Biology subjects

Altman, M. C.

Publications and source records attributed to Altman, M. C..

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

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↗

bioRxiv2024

Reduced function of the adaptor SH2B3 promotes T1D via altered γc cytokine-regulated, T cell intrinsic immune tolerance

Genome-wide association studies have identified SH2B3 as an important non-MHC gene for islet autoimmunity and type 1 diabetes (T1D). In this study, we found a single SH2B3 haplotype significantly associated with increased risk for human T1D, and this haplotype carries the single nucleotide variant rs3184504*T in SH2B3. To better characterize the role of SH2B3 in T1D, we used mouse modeling and found a T cell-intrinsic role for SH2B3 regulating peripheral tolerance. SH2B3 deficiency had minimal effect on TCR signaling or proliferation across antigen doses, yet enhanced cell survival and cytokine signaling including common gamma chain-dependent and interferon-gamma receptor signaling. SH2B3 deficient CD8+T cells showed augmented STAT5-MYC and effector-related gene expression partially reversed with blocking autocrine IL-2 in culture. Using the RIP-mOVA model, we found CD8+ T cells lacking SH2B3 promoted early islet destruction and diabetes without requiring CD4+ T cell help. SH2B3-deficient cells demonstrated increased survival post-transfer compared to control cells despite a similar proliferation profile in the same host. Next, we created a spontaneous NOD.Sh2b3-/-mouse model and found markedly increased incidence and accelerated T1D across sexes. Collectively, these studies identify SH2B3 as a critical mediator of peripheral T cell tolerance limiting the T cell response to self-antigens. Article HighlightsO_LIThe rs3184504 polymorphism, encoding a hypomorphic variant of the negative regulator SH2B3, strongly associates with T1D. C_LIO_LISH2B3 deficiency results in hypersensitivity to cytokines, including IL-2, in murine CD4+ and CD8+ T cells. C_LIO_LISH2B3 deficient CD8+ T cells exhibit a comparable transcriptome to wild-type CD8+ T cells at baseline, but upon antigen stimulation SH2B3 deficient cells upregulate genes characteristic of enhanced JAK/STAT signaling and effector functions. C_LIO_LIWe found a T-cell intrinsic role of SH2B3 leading to severe islet destruction in an adoptive transfer murine T1D model, while global SH2B3 deficiency accelerated spontaneous NOD diabetes across sexes. C_LI

immunology↗

bioRxiv2023

Integrated longitudinal multi-omics study identifies immune programs associated with COVID-19 severity and mortality in 1152 hospitalized participants

Hospitalized COVID-19 patients exhibit diverse clinical outcomes, with some individuals diverging over time even though their initial disease severity appears similar. A systematic evaluation of molecular and cellular profiles over the full disease course can link immune programs and their coordination with progression heterogeneity. In this study, we carried out deep immunophenotyping and conducted longitudinal multi-omics modeling integrating ten distinct assays on a total of 1,152 IMPACC participants and identified several immune cascades that were significant drivers of differential clinical outcomes. Increasing disease severity was driven by a temporal pattern that began with the early upregulation of immunosuppressive metabolites and then elevated levels of inflammatory cytokines, signatures of coagulation, NETosis, and T-cell functional dysregulation. A second immune cascade, predictive of 28-day mortality among critically ill patients, was characterized by reduced total plasma immunoglobulins and B cells, as well as dysregulated IFN responsiveness. We demonstrated that the balance disruption between IFN-stimulated genes and IFN inhibitors is a crucial biomarker of COVID-19 mortality, potentially contributing to the failure of viral clearance in patients with fatal illness. Our longitudinal multi-omics profiling study revealed novel temporal coordination across diverse omics that potentially explain disease progression, providing insights that inform the targeted development of therapies for hospitalized COVID-19 patients, especially those critically ill.

immunology↗

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↗

bioRxiv2020

Asthma-associated variants induce IL33 differential expression through a novel regulatory region

Genome-wide association studies (GWAS) have implicated the IL33 locus in asthma, but the underlying mechanisms remain unclear. Here, we identify a 5 kb region within the GWAS-defined segment that acts as a strong regulatory element in vivo and in vitro. Chromatin conformation capture showed that this 5 kb region loops to the IL33 promoter, potentially regulating its expression. Supporting this notion, we show that genotype at an asthma-associated SNP, rs1888909, located within the 5 kb region, is associated with IL33 gene expression in human airway epithelial cells and IL-33 protein expression in human plasma, potentially through differential binding of OCT-1 (POU2F1) to the asthma-risk allele. Our data demonstrate that asthma-associated variants at the IL33 locus mediate allele-specific regulatory activity and IL33 expression, providing a novel mechanism through which a regulatory SNP contributes to genetic risk of asthma.

