Biology subjects

Woods, M.

Publications and source records attributed to Woods, M..

12 recordsLinked to original sources

bioRxiv2026

Linking coronary microvascular structure and function in preclinical models of coronary microvascular disease

Despite growing awareness of the importance of the coronary microvasculature in cardiac health and disease, Coronary Microvascular Disease (CMVD) remains poorly understood, underdiagnosed, and without targeted therapies. Preclinical models and quantitative tools to measure CMVD are needed. Here, we use two novel quantitative methods to assess coronary microvascular structure (multi-fractal spectrum analysis) and function (Single Photon Emission Computed Tomography (SPECT)-based intramyocardial blood volume (IMBV) imaging) in mouse models of CMVD. Change in IMBV ({bigtriangleup}IMBV), which serves as a quantitative measure of vasodilatory capacity or microvascular function, was reduced with aging, driven by a significant decrease in female mice. Male mice on ApoE-/- background, fed a high-fat diet (HFD) for 6 months, or both had significantly reduced {bigtriangleup}IMBV. We used immunofluorescence to assess both traditional capillary density and global branching structure and vessel heterogeneity using multifractal spectrum analysis. Both were significantly reduced in all groups, and linear regression modeling showed that they were independently associated with {bigtriangleup}IMBV. Finally, we used {bigtriangleup}IMBV to assess the effects of widely used control Adeno-associated viral (AAV) vectors on coronary microvascular function. AAV-overexpression of GFP did not affect function, but Cre-recombinase compromised coronary microvascular structure and function by 16 weeks. In summary, quantitative assessments of coronary microvascular structure and function highlight changes consistent with CMVD seen with aging, female sex, and metabolic insults. Functional changes are partially driven, but not fully defined, by changes in the underlying structure, highlighting the important and incomplete link between structure and function.

physiology↗

bioRxiv2026

Multi-Omics Study of Ancestry in Adults with Intracranial Cancers Glioma (MOSAIC)

BackgroundMost genomic studies of adult-type diffuse gliomas have focused on predominantly European ancestry populations, limiting the generalizability of molecular classifications and precision medicine approaches. We assembled a multi-institutional glioma cohort of diverse patients to investigate how germline ancestry, molecular subtypes, and mutational processes shape tumor biology and clinical outcomes. MethodsWe analyzed 1,102 adults with WHO 2021-classified diffuse gliomas (IDH-mutant, 1p/19q-codeleted oligodendroglioma; IDH-mutant astrocytoma; IDH-wildtype glioma) from seven U.S. institutions. Whole-exome sequencing (WES) of FFPE tumors identified somatic alterations and COSMIC SBS v3.2 mutational signatures. Genetic ancestry was estimated from WES using 1000 Genomes reference populations. Overall survival was assessed using Kaplan-Meier and multivariable models. ResultsThe cohort included 66.9% European (EUR), 21.1% Admixed American/Hispanic (AMR), 10.3% Admixed African (AFR), and 1.6% Asian (AS) ancestry. Survival followed expected molecular hierarchy (median overall survival: oligodendroglioma 15.7 years, astrocytoma 10.6 years, IDH-wildtype glioma 1.9 years). Within oligodendroglioma, AMR patients showed improved survival versus EUR (HR 0.67, 95% CI 0.48-0.94; p=0.011), with similar trends across subtypes. Somatic profiling confirmed canonical subtype-defining alterations and revealed higher ATRX alterations in AFR and AMR IDH-wildtype tumors compared with EUR. ATRX alterations were associated with improved survival only in AFR (p=0.003). Mutational signature analysis identified subtype-specific signatures, including therapy-associated signatures. Chemotherapy-related signatures were more frequent in EUR and AMR than in AFR. ConclusionsThis ancestrally diverse glioma cohort confirms established molecular classifications and identifies ancestry-associated differences in survival, somatic alterations, and mutational processes, indicating the critical need for broad representation to inform precision neuro-oncology. Key PointsO_LIA multi-institutional glioma cohort validates subtype and survival patterns across ancestries. C_LIO_LITherapy-associated mutational signatures differ by ancestry, suggesting distinct treatment-related mutational processes. C_LIO_LIAdmixed American patients show improved survival, particularly in oligodendroglioma. C_LI Importance of the StudyMost genomic studies of adult-type diffuse glioma have focused on populations of predominantly European ancestry which limits the ability to examine variation in tumor biology and clinical outcomes across populations. In this study, we assembled one of the largest ancestrally diverse cohorts of molecularly characterized adult diffuse gliomas, integrating germline ancestry inference with tumor whole-exome sequencing and mutational signature analysis. We confirm that established molecular classifications and survival hierarchies remain robust across ancestry groups. However, we also identified ancestry-associated differences in survival within specific tumor subtypes, higher ATRX alteration frequencies in African American and admixed American patients with IDH-wildtype tumors, and variation in therapy-associated mutational signatures across ancestry groups. These findings highlight the importance of incorporating population differences into genomic studies of glioma and provide a resource for future multi-ancestry investigations of glioma risk, tumor evolution, and treatment response, ultimately supporting more inclusive precision neuro-oncology.

