scholarly journals Transcriptional Regulation of Inflammasomes

2020 ◽  
Author(s):  
Maxence Cornut ◽  
Emilie Bourdonnay ◽  
Thomas Henry
Keyword(s):  
Transcriptional Regulation ◽  
Transcription Factors ◽  
Immune Responses ◽  
Circadian Clock ◽  
Chromatin Structure ◽  
Cell Types ◽  
First Line ◽  
Inflammatory Signals ◽  
Structure Changes ◽  
Different Cell Types

Inflammasomes are multimolecular complexes with potent inflammatory activity. As such, their activity is tightly regulated at the transcriptional and post-transcriptional levels. In this review, we present the transcriptional regulation of inflammasome genes from sensors (e.g NLRP3) to substrates (e.g. IL-1β). Lineage-determining transcription factors shape inflammasome responses in different cell types with profound consequences on the responsiveness to inflammasome-activating stimuli. Pro-inflammatory signals (sterile or microbial) have a key transcriptional impact on inflammasome genes, which is largely mediated by NF-κB and, that translates into higher antimicrobial immune responses. Furthermore, diverse intrinsic (e.g. circadian clock, metabolites) or extrinsic (e.g. xenobiotics) signals are integrated by signal-dependent transcription factors and chromatin structure changes to modulate transcriptionally inflammasome responses. Finally, anti-inflammatory signals (e.g. IL-10) counterbalance inflammasome genes induction to limit deleterious inflammation. Transcriptional regulations thus appear as the first line of inflammasome regulation to raise the defense level in front of stress and infections but also to limit excessive or chronic inflammation.

scholarly journals Transcriptional Regulation of Inflammasomes

2020 ◽  
Vol 21 (21) ◽  
pp. 8087
Author(s):  
Maxence Cornut ◽  
Emilie Bourdonnay ◽  
Thomas Henry
Keyword(s):  
Transcriptional Regulation ◽  
Transcription Factors ◽  
Immune Responses ◽  
Circadian Clock ◽  
Chromatin Structure ◽  
Cell Types ◽  
First Line ◽  
Inflammatory Signals ◽  
Structure Changes ◽  
Different Cell Types

Inflammasomes are multimolecular complexes with potent inflammatory activity. As such, their activity is tightly regulated at the transcriptional and post-transcriptional levels. In this review, we present the transcriptional regulation of inflammasome genes from sensors (e.g., NLRP3) to substrates (e.g., IL-1β). Lineage-determining transcription factors shape inflammasome responses in different cell types with profound consequences on the responsiveness to inflammasome-activating stimuli. Pro-inflammatory signals (sterile or microbial) have a key transcriptional impact on inflammasome genes, which is largely mediated by NF-κB and that translates into higher antimicrobial immune responses. Furthermore, diverse intrinsic (e.g., circadian clock, metabolites) or extrinsic (e.g., xenobiotics) signals are integrated by signal-dependent transcription factors and chromatin structure changes to modulate transcriptionally inflammasome responses. Finally, anti-inflammatory signals (e.g., IL-10) counterbalance inflammasome genes induction to limit deleterious inflammation. Transcriptional regulations thus appear as the first line of inflammasome regulation to raise the defense level in front of stress and infections but also to limit excessive or chronic inflammation.

scholarly journals HIV-2/SIV Vpx antagonises NF-𝜅B activation by targeting p65

2021 ◽  
Author(s):  
Douglas L Fink ◽  
James Cai ◽  
Matthew VX Whelan ◽  
Christopher Monit ◽  
Carlos Maaluquer de Motes ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Immune Responses ◽  
Gene Networks ◽  
Nuclear Translocation ◽  
Cell Types ◽  
Viral Pathogen ◽  
Mona Monkey ◽  
Molecular Patterns ◽  
Different Cell Types

