Biology subjects

Benson, B.

Publications and source records attributed to Benson, B..

10 recordsLinked to original sources

bioRxiv2025

IL-13 Modulates Antiviral Effector and Proinflammatory Pathways in Rhinovirus-Infected Pediatric Bronchial Epithelium

BackgroundRhinovirus (RV) is the most common trigger of viral-induced pediatric asthma exacerbations. The impact of IL-13-driven inflammation, common in pediatric asthma, on airway epithelial antiviral and inflammatory responses to RV remain unclear. ObjectiveDetermine how IL-13-driven T2 inflammation modulates pediatric bronchial epithelial cell responses to RV infection. MethodsBronchial epithelial cells (BECs) were collected from children with (n=50) and without (n=11) asthma. They were differentiated at an air-liquid interface for 21 days, pretreated with IL13 (10ng/mL) for 7 days to model T2 inflammation, then infected with RV-A16 (MOI 0.5). RNA sequencing of BECs was performed prior to and on days 2, 4, 7, and 10 post infection. Linear and generalized additive models partnered with pathway analysis identified differentially expressed gene clusters. ResultsRV infection, IL-13 stimulation, and their interaction each induced differentially expressed genes (7,808; 10,251; and 7,095 genes, respectively; FDR<0.05). IL-13 pretreatment did not alter RV load or a cluster enriched for interferon response and regulation genes, including IFNB1, IFNL1-3, STAT1/2, and CXCL10/11. In contrast, IL-13 reduced expression of distinct antiviral effectors (e.g. MX1/2, RSAD2, IFITM1-3; FDR=1.85x10-) and increased a secondary proinflammatory response cluster enriched for IL-15, TNF, ER stress, and cell-death pathways (FDR=3.63x10-). These clusters correlated with viral load in RV-infected cells, but IL13 pretreatment eliminated those associations. ConclusionsIL-13 does not modify viral load or interferon induction but selectively suppresses epithelial antiviral effector programs and enhances secondary inflammatory pathways during RV infection. These findings provide mechanistic insight into how T2 inflammation contributes to viral-triggered asthma morbidity. Key Messages- IL-13 did not alter rhinovirus viral load or epithelial interferon induction but selectively suppressed antiviral effector programs. This indicates that T2 inflammation reshapes antiviral defenses downstream of interferon signaling rather than impairing interferon production itself. - IL-13 enhances a distinct secondary proinflammatory cluster enriched for IL-15, TNF signaling, ER stress, and cell-death pathways. These late-phase responses may contribute to the heightened airway inflammation and injury observed during viraltriggered exacerbations in T2-high pediatric asthma. - IL-13-driven changes decouple epithelial immune responses from viral load, revealing mechanisms that may persist even with anti-IL-4R/IL-13 therapy. These findings identify epithelial antiviral effector pathways and IL-15/TNF-associated inflammatory programs as potential therapeutic targets for patients who experience breakthrough viral exacerbations despite IL-13 blockade. Capsule SummaryIL-13 did not alter rhinovirus load or epithelial interferon but selectively suppressed antiviral effectors and amplified secondary inflammatory pathways, revealing how T2-inflammation may worsen viral-triggered asthma exacerbations and contribute to breakthrough exacerbations despite IL-4R/IL-13-targeted therapy.

cell biology↗

bioRxiv2025

Transcriptomic Profiling of Bronchial Epithelium Reveals Dysregulated Interferon and Inflammatory Responses to Rhinovirus in Exacerbation-Prone Pediatric Asthma

Host factors influencing susceptibility to rhinovirus-induced asthma exacerbations remain poorly characterized. Using organotypic bronchial epithelial cultures from well-characterized children with asthma and healthy children, this study investigated viral load kinetics and resultant host responses by bulk and single-cell transcriptomics and targeted protein analyses. Bronchial epithelium from exacerbation-prone children exhibited greater rhinovirus replication and a cascade of exaggerated downstream interferon (IFN), inflammatory, epithelial stress, and remodeling responses. These transcriptional patterns were confirmed and further refined using single-cell transcriptomics, revealing cell type-specific contributions--particularly from non-ciliated cell populations including secretory immune response, tuft, and basal cells. We observed that these post-infection differences were associated with lower pre-infection IFN-stimulated gene (ISG) expression and protein levels of the ISG CXCL10. Prophylactic IFN-{beta} treatment reduced viral replication and normalized downstream responses, supporting low baseline (pre-infection) IFN tone as a modifiable causal determinant of host susceptibility to adverse rhinovirus-induced responses in exacerbation-prone children with asthma.