bioinformatics↗

bioRxiv2026

Adaptive Focused Acoustics-integrated proteome profiling of macrophages uncovers low abundant proteins associated with immune homeostasis, inflammatory response, and transport

Efficient and reproducible protein extraction is a critical step in mass spectrometry-based proteomics workflows, particularly for complex host-pathogen systems where low-abundance immune-associated proteins are difficult to detect. Probe sonication methods used for cell lysis requiring mitigation of excessive heat generation, to prevent degradation of biologically important proteins, while also limiting throughput and potentially introducing sample-to-sample variability. In this study, we evaluated adaptive focused acoustics (AFA) technology as an alternative approach for macrophage lysis and protein extraction and digestion within a standard proteomics workflow coupled with mass spectrometry. We observed that AFA technology reduced hands-on processing times and overall workflow timelines and single-sample AFA technology improves proteome coverage, dynamic range, and reproducibility. We also evaluated multiplexed AFA technology for lysis, and we observed an exclusive macrophage proteome and influence on replicate reproducibility and dynamic range detection for low abundant proteins. Moreover, multiplexed AFA technology for macrophage lysis and digestion further increased protein identifications, replicate reproducibility, and dynamic range. Considering the AFA-exclusive proteome, 86 proteins were detected across all AFA-based lysis and digestion methods, including low-abundance proteins associated with macrophage homeostasis, inflammatory response, and transport. Together, these findings demonstrate that AFA technology enhances reproducibility, throughput, and proteome depth for macrophage protein extraction while enabling the detection of biologically relevant low-abundance immune-associated proteins. These improvements provide a strong foundation for future investigation of host-pathogen infection models, where pathogen-derived proteins remain challenging to detect within complex host proteomes.

immunology↗

bioRxiv2026

A structure-guided pipeline yields peptide inhibitors that disarm fungal peptidase-driven virulence and resistance

Fungal infections are a major global health challenge, with current antifungal therapies limited by toxicity, cost, and resistance. For Cryptococcus neoformans, key virulence factors that initiate and sustain infection are regulated by fungal peptidases to produce a polysaccharide capsule, promote immune evasion, and support antifungal resistance. These peptidases represent promising targets for antivirulent therapeutic strategies. Here, we developed a computational pipeline to predict and design peptide- and protein-based inhibitors against cryptococcal peptidases. Specifically, we targeted three virulence-associated peptidases: Rim13 (cysteine), May1 (aspartic), and CnMpr1 (metallo). Cysteine peptidase inhibition decreased capsule/cell size ratios without impeding fungal growth and reduced fungal survival within macrophages. Similarly, aspartic peptidase inhibition enhanced fungal clearance within alveolar macrophages and disrupted biofilm formation with additive effects towards fluconazole susceptibility in resistant strains. Additionally, metallopeptidase inhibition through catalytic zinc chelation and blocked substrate binding led to enhanced enzymatic inhibition and reduced in vitro blood-brain barrier crossing. Moreover, an in vivo larval model assessing inhibitor efficacy produced additive effects with fluconazole and lacked host cell cytotoxicity and fungicidal properties, reinforcing anti-virulence mechanisms and therapeutic potential while limiting the evolution of resistance. Further, global proteome profiling of inhibitor treated cells defined a mechanism of cell wall disruption, impeding fungal virulence. Taken together, the designed peptidase inhibitors exhibited potent antifungal activity without harming mammalian cells, establishing a predictive framework for rational scaffold design of next-generation antifungals that disarm the pathogen enabling immune-mediated clearance.

