Biology subjects

Bates, D.

Publications and source records attributed to Bates, D..

12 recordsLinked to original sources

bioRxiv2026

An endonuclease V protects Bacillus subtilis against a deaminase toxin and a uracil-containing phage

Bacteria deploy polymorphic toxins to inhibit competitors and rely on cognate immunity proteins to prevent self-intoxication. Immunity determinants act by binding and neutralizing incoming toxins, and in the rare cases where toxin-induced damage is also reversed, that activity resides within the immunity protein itself. Whether a conflict system can instead dedicate a separate gene to repairing the damage is unknown. Here we report that an operon in Bacillus subtilis encodes the toxin YwqJ, its cognate immunity protein YwqK, and EndoV an endonuclease that incises DNA at the lesion the toxin creates. YwqJ is a single-stranded DNA cytidine deaminase translocated by the type VIIb secretion system (T7SSb) to mediate contact-dependent interbacterial antagonism. Unexpectedly, EndoV exhibits a preference for uracil over the canonical hypoxanthine, processing genomic uracil in cells and protecting against YwqJ when immunity is absent. Because EndoV acts on the chemical lesion rather than the effector, its protection is indifferent to the source of deamination. EndoVBs accordingly restricts replication of PBS1, a bacteriophage whose genome naturally substitutes uracil for thymine. These findings establish DNA repair as a novel layer of defense within toxin-immunity loci and reveal a DNA repair mechanism that unifies interbacterial antagonism and antiviral immunity.

microbiology↗

bioRxiv2026

SMARCA4, STK11, and KEAP1 co-inactivation associates with poor prognosis and upregulation of the TGF-β pathway in lung adenocarcinoma

BackgroundLung adenocarcinoma (LUAD) is clinically and molecularly defined by oncogenic driver mutations, identification of which has led to the development of driver-targeted therapies and substantial improvements in prognosis for subsets of LUAD patients. Recent studies assessing clinical outcomes in the context of multigenic alterations have identified secondary mutations that might explain differential responses to targeted therapies, chemotherapies and immunotherapies. Genetic inactivation or loss of SMARCA4, which frequently co-occurs with loss-of-function mutations in STK11 and KEAP1, is especially predictive of poor prognosis and shorter overall survival in LUAD patients, regardless of driver status. We sought to examine the clinical and functional associations of SMARCA4 deficiency in LUAD, with or without co-associated STK11/KEAP1 loss-of-function. MethodsWe examined correlation between SMARCA4 loss, gene expression and prognosis through genomic and transcriptomic profiling of clinically annotated LUAD samples. We generated isogenic cell line models with genetic knockouts of SMARCA4 with or without concomitant STK11 and KEAP1 to profile mutationally-defined genotypes of interest in vitro and in vivo. Lastly, we interrogated the functional dependency of SMARCA4/STK11/KEAP1 triple mutant models on TGF-{beta} signaling to assess its potential as a therapeutic target. ResultsSMARCA4/STK11/KEAP1 triple mutant LUAD is associated with poor survival and high frequency of multisite metastasis. SMARCA4/STK11/KEAP1 triple knockout models showed enhanced migration and invasion in vitro, and diversified organotropism in an in vivo intracardiac xenograft metastasis assay. RNA-Seq and DNaseI-Seq of these in vitro models and clinical samples identified upregulation of TGF-{beta} signaling and EMT gene expression signatures, and corresponding changes in chromatin accessibility, in SMARCA4/STK11/KEAP1 triple mutant LUAD. ConclusionsWe identify SMARCA4/STK11/KEAP1 triple mutant LUAD as a prognostically significant disease subset and nominate TGF-{beta} signaling as a potential therapeutic target.

cancer biology↗

bioRxiv2025

Discovery of Isobavachin, a natural flavonoid, as an Apolipoprotein E4 (ApoE4) structure corrector for Alzheimer's disease

