Biology subjects

McArdle, S.

Publications and source records attributed to McArdle, S..

7 recordsLinked to original sources

bioRxiv2025

Unmasking Early Microglial Remodeling in an Alzheimer's Disease Mouse Model

Early neuroimmune remodeling is a critical yet understudied component of Alzheimers disease (AD) pathogenesis. To investigate microglial contributions to AD development prior to overt plaque deposition, we developed an open-source morphometric pipeline to systematically quantify hippocampal microglial structure and activation states in pre-plaque 5xFAD mice. Across [~]11,000 cells, we extracted multidimensional parameters including area, circularity, convex hull, branch points, nearest-neighbor distance, and nuclear features, alongside Iba1 and CD68 intensity measurements. While no significant overt gliosis was observed at this early stage, microglia from 5xFAD mice exhibited subtle trends toward increased structural complexity compared to wild-type controls. Importantly, significant sex-specific differences were detected within the CA1 subregion: male 5xFAD microglia displayed hyper-ramified morphologies consistent with enhanced surveillance states, whereas female microglia demonstrated greater density and a more reactive phenotype. Correlation analyses revealed a conserved association between microglial complexity and Iba1/CD68 expression, independent of sex or genotype, underscoring a fundamental link between cytoskeletal remodeling and phagolysosomal activity. These findings highlight the capacity of morphometric profiling to sensitively detect early, region-specific, and sex-dependent shifts in microglial phenotype before amyloid deposition. By integrating quantitative morphology with canonical molecular markers, this framework provides a robust and unbiased approach for characterizing microglial activation trajectories. Such early readouts may inform biomarker discovery and therapeutic strategies aimed at modulating microglial responses to delay or prevent AD progression.

neuroscience↗

bioRxiv2025

Whole tissue spatial cellular analysis reveals increased macrophage infiltration in pancreata of autoantibody positive donors and patients with type 1 diabetes

While extensive efforts have characterized lymphoid populations that contribute to pancreatic insulitis in type 1 diabetes, significant gaps remain regarding key properties of macrophages in this inflammatory lesion. Hence, we quantified the spatial distribution of macrophages infiltrating human pancreatic tissue sections across disease states. Whole slide images of immunofluoresent stainings were analyzed with a semiautomated machine learning approach to study the distribution of macrophages throughout pancreatic sections from non-diabetic, auto-antibody positive (Aab+), and type 1 diabetes organ donors. Across the entire tissue section, macrophage infiltration was highest in donors with type 1 diabetes, and appeared contingent on the prescence of insulin-containing islets. Aab+ donors had higher macrophage densities in islet and peri-islet regions than non-diabetic individuals, but there was large case-by-case variation. Additionally, a greater proportion of macrophages highly expressed HLA class II (HLA-II) near and within islet regions of the type 1 diabetes group, which correlated with the proportion of stressed beta cells expressing HLA-II. The higher density of macrophages in the Aab+ and type 1 diabetes donors, taken together with higher expression of HLA-II in the type 1 diabetes pancreas, suggests that macrophages play a pivotal role in human type 1 diabetes initiation and progression. Article HighlightsO_LIMacrophage infiltration is increased in all pancreatic regions of patients with type 1 diabetes, and this infiltration appears contingent on the presence of insulin-containing islets. C_LIO_LIAab+ donors have higher macrophage densities in islet and peri-islet regions than non-diabetic individuals, but there is large case-by-case variation within the Aab+ group. C_LIO_LIThe proportion of macrophages highly expressing HLA-II is increased near and within islets only in patients with type 1 diabetes, and this correlates with the proportion of stressed beta cells expressing HLA-II within the islet. C_LIO_LIMacrophages are linked to human type 1 diabetes initiation and progression, hence forming a rationale to examine therapeutic strategies involving this cellular population. C_LI

pathology↗

bioRxiv2025

Integrated histopathology of the human pancreas throughout stages of type 1 diabetes progression