genomics↗

bioRxiv2020

Blood transcriptional module repertoire analysis and visualization using R

Transcriptional modules have been widely used for the analysis, visualization and interpretation of transcriptome data. We have previously described the construction and characterization of generic and reusable blood transcriptional module repertoires. The third and latest version that we have recently made available comprises 382 functionally annotated gene sets (modules) and encompasses 14,168 transcripts. We developed R scripts for performing module repertoire analyses and custom fingerprint visualization. These are made available here along with detailed descriptions. An illustrative public transcriptome dataset and corresponding intermediate output files are also included as supplementary material. Briefly, the steps involved in module repertoire analysis and visualization include: First, the annotation of the gene expression data matrix with module membership information. Second, running of statistical tests to determine for each module the proportion of its constitutive genes which are differentially expressed. Third, the results are expressed "at the module level" as percent of genes increased or decreased and plotted in a fingerprint grid format. A parallel workflow has been developed for computing module repertoire changes for individual samples rather than groups of samples. Such results are plotted in a heatmap format. The use case that is presented illustrates the steps involved in the generation of blood transcriptome repertoire fingerprints of septic patients at both group and individual levels.

bioinformatics↗

bioRxiv2019

A Transcriptome Fingerprinting Assay for Clinical Immune Monitoring

BackgroundWhile our understanding of the role that the immune system plays in health and disease is growing at a rapid pace, available clinical tools to capture this complexity are lagging. We previously described the construction of a third-generation modular transcriptional repertoire derived from genome-wide transcriptional profiling of blood of 985 subjects across 16 diverse immunologic conditions, which comprises 382 distinct modules.\n\nResultsHere we describe the use of this modular repertoire framework for the development of a targeted transcriptome fingerprinting assay (TFA). The first step consisted in down-selection of the number of modules to 32, on the basis of similarities in changes in transcript abundance and functional interpretation. Next down-selection took place at the level of each of the 32 modules, with each one of them being represented by four transcripts in the final 128 gene panel. The assay was implemented on both the Fluidigm high throughput microfluidics PCR platform and the Nanostring platform, with the list of assays target probes being provided for both. Finally, we provide evidence of the versatility of this assay to assess numerous immune functions in vivo by demonstrating applications in the context of disease activity assessment in systemic lupus erythematosus and longitudinal immune monitoring during pregnancy.\n\nConclusionsThis work demonstrates the utility of data-driven network analysis applied to large-scale transcriptional profiling to identify key markers of immune responses, which can be downscaled to a rapid, inexpensive, and highly versatile assay of global immune function applicable to diverse investigations of immunopathogenesis and biomarker discovery.

immunology↗

bioRxiv2019

A Novel Repertoire of Blood Transcriptome Modules Based on Co-expression Patterns Across Sixteen Disease and Physiological States

As the capacity for generating large scale data continues to grow the ability to extract meaningful biological knowledge from it remains a limitation. Here we describe the development of a new fixed repertoire of transcriptional modules. It is meant to serve as a stable reusable framework for the analysis and interpretation of blood transcriptome profiling data. It is supported by customized resources, which include analysis workflows, fingerprint grid plots data visualizations, interactive web applications providing access to a vast number of module-specific functional profiling reports, reference transcriptional profiles and give users the ability to visualize of changes in transcript abundance across the modular repertoire at different granularity levels. A use case focusing on a set of six modules comprising interferon-inducible genes is also provided. Altogether we hope that this resource will also serve as a framework for improving over time our collective understanding of the immunobiology underlying blood transcriptome profiling data.

immunology↗

bioRxiv2017

Ruxolitinib partially reverses functional NK cell deficiency in patients with STAT1 gain-of-function mutations

BackgroundNatural Killer (NK) cells are critical innate effector cells whose development is dependent on the JAK-STAT pathway. NK deficiency can result in severe or refractory viral infections. Patients with Signal Transducer and Activator of Transcription (STAT)1 gain of function (GOF) mutations have increased viral susceptibility.\n\nObjectiveWe sought to investigate NK cell function in STAT1 GOF patients. Methods: NK cell phenotype and function were determined in 16 STAT1 GOF patients.\n\nMethodsNK cell phenotype and function were determined in 16 STAT1 GOF patients.NK cell lines expressing patient mutations were generated with CRISPR-Cas9 mediated gene editing. STAT1 GOF NK cells were treated in vitro with ruxolitinib.\n\nResultsPeripheral blood NK cells from of STAT1 GOF patients had impaired terminal maturation. Specifically, patients with STAT1 GOF mutations have immature CD56dim NK cells with decreased expression of CD16, perforin, CD57 and impaired cytolytic function. STAT1 phosphorylation was elevated but STAT5 was aberrantly phosphorylated in response to IL-2 stimulation. Upstream inhibition of STAT signaling with the small molecule JAK1/2 inhibitor ruxolitinib in vitro and in vivo restored perforin expression in CD56dim NK cells and partially restored NK cell cytotoxic function.\n\nConclusionsProperly regulated STAT1 signaling is critical for NK cell maturation and function. Modulation of elevated STAT1 phosphorylation with ruxolitinib is an important option for therapeutic intervention in patients with STAT1 GOF mutations.

immunology↗