Biology subjects

Ciernia, A. V.

Publications and source records attributed to Ciernia, A. V..

11 recordsLinked to original sources

bioRxiv2026

Sex and APOE Genotype Differentially Shape Microglial Transcriptomic Profiles Across the Hippocampus and Cortex

Female sex and the APOEe4 allele are top risk factors for Alzheimers disease (AD). Microglia play a role in the pathogenesis of AD, yet how sex and APOE genotype affect microglia remain poorly understood. Here, we characterized the transcriptomic and morphological profiles in the hippocampus and cortex of microglia from humanized APOEe3 and APOEe4 mice of males and females. The hAPOEe4 genotype was associated with sex-dependent effects on microglia co-expression modules in both brain regions, involving cellular stress and immunometabolism processes. In females, a hippocampal cell cycle module was supported by reduced microglial proliferation. Cortical modules were enriched for lipid metabolism and immune-related processes whose expression decreased in females but increased in male hAPOEe4. Male, but not female, hAPOEe4 microglia shifted toward an ameboid state in both regions. Together, these findings reveal sex-dependent microglial responses to APOEe4 across brain regions and highlight the need to incorporate sex-specific approaches into AD research.

neuroscience↗

bioRxiv2026

Microbiome-derived Short Chain Fatty Acids modulate microglial inflammatory responses in a sex- and metabolite-specific manner

Microbes residing in the gastrointestinal tract exert immunomodulatory impacts on the brain through the gut-brain axis. Short-chain fatty acids (SCFAs) produced by bacterial fermentation of dietary fiber can enter the brain parenchyma and are implicated in microglia-mediated inflammation. While the gut microbiome is required to maintain microglial homeostasis, the mechanisms by which microbiota-derived metabolites affect microglia remains unknown. We examined the roles of SCFAs, specifically butyrate, propionate and acetate, on microglial function in response to SCFAs both in vitro using BV2 cells and in vivo in mice. We observed in vivo that SCFAs impact microglial transcriptional responses to LPS in a sex- and metabolite-specific manner with butyrate having the strongest effect. Enriched gene sets included signatures associated with LPS-responsive microglia, Arg1-positive microglia, microglial cell cycle related genes and genes affiliated with changes in microglial morphology. We observed a similar effect in vitro, where metabolite administration enhanced phagocytosis, blunted proliferation and nitric oxide production. We then evaluated global histone modification levels following metabolite treatment and detected an enhancement of H3K9ac, H3K27ac, and H3K4me3 both in vivo and in BV2 cells treated with butyrate. Finally, we showed that butyrate is a potent HDAC inhibitor possibly contributing to enhanced acetylation. Hence, our findings suggest that SCFAs impact microglial function in a metabolite- and sex-specific manner, and that butyrate blunts inflammation by regulating microglial histone acetylation. Our results provide a more in-depth understanding of gut microbiome-microglia crosstalk, opening the door for new microbiome- and microglia-targeted therapies. HighlightsXxxx

neuroscience↗

bioRxiv2026

Spatially-resolved integration of microglia morphological diversity and gene expression using Visium with protein co-detection

Microglia exhibit a dynamic range of morphologies that actively shift in response to local environmental cues. There has been a concerted effort as a field to move away from dualistic characterization of all microglia as resting or activated, which is often described in terms of their morphological differences alone, towards more integrated definitions of microglial states based on multiple data types. Recent advances in spatially-resolved transcriptomics offer new ways to understand microglial gene expression in situ. Here, we related microglia morphology to gene expression within a published, spatially-resolved proteogenomics (Visium-SPG) dataset of the human dorsolateral prefrontal cortex as proof of principle to combine the contributions of microglia morphology to regional transcriptomics differences in the brain. The published dataset uniquely combined spatial transcriptomics with immunofluorescent staining for four major brain cell types, including microglia, which enabled us to link microglial morphologies to gene expression in a spatially-resolved manner. Using a computational toolset, MicrogliaMorphology and MicrogliaMorphologyR, we classified individual microglia into morphological subtypes, assigned microglia to spots, and integrated these data with transcriptomic profiles for each Visium-SPG spot. We applied non-negative matrix factorization to account for contributions from multiple cell types, morphological features, and regional context in downstream differential expression modeling. Our approach offers a methodological framework for investigating the relationship between microglial morphology and gene expression in larger cohorts and within disease contexts where changes in microglia morphology are anticipated. Author summaryRecent advances in spatially-resolved transcriptomics and the development of methods to deconvolve cell type signals has offered new ways to understand microglial gene expression in various tissue contexts. In this work, we related microglia morphologies to gene expression within a published spatial transcriptomics dataset of the human dorsolateral prefrontal cortex to assess whether morphologically different microglia are transcriptomically different in the healthy human brain. This dataset uniquely combines spatial transcriptomics with immunofluorescent staining for four major brain cell types, including microglia, enabling the linkage of microglial morphologies to gene expression in a spatially-resolved manner. Using a computational toolset for microglia morphology analysis, we classified individual microglia into morphological subtypes and integrated these data with spatial transcriptomic profiles while accounting for contributions from multiple cell types, morphological features, and regional context. This allowed for the identification of microglia morphology-related genes that are differentially expressed between microglial subtypes and relevant to human brain disorders. Findings together provide proof of principle for exploring the relationship between microglial morphology and gene expression in larger cohorts and diverse experimental contexts.

