CISH is a negative regulator of IL-13-induced CCL26 production in lung fibroblasts

Proteomic and antimicrobial peptide analyses of Buffalo colostrum and mature Milk whey: A comparative study

Buffalo colostrum is the initial mammary secretion after parturition, consisting of nutritional and bioactive components. In this study, we conducted a proteomic analysis of buffalo colostrum whey to identify bioactive proteins and peptides. A total of 107 differentially expressed proteins (DEPs) were identified in buffalo colostrum whey compared to those in mature milk. Gene Ontology analysis revealed that DEPs were primarily associated with immune response and tissue development. KEGG pathway enrichment suggested that colostrum actively enhances nascent immunity involved in interleukin and interferon signaling pathways. Furthermore, candidate antimicrobial peptides (AMPs) of whey protein hydrolysates from buffalo colostrum were characterized, which exhibits broad-spectrum activity against gram-positive and gram-negative pathogens. Overall, this study improves our understanding of protein variations in buffalo lactation, and contributes to the development of AMPs from buffalo colostrum.

Aberrant expression of suppressor of cytokine signaling (SOCS) molecules contributes to the development of allergic diseases

Suppressor of cytokine signalling (SOCS) proteins bind to certain cytokine receptors, Janus kinases and signalling molecules to regulate signalling pathways, thus controlling immune and inflammatory responses. Dysregulated expression of various types of SOCS molecules was indicated in multiple types of allergic diseases. SOCS1, SOCS2, SOCS3, SOCS5, and cytokine-inducible SH2 domain protein (CISH) can differentially exert anti-allergic impacts through different mechanisms, such as suppressing Th2 cell development and activation, reducing eosinophilia, decreasing IgE production, repressing production of pro-allergic chemokines, promoting Treg cell differentiation and activation, suppressing Th17 cell differentiation and activation, increasing anti-allergic Th1 responses, inhibiting M2 macrophage polarization, modulating survival and development of mast cells, reducing pro-allergic activity of keratinocytes, and suppressing pulmonary fibrosis. Although some anti-allergic effects were attributed to SOCS3, it can perform pro-allergic impacts through several pathways, such as promoting Th2 cell development and activation, supporting eosinophilia, boosting pro-allergic activity of eosinophils, increasing IgE production, enhancing the expression of the pro-allergic chemokine receptor, reducing Treg cell differentiation, increasing pro-allergic Th9 responses, as well as supporting mucus secretion and collagen deposition. In this review, we discuss the contrasting roles of SOCS proteins in contexts of allergic disorders to provide new insights regarding the pathophysiology of these diseases and possibly explore SOCS proteins as potential therapeutic targets for alleviating allergies.

A functional genomics pipeline to identify high-value asthma and allergy CpGs in the human methylome

BACKGROUND

DNA methylation of cytosines at cytosine-phosphate-guanine (CpG) dinucleotides (CpGs) is a widespread epigenetic mark, but genome-wide variation has been relatively unexplored due to the limited representation of variable CpGs on commercial high-throughput arrays.

OBJECTIVES

To explore this hidden portion of the epigenome, this study combined whole-genome bisulfite sequencing with in silico evidence of gene regulatory regions to design a custom array of high-value CpGs. This study focused on airway epithelial cells from children with and without allergic asthma because these cells mediate the effects of inhaled microbes, pollution, and allergens on asthma and allergic disease risk.

METHODS

This study identified differentially methylated regions from whole-genome bisulfite sequencing in nasal epithelial cell DNA from a total of 39 children with and without allergic asthma of both European and African ancestries. This study selected CpGs from differentially methylated regions, previous allergy or asthma epigenome-wide association studies (EWAS), or genome-wide association study loci, and overlapped them with functional annotations for inclusion on a custom Asthma&Allergy array. This study used both the custom and EPIC arrays to perform EWAS of allergic sensitization (AS) in nasal epithelial cell DNA from children in the URECA (Urban Environment and Childhood Asthma) birth cohort and using the custom array in the INSPIRE [Infant Susceptibility to Pulmonary Infections and Asthma Following RSV Exposure] birth cohort. Each CpG on the arrays was assigned to its nearest gene and its promotor capture Hi-C interacting gene and performed expression quantitative trait methylation (eQTM) studies for both sets of genes.

RESULTS

Custom array CpGs were enriched for intermediate methylation levels compared to EPIC CpGs. Intermediate methylation CpGs were further enriched among those associated with AS and for eQTMs on both arrays.

CONCLUSIONS

This study revealed signature features of high-value CpGs and evidence for epigenetic regulation of genes at AS EWAS loci that are robust to race/ethnicity, ascertainment, age, and geography.

