Biology subjects

Bearer, E. L.

Publications and source records attributed to Bearer, E. L..

9 recordsLinked to original sources

bioRxiv2026

Multi-Omic and Spatial Profiling Defines Outcome-Associated Tumor States in Head and Neck Adenoid Cystic Carcinoma

Abstract Head and neck adenoid cystic carcinoma (HNACC) shows highly variable clinical behavior that histopathological features only partly predict, and prognostic biomarkers for aggressive disease at diagnosis remain limited. Here, we show by integrating bulk, single-cell, and spatial transcriptomes from 25 HNACC tumors that poor survival is marked by profound loss of myoepithelial tumor cells and expansion of luminal tumor states. Both outcome groups share a myoepithelial-like origin, but aggressive tumors converge on an actively dividing, MYC/E2F-driven luminal state concentrated in discrete spatial niches. Aggressiveness therefore reflects where tumors end along a shared developmental path rather than a distinct lineage or altered immune infiltration. A four-gene classifier capturing this state predicted survival in an independent cohort, outperforming larger signatures and flagging aggressive subgroups in two others. These findings define a lineage proliferation axis linked to HNACC outcome, providing a basis for prospective risk stratification and proliferative-directed therapy.

cancer biology↗

bioRxiv2026

Visualizing micro- nanoplastics in the human brain: Early evidence for roles in microvascular pathology

Our environment has become progressively contaminated with non-biological materials, especially synthetic carbon polymers, plastics. Unsurprisingly some of these make it into the human body as detected by chemical analyses, yet it is unknown whether they cause harm or are innocent bystanders. Building on our observations of glossy deposits and unusual non-biological fluorescent particles in blood vessels, we aimed to determine whether these objects represented plastics. To do this we prepared plastics-enriched pellets from brain and subjected them to pyrolysis gas-chromatography/mass spectroscopy (py-GC/MS), electron microscopy and confocal laser scanning microscopy. Py-GC/MS confirmed the presence of 10 different plastics. Contents of pellets were examined by thin-section EM. We then used laser scanning confocal microscopy to acquire hyperspectral profiles of each type of plastic in suspensions. We found fluorescent particles in all pellets from brains. All 12 plastics in the calibration standard fluoresced. We obtained hyperspectral profiles of single species plastics from industry: Polyethylene, polypropylene and polystyrene. Controls included chemical analysis of brain storage buffer, which had no detectable plastics; and imaging water only and areas on slides lacking tissue. Abundant particles with emission profiles similar to polyethylene and polypropylene decorated the walls of both arterioles and venules. These particles were coincident with glossy deposits we first observed in white matter, suggesting that both features represent plastics. In summary our results demonstrate that synthetic polymers exhibit detectable fluorescence, and particles with similar spectral properties are visible in histologic sections. This opens the door to investigating correlations between plastics and pathology.

pathology↗

bioRxiv2026

Quality Assurance Strategies for Brain State Characterization by MEMRI

BackgroundManganese-enhanced magnetic resonance imaging (MEMRI) is a powerful approach for mapping brain-wide neural activity and axonal projections in vivo. Yet standardized computational frameworks for voxel-wise and atlas-based characterization of brain states across large experimental cohorts remain limited. New methodHere, we present methodological advances for preprocessing and statistical analysis of MEMRI datasets to support scalable, reproducible cohort-level analyses. Quality assurance metrics were developed to evaluate images, cohort-level anatomical alignment, and intensity normalization. Using simulated data, we optimized smoothing, effect-size, and cluster-size thresholds to balance sensitivity and specificity in voxel-wise statistical mapping. We developed InVivoSegment software to apply to our new InVivo Atlas for segmentation of MEMRI data and interpretation of brain-wide activity. ResultsQuality assurance analyses established benchmarks for Mn(II)-induced signal- and contrast-to-noise evaluation, precise cohort-level alignment at 100 m isotropic resolution, and robust intensity normalization. Balanced accuracy and Youdens J statistics were calculated from simulated true positive and noise-only intensities, which defined optimal parameters for smoothing kernel, cluster-size and effect-size thresholds during voxel-wise mapping. Segmentation of simulated data demonstrated reliable transformation of voxel-wise results into regional summaries and identified secondary thresholds that minimize noise-driven artifacts. Comparison with existing methodsApproach to optimize correction parameters for statistical mapping using simulated images improves voxel- and segment-wise sensitivity compared to FDR/FWE-based correction procedures. ConclusionsThese methodological advances enable scalable, reproducible, brain-wide quantification of longitudinal changes in MEMRI studies, strengthen mechanistic investigation of brain-state dynamics relevant to human health, and provide broadly applicable tools for neuroimaging analyses beyond MEMRI applications. HighlightsO_LIQuantitative assurance of image quality complements visual assessment for cohort-level batch processing. C_LIO_LIOptimization of parameters using simulated noise-only images with and without investigator-embedded signal for voxel-wise mapping. C_LIO_LIA new software, "InVivoSegment" together with a labeled atlas, automates reliable user-friendly segmentation of voxel-wise data. C_LIO_LIMethodological advances in MEMRI data processing and computational analyses support scalable voxel- and segment-wise quantification of brain-wide neural activity. C_LI

