The transcription factor NF-κB orchestrates nucleosome remodeling during the primary response to Toll-like receptor 4 signaling

Dual mechanism of inflammation sensing by the hematopoietic progenitor genome

Genomes adapt dynamically to alterations in the signaling milieu, including inflammation that transiently or permanently disrupts genome function. Here, we elucidate how a progenitor cell genome senses and responds to inflammation when the developmental and transcriptional regulator GATA2 is limiting, which causes bone marrow failure in humans and mice and predisposes to leukemia in humans. GATA2low murine progenitors are hypersensitive to inflammatory mediators. We discovered that the hematopoietic transcription factor PU.1 conferred transcriptional activation in GATA2low progenitors in response to Interferon-γ and Toll-Like Receptor 1/2 agonists. In a locus-specific manner, inflammation reconfigured genome activity by promoting PU.1 recruitment to chromatin or tuning activity of PU.1-preoccupied chromatin. The recruitment mechanism disproportionately required IKKβ activity. Inflammation-activated genes were enriched in motifs for RUNX factors that cooperate with GATA factors. Contrasting with the GATA2-RUNX1 cooperativity paradigm, GATA2 suppressed and RUNX1 promoted PU.1 mechanisms to endow the progenitor genome with inflammation-sensing capacity.

Pre-existing epigenetic state and differential NF-κB activation shape type 2 immune cell responses

CD4+ T helper 2 (Th2) cells and group 2 innate lymphoid cells (ILC2s) drive type 2 immune responses via similar effector molecules that are primarily induced by different signals-interleukin (IL)-33 in ILC2s and TCR engagement in Th2 cells. Here, we examined the transcriptional regulation of type 2 immunity, focusing on the NF-κB pathway, which is differentially activated by TCR engagement or cytokine signaling. Conditional deletion of the NF-κB subunits c-Rel and p65 limited the expression of key type 2 genes, including Il13 and Il5, in ILC2s but not in Th2 cells. Genome-wide analysis revealed that the regulatory regions of such genes exist in an open chromatin state in ILC2s, allowing NF-κB binding upon IL-33 stimulation. These regions are less accessible in unstimulated Th2 cells, where NFAT plays a dominant role. Accordingly, p65 deletion impaired ILC2 activation and function during airway inflammation and helminth infection. Thus, innate and adaptive lymphocytes leverage distinct epigenetic landscapes and transcriptional regulators to control shared effector genes.

The NF-κB signaling network in the life of T cells

NF-κB is a crucial transcription factor in lymphocyte signaling. It is activated by environmental cues that drive lymphocyte differentiation to combat infections and cancer. As a key player in inflammation, NF-κB also significantly impacts autoimmunity and transplant rejection, making it an important therapeutic target. While the signaling molecules regulating this pathway are well-studied, the effect of changes in NF-κB signaling levels on T lymphocyte differentiation, fate, and function is not fully understood. Advances in computational biology and new NF-κB-inducible animal models are beginning to clarify these questions. In this review, we highlight recent findings related to T cells, focusing on how environmental cues affecting NF-κB signaling levels determine T cell fate and function.

Accurate and Efficient Detection of Nasopharyngeal Carcinoma Using Multi-Dimensional Features of Plasma Cell-Free DNA

BACKGROUND

The incidence of Nasopharyngeal carcinoma (NPC) is rising in recent years, especially in some non-developed parts of the world. Hence, cost-efficient means for sensitive detection of NPC are vital.

METHODS

We recruited 646 participants, including healthy individuals, patients with benign nasopharyngeal diseases, and NPC patients for plasma cell-free DNA(cfDNA), which underwent low-depth whole-genome sequencing (WGS) to extract multi-dimensional molecular features, including fragmentation pattern, end motif, copy number variation(CNV), and transcription factors(TF). Based on these features, we employed a machine learning algorithm to build prediction models for NPC detection.

RESULTS

We achieved a sensitivity of 95.8% and a specificity of 99.4% to discriminate NPC patients from healthy individuals.

CONCLUSIONS

This study can be a proof-of-concept for these multi-dimensional molecular features to be implemented as a noninvasive approach for the detection and even early detection of NPC.

