIAcute SCI prevents induction of normal stress-induced repair programs in HSCs. C_LIO_LISCI HSPCs exhibit increased chromatin compaction. C_LIO_LISCI compromises HSC genome-maintenance and redox capabilities. C_LIO_LISCI HSCs have defects in normal cell cycle regulation, are hypersensitive to genotoxic stress, and are deficient in long-term reconstitution. C_LIO_LIEarly glucocorticoid receptor (GR) blockade restores long-term hematopoiesis, supporting a GR-dependent but reversible repression mechanism. C_LI

cell biology↗

bioRxiv2025

A secreted citrus protease cleaves an outer membrane protein of the Huanglongbing pathogen

Plants secrete a variety of proteases as a defense response during infection by microbial pathogens. However, the relationship between their catalytic activities and antimicrobial functions remains largely unknown. Particularly, few biologically relevant substrates of these proteases have been identified. Huanglongbing (HLB) has been a major threat to the citrus industry worldwide. The HLB-associated bacterium, Candidatus Liberibacter asiaticus (Las), was previously shown to deploy an inhibitor of papain-like cysteine proteases (PLCPs) to promote disease in citrus. In this study, we identified an outer membrane protein (OMP) of Las, LasOMP1, as a substrate of the citrus PLCP CsRD21a. LasOMP1 is one of the most highly expressed genes in Las. CsRD21a cleaves LasOMP1 and produces cleaved peptide products, which could be detected in vitro and in HLB-diseased citrus plants. We found that CsRD21a targets the N-terminal portion of LasOMP1, potentially at an extracellular loop region. Importantly, transgenic sweet orange overexpressing CsRD21a showed reduced Las titers and delayed disease symptoms, highlighting that engineering this protease is a promising strategy to enhance HLB resistance in citrus. Together, our work reveals a pathogen-derived substrate of plant PLCPs and highlights bacterial OMPs as direct targets of plant defense. Significance StatementHuanglongbing (HLB) is the most devastating disease of citrus with no resistance having been identified in commercial cultivars. Previous work implicated papain-like cysteine proteases (PLCPs) as an important hub of defense in citrus; however, their precise role in HLB tolerance remained unclear. Here, we identify and characterize an outer membrane protein (OMP) from the HLB-associated bacterium as a substrate of the citrus PLCP RD21a. We demonstrate a specific cleavage of the bacterial OMP by citrus RD21a, which may impair pathogen growth and/or activate plant immunity. Importantly, overexpression of RD21a enhances HLB tolerance in sweet oranges. This work identifies OMPs as substrates of plant PLCPs and provides insights into protease defense functions.

plant biology↗

bioRxiv2025

Quantitative Prevalence, Chemical Speciation, and ECM-Embedded Networks of Biogenic Silicon in Animal Tissues Revealed by Refined Analytical Methods

Silicon, abundant in Earths biosphere, plays crucial roles in many organisms. However, its biological functions in animals remain inadequately characterized, primarily constrained by methodological limitations in quantifying, identifying, and visualizing biogenic silicon in tissues. Here, we refined the molybdenum blue colorimetric method (MB) for more accurate silicon quantification, developed integrated mass spectrometry techniques to delineate chemical natures of biogenic silicon, and optimized micro-X-ray fluorescence (micro-XRF) imaging for spatial mapping in animals. Employing these methodologies, we demonstrated that silicon abundance in animals substantially exceeds prior estimates--surpassing essential elements like iron. We also revealed the chemical architectures of diverse silicon compounds and visualized tissue-specific distributions in mice and humans, indicating its predominant localization within extracellular matrix (ECM) and suggesting the formation of silicified networks. These findings establish silicon as a structurally and quantitatively significant element with profound biological implications, warranting its recognition as an essential factor in human physiology and pathology.

biochemistry↗

bioRxiv2025

Lineage Tracing Reveals a Shared Cellular Origin for Supraclavicular Brown and Inguinal Beige Adipocytes