Regulatory mechanism of immune-related genes in patients with hypertension

Hypertension (HT) is among the most common cardiovascular diseases in the world and is an important risk factor for stroke, myocardial infarction, heart failure, and kidney failure. Recent studies have demonstrated that activation of the immune system plays an important role in the occurrence and maintenance of HT. Thus, this research aimed to determine the immune-related biomarkers in HT. In this study, RNA sequencing data of the gene expression profiling datasets (GSE74144) were downloaded from the Gene Expression Omnibus database. Differentially expressed genes between HT and normal samples were identified using the software limma. The immune-related genes associated with HT were screened. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed using the program "clusterProfiler" of the R package. The protein-protein interaction network of these differentially expressed immune-related genes (DEIRGs) was constructed based on the information from the STRING database. Finally, the TF-hub and miRNA-hub gene regulatory networks were predicted and constructed using the miRNet software. Fifty-nine DEIRGs were observed in HT. The Gene Ontology analysis indicated that DEIRGs were mainly enriched in the positive regulation of cytosolic calcium ions, peptide hormones, protein kinase B signaling, and lymphocyte differentiation. The Kyoto Encyclopedia of Genes and Genomes enrichment analysis indicated that these DEIRGs were significantly involved in the intestinal immune network for IgA production, autoimmune thyroid disease, JAK-STAT signaling pathway, hepatocellular carcinoma, and Kaposi sarcoma-associated herpesvirus infection, among others. From the protein-protein interaction network, 5 hub genes (insulin-like growth factor 2, cytokine-inducible Src homology 2-containing protein, suppressor of cytokine signaling 1, cyclin-dependent kinase inhibitor 2A, and epidermal growth factor receptor) were identified. The receiver operating characteristic curve analysis was performed in GSE74144, and all genes with an area under the curve of > 0.7 were identified as the diagnostic genes. Moreover, miRNA-mRNA and TF-mRNA regulatory networks were constructed. Our study identified 5 immune-related hub genes in patients with HT and demonstrated that they were potential diagnostic biomarkers for HT.

Nutritional immunomodulation of Atlantic salmon response to Renibacterium salmoninarum bacterin

We investigated the immunomodulatory effect of varying levels of dietary ω6/ω3 fatty acids (FA) on Atlantic salmon (Salmo salar) antibacterial response. Two groups were fed either high-18:3ω3 or high-18:2ω6 FA diets for 8 weeks, and a third group was fed for 4 weeks on the high-18:2ω6 diet followed by 4 weeks on the high-18:3ω3 diet and termed “switched-diet”. Following the second 4 weeks of feeding (i.e., at 8 weeks), head kidney tissues from all groups were sampled for FA analysis. Fish were then intraperitoneally injected with either a formalin-killed Renibacterium salmoninarum bacterin (5 × 10⁷ cells mL⁻¹) or phosphate-buffered saline (PBS control), and head kidney tissues for gene expression analysis were sampled at 24 h post-injection. FA analysis showed that the head kidney profile reflected the dietary FA, especially for C₁₈ FAs. The qPCR analyses of twenty-three genes showed that both the high-ω6 and high-ω3 groups had significant bacterin-dependent induction of some transcripts involved in lipid metabolism (ch25ha and lipe), pathogen recognition (clec12b and tlr5), and immune effectors (znrf1 and cish). In contrast, these transcripts did not significantly respond to the bacterin in the “switched-diet” group. Concurrently, biomarkers encoding proteins with putative roles in biotic inflammatory response (tnfrsf6b) and dendritic cell maturation (ccl13) were upregulated, and a chemokine receptor (cxcr1) was downregulated with the bacterin injection regardless of the experimental diets. On the other hand, an inflammatory regulator biomarker, bcl3, was only significantly upregulated in the high-ω3 fed group, and a C-type lectin family member (clec3a) was only significantly downregulated in the switched-diet group with the bacterin injection (compared with diet-matched PBS-injected controls). Transcript fold-change (FC: bacterin/PBS) showed that tlr5 was significantly over 2-fold higher in the high-18:2ω6 diet group compared with other diet groups. FC and FA associations highlighted the role of DGLA (20:3ω6; anti-inflammatory) and/or EPA (20:5ω3; anti-inflammatory) vs. ARA (20:4ω6; pro-inflammatory) as representative of the anti-inflammatory/pro-inflammatory balance between eicosanoid precursors. Also, the correlations revealed associations of FA proportions (% total FA) and FA ratios with several eicosanoid and immune receptor biomarkers (e.g., DGLA/ARA significant positive correlation with pgds, 5loxa, 5loxb, tlr5, and cxcr1). In summary, dietary FA profiles and/or regimens modulated the expression of some immune-relevant genes in Atlantic salmon injected with R. salmoninarum bacterin. The modulation of Atlantic salmon responses to bacterial pathogens and their associated antigens using high-ω6/high-ω3 diets warrants further investigation.

