Biology subjects

Cheng, Q. J.

Publications and source records attributed to Cheng, Q. J..

4 recordsLinked to original sources

bioRxiv2023

Dectin-1 ligands produce distinct training phenotypes in human monocytes through differential activation of signaling networks

Cells of the innate immune system retain memory of prior exposures through a process known as innate immune training. {beta}-glucan, a Dectin-1 ligand purified from the Candida albicans cell wall, has been one of the most widely u:lized and well-characterized ligands for inducing innate immune memory. However, many Dectin-1 agonists exist, and it is not known whether all Dectin-1 ligands produce the same phenotype. Using a well-established in vitro model of trained immunity, we compared two commercially available Dectin-1 agonists, zymosan and depleted zymosan, with the gold standard {beta}-glucan in the literature. We found that depleted zymosan, a {beta}-glucan purified from Saccharomyces cerevisiae cell wall through alkali treatment, produced near identical training effects as C. albicans {beta}-glucan. However, untreated zymosan produced a distinct training effect from {beta}-glucans at both the transcript and cytokine level. Training with zymosan diminished, rather than potentiated, induction of key cytokines such as TNF, IL-12, and IL-6. Zymosan activated NFB and AP-1 transcription factors more strongly than {beta}-glucans. The addition of the toll-like receptor (TLR) ligand Pam3CSK4 was sufficient to convert the training effect of {beta}-glucans to a phenotype resembling training with zymosan. We conclude that differential activation of TLR signaling pathways determines the phenotype of innate immune training induced by Dectin-1. These findings bring clarity to the specific question of which Dectin-1 agonists produce prototypical training effects and provide broader insight into how signaling networks regulate innate immune training.

immunology↗

bioRxiv2022

A stimulus-contingent positive feedback loop enables IFN-β dose-dependent activation of pro-inflammatory genes

Type I interferons (IFN) induce powerful anti-viral and innate immune responses via the transcription factor, IFN-stimulated gene factor (ISGF3). However, in some pathological contexts type I IFNs are responsible for exacerbating inflammation. Here, we show that a high dose of IFN-{beta} also activates an inflammatory gene expression program in contrast to IFN-{lambda}3, a type III IFN, which elicits only the common anti-viral gene program. We show that the inflammatory gene program depends on a second, potentiated phase in ISGF3 activation. Iterating between mathematical modeling and experimental analysis we show that the ISGF3 activation network may engage a positive feedback loop with its subunits IRF9 and STAT2. This network motif mediates stimulus-specific ISGF3 dynamics that are dependent on ligand, dose, and duration of exposure, and when engaged activates the inflammatory gene expression program. Our results reveal a previously underappreciated dynamical control of the JAK-STAT/IRF signaling network that may produce distinct biological responses, and suggest that studies of type I IFN dysregulation, and in turn therapeutic remedies, may focus on feedback regulators within it. HIGHLIGHTSO_LIHigh dose IFN-{beta} activates a pro-inflammatory gene program in epithelial cells. C_LIO_LIIFN-{beta}, but not IFN-{lambda}3, induces a second, potentiated phase in ISGF3 activity. C_LIO_LIISGF3 induces its subunits to form a stimulus-contingent positive feedback loop. C_LIO_LIThe positive feedback motif is required for the pro-inflammatory gene program. C_LI

immunology↗

bioRxiv2020

High dose IFN-β activates GAF to enhance expression of ISGF3 target genes in epithelial cells

Interferon {beta} (IFN-{beta}) signaling activates the transcription factor complex ISGF3 to induce gene expression programs critical for antiviral defense and host immune responses. It has also been observed that IFN-{beta} activates a second transcription factor, {gamma}-activated factor (GAF), but the significance of this coordinated activation is unclear. We report that in respiratory epithelial cells high doses of IFN-{beta} indeed activate both ISGF3 and GAF, which bind to distinct genomic locations defined by their respective DNA sequence motifs. In contrast, low doses of IFN-{beta} preferentially activate ISGF3 but not GAF. Surprisingly, in epithelial cells GAF binding does not induce nearby gene expression even when strongly bound to the promoter. Yet expression of interferon stimulated genes is enhanced when GAF and ISGF3 are both active compared to ISGF3 alone. Our data suggest that GAF enhances ISGF3 target gene expression by co-localizing with ISGF3 at some promoters and facilitating chromosome looping between distal enhancers and other promoters. We propose that GAF may function as a dose-sensitive amplifier of ISG expression to enhance antiviral immunity and establish pro-inflammatory states in respiratory epithelial cells. One sentence summaryGAF is transcriptionally inactive in epithelial cells but enhances expression of ISGF3 target genes, thus functioning as a dose-sensitive amplifier of the IFN-{beta} response.

molecular biology↗

bioRxiv2020

NFκB dynamics determine stimulus-responsive epigenomic reprogramming in macrophages

The epigenome defines the cell type, but also shows plasticity that enables cells to tune their gene expression potential to the context of extracellular cues. This is evident in immune sentinel cells such as macrophages, which can respond to pathogens and cytokines with phenotypic shifts that are driven by epigenomic reprogramming1. Recent studies indicate that this reprogramming arises from the activity of transcription factors such as nuclear factor kappa-light-chain-enhancer of activated B cells (NF{kappa}B), which binds not only to available enhancers but may produce de novo enhancers in previously silent areas of the genome2. Here, we show that NF{kappa}B reprograms the macrophage epigenome in a stimulus-specific manner, in response only to a subset of pathogen-derived stimuli. The basis for these surprising differences lies in the stimulus-specific temporal dynamics of NF{kappa}B activity. Testing predictions of a mathematical model of nucleosome interactions, we demonstrate through live cell imaging and genetic perturbations that NF{kappa}B promotes open chromatin and formation of de novo enhancers most strongly when its activity is non-oscillatory. These de novo enhancers result in the activation of additional response genes. Our study demonstrates that the temporal dynamics of NF{kappa}B activity, which encode ligand identity3, can be decoded by the epigenome through de novo enhancer formation. We propose a mechanistic paradigm in which the temporal dynamics of transcription factors are a key determinant of their capacity to control epigenomic reprogramming, thus enabling the formation of stimulus-specific memory in innate immune sentinel cells.

molecular biology↗