MAGEA9 Expression in Vocal Fold Leukoplakia and Its Enhancement of Vocal Fold Leukoplakia Epithelial Cell Proliferation, Migration, and Invasion Through the NF-kB-MMP-2/9 Pathway

PURPOSE

The expression of MAGE-A9 in vocal fold leukoplakia (VFL) tissues and the mechanism underlying its role in the malignant transformation of VFL remain unclear. This study investigated the role of MAGE-A9 in the proliferation, migration, and invasion of VFL epithelial cells as well as the underlying regulatory mechanism.

METHODS

MAGE-A9 expression in VFL tissues was detected by immunohistochemistry. The CCK-8 assay, flow cytometry, and transwell assays were performed to determine the viability, cell cycle distribution and apoptosis, as well as migration and invasion, respectively, of primary cultured VFL epithelial cells. Ki67, cell cycle proteins, and proteins in the NF-kB-MMP-2/9 pathway were assessed by Western blotting.

RESULTS

MAGE-A9 expression was detected in 54.5% (18/33) of vocal fold polyps, 48.9% (44/90) of VFLs, and 84.8% (28/33) of laryngeal cancers. Significantly higher levels of expression were found in laryngeal cancer than in vocal fold polyps and VFL tissues (P < 0.001). The expression of MAGE-A9 tended to increase with the severity of VFL dysplasia. In VFL epithelial cells, the overexpression of MAGE-A9 significantly increased the viability, proliferation, migration, and invasion of the cells and reduced the level of apoptosis. The cell cycle effects of MAGE-A9 overexpression included an increased proportion of cells in the G2 and S phases and a decreased proportion of those in the G1 phase (P = 0.002), leading to an altered G1/S phase transition. MAGE-A9 overexpression also significantly increased p-IKBα, p-p65, MMP2, and MMP9 levels while decreasing those of IKBα. All of the effects of MAGE-A9 were inhibited by treating the cells with the IκBα phosphorylation inhibitor BAY 11-7082.

CONCLUSION

MAGE-A9 expression tended to increase with the severity of dysplasia in VFL and was significantly higher in laryngeal cancer than in VFL. MAGE-A9 was shown to promote the proliferation, migration, and invasion of VFL epithelial cells via the NF-kB pathway and downstream targets such as MMP-2/9.

Suppressed macrophage response to quorum-sensing-active Streptococcus pyogenes occurs at the level of the nucleus

Streptococcus pyogenes, or Group A Streptococus (GAS), a significant human pathogen, employs quorum sensing (QS) systems to coordinate its behavior and genetic regulation in order to enhance survival. Our previous research established that one such QS system, the Rgg2/3 system, can suppress macrophage NFκB activity and production of pro-inflammatory cytokines. Yet, the scope of suppression and the mechanism by which it occurs remains unknown. In this study, we used transcriptomic and phosphoproteomic approaches to address these unanswered questions. We found QS-ON GAS broadly suppressed most inflammatory transcriptional pathways including those of NFκB, type I and type II interferon responses, and intracellular stress responses. Yet, we found no alternative transcriptional programs were activated after QS-ON GAS infection. Additionally, phosphoproteomics showed no disruption in typical inflammatory pathways such as those related to NFκB and MAPK activation, which was confirmed by western blotting and translocation assays. Instead, the proteomic data highlighted a potential role for epigenetic mechanisms of inflammatory regulation. To determine if epigenetic regulation was involved in QS-mediated immunomodulation, DNA methylation was measured and studies were performed inhibiting various histone and chromatin modifiers. These studies also showed no dijerence between QS-ON compared with QS-OFF infected macrophages. These findings expand our understanding of QS-mediated suppression and of GAS virulence strategies that appear to employ unusual methods of restricting inflammation. Uncovering this mechanism will ojer invaluable insight into GAS, itself, as well as understudied immunological pathways.