cell biology↗

bioRxiv2025

Viral replication and interferon responses in bronchial epithelia is enhanced by Th17 cells

RationaleThe impact of Th17 lymphocytes on epithelial responses to rhinovirus infection in asthma is poorly characterized. MethodsBronchial epithelial cells (BECs) from children with asthma were differentiated to an organotypic epithelium and primed via co-culture with healthy donor Th17 lymphocytes for 4 days prior to apical infection with human rhinovirus-16 (RV-16). RNA sequencing with WGCNA analysis was performed to identify modules of gene expression altered by Th17 priming or RV-16 infection in BECs or Th17 cells. Gene expression was correlated with viral copy number and with secreted protein levels. ResultsAnalysis identified 4,030 genes grouped into 9 named modules with differential gene expression in BECs due to Th17 priming and viral infection. Modules with increased expression with Th17 priming and RV-16 infection included Interferon, MAP-kinase and TNF Signaling modules, while expression of Cilia structure/function and Metabolism modules were decreased. Th17 cells co-cultured with RV-16 infected BECs exhibited increased expression of an Interferon and Viral Response Module without detectable direct viral infection of Th17 cells.Increased expression of the Interferon Signaling in BECs and Interferon Response in Th17 cells was correlated with increased viral copy number in BECs. Th17 priming of BECs led to increased secretion of IFN-, IFN-{gamma}, and IL-1{beta} following RV-16 as compared to BECs alone. ConclusionsTh17 lymphocytes enhance epithelial interferon responses to RV-16 infection in bronchial epithelium from asthmatic children.

cell biology↗

bioRxiv2025

Transcriptomic and pathological analysis of the hnRNP network reveals glial involvement in FTLD pathological subtypes

Frontotemporal dementia (FTD) is a neurodegenerative disorder with a strong heritable component. Frontotemporal lobar degeneration (FTLD) refers to the pathological changes seen in FTD, characterised by atrophy of the frontal and temporal lobes and the presence of abnormal protein inclusions. In the case of FTLD with hyperphosphorylated TDP-43 positive inclusions (FTLD-TDP), five pathological subtypes (A, B, C, D, and E) are observed based on the types and distribution of inclusions found in the brain. In all subtypes, there tends to be a large variability in the number of pathological inclusions observed between cases, with limited correlation to clinical manifestations. TDP-43 is an RNA binding protein belonging to the heterogeneous nuclear ribonucleoprotein (hnRNP) family which along with other hnRNPs modulates multiple aspects of RNA processing. HnRNPs other than TDP-43 have been implicated in several neurological diseases, including ALS, FTLD-TDP, FTLD-FUS and Alzheimers disease. Multiple hnRNPs have been found in pathological inclusions in specific subtypes of FTLD-TDP, suggesting potential roles in the disease process. The role of the hnRNP network in FTLD disease pathogenesis, however, has not yet been investigated. This study aimed to comprehensively evaluate the presence and expression of hnRNP proteins in two pathological subtypes of sporadic FTLD-TDP (A and C) as well as the genetic form FTLD-TDP A C9orf72 using immunohistochemistry and gene expression analysis by single-nuclei RNA-sequencing. We found that there was great variability in frequency of TDP-43 pathology across and within FTLD-TDP pathological subtypes. Finally, our findings suggest that distinct global transcriptomic profiles may underlie the different pathological subtypes of FTLD-TDP. The most prominent transcriptomic changes were observed in oligodendrocytes and astrocytes, involving multiple hnRNPs across FTLD subtypes compared to controls. Transcriptomic co-expression analysis further revealed that glial clusters were more strongly associated with RNA processing dysfunction and contribute to disease classification. Together, these findings highlight the involvement of the hnRNP network and glial-specific RNA processing alterations in FTLD-TDP pathophysiology, offering new insight into the molecular distinctions between pathological subtypes and potential targets for future investigation.

neuroscience↗

bioRxiv2024

Human Alveolar and Monocyte-derived Human Macrophage Responses to Mycobacterium tuberculosis