The metabolic importance of brown adipose tissue (BAT) has been recognized, but the origins of BAT, particularly supraclavicular BAT (scBAT), are less clear. Here, we traced the origin of scBAT to Mef2c-anterior heart field (AHF)-marked cells. Mef2c-AHF-marked cells isolated from scBAT can spontaneously differentiate into brown adipocytes, express mesenchymal stem cell markers, and can be isolated from the stromal-vascular fraction (SVF) of wild-type scBAT as [CD31-CD45-SCA-1+CD29+CD34-CD24-] (CD34-) cells. Mef2c-AHF-marked cells substantially overlap with Prrx1-marked cells in scBAT, which also contribute to beige adipocytes in inguinal white adipose tissue (iWAT) during development. Similarly, CD34- cells isolated from the SVF of iWAT can spontaneously differentiate into beige adipocytes in vitro. Using intersectional tracing, we revealed that common progenitors of Mef2c-AHF- and Prrx1-marked cells in scBAT emerge from the developing heart. Thus, these studies reveal a common origin for scBAT and cardiac tissue and a close lineage relationship between scBAT and beige adipocytes of the iWAT.

developmental biology↗

bioRxiv2025

Photolabile oligonucleotides combined with topologically imposed light gradients enable spatially resolved single-cell transcriptomics and epigenomics

The organization of cells within a tissue plays a critical role in tuning cellular function. Several methods have recently been developed to capture the transcriptome of cells while retaining spatial information. However, these genome-wide sequencing methods typically lack the spatial resolution of individual cells and are confined to quantifying positional information within predefined lattice locations, thereby failing to capture large sections of a tissue outside these regions. Further, these methods are generally limited to profiling fixed cells with reduced mRNA capture efficiency compared to standard scRNA-seq. In addition, existing methods lack modularity and cross-platform compatibility, thereby limiting most of these techniques from jointly profiling the epigenetic and transcriptomic state of individual cells. To overcome these limitations, we present scSTAMP-seq (single-cell Spatial Transcriptomic And Multiomic Profiling), an approach that employs cholesterol-tagged photolabile oligonucleotides that incorporate into cell membranes, enabling us to "stamp" the position of cells using spatially imposed light gradients prior to tissue dissociation and single-cell sequencing. Applied to live cells, scSTAMP-seq efficiently captures spatially resolved single-cell transcriptomes at high resolution for all cells within a field of view. Further, we demonstrate that light patterning enables dynamic spatial resolution, including the ability to map the position of individual cells. Finally, we show that scSTAMP-seq is modular and can be seamlessly integrated with various downstream single-cell sequencing technologies. We demonstrate this by performing scRNA-seq using plate- and droplet-based methods, and by performing joint epigenome and transcriptome sequencing from the same cell while preserving positional information. Collectively, these results demonstrate that scSTAMP-seq is a sensitive and high-throughput technology for mapping single-cell transcriptomes and epigenomes at the spatial resolution of individual cells.

genomics↗

bioRxiv2025

Combinatorial protein barcodes enable self-correcting neuron tracing with nanoscale molecular context

Mapping nanoscale neuronal morphology with molecular annotations is critical for understanding healthy and dysfunctional brain circuits. Current methods are constrained by image segmentation errors and by sample defects (e.g., signal gaps, section loss). Genetic strategies promise to overcome these challenges by using easily distinguishable cell identity labels. However, multicolor approaches are spectrally limited in diversity, whereas nucleic acid barcoding lacks a cellfilling morphology signal for segmentation. Here, we introduce PRISM (Protein-barcode Reconstruction via Iterative Staining with Molecular annotations), a platform that integrates combinatorial delivery of antigenically distinct, cell-filling proteins with tissue expansion, multi-cycle imaging, barcode-augmented reconstruction, and molecular annotation. Protein barcodes increase label diversity by >750-fold over multicolor labeling and enable morphology reconstruction with intrinsic error correction. We acquired a [~]10 million {micro}m3 volume of mouse hippocampal area CA2/3, multiplexed across 23 barcode antigen and synaptic marker channels. By combining barcodes with shape information, we achieve an 8x increase in automatic tracing accuracy of genetically labelled neurons. We demonstrate PRISM supports automatic proofreading across micron-scale spatial gaps and reconnects neurites across discontinuities spanning hundreds of microns. Using PRISMs molecular annotation capability, we map the distribution of synapses onto traced neural morphology, characterizing challenging synaptic structures such as thorny excrescences (TEs), and discovering a size correlation among spatially proximal TEs on the same dendrite. PRISM thus supports selfcorrecting neuron reconstruction with molecular context.

