Cytokine-cytokine Receptor Interaction Pathway Research Articles

Transcriptomic analysis reveals the gene expression profiles in the spleen of spotted knifejaw (Oplegnathus punctatus) infected by Vibrio harveyi

As one of the most valuable maricultured species, spotted knifejaw (Oplegnathus punctatus) has high popularity in eastern Asia. In recent years, diseases caused by Vibrio harveyi have brought huge economic losses in spotted knifejaw industry. To better understand the molecular mechanisms of immune response about V. harveyi resistance in spotted knifejaw, a comparative transcriptome analysis was performed on spleen tissues at five different time points post-infection (0, 12, 24, 48 and 72 hpi). A total of 4279 differentially expressed genes (DEGs) were identified. KEGG pathways analysis showed that multiple immune-related pathways were significant regulated, including Toll-like receptor signaling pathway, ECM-receptor interaction pathway, cytokine-cytokine receptor interaction pathway and hematopoietic cell lineage pathway. Weighted gene co-expression network analysis showed that several immune-related pathways of the highest correlation with 12 hpi (cor = 0.89, P = 7e-06) were significantly enriched. In addition, 12 hpi was a turning point for 7 gene clusters out of 9 that were divided according to gene expression patterns. Therefore, we speculated that 12 hpi might be a very critical time point for spotted knifejaw against V. harveyi infection. Additionally, qRT-PCR was carried out to validate the expressions of 12 DEGs. This study provided the first systematical transcriptome analysis of spotted knifejaw against V. harveyi. The results could help us better understand the dynamic immune responses of spotted knifejaw against bacterial infection, and provide useful information for antibacterial defense in spotted knifejaw industry as well.

Multi-staged gene expression profiling reveals potential genes and the critical pathways in kidney cancer

Cancer is among the highly complex disease and renal cell carcinoma is the sixth-leading cause of cancer death. In order to understand complex diseases such as cancer, diabetes and kidney diseases, high-throughput data are generated at large scale and it has helped in the research and diagnostic advancement. However, to unravel the meaningful information from such large datasets for comprehensive and minute understanding of cell phenotypes and disease pathophysiology remains a trivial challenge and also the molecular events leading to disease onset and progression are not well understood. With this goal, we have collected gene expression datasets from publicly available dataset which are for two different stages (I and II) for renal cell carcinoma and furthermore, the TCGA and cBioPortal database have been utilized for clinical relevance understanding. In this work, we have applied computational approach to unravel the differentially expressed genes, their networks for the enriched pathways. Based on our results, we conclude that among the most dominantly altered pathways for renal cell carcinoma, are PI3K-Akt, Foxo, endocytosis, MAPK, Tight junction, cytokine-cytokine receptor interaction pathways and the major source of alteration for these pathways are MAP3K13, CHAF1A, FDX1, ARHGAP26, ITGBL1, C10orf118, MTO1, LAMP2, STAMBP, DLC1, NSMAF, YY1, TPGS2, SCARB2, PRSS23, SYNJ1, CNPPD1, PPP2R5E. In terms of clinical significance, there are large number of differentially expressed genes which appears to be playing critical roles in survival.

Intermittent Hypoxia Attenuates and Reverses Epinephrine‐Induced Changes in Gene Expression in Endothelial Cells