Type 1 diabetes (T1D) is a progressive autoimmune condition that culminates in the loss of insulin-producing beta cells. Pancreatic histopathology provides essential insights into disease initiation and progression yet an integrated perspective of in situ pathogenic processes is lacking due to limited sample availability, the dispersed nature of anatomical lesions, and often restricted analytical dimensionality. Here, we combined multiplexed immunostaining, high-magnification whole-slide imaging, digital pathology, and semi-automated image analysis strategies to interrogate pancreatic tail and head regions obtained from organ donors across T1D stages including at-risk and at-onset cases. Deconvolution of architectural features, endocrine cell composition, immune cell burden, and spatial relations of [~]25,000 islets revealed a series of novel histopathological correlates especially in the prodromal disease stage preceding clinical T1D. Altogether, our comprehensive "single-islet" analyses permit the reconstruction of a revised natural T1D history with implications for further histopathological investigations, considerations of pathogenetic modalities, and therapeutic interventions.

immunology↗

bioRxiv2023

Linked CD4+/CD8+ T cell neoantigen vaccination overcomes immune checkpoint blockade resistance and enables tumor regression

Therapeutic benefit to immune checkpoint blockade (ICB) is currently limited to the subset of cancers thought to possess a sufficient tumor mutational burden (TMB) to allow for the spontaneous recognition of neoantigens (NeoAg) by autologous T cells. We explored whether the response of an aggressive low TMB squamous cell tumor to ICB could be improved through combination immunotherapy using functionally defined NeoAg as targets for endogenous CD4+ and CD8+ T cells. We found that, whereas vaccination with CD4+ or CD8+ NeoAg alone did not offer prophylactic or therapeutic immunity, vaccines containing NeoAg recognized by both subsets overcame ICB resistance and led to the eradication of large established tumors that contained a subset of PD-L1+ tumor-initiating cancer stem cells (tCSC), provided the relevant epitopes were physically linked. Therapeutic CD4+/CD8+ T cell NeoAg vaccination produced a modified tumor microenvironment (TME) with increased numbers of NeoAg-specific CD8+ T cells existing in progenitor and intermediate exhausted states enabled by combination ICB-mediated intermolecular epitope spreading. The concepts explored herein should be exploited for the development of more potent personalized cancer vaccines that can expand the range of tumors treatable with ICB.

immunology↗

bioRxiv2022

Spatial and functional arrangement of Ebola virus polymerase inside phase-separated viral factories

Ebola virus (EBOV) infection induces the formation of membrane-less, cytoplasmic compartments termed viral factories, in which multiple viral proteins gather and coordinate viral transcription, replication and assembly. Key to viral factory function is the recruitment of EBOV polymerase, a multifunctional machine that mediates transcription and replication of the viral RNA genome. We show that intracellularly reconstituted EBOV viral factories are biomolecular condensates, with composition-dependent internal exchange dynamics that likely facilitates viral replication. Within the viral factory, we found the EBOV polymerase clusters into foci. The distance between these foci increases when viral replication is enabled. In addition to the typical droplet-like viral factories, we report the formation of network-like viral factories during EBOV infection. Unlike droplet-like viral factories, network-like factories are inactive for EBOV nucleocapsid assembly. This unique view of EBOV propagation suggests a form-to-function relationship that describes how physical properties and internal structures of biomolecular condensates influence viral biogenesis.

microbiology↗

bioRxiv2022

Treatment of pancreatic cancer with irreversible electroporation and intratumoral CD40 antibody stimulates systemic immune responses that inhibit liver metastasis in an orthotopic model.