The NF-𝜅B family of transcription factors and associated signalling pathways are abundant and ubiquitous in human immune responses. Activation of NF-𝜅B transcription factors by viral pathogen-associated molecular patterns, such as viral RNA and DNA, is fundamental to anti-viral innate immune defences and pro-inflammatory cytokine production that steers adaptive immune responses. Diverse non-viral stimuli, such as lipopolysaccharide and cytokines, also activate NF-𝜅B and the same anti-pathogen gene networks. Viruses adapted to human cells often encode multiple proteins aimed at varied NF-𝜅B pathway targeted to mitigate the anti-viral effects of NF-𝜅B-dependent host immunity. In this study we have demonstrated using numerous assays, in a number of different cell types, that plasmid-encoded or virus-delivered Simian Immunodeficiency Virus (SIV) accessory protein Vpx is a broad antagonist of NF-𝜅B signalling active against diverse innate NF-𝜅B agonists. Using targeted Vpx mutagenesis, we showed that this novel Vpx phenotype is independent of known Vpx cofactor DCAF1 and other cellular binding partners, including SAMHD1, STING and the HUSH complex. We found that Vpx co-immunoprecipitated with canonical NF-𝜅B transcription factor p65 and not NF-𝜅B transcription factor proteins p50 or p100, preventing nuclear translocation of p65, a novel mechanism of NF-𝜅B antagonism by lentiviruses. We found that broad antagonism of NF-𝜅B activation by Vpx was conserved across distantly related lentiviruses as well as for Vpr from SIV Mona monkey (SIVmon), which has Vpx-like SAMHD1-degradation activity.

scholarly journals Effects of Gut Metabolites and Microbiota in Healthy and Marginal Livers Submitted to Surgery

2020 ◽  
Vol 22 (1) ◽  
pp. 44
Author(s):  
Marc Micó-Carnero ◽  
Carlos Rojano-Alfonso ◽  
Ana Isabel Álvarez-Mercado ◽  
Jordi Gracia-Sancho ◽  
Araní Casillas-Ramírez ◽  
...  
Keyword(s):  
Immune Responses ◽  
Ischemia Reperfusion Injury ◽  
Ischemia Reperfusion ◽  
Cell Types ◽  
Microbial Populations ◽  
Operative Outcomes ◽  
Bidirectional Relationship ◽  
Preclinical And Clinical Studies ◽  
Different Cell Types ◽  
Stimulation Of

Microbiota is defined as the collection of microorganisms within the gastrointestinal ecosystem. These microbes are strongly implicated in the stimulation of immune responses. An unbalanced microbiota, termed dysbiosis, is related to the development of several liver diseases. The bidirectional relationship between the gut, its microbiota and the liver is referred to as the gut–liver axis. The translocation of bacterial products from the intestine to the liver induces inflammation in different cell types such as Kupffer cells, and a fibrotic response in hepatic stellate cells, resulting in deleterious effects on hepatocytes. Moreover, ischemia-reperfusion injury, a consequence of liver surgery, alters the microbiota profile, affecting inflammation, the immune response and even liver regeneration. Microbiota also seems to play an important role in post-operative outcomes (i.e., liver transplantation or liver resection). Nonetheless, studies to determine changes in the gut microbial populations produced during and after surgery, and affecting liver function and regeneration are scarce. In the present review we analyze and discuss the preclinical and clinical studies reported in the literature focused on the evaluation of alterations in microbiota and its products as well as their effects on post-operative outcomes in hepatic surgery.

scholarly journals Transcriptional Regulation of Autophagy Genes via Stage-Specific Activation of CEBPB and PPARG during Adipogenesis: A Systematic Study Using Public Gene Expression and Transcription Factor Binding Datasets

Cells ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 1321 ◽  
Author(s):  
Mahmoud Ahmed ◽  
Trang Huyen Lai ◽  
Jin Seok Hwang ◽  
Sahib Zada ◽  
Trang Minh Pham ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcriptional Regulation ◽  
Transcription Factors ◽  
High Throughput Sequencing ◽  
Cell Model ◽  
Cell Types ◽  
Autophagy Gene ◽  
Occupancy Patterns ◽  
Differentiation Stage