microbiology↗

bioRxiv2026

Systematic Infectome-Phenome Profiling Reveals Cryptococcal Infection-Associated Proteins Driving Immune System Remodeling and Immunization Potential

Mortality and morbidity associated with invasive fungal infections continue to rise, driven by the emergence of new pathogens, increasing antifungal resistance, and expanding immunocompromised populations. Despite this growing threat, fungal biology lacks scalable, unbiased strategies to link infection-responsive fungal proteins to functional outcomes that drive virulence and immune modulation. Here, we present an integrated infectome-phenome discovery platform that combines high resolution mass spectrometry-based proteomics with systematic phenotypic profiling to globally interrogate Cryptococcus neoformans-macrophage interactions. This approach reveals coordinated host immune suppression alongside complementary fungal virulence programs and enables the unbiased prioritization of infection-associated fungal proteins. Systematic phenome fingerprinting of candidate mutant strains resolves two functional classes of putative therapeutic relevance: antifungal and antivirulence, with in vitro characterizations corroborated with a murine model of cryptococcosis. Prioritization of a conserved, previously uncharacterized virulence-associated protein, CipC, uncovers altered extracellular vesicle composition and enhanced antigenic properties. Immunization with CipC-derived vesicles elicits a robust and diversified host immune response, implicating fungal extracellular vesicles in immune remodeling and host priming. Together, these findings establish a broadly applicable framework for systematically identifying and functionally characterizing fungal drivers of infection for therapeutic and immunological target discovery with relevance across diverse human fungal pathogens.

microbiology↗

bioRxiv2025

Spatiotemporal dynamics of cryptococcal infection reveal novel immune modulatory mechanisms and antifungal targets

The threat and incidence of fungal diseases are increasing, as is the severity and mortality rates associated with these infections. New strategies to combat fungal infections are urgently needed to overcome rising rates of resistance and the emergence of new pathogens. To promote invasion within a host, fungi use highly adapted and regulated virulence factors, and, in turn, the host adopts an active and dynamic immune response to suppress infection. Understanding the interplay between these processes is crucial to move fungal disease management and treatment forward and improve global health outcomes. Within the present study, we tackle these challenges using state-of-the-art mass spectrometry instrumentation to explore proteome remodeling during active infection of Cryptococcus neoformans at an unprecedented depth with spatiotemporal resolution. Our prioritization of three host organs (i.e., lungs, brain, spleen) critical to initiation, progression, and response of disease discovers tissue-specific remodeling across time. Within the lungs, we revealed early and sustained activation of the host immune response integrated with characterization of a promising new antifungal target, and we propose the discovery of a competitive inhibitor for functional target disruption. Within the brain, proteome remodeling aligns with disease progression, and we define a new mechanistic role for haptoglobin in fungal cell modulation, as well as showcasing an adaptive survival response of C. neoformans within an hypoxic environment. Within the spleen, we reveal new dynamics of immune system activation upon cryptococcal infection. Overall, we provide the deepest integrated view of cryptococcal disease dynamics across temporal and spatial scales, revealing unrecognized mechanisms of host immunity and fungal pathogenesis that offer new avenues for targeted therapeutic intervention and disease management.

microbiology↗

bioRxiv2025

Whole blood proteome dynamics defines predictive diagnostic and prognostic signatures of cryptococcal infection