neuroscience↗

bioRxiv2026

ROIMAPer: An Open Source Framework for Rapid and Accurate Atlas Based Registration of Individual Brain Images in FIJI

The brains remarkable complexity and cellular heterogeneity necessitate precise anatomical annotation to ensure that imaging-based analyses accurately resolve region-specific features. Few computational tools currently exist that allow for the accurate and rapid registration of single brain images to standard brain atlases. To address this limitation, we developed ROIMAPer, a novel FIJI plugin for rapid registration of individual brain slices. ROIMAPer includes eight atlases spanning mouse, rat, and human brain anatomy across multiple developmental stages, making it broadly applicable across diverse experimental contexts. It allows for linear and affine scaling of the reference atlas to the experimental image and is optimized for serial processing of large quantities of images. We demonstrated the accuracy of ROIMAPer through quantification of in situ hybridization data from the Allen Gene Expression Atlas of seven marker genes across major brain regions and of four marker genes across hippocampal subfields. Quantification of marker genes within their assigned brain regions closely matched the ground truth across all major regions. At a finer resolution, marker-gene quantification within hippocampal subregions aligned with the experimental data, although discrepancies with the ground truth were observed for Mcu. Overall, ROIMAPer provides broad utility for open-source brain image analysis from multiple species. Significance StatementWe present an open-source, user-friendly, and accessible tool for registration of individual brain slices to anatomical reference atlases, compatible with the image analysis platform FIJI. The field lacks tools that offer a span of cross-species atlases, FIJI-compatibility, intuitive linear scaling methods, and low user-input without requiring high computational skill. Our tool minimizes user-involvement, allows for processing of larger datasets through more effective resource management, and speeds-up previously tedious processing steps.

neuroscience↗

bioRxiv2024

Characteristics of early career health researchers and experiences of burnout during the COVID-19 pandemic in Canada

IntroductionThe COVID-19 pandemic disrupted research globally. How it impacted Canadian early-career health researchers (ECHRs) remains unclear. We administered a survey to understand the composition of ECHRs in Canada, their job experiences, and experiences of burnout during the COVID-19 pandemic. MethodsA cross-sectional survey was conducted in May 2023 of Canadian ECHRs defined as within 7 years of their first independent research position. Quantitative analyses included a description of respondents by research pillar, socio-demographic and workplace characteristics, and the prevalence of burnout, disengagement or exhaustion. Sample characteristics were compared to national data on ECHRs from a Canadian funding agency. Thematic analysis of free-text responses was also conducted. ResultsA total of 225 respondents met the eligibility criteria. Most respondents were assistant professors and characteristics of our sample were like the national data. The COVID-19 pandemic posed many challenges to student recruitment, and emotional support of students, with over half of the respondents reporting a moderate to significant decline in mental health compared to pre-pandemic. A significant proportion of respondents were experiencing high burnout (62%, 95%CI:56-67%), exhaustion (64%, 95%CI: 57-70%) or disengagement (91%, 95%CI: 87-95%). Thematic analysis identified three themes: ongoing benefits/problems preceding the pandemic, unintended outcomes of strategies to manage/prevent/contain COVID-19, and reasons to stay in their current position. ConclusionsOur survey revealed that Canadian ECHRs reported many diverse challenges during the COVID-19 pandemic and high burnout, putting the sustainability of this workforce at risk. Improved systems are needed to understand the long-term impacts and support the future of the Canadian health research ecosystem.

scientific communication and education↗

bioRxiv2024

Early life intestinal inflammation alters gut microbiome, impairing gut-brain communication and reproductive behavior in mice

