Biology subjects

Sasse, S. K.

Publications and source records attributed to Sasse, S. K..

3 recordsLinked to original sources

bioRxiv2025

Inflammatory cytokines promote interferon regulatory factor (IRF) transcriptional activity in human pulmonary epithelial cells through the induction of IRF1 by nuclear factor-κB

Transcription factors of the interferon regulatory factor (IRF) family play key roles during viral and bacterial infections. However, IRF regulation by inflammatory cytokines, including interleukin (IL)-1{beta} and tumor necrosis factor (TNF) , remains underexplored. Since airway epithelial cells (AECs) modulate lung inflammation, IRF expression was characterized in pulmonary A549 and bronchial BEAS-2B epithelial cells, plus primary human AECs grown in submersion or highly differentiated air-liquid interface culture. Whereas most IRF mRNAs were expressed across models, IRF4 and IRF8 showed consistently low expression, and IRF6 was only expressed highly in primary cells. IRF3 and IRF9 were highly expressed in each model, and while protein expression was confirmed in A549 cells, this remained primarily cytoplasmic post-IL-1{beta} treatment. IRF2 was constitutively nuclear in A549 cells and showed moderate/high mRNA expression in each model. IRF1 mRNA was induced by IL-1{beta}-in primary and A549 cells, where IL-1{beta} and TNF dramatically increased IRF1 protein expression. TNF also increased IRF1 protein in BEAS-2B cells. In A549 cells, an IRF reporter system combined with RNA silencing did not support transcriptional roles for IRF2 or IRF3 but suggested a modest role for IRF9 following IL-1{beta} stimulation. IL-1{beta}-induced IRF1 localized to the nucleus of A549 cells revealing a major transcriptional role. IRF1 expression induced by IL-1{beta}/TNF required NF-{kappa}B and four novel 5' enhancer regions to IRF1 bound the NF-{kappa}B subunit, p65. These regions drove IL-1{beta}/TNF-inducible reporter activity via consensus NF-{kappa}B motifs. Three such regions recruited RNA polymerase-2 and were flanked by the active chromatin mark, histone 3 lysine 27 acetylation which, given the high levels of genetic conservation, support involvement in IRF1 transcription. Finally, IRF1 expression, transcription rate, and enhancer activity induced by IL-1{beta}/TNF were relatively unaffected by glucocorticoid co-treatment. IRF1-dependent gene expression could therefore be insensitive to glucocorticoid and may contribute to glucocorticoid-resistant diseases such as severe asthma.

molecular biology↗

bioRxiv2021

Nascent RNA sequencing defines dynamic aryl hydrocarbon receptor signaling responses to wood smoke particles

Heterogeneity of respirable particulates and compounds complicates understanding transcriptional responses to air pollution. Here, we address this problem through applying precision nuclear run-on sequencing (PRO-seq) to measure nascent transcription and the assay for transposase-accessible chromatin using sequencing (ATAC-seq) to airway epithelial cells after wood smoke particle (WSP) exposure. We used transcription factor enrichment analysis to agnostically identify temporally distinct roles for the TCF/SRF family, the aryl hydrocarbon receptor (AHR), and NFkB in regulating transcriptional changes induced by WSP. Transcription of canonical targets of the AHR, such as CYP1A1 and AHRR, was robustly increased after just 30 minutes of WSP exposure, and we discovered novel AHR-regulated pathways and targets including the DNA methyltransferase, DNMT3L. Transcription of these genes and associated enhancers rapidly returned to near baseline by 120 minutes. The kinetics of AHR- and NFkB-regulated responses to WSP were distinguishable based on the timing of both transcriptional responses and chromatin remodeling, with induction of several cytokines implicated in maintaining NFkB responses through 120 minutes of exposure. In aggregate, our data establish a direct and primary role for AHR in mediating airway epithelial responses to WSP and identify crosstalk between AHR and NFkB signaling in controlling pro-inflammatory gene expression. This work also defines an integrated genomics-based strategy for deconvoluting multiplexed transcriptional responses to heterogeneous environmental exposures.

genomics↗

bioRxiv2019

Nascent transcript analysis of glucocorticoid crosstalk with TNF defines primary and cooperative inflammatory repression

The glucocorticoid receptor (GR) binds to specific DNA sequences and directly induces transcription of anti-inflammatory genes that contribute to cytokine repression, frequently in cooperation with NF-kB. Whether inflammatory repression also occurs through local interactions between GR and inflammatory gene regulatory elements remains controversial. Here, using Global Run-on Sequencing (GRO-seq) in human airway epithelial cells, we show that glucocorticoid signaling represses transcription within 10 minutes. Many repressed regulatory regions reside within hyper-ChIPable genomic regions that are subject to non-specific interactions with some antibodies. When this was accounted for, we determined that transcriptional repression occurs without local GR occupancy. Instead, widespread transcriptional induction through canonical GR binding sites is associated with reciprocal repression of distal TNF-regulated enhancers through a chromatin-dependent process, as evidenced by chromatin accessibility and enhancer-reporter assays. Simultaneously, transcriptional induction of key anti-inflammatory effectors is decoupled from primary repression through cooperation between GR and NF-kB at a subset of regulatory regions. Thus, glucocorticoids exert bimodal restraints on inflammation characterized by rapid primary transcriptional repression without local GR occupancy and secondary anti-inflammatory effects resulting from transcriptional cooperation between GR and NF-kB.

molecular biology↗