Biology subjects

Adams, M.

Publications and source records attributed to Adams, M..

At least 19 recordsLinked to original sources

bioRxiv2026

NF1 splicing reprograms ERα signaling to promote luminal breast cancer progression

Alternative splicing is an emerging driver of cancer progression, yet its role in modulating tumor suppressor function remains incompletely understood. Here, we identify an alternatively spliced NF1 isoform lacking the nuclear localization sequence (NLS; NLS SE) as a clinically and functionally relevant regulator of breast cancer progression. Analysis of TCGA and AURORA cohorts revealed that NF1 NLS SE is enriched in metastatic tumors, preferentially occurs in luminal subtypes, and is associated with decreased overall survival independent of NF1 genomic alterations. Using a CRISPR-engineered MCF7 model, we show that NLS SE expression abolishes nuclear localization of neurofibromin, enhances ERK signaling, and promotes proliferation and resistance to endocrine and MAPK-targeted therapies. Despite increased ER protein levels, transcriptomic analysis revealed suppression of canonical estrogen response programs and activation of KRAS, EMT, and inflammatory pathways. Mechanistically, NLS SE expression increased RNA-bound ER and reprogrammed RNA binding protein networks, including CELF, ESRP1, and SRSF family members, leading to widespread alternative splicing. Together, these findings define NF1 NLS exon skipping as a luminal breast cancer-associated, isoform-level mechanism that disrupts nuclear neurofibromin function, rewires ER signaling towards post-transcriptional regulation, and promotes endocrine-resistant disease. Targeting splicing regulatory networks may represent a therapeutic strategy in NF1-dysregulated breast cancer. O_FIG O_LINKSMALLFIG WIDTH=192 HEIGHT=200 SRC="FIGDIR/small/726647v1_ufig1.gif" ALT="Figure 1"> View larger version (59K): org.highwire.dtl.DTLVardef@d507dborg.highwire.dtl.DTLVardef@1f6f6c9org.highwire.dtl.DTLVardef@c42e1corg.highwire.dtl.DTLVardef@1af38dd_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract.C_FLOATNO NF1 NLS exon skipping drives cytoplasmic retention of neurofibromin and reprograms ER toward post-transcriptional regulatory functions. (A) In cells expressing NLS-containing NF1 isoforms, neurofibromin localizes to the nucleus and constrains ER activity. (B-C) Alternative splicing of the NF1 NLS exon generates the NLS SE isoform, resulting in cytoplasmic retention of neurofibromin. This shift disrupts canonical ER signaling and is associated with increased ER phosphorylation and enhanced RNA-binding activity. ER engages RNA and cooperates with splicing machinery, including phosphorylated SF3B1, to promote transcriptomic remodeling. These changes support a therapy-resistant state characteristic of aggressive, endocrine-resistant breast cancer. C_FIG

cancer biology↗

bioRxiv2026

Endometrial Hyperplasia Risk Is Increased by High-Fat Diet Via Estrogen-Driven Stromal Fibroblast Reprogramming Toward a Pro-Fibrotic State

The uterine endometrium is capable of scarless regeneration under coordinated estrogen and progesterone signaling across the menstrual cycle. Obesity suppresses progesterone production, leading to chronic estrogen exposure and increased endometrial hyperplasia (EH) risk. To define how obesity alters endometrial cell states, endometrial tissues from control and EH-predisposed mice fed either a control diet or a high-fat diet (HFD) were analyzed by single-cell RNA sequencing and tissue phenotyping. HFD reprogrammed endometrial stroma towards an inflammatory, pro-fibrotic state, reducing progesterone receptor-network-associated Aldh1a2+ fibroblasts and expanding estrogen receptor-network-associated Gsn fibroblasts. HFD further impaired macrophage recruitment and promoted hyperplastic epithelial signatures, consistent with increased disease severity in an EH mouse model. Stromal deletion of Estrogen Receptor established stromal estrogen signaling as a driver of HFD-induced extracellular matrix (ECM) accumulation. Collectively, these findings identify HFD-driven fibroblast reprogramming as a central mechanism linking estrogen dominance to stromal fibrosis, defective immune clearance, and heightened EH susceptibility. We propose that, in response to progesterone, fibroblast-mediated ECM remodeling is vital to normal endometrial homeostasis. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=161 SRC="FIGDIR/small/713224v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@1f79ceborg.highwire.dtl.DTLVardef@15f128aorg.highwire.dtl.DTLVardef@ba5604org.highwire.dtl.DTLVardef@16543dc_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO HFD-induced estrogen dominance disrupts endometrial fibroblast homeostasis to predispose the endometrium to diseaseThis study demonstrates that HFD drives estrogen-dependent reprogramming of stromal fibroblasts, characterized by inflammation, stromal ECM accumulation and fibrosis, and a post-ovulatory shift from PGR-network-associated Aldh1a2+ Fibroblasts toward increasing ER-network-associated Gsn+ Fibroblasts. These fibroblast changes are accompanied by a reduction in endometrial macrophages and a transcriptomic shift of HFD epithelium toward hyperplastic epithelium seen in a mouse model of EH. Figure made with BioRender. C_FIG