BackgroundObstructive sleep apnea (OSA) is an independent risk factor for cardiovascular disease; however, the mechanisms are not completely known. OSA‐induced endothelial cell (EC) dysfunction and activation, which precede the development of cardiovascular disease may play a role, but how OSA causes EC dysfunction are not well‐understood. Intermittent hypoxia (IH) and sympathetic activation leading to elevated catecholamines (i.e., epinephrine) are hallmarks of OSA. We have recently demonstrated that IH causes EC activation not directly but via the IH‐induced sympathetic activation and catecholamines (i.e., epinephrine). The objective of this study was to investigate the effect of IH and epinephrine on EC gene expression in an unbiased fashion. We hypothesized that IH and epinephrine cause differential expression of genes in ECs contributing to EC dysfunction in OSA.MethodsWe exposed primary human aortic ECs to normoxia or IH (alternating between 5% O2 for 2 minutes and 20% O2 for 5 minutes) in the presence or absence of epinephrine (10μM) for 60 cycles and isolated RNA for sequencing at the end of exposure.ResultsEpinephrine induced significantly higher number of differentially expressed genes (DEGs) compared to IH alone. The majority (92%) of DEGs identified under IH were also seen in response to epinephrine (Figure 1). These common DEGs were enriched in leukocyte migration, extracellular matrix organization, cell adhesion and blood vessel development. IH‐related genes were also enriched in NOD‐like receptor signaling pathway, lipid and atherosclerosis, cytokine‐cytokine receptor interaction and chemokine signaling pathways, whereas epinephrine related genes were enriched in Ras signaling, MAPK signaling, PI3K‐Akt signaling and Phospholipase D signaling pathways as well as cytokine‐cytokine receptor interaction. Combining IH with epinephrine had significant impact on epinephrine‐induced gene expression under normoxic conditions and attenuated and reversed the epinephrine‐induced changes on gene expression.ConclusionsThe effect of epinephrine on gene expression is greater than IH alone in terms of the number of genes and their level of expression. The majority of genes that are differentially expressed in response to IH were also regulated by epinephrine resulting in activation of similar biologic processes by IH and epinephrine. We also identified new biologic and signaling pathways affected by IH and epinephrine alone and in combination. Further investigation of these IH‐ and epinephrine‐regulated genes and pathways will increase our understanding of the mechanisms by which OSA causes EC dysfunction and cardiovascular disease.

Cross-Platform in-silico Analyses Exploring Tumor Immune Microenvironment with Prognostic Value in Triple-Negative Breast Cancer.

IntroductionOnly a proportion of triple-negative breast cancer (TNBC) is immunotherapy-responsive. We hypothesized that the tumor microenvironment (TME) influences the outcomes of TNBC and investigated the relevant signaling pathways.Materials and MethodsImmune score (IS) and stromal score (SS) were calculated using the ESTIMATE and correlated with the overall survival (OS) in TNBC. RNA-seq data from 115 TNBC samples and 112 normal adjacent tissues were retrieved. Validations in the methylation levels in 10 TNBC and five non-TNBC cell lines were obtained. Cox model overall survival (OS) validated the derived transcription factor (TF) genes in cBioPortal breast cancer patients.ResultsSS-low predicts a higher OS compared with SS-high patients (P = 0.0081 IS-high/SS-low patients had better OS (P = 0.045) than IS-low/SS-high patients. More macrophages were polarized to the M2 state in patients with IS-low/SS-high patients (P < 0.001). Moreover, CIBERSORTx showed more CD8+ cytotoxic T-cells in IS-high/SS-low patients (p = 0.0286) and more resting NK cells in the IS-low/SS-high TME (P = 0.0108). KEGG pathway analysis revealed that overexpressed genes were enriched in the IL-17 and cytokine-cytokine receptor interaction pathways. The lncRNA DRAIC, a tumor suppressor, was consistently deactivated in the 10 TNBC cell lines. On the cBioPortal platform, we validated that 13% of ER-negative, HER2-unamplified BC harbored IL17RA deep deletion and 25% harbored TRAF3IP2 amplification. On cBioPortal datasets, the nine altered TF genes derived from the X2K analysis showed significantly worse relapse-free survival in 2377 patients and OS in 4819 invasive BC patients than in the unaltered cohort.ConclusionOf note, the results of this integrated in silico study can only be generalized to approximately 17% of patients with TNBC, in which infiltrating stromal cells and immune cells play a determinant prognostic role.

Construction Immune Related Feed-Forward Loop Network Reveals Angiotensin II Receptor Blocker as Potential Neuroprotective Drug for Ischemic Stroke.