Pro-inflammatory macrophage activation does not require inhibition of oxidative phosphorylation

Pro-inflammatory macrophage activation is a hallmark example of how mitochondria serve as signaling organelles. Oxidative phosphorylation sharply decreases upon classical macrophage activation, as mitochondria are thought to shift from ATP production towards accumulating signals that amplify effector function. However, evidence is conflicting regarding whether this collapse in respiration is essential or dispensable. Here we systematically examine this question and show that reduced oxidative phosphorylation is not required for pro-inflammatory macrophage activation. Different pro-inflammatory stimuli elicit varying effects on bioenergetic parameters, and pharmacologic and genetic models of electron transport chain inhibition show no causative link between respiration and macrophage activation. Furthermore, the signaling metabolites succinate and itaconate can accumulate independently of characteristic breaks in the TCA cycle in mouse and human macrophages, and peritoneal macrophages can be activated in vivo without inhibition of oxidative phosphorylation. The results indicate there is plasticity in the metabolic phenotypes that can support pro-inflammatory macrophage activation.

Integration of transcriptomics and metabolomics reveals the mechanism of Glycyrrhizae Radix Et Rhizoma extract inhibiting CCL5 in the treatment of acute pharyngitis

BACKGROUND

Acute pharyngitis (AP) is a common condition marked by inflammation of the oropharynx, which can lead to severe throat swelling, breathing difficulties, and even suffocation, significantly impacting quality of life. Despite the beneficial anti-inflammatory activity of Glycyrrhizae Radix Et Rhizoma (GRER) and Isoliquiritigenin (ISL), their pharmacological mechanisms against AP remain unclear.

PURPOSE

This study explores the mechanisms by which GRER treats AP, utilizing both transcriptomics and metabolomics approaches.

METHODS

We identified the chemical components of GRER and those that enter the bloodstream using UPLC-MS/MS. Based on15 % ammonia-induced AP model, this study integrates transcriptomics and metabolomics to investigate the mechanism of GRER and ISL in the AP treatment.

RESULTS

The results indicated that GRER has significantly protective and anti-inflammatory effects against AP. Our analysis identified 144 components of GRER in vitro and 17 components in vivo. Network pharmacology and quantitative analysis highlighted ISL as a key active ingredient responsible for GRER's anti-AP effects. Transcriptomics and metabolomics results indicate that GRER and its active ingredient ISL exert therapeutic effects on AP by inhibiting the expression of CCL5 in pharyngeal tissue, thereby downregulating the levels of pro-inflammatory metabolites malic acid and fumaric acid in the tricarboxylic acid (TCA) cycle pathway.

CONCLUSION

The data in this article demonstrated that GRER and ISL has significantly anti-inflammatory effects and protective effects for AP by regulating CCL5 expression to reduce the levels of pro-inflammatory metabolites within TCA cycle pathway. It provides a scientific basis for prevention and treatment of AP.

Innate Immune Memory is Stimulus Specific

Innate immune memory (also termed trained immunity) is defined in part by its ability to cross-protect against heterologous pathogens, and can be generated by many different stimuli, suggesting a "universal" trained state. However, different stimuli could form distinct memories, leading to stimulus-specific trained responses. Here, we use primary human monocyte-derived macrophages to demonstrate phenotypic and epigenetic stimulus specificity of innate immune memory six days after initial exposure. Quantification of cytokine production with single-molecule RNA imaging demonstrates stimulus-specific patterns of response to restimulation at the single cell level. Differential licensing of inflammatory transcription factors is associated with encoding of specificities in chromatin. Trained cells show stronger responses to secondary stimuli that are more similar to the initial stimulus they experienced, suggesting a functional role for these stimulus-specific memories. Rather than activating a universal training state, our findings demonstrate that different stimuli impart specific memories that generate distinct training phenotypes in macrophages.