RationaleAlveolar macrophages (AMs) and recruited monocyte-derived macrophages (MDMs) mediate early lung immune responses to Mycobacterium tuberculosis (Mtb). Differences in the response of these distinct cell types is poorly understood and may provide insight into mechanisms of TB pathogenesis. ObjectivesTo determine whether Mtb induces unique and essential anti-microbial pathways in human AMs compared to MDMs. MethodsUsing paired human AMs and 5-day MCSF-derived MDMs from 6 healthy volunteers, we infected cells with Mtb H37Rv for 6 hours, isolated RNA, and analyzed transcriptomic profiles with RNASeq. Main ResultsWe found 681 genes that were Mtb-dependent in AMs compared to MDMs and 4538 that were Mtb-dependent in MDMs but not AMs (FDR < 0.05). Using hypergeometric enrichment of DEGs in Broad Hallmark gene sets, we found that Type I and II IFN Response were the only gene sets selectively induced in Mtb-infected AM (FDR <0.05). In contrast, MYC targets, unfolded protein response and MTORC1 signaling, were selectively enriched in MDMs (FDR < 0.05). IFNA1, IFNA8, IFNE, and IFNL1 were specifically and highly upregulated in AMs compared to MDMs at baseline and/or after Mtb infection. IFNA8 modulated Mtb-induced pro-inflammatory cytokines and, compared to other interferons, stimulated unique transcriptomes. Several DNA sensors and Interferon Regulatory Factors had higher expression at baseline and/or after Mtb infection in AMs compared to MDMs. ConclusionsThese findings demonstrate that Mtb infection induced unique transcriptional responses in human AMs compared to MDMs, including upregulation of the IFN response pathway and specific DNA sensors.

immunology↗

bioRxiv2023

A Brain-Wide Map of Neural Activity during Complex Behaviour

A key challenge in neuroscience is understanding how neurons in hundreds of interconnected brain regions integrate sensory inputs with prior expectations to initiate movements and thereby make decisions. It is difficult to meet this challenge if different laboratories apply different analyses to different recordings in different regions during different behaviours. Here, we report a comprehensive set of recordings from 621733 neurons across 139 mice in 12 labs performing a decision-making task with sensory, motor, and cognitive components, obtained with 699 Neuropixels probe insertions covering 279 brain areas in the left forebrain and midbrain and the right hindbrain and cerebellum. We provide an initial appraisal of this brain-wide map, assessing how neural activity encoded key task variables. Representations of visual stimuli appeared transiently in classical visual areas after stimulus onset and then spread to ramp-like activity in a collection of mid- and hindbrain regions that also encoded choices. Neural responses correlated with motor action almost everywhere in the brain. Responses to reward delivery and consumption versus negative feedback were also widespread. This publicly available dataset represents an unprecedented resource for understanding how computations distributed across and within brain areas drive behaviour.

neuroscience↗

bioRxiv2023

Brain-wide representations of prior information in mouse decision-making

The neural representations of prior information about the state of the world are poorly understood. To investigate them, we examined brain-wide Neuropixels recordings and widefield calcium imaging collected by the International Brain Laboratory. Mice were trained to indicate the location of a visual grating stimulus, which appeared on the left or right with prior probability alternating between 0.2 and 0.8 in blocks of variable length. We found that mice estimate this prior probability and thereby improve their decision accuracy. Furthermore, we report that this subjective prior is encoded in at least 20% to 30% of brain regions which, remarkably, span all levels of processing, from early sensory areas (LGd, VISp) to motor regions (MOs, MOp, GRN) and high level cortical regions (ACAd, ORBvl). This widespread representation of the prior is consistent with a neural model of Bayesian inference involving loops between areas, as opposed to a model in which the prior is incorporated only in decision-making areas. This study offers the first brain-wide perspective on prior encoding at cellular resolution, underscoring the importance of using large scale recordings on a single standardized task.

neuroscience↗

bioRxiv2022

kimma: flexible linear mixed effects modeling with kinship for RNA-seq data

We introduce kimma (Kinship In Mixed Model Analysis), an open-source R package for flexible linear mixed effects modeling of RNA-seq including covariates, weights, random effects, covariance matrices, and fit metrics. In simulated datasets, kimma detects differentially expressed genes (DEGs) with similar specificity, sensitivity, and computational time as limma unpaired and dream paired models. Unlike other software, kimma supports covariance matrices as well as fit metrics like AIC. Utilizing genetic kinship covariance, kimma revealed that kinship impacts model fit and DEG detection in a related cohort. Thus, kimma equals or outcompetes current DEG pipelines in sensitivity, computational time, and model complexity.