The ubiquitin ligase Cul5 regulates CD4+ T cell fate choice and allergic inflammation

Antigen encounter directs CD4⁺ T cells to differentiate into T helper or regulatory cells. This process focuses the immune response on the invading pathogen and limits tissue damage. Mechanisms that govern T helper cell versus T regulatory cell fate remain poorly understood. Here, we show that the E3 ubiquitin ligase Cul5 determines fate selection in CD4⁺ T cells by regulating IL-4 receptor signaling. Mice lacking Cul5 in T cells develop Th2 and Th9 inflammation and show pathophysiological features of atopic asthma. Following T cell activation, Cul5 forms a complex with CIS and pJak1. Cul5 deletion reduces ubiquitination and subsequent degradation of pJak1, leading to an increase in pJak1 and pSTAT6 levels and reducing the threshold of IL-4 receptor signaling. As a consequence, Cul5 deficient CD4⁺ T cells deviate from Treg to Th9 differentiation in low IL-4 conditions. These data support the notion that Cul5 promotes a tolerogenic T cell fate choice and reduces susceptibility to allergic asthma.

Cytokine signaling influences the differentiation of CD4⁺ T cells into varying functional subsets. Here the authors show that an E3 ubiquitin ligase Cul5 alters T_H2 and T_H9 development and absence of Cul5 in T cells results in higher levels of allergy-associated IL-4 and IL-9 secreting T cells.

Effect Mechanism of Electroacupuncture at ST36 on the Injured Extensor Digitorum Longus in the Jumping Rat Model Based on mRNA-Seq Analysis

The key target and regulatory mechanism of electroacupuncture of Zusanli (ST36) on extensor longus muscle injury in a jumping rat model were investigated. To this end, 24 female SD rats were randomly divided into the following four groups: no-treatment control group (NON), 6-week jumping group (J6O), electroacupuncture group after 6-week jumping (J6A), and natural recovery group after 6-week jumping (J6N). After 6 weeks of jumping, in the electroacupuncture group (J6A), electroacupuncture stimulation was applied at Zusanli(ST36) for 20 min per day over the course of 5 days. In the natural recovery group (J6N), rats were fastened with a special apparatus without electroacupuncture stimulation for 20 min at the same time. Transmission electron microscopy, transcriptome sequencing and analysis, Western blotting assay and immunofluorescence staining were performed at the end of our experiment. The recovery effect of J6A rats was more obvious than that of J6N rats and J6O rats as indicated by changes of infiltration of inflammatory cells and morphological structure. Notably, the morphological structure of J6A rats was closer to NON rats in the observation of transmission electron microscopy. CISH/STAT3 regulation was identified by mRNA-seq. The pro-inflammatory response to STAT3 activation was alleviated through up-regulating the expression of CISH protein in J6A rats relative to J6O rats. The level of BAX was decreased and the level of Bcl-2 level was increased in J6A rats relative to J6O rats. Moreover, when compared to J6N rats, the level of Bcl-2 was significantly up-regulated in J6A rats. Increased caspase-3 expression but decreased CDKN2α expression was shown in J6A rats relative to NON rats. These results indicate that the potential mechanism underlying electroacupuncture stimulation of Zusanli (ST36) in repairing the injured extensor digitorum longus following overused jumping may be attributed to CISH/STAT3 regulation of proteins associated with inflammation, apoptosis, and proliferation.

CISH constrains the tuft-ILC2 circuit to set epithelial and immune tone

Innate lymphoid cells (ILCs) are tissue-resident effectors poised to activate rapidly in response to local signals such as cytokines. To preserve homeostasis, ILCs must employ multiple pathways, including tonic suppressive mechanisms, to regulate their primed state and prevent inappropriate activation and immunopathology. Such mechanisms remain incompletely characterized. Here we show that cytokine-inducible SH2-containing protein (CISH), a suppressor of cytokine signaling (SOCS) family member, is highly and constitutively expressed in type 2 innate lymphoid cells (ILC2s). Mice that lack CISH either globally or conditionally in ILC2s show increased ILC2 expansion and activation, in association with reduced expression of genes inhibiting cell-cycle progression. Augmented proliferation and activation of CISH-deficient ILC2s increases basal and inflammation-induced numbers of intestinal tuft cells and accelerates clearance of the model helminth, Nippostrongylus brasiliensis, but compromises innate control of Salmonella typhimurium. Thus, CISH constrains ILC2 activity both tonically and after perturbation, and contributes to the regulation of immunity in mucosal tissue.