physiology↗

bioRxiv2026

Modeling Reliable Detection Range of Cetaceans Imaged with Infrared Cameras

Infrared (IR) imaging systems are used on vessels, platforms, and drones to detect cetaceans several kilometers away, helping to mitigate harm from maritime activities like vessel strikes and pile driving. To ensure operational effectiveness, the reliable detection range (RDR) --the distance at which 100% detection probability is achieved--is a critical metric. This study presents a radiometric model for calculating RDR across a wide range of environmental conditions and system parameters, which enables the evaluation of IR system performance without extensive at-sea data collection.

ecology↗

bioRxiv2025

Neotropical bats as bioindicators for emerging zoonoses in Central America: A case study identifying Trypanosoma cruzi in bats from Belize using metagenomic next-generation sequencing

Emerging zoonoses remain a global public health concern. Surveillance of infectious and vector-borne diseases is vital for predicting and mitigating detrimental effects of zoonotic spillover events. Beyond assessing what microorganisms are circulating in specific environments, it is important to understand how potential reservoir hosts, especially animals such as bats, participate in pathogen transmission. Bats can host and potentially spread infections caused by bacteria, viruses, fungi, and protozoa. However, bats can also act as bioindicators that test positive for pathogenic microorganisms without necessarily contributing to the pathogen replication cycle. Metagenomic next-generation sequencing (mNGS) provides an efficient means to broadly screen for pathogens, although microorganism selectivity can sometimes be lower than targeted approaches. Pairing mNGS results with higher-sensitivity tests such as quantitative PCR (qPCR) can validate results and together these tools provide a relatively fast and reliable method for conducting surveillance. To test this approach, we surveyed the types of microorganisms circulating in Belize by collecting 263 blood samples from 20 different bat species captured in the Orange Walk District in 2019, 2022, and 2023. We used mNGS to initially characterize the microbial communities and qPCR to confirm presence and intensity of human pathogens of interest. We detected 1,430 different microorganisms with some relevance to human or animal health, including the protozoan Trypanosoma cruzi which was detected in the phyllostomid bats Desmodus rotundus and Artibeus jamaicensis. qPCR confirmed the presence and intensity of Trypanosoma cruzi in mNGS-positive bat samples. We documented the types of pathogenic microorganisms circulating throughout the bat community in northern Belize to demonstrate the capacity for bats to serve as bioindicators. Author SummaryTracking the spread of new and emerging zoonotic diseases is a major component of global health research. Pathogen surveillance is a vital part of predicting and reducing the consequences of disease outbreaks. Bats are a diverse group of mammals that can host and potentially transmit many pathogens that pose potential risks to human and environmental health. Our study surveyed blood samples (n=263) from 20 bat species collected from the Orange Walk District of Belize in 2019, 2022, and 2023. Metagenomic next-generation sequencing identified 1,430 different microorganisms that are considered potentially relevant to human or animal health. Among the microorganisms detected was Trypanosoma cruzi (T. cruzi), the protozoan causative agent of Chagas disease. T. cruzi was of particular interest due to its presence throughout the Americas and relevance to public health. We surveyed the types of microorganisms circulating throughout bat populations in northern Belize to demonstrate the ability of bats to act as bioindicators.

microbiology↗

bioRxiv2025

Maternal SETDB1 enables development beyond cleavage stages by extinguishing the MERVL-driven 2-cell totipotency transcriptional program in the mouse embryo