neuroscience↗

bioRxiv2025

Gene-Expression Programs in Salivary Gland Adenoid Cystic Carcinoma Analyzed Using Single-Cell and Spatial Transcriptomics

Adenoid cystic carcinoma of the salivary gland (SGACC) is a highly aggressive malignancy characterized by poor patient survival outcomes. While several studies have analyzed the transcriptome of the salivary gland at the bulk and single-cell level, no spatial transcriptomic analyses of this tissue have been published. Most of the existing publications on SGACC have predominantly relied on bulk and single cell RNA sequencing approaches, which do not resolve the spatially localized transcriptional heterogeneity nor have the resolution for defining molecular markers within tumor subpopulations. SGACC is clinically notable for the presence of multiple tumor clones, distinct spatial phenotypes, and its indolent yet invasive nature coupled with a high propensity for distant metastasis. These features may reflect co-expression of tumor-associated markers across diverse cellular niches, and a resultant biological complexity which causes standard treatment such as surgical resection, radiation therapy, and chemotherapy to be largely ineffective in significantly improving long-term survival, and highlights the need for more precise, targeted therapeutic strategies. Herein, we analyzed single cell (n = 4) and high-resolution spatial transcriptomics samples (n = 5) to characterize cancer cell populations in MYB- and non-MYB-expressing cell states, delineated gene expression signatures, and identified critical molecular interactions specific to SGACC. We used Visum HD to obtain spatial transcriptomics data at 2{micro}m squared high resolution. This allowed a multi-omics approach comprising single cell and spatial transcriptomic methods to enable the discovery of novel transcriptional signatures and microenvironmental features not captured by conventional methods. Spatial mapping revealed marked cellular heterogeneity and demonstrated how tissue environments influence cellular transcriptomics. To tumor heterogeneity, we focused on tumorigenic cell populations, profiled plasma and T cell enrichment within the tumor microenvironment and identified key pathways and transcriptional drivers including the MYB-NFIB fusion underlying the tumor cluster formation. Our findings indicate an upregulation of genes involved in extracellular matrix remodeling, autophagy, and reactive stromal cell populations. We further found evidence of partial epithelial-mesenchymal transition (P-EMT) programming within MYB-expressing tumor clusters. Pathway analysis revealed that mutations in the spatial query sample prominently affect the PI3K-AKT and IL-17 signaling pathways, together with a downregulation of canonical Wnt signaling in some regions of the tissue architecture adjacent to immune cells. Collectively, these results underscore the complex regulatory landscape of SGACC and offer insights into its cellular dynamics and possible therapeutic vulnerabilities.

cancer biology↗

bioRxiv2024

White matter hyperintensities and microplastics

SynopsisWhite matter hyperintensities are abnormalities that appear in MRI scans of living patients but are not apparent in MRI post-mortem. GoalOur goal is to understand the cellular/biological basis of white matter hyperintensities (WMH). ApproachWe aligned post-mortem MR scans with those collected ante-mortem and performed histopathology and pyrGC/MS for plastics on regions with WMH. ResultPyrGC/MS detected large amounts of plastics and we determined their cellular locations with a novel optical imaging approach in regions with small vessel disease and Abeta plaques. ImpactMicroplastics in the brains of people with cognitive impairment may be due to pre-existing vascular injury or contribute to it. Many questions remain: Where do they come from, do they impair function? Can they be diagnosed by MRI ante-mortem?