IRF1 cooperates with ISGF3 or GAF to form innate immune de novo enhancers in macrophages

Macrophages exposed to immune stimuli reprogram their epigenomes to alter their subsequent functions. Exposure to bacterial lipopolysaccharide (LPS) causes widespread nucleosome remodeling and the formation of thousands of de novo enhancers. We dissected the regulatory logic by which the network of interferon regulatory factors (IRFs) induces the opening of chromatin and the formation of de novo enhancers. We found that LPS-activated IRF3 mediated de novo enhancer formation indirectly by activating the type I interferon (IFN)-induced ISGF3. However, ISGF3 was generally needed to collaborate with IRF1, particularly where chromatin was less accessible. At these locations, IRF1 was required for the initial opening of chromatin, with ISGF3 extending accessibility and promoting the deposition of H3K4me1, marking poised enhancers. Because IRF1 expression depends on the transcription factor NF-κB, which is activated in infected but not bystander cells, IRF-regulated enhancers required activation of both the IRF3 and NF-κB branches of the innate immune signaling network. However, type II IFN (IFN-γ), which is typically produced by T cells, may also induce IRF1 expression through the STAT1 homodimer GAF. We showed that, upon IFN-γ stimulation, IRF1 was also responsible for opening inaccessible chromatin sites that could then be exploited by GAF to form de novo enhancers. Together, our results reveal how combinatorial logic gates of IRF1-ISGF3 or IRF1-GAF restrict immune epigenomic memory formation to macrophages exposed to pathogens or IFN-γ-secreting T cells but not bystander macrophages exposed transiently to type I IFN.

Linking signal input, cell state, and spatial context to inflammatory responses

Signal integration is central to a causal understanding of appropriately scaled inflammatory responses. Here, we discuss recent progress in our understanding of the stimulus-response linkages downstream of pro-inflammatory inputs, with special attention to (1) the impact of cell state on the specificity of evoked gene expression and (2) the critical role of the spatial context of stimulus exposure. Advances in these directions are emerging from new tools for inferring cell-cell interactions and the activities of cytokines and transcription factors in complex microenvironments, enabling analysis of signal integration in tissue settings. Building on data-driven elucidation of factors driving inflammatory outcomes, mechanistic modeling can then contribute to a quantitative understanding of regulatory events that balance protective versus pathological inflammation.

Advances in protein subunit vaccines against H1N1/09 influenza

The A/H1N1pdm09 influenza virus, which caused the 2009 pandemic, has since become a recurring strain in seasonal influenza outbreaks. Given the ongoing threat of influenza, protein subunit vaccines have garnered significant attention for their safety and effectiveness. This review seeks to highlight the latest developments in protein subunit vaccines that specifically target the A/H1N1pdm09 virus. It will also examine the structure and replication cycle of influenza A viruses and compare different types of influenza vaccines. Additionally, the review will address key aspects of H1N1 protein subunit vaccine development, such as antigen selection, protein expression systems, and the use of adjuvants. The role of animal models in evaluating these vaccines will also be discussed. Despite challenges like antigenic variability and the complexities of vaccine production and distribution, protein subunit vaccines remain a promising option for future influenza prevention efforts.

Viral imitation is the sincerest form of epigenetic flattery

Viruses use multiple strategies to successfully generate progeny and overcome host defenses. In recent years, it has become increasingly evident that epigenetic mechanisms of host gene regulation are vulnerable to viral manipulation. In the form of histone mimicry, viral invasion of host chromatin is a striking example of how viruses have evolved to invade every aspect of cellular function for viral benefit. In this perspective, we will review how three viruses-influenza A, SARS-CoV-2, and Cotesia plutellae bracovirus-use histone mimicry to promote viral success through immune evasion. These examples highlight the importance of this burgeoning field and point toward the wealth of knowledge we have yet to uncover.

Transcriptional function of E2A, Ebf1, Pax5, Ikaros and Aiolos analyzed by in vivo acute protein degradation in early B cell development

Early B cell lymphopoiesis depends on E2A, Ebf1, Pax5 and Ikaros family members. In the present study, we used acute protein degradation in mice to identify direct target genes of these transcription factors in pro-B, small pre-B and immature B cells. E2A, Ebf1 and Pax5 predominantly function as transcriptional activators by inducing open chromatin at their target genes, have largely unique functions and are essential for early B cell maintenance. Ikaros and Aiolos act as dedicated repressors to cooperatively control early B cell development. The surrogate light-chain genes Igll1 and Vpreb1 are directly activated by Ebf1 and Pax5 in pro-B cells and directly repressed by Ikaros and Aiolos in small pre-B cells. Pax5 and E2A contribute to V(D)J recombination by activating Rag1, Rag2, Dntt, Irf4 and Irf8. Similar to Pax5, Ebf1 also represses the cohesin-release factor gene Wapl to mediate prolonged loop extrusion across the Igh locus. In summary, in vivo protein degradation has provided unprecedented insight into the control of early B cell lymphopoiesis by five transcription factors.