SOCS Proteins in Immunity, Inflammatory Diseases, and Immune-Related Cancer

Cytokine signaling represents one of the cornerstones of the immune system, mediating the complex responses required to facilitate appropriate immune cell development and function that supports robust immunity. It is crucial that these signals be tightly regulated, with dysregulation underpinning immune defects, including excessive inflammation, as well as contributing to various immune-related malignancies. A specialized family of proteins called suppressors of cytokine signaling (SOCS) participate in negative feedback regulation of cytokine signaling, ensuring it is appropriately restrained. The eight SOCS proteins identified regulate cytokine and other signaling pathways in unique ways. SOCS1–3 and CISH are most closely involved in the regulation of immune-related signaling, influencing processes such polarization of lymphocytes and the activation of myeloid cells by controlling signaling downstream of essential cytokines such as IL-4, IL-6, and IFN-γ. SOCS protein perturbation disrupts these processes resulting in the development of inflammatory and autoimmune conditions as well as malignancies. As a consequence, SOCS proteins are garnering increased interest as a unique avenue to treat these disorders.

MiR-944/CISH mediated inflammation via STAT3 is involved in oral cancer malignance by cigarette smoking

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Down-regulation of CISH in OSCC tissues and cell lines.

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CISH mediates cellular functions through STAT3 inhibition.

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MiR-944 regulates cellular functions through direct binding of CISH.

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Cigarette smoking-mediated miR-944/CISH/STAT3 axis plays a role in oral carcinogenesis.

The cytokine-inducible Src homology 2-containing protein (CISH) is an endogenous suppressors of signal transduction and activator of transcription (STAT) and acts as a key negative regulator of inflammatory cytokine responses. Downregulation of CISH has been reported to associate with increased activation of STAT and enhanced inflammatory pathways. However, whether microRNAs (miRNAs) play a crucial role in CISH/STAT regulation in oral squamous cell carcinoma (OSCC) remains unknown. The expression of CISH on OSCC patients was determine by quantitative real-time PCR (qRT-PCR) and immunohistochemistry. Specific targeting by miRNAs was determined by software prediction, luciferase reporter assay, and correlation with target protein expression. The functions of miR-944 and CISH were accessed by transwell migration and invasion analyses using gain- and loss-of-function approaches. Enzyme-linked immunosorbent assay (ELISA) and qRT-PCR were used to evaluate the pro-inflammation cytokines expression under the miR-944, CISH, NNK or combinations treatment. We found that the CISH protein, which modulates STAT3 activity, as a direct target of miR-944. CISH protein was significantly down-regulated in OSCC patients and cell lines and its level was inversely correlated with miR-944 expression. The miR-944-induced STAT3 phosphorylation, pro-inflammation cytokines secretion, migration and invasion were abolished by CISH restoration, suggesting that the oncogenic activity of miR-944 is CISH dependent. Furthermore, tobacco extract (NNK) may contribute to miR-944 induction and STAT3 activation. Antagomir-mediated inactivation of miR-944 prevented the NNK-induced STAT3 phosphorylation and pro-inflammation cytokines secretion. Altogether, these data demonstrate that NNK-induced miR944 expression plays an important role in CISH/STAT3-mediated inflammatory response and activation of tumor malignancy.

mirTime: identifying condition-specific targets of microRNA in time-series transcript data using Gaussian process model and spherical vector clustering

Background

MicroRNAs, small noncoding RNAs, are conserved in many species, and they are key regulators that mediate post-transcriptional gene silencing. Since biologists cannot perform experiments for each of target genes of thousands of microRNAs in numerous specific conditions, prediction on microRNA target genes has been extensively investigated. A general framework is a two-step process of selecting target candidates based on sequence and binding energy features and then predicting targets based on negative correlation of microRNAs and their targets. However, there are few methods that are designed for target predictions using time-series gene expression data.

Results

In this article, we propose a new pipeline, mirTime, that predicts microRNA targets by integrating sequence features and time-series expression profiles in a specific experimental condition. The most important feature of mirTime is that it uses the Gaussian process regression model to measure data at unobserved or unpaired time points. In experiments with two datasets in different experimental conditions and cell types, condition-specific target modules reported in the original papers were successfully predicted with our pipeline. The context specificity of target modules was assessed with three (correlation-based, target gene-based and network-based) evaluation criteria. mirTime showed better performance than existing expression-based microRNA target prediction methods in all three criteria.

Availability and implementation

mirTime is available at https://github.com/mirTime/mirtime.

Supplementary information

Supplementary data are available at Bioinformatics online.