Loss of maternal SETDB1, a histone H3K9 methyltransferase, leads to developmental arrest prior to implantation, with very few mouse embryos advancing beyond the 8-cell stage, which is currently unexplained. We genetically investigate SETDB1s role in the epigenetic control of the transition from totipotency to pluripotency--a process demanding precise timing and forward directionality. Through single-embryo total RNA sequencing of 2-cell and 8-cell embryos, we find that Setdb1mat-/+ embryos fail to extinguish 1-cell and 2-cell transient genes--alongside persistent expression of MERVL retroelements and MERVL-driven chimeric transcripts that define the totipotent state in mouse 2-cell embryos. Comparative bioinformatics reveals that SETDB1 acts at MT2 LTRs and MERVL-driven chimeric transcripts, which normally acquire H3K9me3 during early development. The dysregulated targets substantially overlap with DUXBL-responsive genes, indicating a shared regulatory pathway for silencing the 2-cell transcriptional program. We establish maternal SETDB1 as a critical chromatin regulator required to extinguish retroelement-driven totipotency networks and ensure successful preimplantation development.

genetics↗

bioRxiv2025

The adhesion molecules β7 integrin and L-selectin contribute to cholestatic liver disease in male mice

Background & AimsPrimary sclerosing cholangitis (PSC) is a long-term progressive disease, often occurring in conjunction with inflammatory bowel disease (IBD). Dysregulated immune cell migration and gut microbiota alterations are implicated in disease progression. Livers of PSC patients show upregulation of the endothelial ligand mucosal addressin cell-adhesion molecule-1 (MAdCAM-1). Here we examined the role of the leukocytic adhesion molecules (AM) {beta}7 integrin and L-selectin, both binding partners of MAdCAM-1, in an experimental mouse model resembling aspects of human PSC. MethodsWild type (WT), {beta}7 integrin-deficient ({beta}7-/-), L-selectin-deficient (L-sel-/-), and L-selectin/{beta}7 integrin double-deficient (L-sel-/-/{beta}7-/-) male mice were compared in the model of 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC)-induced cholangiopathy. The extent of pathology was evaluated by serum parameters, histology, flow cytometry, and expression of inflammatory mediators. Fecal microbiota changes were assessed by 16S rRNA amplicon sequencing and intestinal permeability was measured by FITC-dextran assay. ResultsAM-deficient mice were markedly protected from DDC-induced cholangiopathy. Hepatic immune cell populations of AM-deficient mice differed significantly from those of WT mice. Adoptively transferred {beta}7-/- CD8+ T cells caused significantly less liver damage than CD8+ WT T cells in DDC-treated {beta}7-/- mice. DDC-feeding caused substantial changes in fecal microbiota profiles, which differed between the mouse strains, and a strong increase in intestinal permeability that was significantly lower in {beta}7-/- than WT mice. Conclusions{beta}7 integrin and L-selectin contribute to DDC-induced cholangiopathy with {beta}7 integrin-expressing CD8+ T cells playing a crucial role in promoting pathogenesis. In addition, AM-expressing immune cells may contribute to the inflammatory process by causing unfavorable gut microbiota shifts and destabilizing the gut barrier. Synopsis{beta}7 integrin- and/or L-selectin-deficient mice are less susceptible to 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC)-induced experimental cholangiopathy. {beta}7 integrin-expressing CD8+ T cells contribute to DDC-induced pathogenesis. {beta}7 integrin promotes DDC-induced gut barrier dysfunction and microbiota shifts, potentially exacerbating hepatic injury.

immunology↗

bioRxiv2025

YAP signaling promotes resistance to MEK and AKT inhibition in NF1-related MPNSTs

Neurofibromatosis type 1 (NF1) is a tumor predisposition syndrome caused by loss of function of the neurofibromin protein. Malignant peripheral nerve sheath tumors (MPNSTs) are a rare and deadly sarcoma with few therapeutic options that are the leading cause of death for patients with NF1. To date, no targeted therapies have been approved for MPNST treatment, highlighting the need for an understanding of adaptive signaling mechanisms that drive resistance. We developed a preclinical model of drug resistance using a cross-over drug holiday design and evaluated patterns of response and resistance to MEK and AKT inhibitors, two pathways that are dysregulated by loss of neurofibromin. We show that the mTOR and YAP/TEAD pathways are activated by MEK inhibitor exposure, yet blockade of these pathways in resistant MPNST PDX models does not significantly reduce tumor growth, despite strong in vitro synergy between trametinib and the novel TEAD inhibitor, GNE-7883. Using spatial transcriptomics, we uncovered phenotypic inertia as a key mechanism of drug resistance in MPNST, in addition to signaling plasticity. Further, we found that resistance is mediated by sustained ERK, YAP, and MYC driven transcriptional programs. In the future, preclinical studies should focus on addressing intratumoral heterogeneity and how it evolves over time.