BackgroundPancreatic cancer (PC) has a poor prognosis, and most patients present with either locally advanced or distant metastatic disease. Irreversible Electroporation (IRE) is a non-thermal method of ablation used clinically in locally advanced PC, but most patients eventually develop distant recurrence. We have previously shown that IRE alone is capable of generating protective, neoantigen-specific immunity. Here we aim to generate meaningful therapeutic immune effects by combining IRE with local (intratumoral) delivery of a CD40 agonistic antibody (CD40Ab). MethodsKPC46 organoids were generated from a tumor-bearing male KrasLSL-G12D-p53LSL-R172H-Pdx-1-Cre (KPC) mouse. Orthotopic tumors were established in the pancreatic tail of B6/129 F1J mice via laparotomy. Mice were randomized to treatment with either sham laparotomy, IRE alone, CD40Ab alone, or IRE followed immediately by CD40Ab injection. Metastatic disease and immune infiltration in the liver were analyzed 14 days post-procedure using flow cytometry and multiplex immunofluorescence imaging with spatial analysis. Candidate neoantigens were identified by mutanome profiling of tumor tissue for ex vivo functional analyses. ResultsThe combination of IRE+CD40Ab improved median survival to greater than 35 days, significantly longer than IRE (21 days) or CD40Ab (24 days) alone (p<0.01). CD40Ab decreased metastatic disease burden, with less disease in the combination group than in the sham group or IRE alone. Immunohistochemistry of liver metastases revealed a more than two-fold higher infiltration of CD8+ T-cells in the IRE+CD40Ab group than in any other group (p<0.01). Multiplex immunofluorescence imaging revealed a 4-6-fold increase in the density of CD80+CD11c+ activated dendritic cells (p<0.05), which were spatially distributed throughout the tumor unlike the sham group, where they were restricted to the periphery. In contrast, CD4+FoxP3+ T-regulatory cells (p<0.05) and Ly6G+ MDSCs (P<0.01) were reduced and restricted to the tumor periphery in the IRE+CD40Ab group. T-cells from the IRE+CD40Ab group recognized significantly more peptides representing candidate neoantigens than did T-cells from the IRE or untreated control groups. ConclusionsIRE can induce local tumor regression and neoantigen-specific immune responses. Addition of CD40Ab to IRE improved dendritic cell activation and neoantigen recognition, while generating a strong systemic anti-tumor T-cell response that inhibited metastatic disease progression. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=89 SRC="FIGDIR/small/510847v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@1a42713org.highwire.dtl.DTLVardef@16be8org.highwire.dtl.DTLVardef@15362eaorg.highwire.dtl.DTLVardef@182f988_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2018

PRESTO, a new tool for integrating large-scale -omics data and discovering disease-specific signatures

BackgroundCohesive visualization and interpretation of hyperdimensional, large-scale -omics data is an ongoing challenge, particularly for biologists and clinicians involved in current highly complex sequencing studies. Multivariate studies are often better suited towards non-linear network analysis than differential expression testing. Here, we present PRESTO, a PREdictive Stochastic neighbor embedding Tool for Omics, which allows unsupervised dimensionality reduction of multivariate data matrices with thousands of subjects or conditions. PRESTO is intuitively integrated into an interactive user interface that helps to visualize the multidimensional patterns in genome-wide transcriptomic data from basic science and clinical studies.\n\nResultsPRESTO was tested with multiple input omics platforms, including microarray and proteomics from both mouse and human clinical datasets. PRESTO can analyze up to tens of thousands of genes and shows no increase in processing time with a large number of samples or patients. In complex datasets, such as those with multiple time points, several patient groups, or diverse mouse strains, PRESTO outperformed conventional methods. Core co-expressed gene networks were intuitively grouped in clusters, or gates, after dimensionality reduction and remained consistent across users. Networks were identified and assigned to physiological and pathological functions that cannot be gleaned from conventional bioinformatics analyses. PRESTO detected gene networks from the natural variations among mouse macrophages and human blood leukocytes. We applied PRESTO to clinical transcriptomic and proteomic data from large patient cohorts and detected disease-defining signatures in antibody-mediated kidney transplant rejection, renal cell carcinoma, and relapsing acute myeloid leukemia (AML). In AML, PRESTO confirmed a previously described gene signature and found a new signature of 10 genes that is highly predictive of patient outcome.\n\nConclusionsPRESTO offers an important integration of powerful bioinformatics tools with an interactive user interface that increases data analysis accessibility beyond bioinformaticians and coders. Here, we show that PRESTO out performs conventional methods, such as DE analysis, in multi-dimensional datasets and can identify biologically relevant co-expression gene networks. In paired samples or time points, co-expression networks could be compared for insight into longitudinal regulatory mechanisms. Additionally, PRESTO identified disease-specific signatures in clinical datasets with highly significant diagnostic and prognostic potential.

bioinformatics↗