Ischemic stroke (IS) accounts for the leading cause of disability and mortality in China. Increasing researchers are studying the effects of neuroprotective agents on IS. However, the molecular mechanisms of feed-forward loops (FFLs) associated with neuroprotection in the pathogenesis of IS need to be further studied. A protein-protein interaction (PPI) network of IS immune genes was constructed to decipher the characters and excavate 3 hub genes (PI3K, IL6, and TNF) of immunity. Then, we identified two hub clusters of IS immune genes, and the cytokine-cytokine receptor interaction pathway was discovered on the pathway enrichment results of both clusters. Combined with GO enrichment analysis, the cytokines participate in the inflammatory response in the extracellular space of IS patients. Next, a transcription factor (TF)–miRNA–immune gene network (TMIGN) was established by extracting four regulatory pairs (TF–miRNA, TF–gene, miRNA–gene, and miRNA–TF). Then, we detected 3-node regulatory motif types in the TMIGN network. According to the criteria we set for defining 3-node motifs, the motif with the highest Z-score (3-node composite FFL) was picked as the statistically evident motif, which was merged to construct an immune-associated composite FFL motif-specific sub-network (IA-CFMSN), which contained 21 3-node FFLs composed of 13 miRNAs, 4 TFs, 9 immune genes, and 1 TF& immune gene, among which TP53 and VEGFA were prominent TF and immune gene, respectively. In addition, the immune genes in IA-CFMSN were used for identifying associated pathways and drugs to further clarify the immune regulation mechanism and neuroprotection after IS. As a result, 5 immune genes targeted by 20 drugs were identified and the Angiotensin II Receptor Blockers (ARBs) target AGTR1 was found to be a neuroprotective drug for IS. In the present study, the construction of IA-CFMSN provides IS immune-associated FFLs for further experimental studies, providing new prospects for the discovery of new biomarkers and potential drugs for IS.

Identification of Down-Regulated ADH1C is Associated With Poor Prognosis in Colorectal Cancer Using Bioinformatics Analysis.

Colorectal cancer (CRC) is the second most deadly cancer in the whole world, with the underlying mechanisms largely indistinct. Therefore, we aimed to identify significant pathways and genes involved in the initiation, formation and poor prognosis of CRC using bioinformatics methods. In this study, we compared gene expression profiles of CRC cases with those from normal colorectal tissues from three chip datasets (GSE33113, GSE23878 and GSE41328) to identify 105 differentially expressed genes (DEGs) that were common to the three datasets. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses showed that the highest proportion of up-regulated DEGs was involved in extracellular region and cytokine-cytokine receptor interaction pathways. Integral components of membrane and bile secretion pathways were identified as containing down-regulated DEGs. 13 hub DEGs were chosen and their expression were further validated by GEPIA. Only four DEGs (ADH1C, CLCA4, CXCL8 and GUCA2A) were associated with a significantly lower overall survival after the prognosis analysis. Lower ADH1C protein level and higher CXCL8 protein level were verified by immunohistochemical staining and western blot in clinical CRC and normal colorectal tissues. In conclusion, our study indicated that the extracellular tumor microenvironment and bile metabolism pathways play critical roles in the formation and progression of CRC. Furthermore, we confirmed ADH1C being down-regulated in CRC and reported ADH1C as a prognostic predictor for the first time.

Abstract 029: Proteins Linking Chronic Kidney Disease To Incident Heart Failure In Adults With Chronic Kidney Disease: The Atherosclerosis Risk In Communities Study

Introduction: Decreased estimated glomerular filtration rate (eGFR), a kidney dysfunction marker, associates independently with an increased incident heart failure (HF) risk. Identifying mechanisms linking kidney dysfunction to incident HF may reveal potential therapeutic targets. We performed a proteome-wide analysis to identify eGFR-related pathways associated with incident HF. Methods: We studied ARIC participants at Visit 3 (n=10412) and Visit 5 (n=4841) who were free of HF and had aptamer-based proteomic data (SomaLogic, Boulder, CO). Multivariable linear regression models identified proteins associated with eGFR at Visits 3 and 5 at Bonferroni-adjusted P &lt; 1x10 -5 . Incident HF associations were assessed for eGFR-related proteins with multivariable Cox proportional hazards regression models at Bonferroni-adjusted P &lt; 1x10 -5 . All regression models were adjusted for demographics, hypertension, diabetes, coronary artery disease, atrial fibrillation, smoking status, eGFR and albuminuria. Pathway analysis (g:Profiler/KEGG) was performed using proteins associated with incident HF at a false discovery rate (FDR) of &lt; 0.05. Results: The mean age at Visit 3 was 62±6 years, 52% were women, 22% were Black, and 1127 incident HF events occurred post-Visit 3 (median follow-up: 14.8 years). The mean age at Visit 5 was 76±5 years, 58% were women, 18% were Black, and 488 incident HF events occurred post-Visit 5 (median follow-up: 7.2 years). One thousand and seventy-three proteins associated with eGFR at Visits 3 and 5 (P &lt; 1x10 -5 ). Of these eGFR-related proteins, 18 associated with incident HF at Visits 3 and 5 (P &lt; 5x10 -5 ) ( Figure ). Complement and coagulation cascades and cytokine-cytokine receptor interaction pathways were enriched within the 226 proteins associated with incident HF at FDR &lt; 0.05. Conclusions: Kidney dysfunction-related changes in innate immunity and thrombosis associate with an increased risk of incident HF.