Autophagy is the cell self-eating mechanism to maintain cell homeostasis by removing damaged intracellular proteins or organelles. It has also been implicated in the development and differentiation of various cell types including the adipocyte. Several links between adipogenic transcription factors and key autophagy genes has been suggested. In this study, we tried to model the gene expression and their transcriptional regulation during the adipocyte differentiation using high-throughput sequencing datasets of the 3T3-L1 cell model. We applied the gene expression and co-expression analysis to all and the subset of autophagy genes to study the binding, and occupancy patterns of adipogenic factors, co-factors and histone modifications on key autophagy genes. We also analyzed the gene expression of key autophagy genes under different transcription factor knockdown adipocyte cells. We found that a significant percent of the variance in the autophagy gene expression is explained by the differentiation stage of the cell. Adipogenic master regulators, such as CEBPB and PPARG target key autophagy genes directly. In addition, the same factor may also control autophagy gene expression indirectly through autophagy transcription factors such as FOXO1, TFEB or XBP1. Finally, the binding of adipogenic factors is associated with certain patterns of co-factors binding that might modulate the functions. Some of the findings were further confirmed under the knockdown of the adipogenic factors in the differentiating adipocytes. In conclusion, autophagy genes are regulated as part of the transcriptional programs through adipogenic factors either directly or indirectly through autophagy transcription factors during adipogenesis.

The innate immune system

2020 ◽  
pp. 307-314
Author(s):  
Paul Bowness
Keyword(s):  
Immune System ◽  
Immune Responses ◽  
Innate Immune System ◽  
Cell Types ◽  
Innate Immune ◽  
Microbial Pathogens ◽  
Innate Immune Responses ◽  
Adaptive Immune ◽  
System P ◽  
Different Cell Types

The innate immune system comprises evolutionarily ancient mechanisms that mediate first-line responses against microbial pathogens, and are also important in priming and execution of adaptive immune responses, and in defence against tumours. These responses, which recognize microbial non-self, damaged self, and absent self, are characterized by rapidity of action and they involve various different cell types, cell-associated receptors, and soluble factors. Previously thought to lack plasticity or memory, certain innate immune responses have recently been shown to be capable of ‘learning’ or ‘training’. Most cells of the innate immune system are derived from the myeloid precursors in the bone marrow. These include monocytes and their derivatives—macrophages and dendritic cells, blood granulocytes (neutrophils, basophils, and eosinophils), and tissue mast cells.

scholarly journals A single-cell atlas reveals shared and distinct immune responses and metabolism during SARS-CoV-2 and HIV-1 infections

2022 ◽  
Author(s):  
Tony Pan ◽  
Guoshuai Cao ◽  
Erting Tang ◽  
Yu Zhao ◽  
Pablo Penaloza-MacMaster ◽  
...  
Keyword(s):  
Immune Responses ◽  
Single Cell ◽  
Immune Cells ◽  
Viral Infections ◽  
Rho Gtpase ◽  
Cell Types ◽  
Disease Biology ◽  
Similarities And Differences ◽  
Different Cell Types ◽  
Hiv 1

SARS-CoV-2 and HIV-1 are RNA viruses that have killed millions of people worldwide. Understanding the similarities and differences between these two infections is critical for understanding disease progression and for developing effective vaccines and therapies, particularly for 38 million HIV-1+ individuals who are vulnerable to SARS-CoV-2 co-infection. Here, we utilized single-cell transcriptomics to perform a systematic comparison of 94,442 PBMCs from 7 COVID-19 and 9 HIV-1+ patients in an integrated immune atlas, in which 27 different cell types were identified using an accurate consensus single-cell annotation method. While immune cells in both cohorts show shared inflammation and disrupted mitochondrial function, COVID-19 patients exhibit stronger humoral immunity, broader IFN-I signaling, elevated Rho GTPase and mTOR pathway activities, and downregulated mitophagy. Our results elucidate transcriptional signatures associated with COVID-19 and HIV-1 that may reveal insights into fundamental disease biology and potential therapeutic targets to treat these viral infections.