Despite recent advances in understanding the connection between the gut microbiota and the adult brain, there remains a wide knowledge gap in how gut inflammation impacts brain development. We hypothesized that intestinal inflammation in early life would negatively affect neurodevelopment through dysregulation of microbiota communication to the brain. We therefore developed a novel pediatric chemical model of inflammatory bowel disease (IBD), an incurable condition affecting millions of people worldwide. IBD is characterized by chronic intestinal inflammation, and has comorbid symptoms of anxiety, depression and cognitive impairment. Significantly, 25% of patients with IBD are diagnosed during childhood, and the effect of chronic inflammation during this critical period of development is largely unknown. This study investigated the effects of early-life gut inflammation induced by DSS (dextran sulfate sodium) on a range of microbiota, endocrine, and behavioral outcomes, focusing on sex-specific impacts. DSS-treated mice exhibited increased intestinal inflammation, altered microbiota membership, and changes in microbiota-mediated circulating metabolites. The majority of behavioral measures were unaffected, with the exception of impaired mate-seeking behaviors in DSS-treated males. DSS-treated males also showed significantly smaller seminal vesicles, lower circulating androgens, and decreased intestinal hormone-activating enzyme activity. In the brain, microglia morphology was chronically altered with DSS treatment in a sex-specific manner. The results suggest that early-life gut inflammation causes changes in gut microbiota composition, affecting short-chain fatty acid (SCFA) producers and glucuronidase (GUS) activity, correlating with altered SCFA and androgen levels. The findings emphasize the developmental sensitivity to inflammation-induced changes in endocrine signalling and underscore long-lasting physiological and microbiome changes associated with juvenile IBD. HighlightsEarly-life gut inflammation produces sex-specific effects on i) microbiome, ii) sex hormones and iii) behaviour. Both sexes show disrupted gut bacterial members that regulate sex hormone levels. Male mice demonstrate deficits in mate seeking, which may be mediated by reduced androgen levels. Both male and female mice demonstrate shifts in hippocampal microglial morphology.

neuroscience↗

bioRxiv2024

Repeated LPS induces training and tolerance of microglial responses across brain regions

BackgroundNeuroinflammation is involved in the pathogenesis of almost every central nervous system disorder. As the brains innate immune cells, microglia fine tune their activity to a dynamic brain environment. Previous studies have shown that repeated bouts of peripheral inflammation can trigger long-term changes in microglial gene expression and function, a form of innate immune memory. Methods and ResultsIn this study, we used multiple low-dose lipopolysaccharide (LPS) injections in adult mice to study the acute cytokine, transcriptomic, and microglia morphological changes that contribute to the formation of immune memory in the frontal cortex, hippocampus, and striatum, as well as the long-term effects of these changes on behavior. Training and tolerance of gene expression was shared across regions, and we identified 3 unique clusters of DEGs (2xLPS-sensitive, 4xLPS-sensitive, LPS-decreased) with different biological functions. 2xLPS-sensitive DEG promoters were enriched for binding sites for IRF and NFkB family transcription factors, two key regulators of innate immune memory. We quantified shifts in microglia morphological populations and found that while the proportion of ramified and rod-like microglia mostly remained consistent within brain regions and sexes with LPS treatment, there was a shift from ameboid towards hypertrophic morphological states across immune memory states and a dynamic emergence and resolution of trains of rod-like microglia with repeated LPS. ConclusionsTogether, findings support the dynamic regulation of microglia during the formation of immune memories in the brain and support future work to exploit this model in brain disease contexts.

neuroscience↗

bioRxiv2023

Development of a high-throughput pipeline to characterize microglia morphological states at a single-cell resolution

As rapid responders to their environments, microglia engage in functions that are mirrored by their cellular morphology. Microglia are classically thought to exhibit a ramified morphology under homeostatic conditions which switches to an ameboid form during inflammatory conditions. However, microglia display a wide spectrum of morphologies outside of this dichotomy, including rod-like, ramified, ameboid, and hypertrophic states, which have been observed across brain regions, neurodevelopmental timepoints, and various pathological contexts. We used dimensionality reduction and clustering approaches to consider contributions of multiple morphology measures together to define a spectrum of microglial morphological states. Using ImageJ tools, we first developed a semi-automated approach to characterize 27 morphology features from hundreds to thousands of individual microglial cells in a brain subregion-specific manner. Within this pool of morphology measures, we defined distinct sets of highly correlated features that describe different aspects of morphology, including branch length, branching complexity, territory span, and cell circularity. When considered together, these sets of features drove different morphological clusters. Furthermore, our analysis toolset captured morphological states similarly and robustly when applied to independent datasets and using different immunofluorescent markers for microglia. We have compiled our morphology analysis pipeline into an accessible, easy to use, and fully open-source ImageJ macro and R package that the neuroscience community can expand upon and directly apply to their own analyses. Outcomes from this work will supply the field with new tools to systematically evaluate the heterogeneity of microglia morphological states across various experimental models and research questions.