Across the globe, fungi are impacting the lives of millions of people through the development of infections ranging from superficial to systemic with limited treatment options. To effectively combat fungal disease, rapid and reliable diagnostic methods are required, including current methodologies using antigen detection, culturing, microscopy, and molecular tools. However, the flexibility of these platforms to diagnose infection using non-invasive methods and predict the outcome of disease are limited. In this study, we apply state-of-the-art mass spectrometry-based proteomics to perform dual perspective (i.e., host and pathogen) profiling of cryptococcal infection. Whole blood collected over a temporal scale following murine model challenged with the human fungal pathogen, Cryptococcus neoformans, detected >3,000 host proteins and 160 fungal proteins. From the host perspective, temporal regulation of known immune-associated proteins, including eosinophil peroxidase and lipocalin-2, along with suppression of lipoproteins, demonstrated infection- and time-dependent host remodeling. Conversely, from the pathogen perspective, known and putative virulence-associated proteins were detected, including proteins associated with fungal extracellular vesicles and host immune modulation. We also observed and validated a new mechanism of immune system response to C. neoformans through modulation of haptoglobin. Further, we assessed the predictive power of dual perspective proteome profiling toward prognostics of cryptococcal infection and report a previously undisclosed integration among virulence factor production, immune system modulation, and individual model survival. Together, our findings pose novel biomarkers of cryptococcal infection from whole blood and highlight the potential of personal proteome profiles to determine the prognosis of cryptococcal infection, a new parameter in fungal disease management.

microbiology↗

bioRxiv2024

Dopamine increases protein synthesis in hippocampal neurons enabling dopamine-dependent LTP

The reward and novelty related neuromodulator dopamine plays an important role in hippocampal long- term memory, which is thought to involve protein synthesis-dependent synaptic plasticity. However, the direct effects of dopamine on protein synthesis, and the functional implications of newly synthesized proteins for synaptic plasticity, have not yet been investigated. We have previously reported that timing- dependent synaptic depression (t-LTD) can be converted into potentiation by dopamine application during synaptic stimulation (Brzosko et al., 2015) or postsynaptic burst activation (Fuchsberger et al., 2022). Here we show that dopamine increases protein synthesis in mouse hippocampal CA1 neurons, enabling dopamine-dependent long-term potentiation (DA-LTP), which is mediated via the Ca2+-sensitive adenylate cyclase (AC) subtypes 1/8, cAMP, and cAMP-dependent protein kinase (PKA). We found that neuronal activity is required for the dopamine-induced increase in protein synthesis. Furthermore, dopamine induced a protein synthesis-dependent increase in the AMPA receptor subunit GluA1, but not GluA2. We found that DA-LTP is absent in GluA1 knock-out mice and that it requires calcium-permeable AMPA receptors. Taken together, our results suggest that dopamine together with neuronal activity controls synthesis of plasticity-related proteins, including GluA1, which enable DA-LTP via a signalling pathway distinct from that of conventional LTP.

neuroscience↗

bioRxiv2020

Control of fluid flow by Adgrd1 is essential for mammalian oviductal embryo transport

Dysfunction of oviductal embryo transport can lead to ectopic pregnancy which affects 1 to 2% of all conceptions in the United States and Europe, and is the most common cause of pregnancy-related death in the first trimester1, 2. Ectopic pregnancies almost always occur in the Fallopian tube, emphasizing the critical role of oviductal transport in human reproduction3. Oviductal transit is regulated and involves a valve-like "tubal-locking" phenomenon that temporarily arrests oocytes at the ampullary-isthmic junction (AIJ) where fertilization occurs4. Here, we show that female mice lacking the orphan adhesion G-protein coupled receptor Adgrd1 are sterile because they are unable to unlock the restraining mechanism at the AIJ, inappropriately retaining embryos within the oviduct. Adgrd1 is expressed on the oviductal epithelium and the post-ovulatory attenuation of tubal fluid production is dysregulated in Adgrd1-deficient mice. We identified Plxdc2 as an activating ligand for Adgrd1 displayed on the surface of cumulus cells. Our findings suggest that regulating oviductal luminal fluid production by Adgrd1 controls embryo transit, and provides important insights into the genetic regulation and molecular mechanisms involved embryo tubal transport.