cancer biology↗

bioRxiv2025

Limited Water Stress Triggers Adaptive Leaf Trait Response in Australian Commercial Rice Without Compromising Grain Yield and Quality

Water scarcity poses significant challenge for the Australian rice industry, driving the need for varieties with improved water use efficiency (WUE). This study evaluated 18 Australian elite japonica, two indica rice lines, and the West African japonica cultivar Moroberekan to assess stomatal and non-stomatal leaf traits contributing to WUE. Plants were cultivated under controlled glasshouse conditions with two water treatments: ponded (PW) and limited water (LW) maintained at 60-65% field capacity throughout the vegetative stage. Under LW, plants exhibited decreased photosynthetic efficiency, stomatal conductance, and stomatal density but increased cuticular and epicuticular wax (CEW) deposition, which helped conserve water. The rice cultivar Sherpa exhibited reduced sensitivity to regulation of gas exchange, stomatal adjustments and photosynthetic efficiency, and the greatest CEW deposition among the japonica varieties, indicating potential for improved WUE. Thousand grain weight showed no significant differences between the two water treatments. Brown rice yield and milling recovery were also unaffected. Spectral analysis of dehulled seeds suggested that LW stress increased protein content but had no effect on lipids and starch. These findings demonstrate that LW during the vegetative stage can induce water-conserving traits without compromising yield or grain quality; providing valuable insights for developing water-efficient rice varieties. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=70 SRC="FIGDIR/small/655428v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@11820bcorg.highwire.dtl.DTLVardef@10d1940org.highwire.dtl.DTLVardef@f4f3c2org.highwire.dtl.DTLVardef@1af7748_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightWater scarcity elicits a range of stomatal and non-stomatal responses in Australian commercial rice varieties without compromising yield and grain quality while enhancing water conservation.

plant biology↗

bioRxiv2025

Long non-coding RNA hsr-omega provides scaffolding for the nuclear domain B-body.

Nuclear domains (NDs)--such as nucleoli or nuclear speckles--are membraneless, organelle-like compartments that concentrate and retain nuclear proteins. Despite their ubiquitous presence in the cell, the organization, regulation, and functions of many NDs remain poorly understood. The B-body is a prominent nuclear domain observed in developing flight muscles of Drosophila. In this study, we expand the understanding of B-body composition and function. We identify several additional RNA-binding proteins (RBPs) as B-body components and show that some proteins can dynamically disappear from this ND. We further demonstrate that the B-body contains an RNA component, which was identified as the long non-coding RNA hsr{omega}. Genetic analyses reveal that hsr{omega} acts as a structural scaffold for the B-body, and its depletion leads to B-body disassembly. In contrast, loss of the resident protein Bruno (Bru), a splicing factor, does not compromise B-body integrity. Finally, we show that imbalance in the hsr{omega}/Bru ratio promotes Bru aggregation, suggesting that the B-body plays a role in maintaining nuclear protein homeostasis.

cell biology↗

bioRxiv2025

Application of machine learning to discriminate photoreceptor cell species in xenotransplanted chimeric retinas