Collaboration between distinct SWI/SNF chromatin remodeling complexes directs enhancer selection and activation of macrophage inflammatory genes

Macrophages elicit immune responses to pathogens through induction of inflammatory genes. Here, we examined the role of three variants of the SWI/SNF nucleosome remodeling complex-cBAF, ncBAF, and PBAF-in the macrophage response to bacterial endotoxin (lipid A). All three SWI/SNF variants were prebound in macrophages and retargeted to genomic sites undergoing changes in chromatin accessibility following stimulation. Cooperative binding of all three variants associated with de novo chromatin opening and latent enhancer activation. Isolated binding of ncBAF and PBAF, in contrast, associated with activation and repression of active enhancers, respectively. Chemical and genetic perturbations of variant-specific subunits revealed pathway-specific regulation in the activation of lipid A response genes, corresponding to requirement for cBAF and ncBAF in inflammatory and interferon-stimulated gene (ISG) activation, respectively, consistent with differential engagement of SWI/SNF variants by signal-responsive transcription factors. Thus, functional diversity among SWI/SNF variants enables increased regulatory control of innate immune transcriptional programs, with potential for specific therapeutic targeting.

Examining NF-κB genomic interactions by ChIP-seq and CUT&Tag

An understanding of the mechanisms and logic by which transcription factors coordinate gene regulation requires delineation of their genomic interactions at a genome-wide scale. Chromatin immunoprecipitation-sequencing (ChIP-seq) and more recent techniques, including CUT&Tag, typically reveal thousands of genomic interactions by transcription factors, but without insight into their functional roles. Due to cost and time considerations, optimization of ChIP experimental conditions is typically carried out only with representative interaction sites rather than through genome-wide analyses. Here, we describe insights gained from the titration of two chemical crosslinking reagents in genome-wide ChIP-seq experiments examining two members of the NF-κB family of transcription factors: RelA and c-Rel. We also describe a comparison of ChIP-seq and CUT&Tag. Our results highlight the large impact of ChIP-seq experimental conditions on the number of interactions detected, on the enrichment of consensus and non-consensus DNA motifs for the factor, and on the frequency with which the genomic interactions detected are located near potential target genes. We also found considerable consistency between ChIP-seq and CUT&Tag results, but with a substantial fraction of genomic interactions detected with only one of the two techniques. Together, the results demonstrate the dramatic impact of experimental conditions on the results obtained in a genome-wide analysis of transcription factor binding, highlighting the need for further scrutiny of the functional significance of these condition-dependent differences.

Systematic single-cell analysis reveals dynamic control of transposable element activity orchestrating the endothelial-to-hematopoietic transition

BACKGROUND

The endothelial-to-hematopoietic transition (EHT) process during definitive hematopoiesis is highly conserved in vertebrates. Stage-specific expression of transposable elements (TEs) has been detected during zebrafish EHT and may promote hematopoietic stem cell (HSC) formation by activating inflammatory signaling. However, little is known about how TEs contribute to the EHT process in human and mouse.

RESULTS

We reconstructed the single-cell EHT trajectories of human and mouse and resolved the dynamic expression patterns of TEs during EHT. Most TEs presented a transient co-upregulation pattern along the conserved EHT trajectories, coinciding with the temporal relaxation of epigenetic silencing systems. TE products can be sensed by multiple pattern recognition receptors, triggering inflammatory signaling to facilitate HSC emergence. Interestingly, we observed that hypoxia-related signals were enriched in cells with higher TE expression. Furthermore, we constructed the hematopoietic cis-regulatory network of accessible TEs and identified potential TE-derived enhancers that may boost the expression of specific EHT marker genes.

CONCLUSIONS

Our study provides a systematic vision of how TEs are dynamically controlled to promote the hematopoietic fate decisions through transcriptional and cis-regulatory networks, and pre-train the immunity of nascent HSCs.