neuroscience↗

bioRxiv2025

Staphylococcus aureus inhibits the NLRP3 inflammasome in macrophages during the early phases of intracellular infection, but not the late phases

Staphylococcus aureus (S. aureus) is a highly virulent pathogen responsible for chronic infections such as osteomyelitis. Although its interaction with the host immune system has been widely studied, the specific role of inflammasomes in regulating the infection within macrophages remains unclear. We investigated this question using bone marrow-derived macrophages infected with S. aureus and observed a significant reduction in intracellular bacterial load beginning at 18 hours post-infection (hpi), which continued through 96 hpi. Notably, robust activation of the NLRP3 inflammasome--including inflammasome assembly, IL-1{beta} and GSDMD maturation, and pyroptosis--occurred only after 18 hpi. This led us to hypothesize that S. aureus suppresses inflammasome activation during early infection. Supporting this, infected BMDMs failed to respond robustly to LPS and nigericin up to 18 hpi, with partial recovery at later timepoints, suggesting that S. aureus initially inhibits NLRP3 signaling to persist within macrophages but is later counteracted by the host response.

immunology↗

bioRxiv2025

A Rare Multipotent Peg-like Epithelial Cell is a Candidate Cell-of-Origin for High-Grade Serous Ovarian Cancer

To illuminate the origins of high-grade serous ovarian cancer (HGSOC), the most lethal and common form of ovarian cancer, we have created a comprehensive living organoid biobank of human fallopian tube tissue, which is thought to be the origin of this cancer. Through optimized culture protocols and integrated multi-omic profiling--including single-cell RNA sequencing, chromatin accessibility (ATAC) analysis, proteomics, and secretomics--we assembled the largest molecular atlas of the fallopian tube epithelium to date. This resource revealed diverse epithelial lineages and regulatory networks, including a rare, multipotent epithelial subpopulation with hybrid epithelial-mesenchymal features. Spatially localized to the basal epithelium and resembling mesonephric developmental precursors, these cells exhibit transcriptomic and proteomic similarities to the mesenchyme-like subtype of HGSOC, implicating them as potential cells-of-origin. Their molecular identity is preserved in organoid models, enabling future mechanistic and translational studies. This resource, which advances fundamental understanding of epithelial hierarchy and cancer susceptibility, provides a platform to inform early detection and prevention strategies for aggressive forms of ovarian cancer. HighlightsO_LIEstablishment of a clinically annotated fallopian tube organoid biobank enables delineation of epithelial lineage hierarchies and differentiation capacity. C_LIO_LIMulti-omics integration defines robust, lineage-specific transcriptional and regulatory networks in the fallopian tube epithelium. C_LIO_LIA rare basal epithelial subpopulation with mesenchymal features aligns with a mesenchyme-like subtype of high-grade serous ovarian cancer. C_LIO_LIRare basal peg cells exhibit fetal mesonephric developmental transcriptional programs and are maintained ex-vivo in fallopian tube organoids. C_LI

cancer biology↗

bioRxiv2025

Combining brainwide activity imaging and electron microscopy reveals novel nociceptive circuits