Photoreceptor transplantation is being studied to improve visual function in retinal diseases causing blindness, such as age-related macular degeneration, hereditary eye diseases, and traumatic retinopathy, among others. Preclinical studies often involve the delivery of exogenous human photoreceptor cells into the retinas of animal models. In such experiments, a key readout is the differential frequency of donor cell somatic integration versus artificial labeling secondary to material transfer of cytosolic or nuclear labels from donor to recipient cells. For this analysis, the ability to recognize photoreceptor nuclei as being of donor (human) versus animal is key, but purely immunohistology discrimination can be challenging because of antigenic species overlap or intercellular antigen transfer. To address this challenge, we sought to develop and validate a computational technique to discriminate between photoreceptor cells of different animal species based on machine learning of nuclear morphology. Here, we aimed to evaluate the feasibility of using computer-assisted detection of separate nuclei and employing random forest classification to automate the species differentiation, among DAPI-stained photoreceptors after xeno-transplantation of human photoreceptors into the retinas of mice and pigs. Our models were trained on single-species samples and validated with mixed-species samples. We then transplanted human embryonic stem cell-derived retinal organoid cells into rodent and pig retinal degeneration models. The random forest model accurately determined cell identity post-xenotransplantation, validated by histological assessment using an anti-human nuclear antibody. Our results support the potential efficacy of employing machine learning image analysis and classification techniques that may promote experimental rigor, minimize observer bias, and enable high throughput semi-automated workflows for transplantation outcomes analysis. The methodological framework reported here may enable a more nuanced and precise analysis of the behavior of transplanted photoreceptors for the purposes of human retinal regeneration.

neuroscience↗

bioRxiv2024

Lineage labeling with zebrafish hand2 Cre and CreERT2 recombinase CRISPR knock-ins

BackgroundThe ability to generate endogenous Cre recombinase drivers using CRISPR- Cas9 knock-in technology allows lineage tracing, cell type specific gene studies, and in vivo validation of inferred developmental trajectories from phenotypic and gene expression analyses. This report describes endogenous zebrafish hand2 Cre and CreERT2 drivers generated with GeneWeld CRISPR-Cas9 precision targeted integration. Resultshand2-2A-cre and hand2-2A-creERT2 knock-ins crossed with ubiquitous loxP-based Switch reporters led to broad labeling in expected mesodermal and neural crest-derived lineages in cardiac, pectoral fins, pharyngeal arch, liver, intestine, and mesothelial tissues, as well as enteric neurons. Novel patterns of hand2 lineage tracing appeared in venous blood vessels. CreERT2 induction at 24 hours reveals late emerging hand2 progenitors in the 24 - 48 hour embryo contribute to the venous and intestinal vasculature. Induction in 3 dpf larva restricts hand2 lineage labeling to mesoderm-derived components of the branchial arches, heart, liver and enteric neurons. Conclusionshand2 progenitors from the lateral plate mesoderm and ectoderm contribute to numerous lineages in the developing embryo. Later emerging hand2 progenitors become restricted to a subset of lineages in the larva. The hand2 Cre and CreERT2 drivers establish critical new tools to investigate hand2 lineages in zebrafish embryogenesis and larval organogenesis. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=117 SRC="FIGDIR/small/626907v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@12f58cborg.highwire.dtl.DTLVardef@16e95c8org.highwire.dtl.DTLVardef@12b8e9dorg.highwire.dtl.DTLVardef@a01848_HPS_FORMAT_FIGEXP M_FIG C_FIG Zebrafish hand2 Cre and CreERT2 drivers generated with GeneWeld CRISPR/Cas9 precision targeted integration label numerous lineages from the mesoderm and ectoderm. Temporal CreERT2 Tamoxifen regulated switching re{-} veals late emerging hand2 progenitors contribute to the embryonic venous vasculature and larval organs.

developmental biology↗

bioRxiv2024

Modest functional diversity decline and pronounced composition shifts of microbial communities in a uranium-contaminated aquifer

BackgroundMicrobial taxonomic diversity declines with increased environmental stress. Yet, few studies have explored whether phylogenetic and functional diversities track taxonomic diversity along the stress gradient. Here, we investigated bacterial communities within an aquifer in Oak Ridge, Tennessee, USA, which is characterized by a broad spectrum of stressors, including extremely high levels of nitrate, heavy metals like cadmium and chromium, radionuclides such as uranium, and extremely low pH (<3). ResultsBoth taxonomic and phylogenetic -diversities were reduced in the most impacted wells, while the decline in functional -diversity was modest and statistically insignificant, indicating a more robust buffering capacity to environmental stress. Differences in functional gene composition (i.e., functional {beta}-diversity) were pronounced in highly contaminated wells, while convergent functional gene composition was observed in uncontaminated wells. The relative abundances of most carbon degradation genes were decreased in contaminated wells, but genes associated with denitrification, adenylylsulfate reduction, and sulfite reduction were increased. Compared to taxonomic and phylogenetic compositions, environmental variables played a more significant role in shaping functional gene composition, suggesting that niche selection could be more closely related to microbial functionality than taxonomy. ConclusionsOverall, we demonstrated that despite a reduced taxonomic -diversity, microbial communities under stress maintained functionality underpinned by environmental selection.