neuroscience↗

bioRxiv2023

Reconfiguration of Brain-Wide Neural Activity After Early Life Adversity

Early life adversity (ELA) predisposes individuals to physical and mental disorders lifelong. How ELA affects brain functions, leading to these vulnerabilities, is a mystery. To understand ELAs impacts, investigations into neural activity affected by ELA must go beyond localized areas toward simultaneous recordings from multiple widely distributed regions over time. Such studies will expose relative activity between regions and discover shifts in regional activity in response to different experiences. Here, we performed longitudinal manganese-enhanced magnetic resonance imaging (MEMRI) to measure degrees of brain-wide neural activity in ELA-exposed mice across a series of experiences in adulthood. To ascertain whether ELA resulted in atypical brain activity, results were compared to those of the standard mouse (Std). MEMRI captured activity in the freely moving home cage condition, and short- and long-term after exposure to TMT, a naturalistic predator threat. Images were normalized and aligned then analyzed with statistical mapping and automated segmentation. We found that neural activity in the home cage was greater in ELA compared to Std in multiple striatal-pallidal and hypothalamic regions. Upon acute threat, neural activity in Std increased in these regions to become more similar to that in ELA, while new hyperactive responses in ELA emerged in the midbrain and hindbrain. Nine days after acute threat, heightened neural activity in ELA persisted within locus coeruleus and increased within posterior amygdala, ventral hippocampus, and dorsomedial and ventromedial hypothalamus. These results reveal functional imbalances that arise between multiple brain-systems after ELA, which are dependent upon context and cumulative experiences into adulthood. Significance StatementEarly life adversity (ELA) is a crucial determinant of adult health. Yet the neurobiological basis for this remains elusive. Localized brain regions display atypical neural activity in rodents who experienced ELA, but how this contributes to overall brain state dynamics has been unknown. Here, we used longitudinal manganese-enhanced MRI to detect brain-wide activities altered by ELA in the adult across a series of conditions: freely moving, experiencing threat or its aftermath. Computational analyses revealed that ELA produced widespread dynamic reconfiguration of brain-wide neural activity in response to threat, shown here for the first time. Dynamic brain state remodeling after ELA provides critical insights into human mental health vulnerabilities associated with adverse childhood experiences (ACEs), and suggests plausible targets for intervention.

neuroscience↗

bioRxiv2023

Harnessing axonal transport to map reward circuitry: Differing brain-wide projections from medial forebrain domains

Neurons project long axons that contact other distant neurons. Projections can be mapped by hijacking endogenous membrane trafficking machinery by introducing tracers. To witness functional connections in living animals, we developed a tracer detectible by magnetic resonance imaging (MRI), Mn(II). Mn(II) relies on kinesin-1 and amyloid-precursor protein to travel out axons. Within 24h, projection fields of cortical neurons can be mapped brain-wide with this technology. MnCl2 was stereotactically injected either into anterior cingulate area (ACA) or into infralimbic/prelimbic (IL/PL) of medial forebrain (n=10-12). Projections were imaged, first by manganese-enhanced MRI (MEMRI) live, and then after fixation by microscopy. MR images were collected at 100{micro}m isotropic resolution ([~]5 neurons) in 3D at four time points: before and at successive time points after injections. Images were preprocessed by masking non-brain tissue, followed by intensity scaling and spatial alignment. Actual injection locations, measured from post-injection MR images, were found to be 0.06, 0.49 and 0.84mm apart between cohorts, in R-L, A-P, and D-V directions respectively. Mn(II) enhancements arrived in hindbrains by 24h in both cohorts, while co-injected rhodamine dextran was not detectible beyond immediate subcortical projections. Data-driven unbiased voxel-wise statistical maps after ACA injections revealed significant progression of Mn(II) distally into deeper brain regions: globus pallidus, dorsal striatum, amygdala, hypothalamus, substantia nigra, dorsal raphe and locus coeruleus. Accumulation was quantified as a fraction of total volume of each segment containing significantly enhanced voxels (fractional accumulation volumes), and results visualized in column graphs. Unpaired t-tests between groups of brain-wide voxel-wise intensity profiling by either region of interest (ROI) measurements or statistical parametric mapping highlighted distinct differences in distal accumulation between injection sites, with ACA projecting to periaqueductal gray and IL/PL to basolateral amygdala (p<0.001 FDR). Mn(II) distal accumulations differed dramatically between injection groups in subdomains of the hypothalamus, with ACA targeting dorsal medial, periventricular region and mammillary body nuclei, while IL/PL went to anterior hypothalamic areas and lateral hypothalamic nuclei. Given that these hypothalamic subsegments communicate activity in the central nervous system to the body, these observations describing distinct forebrain projection fields will undoubtedly lead to newer insights in mind-body relationships.

neuroscience↗

bioRxiv2020

Effects of physiological deficits in pineal melatonin on Triple Negative Breast Cancer.