The dynamic immune responses of Mandarin fish (Siniperca chuatsi) to ISKNV in early infection based on full-length transcriptome analysis and weighted gene co-expression network analysis

Mandarin fish (Siniperca chuatsi) been seriously harmed by infectious spleen and kidney necrosis virus (ISKNV) in recent years, but the early immune response mechanism of infection is still unknown. Here, we performed RNA sequencing on the spleens of mandarin fish infected with ISKNV at 0, 12, 24, 48, and 72 h post-infection (hpi) using short-read Illumina RNA sequencing and long-read Pacific Biosciences isoform sequencing to generate a full-length transcriptome. The immune responses of mandarin fish infected with ISKNV at the molecular level were characterized by RNA-seq analysis and weighted gene co-expression network analysis (WGCNA). A total of 26,528 full-length transcript sequences were obtained. There were 2,729 (1,680 up-regulated and 1,112 down-regulated), 1,874 (1,136 up-regulated and 738 down-regulated), 2,032 (1,158 up-regulated and 847 down-regulated), and 4,176 (2,233 up-regulated and 1,943 down-regulated) differentially expressed genes (DEGs) in mandarin fish at 12, 24, 48, and 72 hpi, compared with uninfected fish, respectively. A total of four modules of co-expressed DEGs identified by WGCNA were significantly positively correlated to the four time points after infection, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the immune-related DEGs in all these modules were mainly enriched in Phagosome, Endocytosis, Herpes simplex infection, and Cytokine-cytokine receptor interaction pathways. Further analysis showed that oher signaling pathways, including CAMs, NOD-like receptor and ER protein processing, Intestinal immune network for IgA production, TLR pathway, and Apoptosis significantly enriched in four modules corresponding to 12, 24, 48, and 72 hpi respectively, had specifically participated in the immune response. Hub genes identified based on the high-degree nodes in the WGCN, including CAM3, IL-8, CCL21, STING, SNX1, PFR and TBK1, and some DEGs such as MHCI, MHCII, TfR, STING, TNF α, TBK1, IRF1, and NF-kB, BCR, IgA and Bcl-XL had involved in dynamic molecular response of mandarin fish to ISKNV infection. In sum, this study provides a set of full-length transcriptome of the spleen tissue of mandarin fish for the first time and revealed a group of immune genes and pathways involved in different temporal responses to ISKNV infection, which has implications for resource conservation and aiding the development of strategies to prevent virus early infection for mandarin fish.

Elucidating the material basis and potential mechanisms of Ershiwuwei Lvxue Pill acting on rheumatoid arthritis by UPLC-Q-TOF/MS and network pharmacology.

Ershiwuwei Lvxue Pill (ELP, མགྲིན་མཚལ་ཉེར་ལྔ།), a traditional Tibetan medicine preparation, has been used hundreds of years for the clinical treatment of rheumatoid arthritis (RA) in the highland region of Tibet, China. Nevertheless, its chemical composition and therapeutic mechanism are unclear. This study aimed to uncover the potentially effective components of ELP and the pharmacological mechanisms against RA by combing UPLC-Q-TOF/MS and network pharmacology. In this study, 96 compounds of ELP were identified or tentatively characterized based on UPLC-Q-TOF/MS analysis. Then, a total of 22 potential bioactive compounds were screened by TCMSP with oral bioavailability and drug-likeness. Preliminarily, 10 crucial targets may be associated with RA through protein-protein interaction network analysis. The functional enrichment analysis indicated that ELP exerted anti-RA effects probably by synergistically regulating many biological pathways, such as PI3K-Akt, Cytokine-cytokine receptor interaction, JAK-STAT, MAPK, TNF, and Toll-like receptor signaling pathway. In addition, good molecular docking scores were highlighted between five promising bioactive compounds (ellagic acid, quercetin, kaempferol, galangin, coptisine) and five core targets (PTGS2, STAT3, VEGFA, MAPK3, TNF). Overall, ELP can exert its anti-RA activity via multicomponent, multitarget, and multichannel mechanisms of action. However, further studies are needed to validate the biological processes and effect pathways of ELP.