microbiology↗

bioRxiv2024

Bone marrow microenvironment signatures associate with patient survival after guadecitabine and atezolizumab therapy in HMA-resistant MDS

Almost 50% of patients with myelodysplastic syndrome (MDS) are refractory to first-line hypomethylating agents (HMAs), which presents a significant clinical challenge considering the lack of options for salvage. Past work revealed that immune checkpoint molecules on peripheral myeloblasts and immune cells are up-regulated after HMA treatment. Therefore, we conducted a Phase I/II clinical trial combining guadecitabine (an HMA) and atezolizumab (an immune checkpoint inhibitor) to treat HMA-relapsed or refractory (HMA-R/R) MDS patients. This combination therapy showed median overall survival of 15.1 months relative to historical controls (4-6 months). Here, we profiled the cell composition and gene expression signatures of cells from bone marrow aspirates from trial participants with short-term (<15 months) or long-term (>15 months) survival at single-cell resolution. Long-term survivors showed a significant reduction of immunosuppressive monocytes, and an expansion of effector lymphocytes after combination therapy. Further immune profiling suggests that gamma delta T cell activation through primed dendritic cells was associated with global interferon activation in the bone marrow microenvironment of long-term survivors. Short-term survivors exhibited elevated inflammation and senescence-like gene signatures that were not resolved by combination therapy. We propose that distinct bone marrow microenvironment features, such as senescence-associated inflammation or immunosuppressive monocyte presence, could improve patient stratification for HMA and immunotherapy combinations in HMA-R/R MDS patients.

cancer biology↗

bioRxiv2024

Microplate micromilling: A customizable platform to support the prototyping, development and testing of microphysiological culture models

The development of microphysiological cell culture models (MPMs) that align with the throughput demands of drug and chemical testing are needed to help reduce animal testing, aide in the discovery of new drugs, and identify harmful chemical exposures. To address this need, we have developed a process for rapid prototyping MPM devices using computer numerical control (CNC) micromilling of commercially available microplates. Microchannels are cut out of the existing microplate structure and ports are drilled into the bottom of the wells to interface the wells. To test versatility and benchmark to another rapid-prototyping approach, we manufactured common microfluidic features into microplates using four different CNC mills as well as a 3D printer. Cell viability was assessed for polystyrene (PS) well plates and two 3D printed resins (MED610 and VeroClear) with the PS showing >2.5-fold increase in cell growth after three days. Machines were tested on their ability to create common device features including a traditional microfluidic device as well as a custom design incorporating complex geometries. Features were measured by confocal microscopy. We found that features including 1000{micro}m ports, 800{micro}m microchannels, 200{micro}m phase-guides, and 500{micro}m post arrays were machined and the range of CVs for features were 1.02-4.42, 1.32-3.50, 2.34-16.58, 6.25-16.40 respectively, while the 3D printed features exhibited maximal CVs of 20.98, 11.68, 23.60, and 10.01 for the same features. Predictably, more expensive machines generally showed higher accuracy and lower variation, but many features could be created accurately and precisely by inexpensive (<$3000) machines facilitating the broader use of this technology to create a user customizable platform to support the prototyping, development, and testing of human relevant models with broad applications across the life sciences. Graphical abstractMultiple CNC mills are assessed on accuracy and precision of microfluidic features of interest for microphysiological model development creation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/615399v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@1be08eorg.highwire.dtl.DTLVardef@33b0a4org.highwire.dtl.DTLVardef@192167borg.highwire.dtl.DTLVardef@200b7_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2024

Parkinson's disease-associated shifts between DNA methylation and DNA hydroxymethylation in human brain