neuroscience↗

bioRxiv2022

Histone deacetylase 3 regulates microglial function through histone deacetylation

BackgroundAs the primary innate immune cells of the brain microglia respond to damage and disease through pro-inflammatory release of cytokines and neuroinflammatory molecules. Histone acetylation is an activating transcriptional mark that regulates gene expression, which is altered in states of disease. Inhibition of histone deacetylase 3 (Hdac3) has been utilized in pre-clinical models of disease to dampen inflammation, but the molecular mechanisms underlying Hdac3s regulation of inflammatory gene expression in microglia is not well understood. MethodsFunctional changes in immortalized microglia were characterized using a Hdac3 specific inhibitor RGFP966 in response to an immune challenge lipopolysaccharide (LPS). Flow cytometry and cleavage under tags & release using nucleases (CUT & RUN) were used to investigate global and promoter-specific histone acetylation changes, resulting in altered gene expression. ResultsHdac3 inhibition enhanced neuroprotective functions of microglia in response to LPS through reduced nitric oxide release and increased baseline phagocytosis. Inhibition of Hdac3 enhanced histone acetylation globally and at specific gene loci, resulting in the release of gene repression at baseline and enhanced responses to LPS. ConclusionThe findings suggest Hdac3 serves as a negative regulator of microglial gene expression, and that inhibition of Hdac3 facilitates the microglial response to inflammation and its subsequent resolution. Together, this work provides new mechanistic insights into therapeutic applications of Hdac3 inhibition which mediate reduced neuroinflammatory insults through microglial response.

neuroscience↗

bioRxiv2021

MGEnrichment: a web application for microglia gene list enrichment analysis

Gene expression analysis is becoming increasingly utilized in neuro-immunology research, and there is a growing need for non-programming scientists to be able to analyze their own genomic data. MGEnrichment is a web application developed both to disseminate to the community our curated database of microglia-relevant gene lists, and to allow non-programming scientists to easily conduct statistical enrichment analysis on their gene expression data. Users can upload their own gene IDs to assess the relevance of their expression data against gene lists from other studies. We include example datasets of differentially expressed genes (DEGs) from human postmortem brain samples from Autism Spectrum Disorder (ASD) and matched controls. We demonstrate how MGEnrichment can be used to expand the interpretations of these DEG lists in terms of regulation of microglial gene expression and provide novel insights into how ASD DEGs may be implicated specifically in microglial development, microbiome responses and relationships to other neuropsychiatric disorders. This tool will be particularly useful for those working in microglia, autism spectrum disorders, and neuro-immune activation research. MGEnrichment is available at https://ciernialab.shinyapps.io/MGEnrichmentApp/ and further online documentation and datasets can be found at https://github.com/ciernialab/MGEnrichmentApp. The app is released under the GNU GPLv3 open source license.

neuroscience↗

bioRxiv2020

Genetic variants drive altered epigenetic regulation of endotoxin tolerance in BTBR macrophages

The BTBR T+Itpr3tf/J (BTBR) mouse has been used as a complex genetic model of Autism Spectrum Disorders (ASD). While the specific mechanisms underlying BTBR behavioral phenotypes are poorly understood, prior studies have implicated profound differences in innate immune system control of pro-inflammatory cytokines. Innate immune activation and elevated pro-inflammatory cytokines are also detected in blood of children with ASD. In this study, we examined how underlying BTBR genetic variants correspond to strain-specific changes in chromatin accessibility, resulting in a pro-inflammatory response specifically in BTBR bone marrow derived macrophages (BMDM). In response to repeated lipopolysaccharide (LPS) treatments, C57BL/6J (C57) BMDM exhibited intact endotoxin tolerance. In contrast, BTBR BMDM exhibited hyper-responsive expression of genes that were normally tolerized in C57. This failure in formation of endotoxin tolerance in BTBR was mirrored at the level of chromatin accessibility. Using ATAC-seq, we specifically identified promoter and enhancer regions with strain-specific differential chromatin accessibility both at baseline and in response to LPS. Regions with strain-specific differences in chromatin accessibility were significantly enriched for BTBR genetic variants, such that an average of 22% of the differential chromatin regions had at least one variant. Together, these results demonstrate that BTBR genetic variants contribute to altered chromatin responsiveness to endotoxin challenge and a failure in formation of tolerance, resulting in a hyper-responsive innate immunity in BTBR. These findings provide evidence for an interaction between complex genetic variants and differential epigenetic regulation of innate immune responses. Our findings also provide novel mechanistic insight into the complex genetic architecture and immune abnormalities observed in ASD.

molecular biology↗