bioinformatics↗

bioRxiv2022

Peripheral blood T-cell deficiency and hyperinflammatory monocyte responses associate with MAC lung disease

RationaleAlthough nontuberculous mycobacterial (NTM) disease is a growing problem, available treatments are suboptimal and diagnostic tools are inadequate. Immunological mechanisms of susceptibility to NTM disease are poorly understood. ObjectiveTo understand NTM pathogenesis, we evaluated innate and antigen-specific adaptive immune responses to Mycobacterium avium complex (MAC) in individuals with MAC lung disease (MACDZ). MethodsWe synthesized 15mer MAC-, NTM-, or MAC/Mtb-specific peptides and stimulated peripheral blood mononuclear cells (PBMC) with pools of these peptides. We measured T-cell responses by cytokine production, expression of surface markers, and analysis of global gene expression in 27 MACDZ individuals and 32 healthy controls. We also analyzed global gene expression in Mav-infected and uninfected peripheral blood monocytes from 17 MACDZ and 17 healthy controls. Measurements and Main ResultsWe were unable to detect T-cell responses against the peptide libraries or Mav lysate that has increased reactivity in MACDZ subjects compared to controls. T-cell responses to non-mycobacteria derived antigens were preserved. MACDZ individuals had a lower frequency of Th1 and Th1* T-cell populations. By contrast, global gene expression analysis demonstrated upregulation of proinflammatory pathways in uninfected and Mav-infected monocytes derived from MACDZ subjects compared to controls. ConclusionsPeripheral blood T-cell responses to Mycobacterial antigens and the frequency of Th1 and Th1* cell populations are diminished in individuals with MAC disease. In contrast, MACDZ subjects had hyperinflammatory monocyte responses. Together, these data suggest a novel immunologic defect which underlies MAC pathogenesis and includes concurrent innate and adaptive dysregulation.

immunology↗

bioRxiv2020

Gut metabolites are more predictive of disease- and cohoused- states than gut bacterial features in a mouse model of polycystic ovary syndrome

Polycystic ovary syndrome (PCOS) impacts [~]10% of reproductive-aged women worldwide. In addition to infertility, women with PCOS suffer from metabolic dysregulation which increases their risk of developing type 2 diabetes, cardiovascular disease and non-alcoholic fatty liver disease. Studies have shown differences in the gut microbiome of women with PCOS compared to controls, a pattern replicated in mouse models. Recently, using a letrozole-induced mouse model of PCOS, we demonstrated that cohousing was protective against development of metabolic and reproductive phenotypes and showed via 16S amplicon sequencing that this protection correlated with time-dependent shifts in gut bacteria. Here, we applied untargeted metabolomics and shotgun metagenomics approaches to further analyze the longitudinal samples from the cohousing experiment. Analysis of beta diversity found that untargeted metabolites had the strongest correlation to both disease and cohoused states and that shifts in metabolite diversity were detected prior to shifts in bacterial diversity. In addition, log2-fold analyses found numerous metabolite features, particularly bile acids (BA), to be highly differentiated between placebo (P) and letrozole (LET), as well as cohoused LET versus LET. Our results indicate that changes in gut metabolites, particularly BAs, are associated with a PCOS-like phenotype in the LET mouse model as well as the protective effect of cohousing. Our results also suggest that transfer of metabolites via coprophagy occurs rapidly and may precipitate changes in bacterial diversity. This study joins a growing body of research highlighting changes in primary and secondary bile acids that may provide a link between host metabolism and gut microbes relevant to the pathology of PCOS. IMPORTANCEUsing a combination of untargeted metabolomics and metagenomics, we performed a comparative longitudinal analysis of the feces collected in a cohousing study with a PCOS mouse model. Our results showed that gut metabolite composition experienced earlier and more pronounced differentiation in both the disease model and cohoused mice compared with the microbial composition. Notably, statistical and machine learning approaches identified shifts in the relative abundance of primary and secondary BA, which have been implicated as modifiers of gut microbial growth and diversity. Network correlation analysis showed strong associations between particular BA and bacterial species, particularly members of Lactobacillus, and that these correlations were time and treatment dependent. Our results provide novel insights into host/microbe relationships related to hyperandrogenism in females and indicate that focused research into small molecule control of gut microbial diversity and host physiology may provide new therapeutic options for the treatment of PCOS.

microbiology↗