Epigenetic mechanisms are mediators of interactions between aging, genetics, and environmental factors in sporadic Parkinsons disease (PD). Multiple studies have explored the DNA modifications in PD, but few focus on 5-hydroxymethylcytosine (5-hmC), which is important in the central nervous system and sensitive to environmental exposures. To date, studies have not differentiated between 5-methylcytosine (5-mC) and 5-hmC or have analyzed them separately. In this study, we modeled paired 5-mC and 5-hmC data simultaneously. We identified 108 cytosines with significant PD-associated shifts between these marks in an enriched neuronal population from PD postmortem parietal cortex, within 83 genes and 34 enhancers associated with 67 genes. These data potentially link epigenetic regulation of genes related to LRRK2 and endolysosomal sort (RAB32 and AGAP1), and genes involved in neuroinflammation, the inflammasome, and neurodevelopment with early changes in PD and suggest that there are significant shifts between 5mC and 5hmC associated with PD in genes not captured by standard methods.

neuroscience↗

bioRxiv2024

Developmental origins of Parkinson's disease risk: perinatal exposure to the organochlorine pesticide dieldrin leads to sex-specific DNA modifications in critical neurodevelopmental pathways in the mouse midbrain

Epidemiological studies show that exposure to the organochlorine pesticide dieldrin is associated with increased risk of Parkinsons disease (PD). Animal studies support a link between developmental dieldrin exposure and increased neuronal susceptibility in the -synuclein preformed fibril (-syn PFF) and MPTP models in adult male C57BL/6 mice. In a previous study, we showed that developmental dieldrin exposure was associated with sex-specific changes in DNA modifications within genes related to dopaminergic neuron development and maintenance at 12 weeks of age. Here, we used capture hybridization-sequencing with custom baits to interrogate DNA modifications across the entire genetic loci of the previously identified genes at multiple time points - birth, 6 weeks, 12 weeks, and 36 weeks old. We identified largely sex-specific dieldrin-induced changes in DNA modifications at each time point that annotated to pathways important for neurodevelopment, potentially related to critical steps in early neurodevelopment, dopaminergic neuron differentiation, synaptogenesis, synaptic plasticity, and glial-neuron interactions. Despite large numbers of age-specific DNA modifications, longitudinal analysis identified a small number of DMCs with dieldrin-induced deflection of epigenetic aging. The sex-specificity of these results adds to evidence that sex-specific responses to PD-related exposures may underly sex-specific differences in disease. Overall, these data support the idea that developmental dieldrin exposure leads to changes in epigenetic patterns that persist after the exposure period and disrupt critical neurodevelopmental pathways, thereby impacting risk of late life diseases, including PD.

neuroscience↗

bioRxiv2024

Characterization of Collaborative Cross mouse founder strain CAST/EiJ as a novel model for lethal COVID-19

Mutations in SARS-CoV-2 variants of concern (VOCs) have expanded the viral host range beyond primates, and a limited range of other mammals, to mice, affording the opportunity to exploit genetically diverse mouse panels to model the broad range of responses to infection in patient populations. Here we surveyed responses to VOC infection in genetically diverse Collaborative Cross (CC) founder strains. Infection of wild-derived CC founder strains produced a broad range of viral burden, disease susceptibility and survival, whereas most other strains were resistant to disease despite measurable lung viral titers. In particular, CAST/EiJ, a wild-derived strain, developed high lung viral burdens, more severe lung pathology than seen in other CC strains, and a dysregulated cytokine profile resulting in morbidity and mortality. These inbred mouse strains may serve as a valuable platform to evaluate therapeutic countermeasures against severe COVID-19 and other coronavirus pandemics in the future.

immunology↗

bioRxiv2024

Molecular basis of foreign DNA recognition by BREX anti-phage immunity system

Anti-phage systems of the BREX (BacteRiophage EXclusion) superfamily rely on epigenetic DNA methylation to discriminate between the host and invading DNA, but their mechanism of protection remains enigmatic. We demonstrate that in Type I BREX systems, both defense and methylation are based on site-specific DNA recognition by the BrxX (PglX) methyltransferase and require the S-adenosyl methionine cofactor. We present a 2.2-[A] cryoEM structure of Escherichia coli BrxX bound to target dsDNA, which reveals the molecular details of DNA recognition by BREX and paves the way for rational engineering of BREX specificity. We show that BrxX alone does not support methylation, and BREX activity requires an assembly of a supramolecular BrxBCXZ immune complex. Finally, we present a cryoEM structure of BrxX bound to a phage-encoded inhibitor Ocr that sequesters an inactive dimeric form of BrxX. Together, these results allow us to propose a model of BREX-mediated DNA sensing and anti-phage defense.

molecular biology↗