Alzheimers disease (AD) is a progressive neurodegenerative disease characterized by extensive neurodegeneration and consequent severe memory loss. Apolipoprotein E4 (ApoE4) is the strongest genetic risk factor for AD, with its pathological effects linked to structural instability and altered interactions with lipids and other important disease proteins including amyloid beta (A{beta}) and tau ({tau}). Therefore, correcting and stabilizing the ApoE4 structure has emerged as a promising therapeutic strategy for mitigating its detrimental effects. In this study, we investigated naturally occurring bioavailable flavonoids as ApoE4 stabilizers, focusing on their potential to modulate ApoE4 structure and function. Comprehensive investigation of a focused database using our integrated computational and experimental screening protocol led to the identification of Isobavachin as a potential corrector and stabilizer of ApoE4 structure. In addition, a few other bioavailable flavonoids with similar stabilizing properties were identified, albeit to a much lesser extent as compared to Isobavachin. The findings support the therapeutic potential of flavonoids as ApoE4 modulators and highlight Isobavachin as a lead candidate for further preclinical evaluation. These results provide new insights into the pharmacological targeting of ApoE4 and open avenues for the development of flavonoid-based, ApoE-directed therapies for AD.

neuroscience↗

bioRxiv2020

Atlas and developmental dynamics of mouse DNase I hypersensitive sites

Early mammalian development is orchestrated by genome-encoded regulatory elements populated by a changing complement of regulatory factors, creating a dynamic chromatin landscape. To define the spatiotemporal organization of regulatory DNA landscapes during mouse development and maturation, we generated nucleotide-resolution DNA accessibility maps from 15 tissues sampled at 9 intervals spanning post-conception day 9.5 through early adult, and integrated these with 41 adult-stage DNase-seq profiles to create a global atlas of mouse regulatory DNA. Collectively, we delineated >1.8 million DNase I hypersensitive sites (DHSs), with the vast majority displaying temporal and tissue-selective patterning. Here we show that tissue regulatory DNA compartments show sharp embryonic-to-fetal transitions characterized by wholesale turnover of DHSs and progressive domination by a diminishing number of transcription factors. We show further that aligning mouse and human fetal development on a regulatory axis exposes disease-associated variation enriched in early intervals lacking human samples. Our results provide an expansive new resource for decoding mammalian developmental regulatory programs.

genomics↗

bioRxiv2020

A mechanistic model of the BLADE platform predicts performance characteristics of 256 different synthetic DNA recombination circuits

Boolean logic and arithmetic through DNA excision (BLADE) is a recently developed platform for implementing inducible and logical control over gene expression in mammalian cells, which has the potential to revolutionise cell engineering for therapeutic applications. This 2-input 2-output platform can implement 256 different logical circuits that exploit the specificity and stability of DNA recombination. Here, we develop the first mechanistic mathematical model of the 2-input BLADE platform based on Cre- and Flp-mediated DNA excision. After calibrating the model on experimental data from two circuits, we demonstrate close agreement between model outputs and data on the other 111 circuits that have so far been experimentally constructed using the 2-input BLADE platform. Model simulations of the remaining 143 circuits that have yet to be tested experimentally predict excellent performance of the 2-input BLADE platform across the range of possible circuits. Circuits from both the tested and untested subsets that perform less well consist of a disproportionally high number of STOP sequences. Model predictions suggested that circuit performance declines with a decrease in recombinase expression and new experimental data was generated that confirms this relationship.

synthetic biology↗

bioRxiv2020

Promoter keyholes enable specific and persistent multi-gene expression programs in primary T cells without genome modification

Human genes are regulated quantitatively, yet the ability to specify the expression level of a native gene accurately and specifically using a defined reagent has remained elusive. Here we show that precise targeting of KRAB repressive domain within regulatory DNA unlocks an endogenous quantitative dial that can be engaged at nucleotide resolution to program expression levels across a wide physiologic range, with single-gene specificity and high reproducibly in primary cells.