BackgroundTriple negative breast cancer (TNBC) is aggressive and treatment resistant. Evidence suggests that deficits in melatonin signaling increase TNBC risk: conditions that suppress melatonin increased incidence, low melatonin receptor expression correlates with worse prognosis, and high-dose melatonin can inhibit TNBC. Together this suggests that normalizing pineal melatonin could reduce TNBC incidence and/or mortality. The goal of this study was to determine whether small physiological deficits in melatonin alone, can increase risk for TNBC, and how normal melatonin would be protective. MethodsThe effect of melatonin treatment on 4t1 cells in vitro was measured using the MTT cell viability assay, and gene expression of breast cancer and melatonin signaling markers. The effect of pineal gland status on 4t1 cell allografts was tested in C3Sn mice (Mus Musculus) with either an intact pineal (control) or surgical removal of the pineal causing a ~50% deficit in plasma melatonin. Orthotopic tumors were assessed by histopathology and metastasis by strain specific qPCR against 4t1 cell and host gDNA. ResultsMelatonin treatment induced significant changes in gene expression, with a significant reduction in derived PAM50 Risk of Recurrence score (ROR in Not treated = 65.5 {+/-} 10.6 Mean SEM; Treated with 25pg/ml of melatonin 20.8 {+/-} 8.3; P = 0.008), suggesting melatonin treatment would improve prognosis. A ~50% reduction in plasma melatonin increased orthotopic tumors, but this was non-significant, and had no effect on metastasis from tail vein allograft. ConclusionsPhysiological deficits in melatonin do alter the oncogenic status of 4t1 tumor cells but this has only a limited effect on growth and metastasis in vivo. Lack of significance in orthotopic tumor formation may be due to small sample size, and it is possible that any protective effect of melatonin occurs earlier in tumor development than we have tested.

cancer biology↗

bioRxiv2020

Evolution of brain-wide activity in the awake behaving mouse after acute fear by longitudinal manganese-enhanced MRI

Life threatening fear after a single exposure evolves in a subset of vulnerable individuals to anxiety, which may persist for their lifetime. Yet neither the whole brains response to innate acute fear nor how brain activity evolves over time is known. Sustained neuronal activity may be a factor in the development of anxiety. We couple two experimental protocols to obtain a fear response leading to anxiety. Predator stress (PS) is a naturalistic approach that induces fear in rodents; and the serotonin transporter knockout (SERT-KO) mouse responds to PS with sustained defensive behavior. Behavior was monitored before, during and at short and long times after PS in WT and SERT-KO mice. Both genotypes responded to PS with defensive behavior, and SERT-KO retained defensive behavior for 23 days, while wild type (WT) mice return to baseline exploratory behavior by 9 days. Thus, differences in neural activity between WT and SERT-KO at 9 days after PS will identify neural correlates of persistent defensive behavior. We used longitudinal manganese-enhanced magnetic resonance imaging (MEMRI) to identify brain-wide neural activity between behavioral sessions. Mn2+ accumulation in active neurons occurs in awake behaving mice and is retrospectively imaged. To confirm expected effects of PS, behavior was monitored throughout. Following the same two cohorts of mice, WT and SERT-KO, longitudinally allowed unbiased quantitative comparisons of brain-wide activity by statistical parametric mapping (SPM). During natural behavior in WT, only low levels of activity-induced Mn2+-accumulation were detected, while much more accumulation appeared immediately after PS in both WT and SERT-KO, and evolved at 9 days to a new activity pattern at p<0.0001, uncorr., T=5.4. Patterns of accumulation differed between genotypes, with more regions of the brain and larger volumes within regions involved in SERT-KO than WT. A new computational segmentation analysis, using our InVivo Atlas based on a manganese-enhanced MR image of a living mouse, revealed dynamic changes in the volume of significantly enhanced voxels within each segment that differed between genotypes across 45 of 87 segmented regions. At Day 9 after PS, the striatum and ventral pallidum were active in both genotypes but more so in the anxious SERT-KO. SERT-KO also displayed sustained or increased volume of Mn2+ accumulation between Post-Fear and Day 9 in eight segments where activity was decreased or silenced in WT. Staining of the same mice fixed at the conclusion of imaging sessions for c-fos, a marker of neural activity, confirmed that MEMRI detected active neurons. Intensity measurements in 12 regions of interest (ROIs) supported the SPM results. Between group comparisons by SPM and of ROI measurements identified specific regions differing between time points and genotypes Thus we report brain-wide activity in response to a single exposure of acute fear, and, for the first time, its evolution to new activity patterns over time in individuals vulnerable to anxiety. Our results demonstrate the power of longitudinal MEMRI to discover how brain-wide activity evolves during recovery or persistence of fear responses leading to anxiety.

physiology↗