scholarly journals Single-Cell Regulatory Network Inference and Clustering Identifies Cell-Type Specific Expression Pattern of Transcription Factors in Mouse Sciatic Nerve

2021 ◽  
Vol 15 ◽  
Author(s):  
Mingchao Li ◽  
Qing Min ◽  
Matthew C. Banton ◽  
Xinpeng Dun
Keyword(s):  
Transcription Factors ◽  
Sciatic Nerve ◽  
Single Cell ◽  
Cell Types ◽  
Cell Type ◽  
Specific Expression ◽  
Single Cell Rna Sequencing ◽  
Cell Type Specific Expression ◽  
Cell Type Specific ◽  
Different Cell Types

Advances in single-cell RNA sequencing technologies and bioinformatics methods allow for both the identification of cell types in a complex tissue and the large-scale gene expression profiling of various cell types in a mixture. In this report, we analyzed a single-cell RNA sequencing (scRNA-seq) dataset for the intact adult mouse sciatic nerve and examined cell-type specific transcription factor expression and activity during peripheral nerve homeostasis. In total, we identified 238 transcription factors expressed in nine different cell types of intact mouse sciatic nerve. Vascular smooth muscle cells have the lowest number of transcription factors expressed with 17 transcription factors identified. Myelinating Schwann cells (mSCs) have the highest number of transcription factors expressed, with 61 transcription factors identified. We created a cell-type specific expression map for the identified 238 transcription factors. Our results not only provide valuable information about the expression pattern of transcription factors in different cell types of adult peripheral nerves but also facilitate future studies to understand the function of key transcription factors in the peripheral nerve homeostasis and disease.

scholarly journals The Role of MicroRNAs in Regulatory T Cells

2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Chao Liu ◽  
Nannan Li ◽  
Guijian Liu
Keyword(s):  
T Cells ◽  
Regulatory T Cells ◽  
Immune Responses ◽  
Small Rnas ◽  
Target Genes ◽  
Cell Types ◽  
Immune Disorders ◽  
Ongoing Research ◽  
Different Cell Types

MicroRNAs are a class of conserved, 20 nt-23 nt long, noncoding small RNAs that inhibit expression of their respective target genes in different cell types. Regulatory T cells (Tregs) are a subpopulation of T cells that negatively regulate immune responses, which is essential to immune homeostasis. Recent studies have indicated that microRNAs play an important role in the proliferation, differentiation, and functions of Treg. Here, we review the recent progress in understanding the roles of microRNAs in Treg and their dysregulation in immune-related diseases. This ongoing research continues to expand the understanding of Treg regulation and the mechanisms of immune disorders.

scholarly journals Post-transcriptional regulation across human tissues

2015 ◽  
Author(s):  
Alexander Franks ◽  
Edoardo Airoldi ◽  
Nikolai Slavov
Keyword(s):  
Transcriptional Regulation ◽  
Cell Types ◽  
Tissue Type ◽  
Mrna Levels ◽  
Human Tissues ◽  
Protein Levels ◽  
Physiological Variability ◽  
Reliable Quantification ◽  
Post Transcriptional Regulation ◽  
Different Cell Types

AbstractTranscriptional and post-transcriptional regulation shape tissue-type-specific proteomes, but their relative contributions remain contested. Estimates of the factors determining protein levels in human tissues do not distinguish between (i) the factors determining the variability between the abundances of different proteins, i.e., mean-level-variability and, (ii) the factors determining the physiological variability of the same protein across different tissue types, i.e., across-tissues variability. We sought to estimate the contribution of transcript levels to these two orthogonal sources of variability, and found that scaled mRNA levels can account for most of the mean-level-variability but not necessarily for across-tissues variability. The reliable quantification of the latter estimate is limited by substantial measurement noise. However, protein-to-mRNA ratios exhibit substantial across-tissues variability that is functionally concerted and reproducible across different datasets, suggesting extensive post-transcriptional regulation. These results caution against estimating protein fold-changes from mRNA fold-changes between different cell-types, and highlight the contribution of post-transcriptional regulation to shaping tissue-type-specific proteomes.

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