synthetic biology↗

bioRxiv2020

Global reference mapping and dynamics of human transcription factor footprints

Combinatorial binding of transcription factors to regulatory DNA underpins gene regulation in all organisms. Genetic variation in regulatory regions has been connected with diseases and diverse phenotypic traits1, yet it remains challenging to distinguish variants that impact regulatory function2. Genomic DNase I footprinting enables quantitative, nucleotide-resolution delineation of sites of transcription factor occupancy within native chromatin3-5. However, to date only a small fraction of such sites have been precisely resolved on the human genome sequence5. To enable comprehensive mapping of transcription factor footprints, we produced high-density DNase I cleavage maps from 243 human cell and tissue types and states and integrated these data to delineate at nucleotide resolution ~4.5 million compact genomic elements encoding transcription factor occupancy. We map the fine-scale structure of ~1.6 million DHS and show that the overwhelming majority is populated by well-spaced sites of single transcription factor:DNA interaction. Cell context-dependent cis-regulation is chiefly executed by wholesale actuation of accessibility at regulatory DNA versus by differential transcription factor occupancy within accessible elements. We show further that the well-described enrichment of disease- and phenotypic trait-associated genetic variants in regulatory regions1,6 is almost entirely attributable to variants localizing within footprints, and that functional variants impacting transcription factor occupancy are nearly evenly partitioned between loss- and gain-of-function alleles. Unexpectedly, we find that the global density of human genetic variation is markedly increased within transcription factor footprints, revealing an unappreciated driver of cis-regulatory evolution. Our results provide a new framework for both global and nucleotide-precision analyses of gene regulatory mechanisms and functional genetic variation.

genomics↗

bioRxiv2019

Anatomically Informed 3D Printed CT phantoms: The First Step of a Pipeline To Identify Robust Quantitative Radiomic Features

PurposeThis study investigates the robustness of quantitative radiomic features derived from computed tomography (CT) images of a novel patient informed 3-D printed phantom, which captures the morphological heterogeneity of tumors and normal tissue observed on CT scans.\n\nMethodsUsing a novel voxel-based multi-material three-dimensional (3D) printer, an anthropomorphic phantom that was modeled after diseased tissue seen on 6 patient CT scans was manufactured. Four patients presented with pancreatic adenocarcinoma tumors (PDAC), 1 with non-small cell lung carcinoma (NSCLC) and 1 with advanced stage hepatic cirrhosis. The 5 tumors were segmented, extracted and then imbedded into CT images of the heterogenous portion of the cirrhotic liver. The composite scan of the implanted tumor within the background cirrhotic liver was then 3D printed. The resultant phantom was scanned sequentially, 30 times with a clinical CT scanner using a reference CT protocol. One hundred and four quantitative radiomic features were then extracted from images of each lesion to determine their repeatability. Repeatability of each radiomic feature was evaluated using the within subject coefficient of variation (wCV, %). A feature with a wCV (%) > 10% was considered as being unrepeatable. A subset of the repeatable features that were also found to be prognostic for lung and pancreatic cancers were then assessed for their percent deviation (pDV, %) from reference values. The reference values were those derived from the repeatability portion of this study. The assessment was conducted by re-scanning the phantom with 11 different clinically relevant sets of scanning parameters. Deviation of radiomic features derived from images of each tumor across all sets of scanning parameters was assessed using the percent deviation relative to the reference values.\n\nResultsTwenty nine of the 104 features presented with wCV (%) > 10%. The lack of repeatability was found to depend on tumor type. The only class of radiomic features with a wCV (%) < 10% were those calculated using the neighboring grey level dependence-based matrices (NGLDM). Notably, skewness, first information correlation, cluster shade, Haralick correlation, autocorrelation, busyness, complexity, high gray level zone emphasis, small area high gray level emphasis, large area low gray level emphasis, large area high gray level emphasis, short run high grey level emphasis, and valley radiomic features had wCV (%) values > 10% for select tumors within the phantom. Two radiomic features prognostic for NSCLC, energy and grey level non-uniformity, had pDVs (%) that exceeded 30% across all scanning techniques. The pDV (%) for the 4 radiomic features prognostic for PDAC tumors depended on tumor type and selected scanning parameter. Application of the lung kernel caused the largest pDVs (%). Scans acquired with the reduced tube current of 100 mA and reconstructed with the bone kernel yielded pDVs (%) within {+/-} 10%.\n\nConclusionWe demonstrated the feasibility with which patient informed 3D printed phantoms can be manufactured directly from lesions seen on CT scans, and demonstrate their potential use for the assessment of robust quantitative radiomic features.

biophysics↗

bioRxiv2018

Gamblers: an Antibiotic-induced Evolvable Cell Subpopulation Differentiated by Reactive-oxygen-induced General Stress Response