Efficacy of glucocorticoids, chloroquine and vitamin A on cytokine release syndrome: a network pharmacology study.

To verify the efficacy of glucocorticoids, chloroquine and vitamin A in the treatment of cytokine release syndrome (CRS), and to investigate the underlying mechanisms, based on network pharmacology. We used network pharmacology analysis and found 20 co-targeted genes of glucocorticoids, chloroquine, vitamin A and CRS. The pharmacological functions and therapeutic pathways of the genes were analyzed by gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment. The candidate naturally bioactive compounds against the key genes were predicted by Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform. The anti-inflammatory activity of luteolin was assessed by real-time polymerase chain reaction. Among the 20 co-targeted genes of glucocorticoids, chloroquine and vitamin A, interleukin 10 (IL-10), interleukin 2 (IL-2), interleukin 4 (IL-4) and tumor necrosis factor-α (TNF-α) were the key cytokines against CRS. The key pathway involved in the pharmacological mechanism could be cytokine-cytokine receptor interaction pathway, T cell receptor signaling pathway, Janus Kinase-signal transducer and activator of transcription signaling pathway and phosphatidylinositol 3-kinase-protein kinase B signaling pathway. Luteolin targeted by IL-10, IL-4, IL-2 and TNF-α could be one candidate drug for the treatment of CRS. This study comprehensively elucidates the pharmacological mechanism for the treatment of CRS and provides a new method for the discovery of drugs for this disease.

RNA-seq analysis of phagocytic cells from murine epididymal white adipose tissue shows immunosenescence and age-related phosphorus metabolism.

The underlying state of alterations in adipose tissue is hypothesized to be as a result of age-related changes. Young and aged mice have been documented to show distinct gene expression and distinct macrophage-specific adipose tissue regulation. However, more biological understanding is required to know the processes associated with these conditions in relation to the aging process. Transcriptional profiling with RNA-seq analysis was used to determine differentially expressed genes in young (2months old) and aged (20months old) mice macrophage-enriched phagocytic stromal vascular fractions of pooled epididymal white adipose tissue using data obtained from gene expression omnibus. Results showed distinct differentially expressed genes in young and aged mice with a p value cutoff of 0.05 and dissimilarities in the young and aged epididymal white adipose tissue phagocytic cells. Functional enrichment showed activation of cytokine-cytokine receptor interaction pathways, phosphorus metabolic processes and inflammatory pathways such as IL-17, TNF, NF-kappa B, and TGF-β, while AMPK, PPAR and oxidative phosphorylation were suppressed. The analysis showed that aging is linked with phagocytic cell decline, accumulated cellular damages, inflammation, immunosenescence and increased phosphorus metabolism. Interventions that reduce phosphate-containing compound could improve phosphorus metabolism in old age to prolong lifespan and better health.

Transcriptome analysis of grass carp (Ctenopharyngodon idella) and Holland's spinibarbel (Spinibarbus hollandi) infected with Ichthyophthirius multifiliis