To understand how brains work, it is necessary to connect neural activity to synaptic-resolution circuit architecture. Recent advances in light-sheet microscopy (LSM) enable whole-brain, cellular-resolution imaging of activity of all neuronal cell bodies, however, most neurons from such datasets cannot be identified. In most organisms, neurons are identifiable based on their projections (and not based on their cell body position) which, when densely labelled, cannot be resolved using LSM. Here, we present a novel methodology to overcome this by combining whole-brain activity imaging with subsequent volume electron microscopy imaging of the same brain to visualise neuronal projections and identify neurons with interesting activity. We used this approach to identify brain neurons that process input from multisensory (nociceptive and mechanosensory) Basin interneurons that trigger vigorous escape in Drosophila larvae in response to threatening somatosensory stimuli. After whole-brain imaging of neuronal activity during Basin activation, we imaged the same brain with an enhanced focused ion-beam electron microscope (eFIB-SEM). We registered the functional and anatomical volumes and reconstructed (in the eFIB-SEM volume) the projections of neurons that responded to Basin activation to determine their developmental lineage and identity. This revealed a distributed network for processing threatening somatosensory stimuli that trigger vigorous escape spanning 25 distinct lineages and many distinct brain areas, and included direct brain targets of Basin neurons that integrate somatosensory information with other modalities, as well as brain output neurons (descending neurons [DN]) that likely contribute to action-selection. Our workflow provides a powerful framework for mapping neuronal activity onto structure across an entire brain, yielding novel insights into the distributed central processing of noxious stimuli.

neuroscience↗

bioRxiv2025

In vivo genome-wide CRISPR screens in human T cells to enhance T cell therapy for solid tumors

Large-scale CRISPR screening in human T cells holds significant promise for identifying genetic modifications that can enhance cellular immunotherapy. However, many genetic regulators of T cell performance in solid tumors may not be readily revealed in vitro. In vivo screening in tumor-bearing mice offers greater physiological relevance, but has historically been limited by low intratumoral T cell recovery. Here, we developed a new model system that achieves significantly higher human T cell recovery from tumors, enabling genome-wide in vivo screens with small numbers of mice. Tumor-infiltrating T cells in this model exhibit hallmarks of dysfunction compared to matched splenic T cells, creating an ideal context for screening for genetic modifiers of T cell activity in the tumor microenvironment. Using this platform, we performed two genome-wide CRISPR knockout screens to identify genes regulating T cell intratumoral abundance and effector function (e.g., IFN-{gamma} production). The intratumoral abundance screen uncovered the P2RY8-G13 GPCR signaling pathway as a negative regulator of human T cell infiltration into tumors. The effector function screen identified GNAS (Gs), a central signaling mediator downstream of multiple GPCRs that sense different suppressive ligands, as a key regulator of T cell dysfunction in tumors. Targeted GNAS knockout rendered T cells resistant to multiple suppressive cues and significantly improved therapeutic performance across diverse solid tumor models. Moreover, combinatorial knockout of P2RY8 (trafficking) and GNAS (effector function) further enhanced overall tumor control, demonstrating that genetic modifications targeting distinct T cell phenotypes can be combined to improve therapeutic potency. This flexible and scalable in vivo screening platform can be adapted to diverse tumor models and pooled CRISPR libraries, enabling future discovery of genetic strategies that equip T cell therapies to overcome barriers imposed by solid tumors.

immunology↗

bioRxiv2025

ADAMTS3 as a promising novel biomarker for the diagnosis of hepatocellular carcinoma

Early diagnosis of hepatocellular carcinoma (HCC) still represents a significant challenge. The rising of obesity and non-viral liver disease associated HCC further limits the effectiveness of conventional screening approaches such as ultrasonography and alpha-fetoprotein (AFP) testing. In this context, the identification of potential effective biomarkers for rapid and precise diagnosis of HCC still represents an extremely important task. Here, we identify ADAMTS3 as a novel mechanistic serum biomarker for HCC that addresses this shifting etiological landscape. Transcriptome analysis of four independent cohorts-including HCC patients, individuals with obesity-or non-viral liver disease, and healthy controls- reveals four secreted proteins associated with HCC progression. Among them, ADAMTS3 demonstrates strong diagnostic performance by ROC (receiver operating characteristic) and LASSO (least absolute shrinkage and selection operator) analysis. High ADAMTS3 expression correlates with aggressive molecular signature, characterized by enhanced proliferative signaling, suppressed immune effector responses, and a reprogrammed immune microenvironment marked by reduced NK cell infiltration and increased accumulation of immunosuppressive tumor-associated macrophages, driven by extracellular matrix stiffening. Knockdown of ADAMTS3 in cell lines significantly reduced proliferation, and clonogenic potential. Reintroduction of ADAMTS3 partially rescued both phenotypes, further confirming its role in promoting HCC cell growth. Optical tweezer-based measurements further reveal reduced cell stiffness upon ADAMTS3 deficiency, highlighting its role in extracellular matrix (ECM) remodeling. Finally, to provide a simple strategy for HCC diagnosis based on this novel biomarker, we demonstrated a DNA origami-based SERS biosensor capable of detecting ADAMTS3 at 10-11 M. Together, these findings identify ADAMTS3 as a mechanistic biomarker and demonstrate a translational sensing strategy for non-invasive HCC early screening.