Antibiotics can induce mutations that cause antibiotic resistance. Yet, despite their importance, mechanisms of antibiotic-promoted mutagenesis remain elusive. We report that the fluoroquinolone antibiotic ciprofloxacin (cipro) induces mutations that cause drug resistance by triggering differentiation of a mutant-generating cell subpopulation, using reactive oxygen species (ROS) to signal the sigma-S ({sigma}S) general-stress response. Cipro-generated DNA breaks activate the SOS DNA-damage response and error-prone DNA polymerases in all cells. However, mutagenesis is restricted to a cell subpopulation in which electron transfer and SOS induce ROS, which activate the {sigma}S response, allowing mutagenesis during DNA-break repair. When sorted, this small {sigma}S-response-\"on\" subpopulation produces most antibiotic cross-resistant mutants. An FDA-approved drug prevents {sigma}S induction specifically inhibiting antibiotic-promoted mutagenesis. Furthermore, SOS-inhibited cell division, causing multi-chromosome cells, is required for mutagenesis. The data support a model in which within-cell chromosome cooperation together with development of a \"gambler\" cell subpopulation promote resistance evolution without risking most cells.

microbiology↗

bioRxiv2018

Cryptic Promoter Activation Drives POU5F1 (OCT4) Expression in Renal Cell Carcinoma

Transcriptional dysregulation drives cancer formation but the underlying mechanisms are still poorly understood. As a model system, we used renal cell carcinoma (RCC), the most common malignant kidney tumor which canonically activates the hypoxia-inducible transcription factor (HIF) pathway. We performed genome-wide chromatin accessibility and transcriptome profiling on paired tumor/normal samples and found that numerous transcription factors with a RCC-selective expression pattern also demonstrated evidence of HIF binding in the vicinity of their gene body. Some of these transcription factors influenced the tumors regulatory landscape, notably the stem cell transcription factor POU5F1 (OCT4). Unexpectedly, we discovered a HIF-pathway-responsive cryptic promoter embedded within a human-specific retroviral repeat element that drives POU5F1 expression in RCC via a novel transcript. Elevat POU5F1 expression levels were correlated with advanced tumor stage and poorer overall survival in RCC patients. Thus, integrated transcriptomic and epigenomic analysis of even a small number of primary patient samples revealed remarkably convergent shared regulatory landscapes and a novel mechanism for dysregulated expression of POU5F1 in RCC.

cancer biology↗

bioRxiv2018

Bacteria-to-human protein networks reveal origins of endogenous DNA damage

DNA damage provokes mutations and cancer, and results from external carcinogens or endogenous cellular processes. Yet, the intrinsic instigators of DNA damage are poorly understood. Here we identify proteins that promote endogenous DNA damage when overproduced: the DNA-damaging proteins (DDPs). We discover a large network of DDPs in Escherichia coli and deconvolute them into six DNA-damage-causing function clusters, demonstrating DDP mechanisms in three: reactive-oxygen increase by transmembrane transporters, chromosome loss by replisome binding, and replication stalling by transcription factors. Their 284 human homologs are over-represented among known cancer drivers, and their expression in tumors predicts heavy mutagenesis and poor prognosis. Half of tested human homologs, when overproduced in human cells, promote DNA damage and mutation, with DNA-damaging mechanisms like those in E. coli. Together, our work reveals DDP networks that provoke endogenous DNA damage and may indicate functions of many human known and newly implicated cancer-promoting proteins.

cancer biology↗

bioRxiv2018

Engineering Translational Resource Allocation Controllers: Mechanistic Models, Design Guidelines, and Potential Biological Implementations

The use of orthogonal ribosomes in combination with dynamic resource allocation controllers is a promising approach for relieving the negative effects of cellular resource limitations on the modularity of synthetic gene circuits. Here, we develop a detailed mechanistic model of gene expression and resource allocation, which when simplified to a tractable level of complexity, allows the rational design of translational resource allocation controllers. Analysis of this model reveals a fundamental design trade-off; that reducing coupling acts to decrease gene expression. Through a sensitivity analysis of the experimentally tuneable controller parameters, we identify how each controller design parameter affects the overall closed-loop behaviour of the system, leading to a detailed set of design guidelines for optimally managing this trade-off. Based on our designs, we evaluated a number of alternative potential experimental implementations of the proposed system using commonly available biological components. Finally, we show that the controller is capable of dynamically allocating ribosomes as needed to restore modularity in a number of more complex synthetic circuits, such as the repressilator, and activation cascades composed of multiple interacting modules.

synthetic biology↗