molecular biology↗

bioRxiv2019

Machine Learning Methods to Identify Genetic Correlates of Radiation-Associated Contralateral Breast Cancer in the WECARE Study

The purpose of this study is to identify germline single nucleotide polymorphisms (SNPs) that optimally predict radiation-associated contralateral breast cancer (RCBC) and to provide new biological insights into the carcinogenic process. Fifty-two women with contralateral breast cancer and 153 women with unilateral breast cancer were identified within the Womens Environmental Cancer and Radiation Epidemiology (WECARE) Study who were at increased risk of RCBC because they were [≤] 40 years of age at first diagnosis of breast cancer and received a scatter radiation dose > 1 Gy to the contralateral breast. A previously reported algorithm, preconditioned random forest regression, was applied to predict the risk of developing RCBC. The resulting model produced an area under the curve of 0.62 (p=0.04) on hold-out validation data. The biological analysis identified the cyclic AMP-mediated signaling and Ephrin-A as significant biological correlates, which were previously shown to influence cell survival after radiation in an ATM-dependent manner. The key connected genes and proteins that are identified in this analysis were previously identified as relevant to breast cancer, radiation response, or both. In summary, machine learning/bioinformatics methods applied to genome-wide genotyping data have great potential to reveal plausible biological correlates associated with the risk of RCBC.

bioinformatics↗

bioRxiv2018

ATM orchestrates the DNA-damage response to counter toxic non-homologous end-joining at broken replication forks

Mutations in the ATM tumor suppressor confer hypersensitivity to DNA-damaging agents. To explore genetic resistance mechanisms, we performed genome-wide CRISPR-Cas9 screens in cells treated with the DNA topoisomerase poison topotecan. Thus, we establish that loss of terminal components of the non-homologous end-joining (NHEJ) machinery or the BRCA1-A complex specifically confers topotecan resistance to ATM-deficient cells. We show that hypersensitivity of ATM-mutant cells to topotecan or the poly-(ADP-ribose) polymerase inhibitor olaparib is due to delayed homologous recombination repair at DNA-replication-fork-associated double-strand breaks (DSBs), resulting in toxic NHEJ-mediated chromosome fusions. Accordingly, restoring legitimate repair in ATM-deficient cells, either by preventing NHEJ DNA ligation or by enhancing DSB-resection by BRCA1-A complex inactivation, markedly suppresses this toxicity. Our work suggests opportunities for patient stratification in ATM-deficient cancers and when using ATM inhibitors in the clinic, and identifies additional therapeutic vulnerabilities that might be exploited when such cancers evolve drug resistance.\n\nOne Sentence SummaryATM counteracts toxic NHEJ at broken replication forks

cell biology↗

bioRxiv2017

Establishment In Culture Of Expanded Potential Stem Cells

Mouse embryonic stem cells are derived from in vitro explantation of blastocyst epiblasts1,2 and contribute to both the somatic lineage and germline when returned to the blastocyst3 but are normally excluded from the trophoblast lineage and primitive endoderm4-6. Here, we report that cultures of expanded potential stem cells (EPSCs) can be established from individual blastomeres, by direct conversion of mouse embryonic stem cells (ESCs) and by genetically reprogramming somatic cells. Remarkably, a single EPSC contributes to the embryo proper and placenta trophoblasts in chimeras. Critically, culturing EPSCs in a trophoblast stem cell (TSC) culture condition permits direct establishment of TSC lines without genetic modification. Molecular analyses including single cell RNA-seq reveal that EPSCs share cardinal pluripotency features with ESCs but have an enriched blastomere transcriptomic signature and a dynamic DNA methylome. These proof-of-concept results open up the possibility of establishing cultures of similar stem cells in other mammalian species.

developmental biology↗