cancer biology↗

bioRxiv2025

A Protein Antibiotic Inhibits the BAM Complex to Kill Without Cell Entry

Many antibiotics are ineffective against Gram-negative pathogens such as Pseudomonas aeruginosa because they cannot penetrate the bacterial outer membrane. Here, we show that protein antibiotics called L-type pyocins kill P. aeruginosa by inhibiting the {beta}-barrel assembly machinery (BAM) complex at the cell surface, halting outer-membrane protein assembly. Using single-particle cryo-electron microscopy, we show that L-type pyocins bind a surface-exposed region of BamA and deploy a C-terminal peptide that competitively inhibits the BAM complex, demonstrating that cell entry is not required for antibiotic activity. We combine genetics, multi-omics and cryo-electron tomography to show that BAM complex inhibition by L-type pyocins or the peptide antibiotic darobactin triggers a multifaceted transcriptomic, proteomic and morphological response. Despite this, BAM inhibition ultimately leads to a catastrophic loss of membrane integrity and cell death. These results validate BAM as a target for antibiotics that do not enter the cell and define an engineerable system for their development.

microbiology↗

bioRxiv2025

Systematic evaluation of the impact of promoter proximal short tandem repeats on expression

Genetic variation at thousands of short tandem repeats (STRs), which consist of consecutive repeated sequences of 1-6bp, has been statistically associated with gene expression and other molecular phenotypes in humans. However, the causality and regulatory mechanisms for most of these STRs remains unknown. Massively parallel reporter assays (MPRA) enable testing the regulatory activity of a large number of synthesized variants, but have not been applied to STRs due to experimental and computational challenges. Here, we optimized an MPRA framework based on random barcoding to study the impact of variation in repeat copy number on expression. We first performed an MPRA on sequences derived from 30,516 promoter-proximal STR loci along with up to 152bp of genomic context, testing 3-4 variants with differing repeat copy numbers for each locus in HEK293T cells. We identified 1,366 loci with significant associations between repeat copy number and expression, which were enriched for positive effect sizes (P=2.08e-110). We then designed a second MPRA in which we performed deeper perturbations, including systematic manipulation of the repeat unit sequence, orientation, and copy number, with 200-300 perturbations for each of the 300 loci with the strongest signals. Our results revealed that the repeat unit sequence is the primary driver of differences in the relationship between copy number and expression across loci, whereas orientation and flanking sequence have weaker effects, primarily for AT-rich repeat units. The high resolution of these perturbations enabled us to detect non-linear effects, most notably for AAAC/GTTT repeats, which emerge only beyond a certain copy number threshold. Finally, we observed that a subset of STRs in our library show expression levels that are tightly linked with predicted DNA secondary structure formation. We repeated our perturbation MPRA in HeLa S3 cells under wildtype and RNase H1 knockdown conditions, which, via reduction in RNase H1 activity, are expected to hinder resolution of R-loops. This demonstrated that associations between copy number and expression at G-quadruplex-forming CCCCG/CGGGG repeats are particularly sensitive to loss of RNase H1, providing support for an R-loop mediated mechanism for these repeats. Altogether, we establish STRs as a critical component of the non-coding regulatory grammar and provide a framework for understanding how this dynamic form of genetic variation shapes gene expression.

genomics↗