Ichthyophthirius multifiliis is a protozoan ciliate that causes white spot disease (also known as ichthyophthiriasis) in freshwater fish. Holland's spinibarbel (Spinibarbus hollandi) was less susceptible to white spot disease than grass carp (Ctenopharyngodon Idella). In this study, grass carp and Holland's spinibarbel are infected by I. multifiliis and the amount of infection is 10,000 theronts per fish. All grass carp died within 12 days after infection, and the survival rate of Holland's spinibarbel was more than 80%. In order to study the difference in sensitivity of these two fish species to I. multifiliis, transcriptome analysis was conducted using gill, skin, liver, spleen and head kidney of Holland's spinibarbel and grass carp at 48 h post-infection with I. multifiliis. A total of 489,296,696 clean reads were obtained by sequencing. A total of 105 significantly up-regulated immune-related genes were obtained by Gene Ontology (GO) classification and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis in grass carp. Cluster of differentiation 40 (CD40), cluster of differentiation 80 (CD 80), tumor necrosis factor-alpha (TNF-α), toll-like receptor 4 (TLR-4), interleukin 1 beta (IL-1β) and other inflammatory-related genes in grass carp were enriched in the cytokine-cytokine receptor interaction pathway and toll-like receptor pathway. In Holland's spinibarbel, a total of 46 significantly up-regulated immune-related genes were obtained by GO classification and KEGG pathway enrichment analysis. Immune-related genes, such as Immunoglobin heavy chain (IgH), cathepsin S (CTSS), complement C1q A chain (C1qA), complement component 3 (C3) and complement component (C9) were enriched in phagosome pathway, lysosome pathway and complement and coagulation concatenation pathway. C3 was significantly up-regulated in gill and head kidney. Fluorescence in situ hybridization (FISH) showed that the C3 gene was highly expressed in gill tissue of Holland's spinibarbel infected with I. multifiliis. A small amount of C3 gene was expressed in the gill arch of grass carp after infected with I. multifiliis. In conclusion, the severe inflammatory response in vivo after infecting grass carp with I. multifiliis might be the main cause of the death of grass carp. The extrahepatic expression of the gene of Holland's spinibarbel might play an important role in the immune defense against I. multifiliis.

Epigenetic regulation of inflammation by microRNAs in post-infectious bronchiolitis obliterans.

ObjectivesPost‐infectious bronchiolitis obliterans (PiBO) is a rare, chronic disease initiated by severe infection and followed by perpetuating inflammation and obliteration of the small airways. MicroRNAs (miRNAs) have been proposed to play a central role as epigenetic regulators, which control resolution and prevent the uncontrolled progress of inflammation. The aim of this study was to define biomarkers on the level of post‐transcriptional gene regulation in order to characterise PiBO.MethodsA total of 39 patients with well‐defined PiBO and 31 controls from two centres, Barcelona, Spain, and Frankfurt, Germany, were analysed by next‐generation sequencing (NGS). The evaluation of the biological targets of the miRNAs was performed by pathway enrichment analysis and protein–protein interaction network analysis respectively.ResultsPatients with PiBO had significantly lower lung function values and increased airway inflammation in induced sputum as indicated by total cell counts, neutrophils, IL‐1β, IL‐6, IL‐8 and TGF‐β compared to controls.Next‐generation sequencing analysis revealed a total of 22 dysregulated miRNAs, which passed significance threshold for Padj ≤ 0.001 with 17 being upregulated and 5 being downregulated. Of these dysregulated miRNAs, miR‐335‐5p, miR‐186‐5p, miR‐30b‐5p and miR‐30c‐5p were further validated using qRT‐PCR. Interestingly, these miRNAs are functionally implicated in cytokine–cytokine receptor interaction, TGF‐β signalling and FoxO signalling pathway and significantly correlated with lung function values (FEV1).ConclusionOur results demonstrate an aberrant miRNA expression profile in PiBO, which impacts pathways responsible for the regulation of inflammation and fibrosis. The defined miRNAs are useful biomarkers and should be assessed as potential target in the field of miRNA therapeutics.

Transcriptome analysis of the early stage ifnlr1-mutant zebrafish indicates the immune response to auditory dysfunction

BackgroundIFNLR1 has been recently identified to be related to autosomal dominant nonsyndromic sensorineural hearing loss (ADNSHL). It is reported to be expressed in the inner ear of mice and the lateral line of zebrafish. However, it remains unclear how defects in this gene lead to hearing loss. ObjectivesTo elucidate the global gene expression changes in zebrafish when the expression of ifnlr1 is downregulated. MethodsTranscriptome analysis was performed on ifnlr1 morpholino knockdown zebrafish and the control zebrafish using RNA-seq technology. ResultsThe results show that 262 differentially expressed genes (DEGs) were up-regulated while 146 DEGs were down-regulated in the E4I4–Mo zebrafish larvae compared to the control-Mo. Six pathways were significantly enriched, including steroid biosynthesis pathway, adipocytokine signaling pathway, cytokine-cytokine receptor interaction pathway, p53 signaling pathway, AGE-RAGE signaling pathway in diabetic complications, and terpenoid backbone biosynthesis pathway. Among them, three pathways (steroid biosynthesis pathway, cytokine-cytokine receptor interaction pathway and p53 signaling pathway) are immune-associated. ConclusionsThe transcriptome analysis results contribute to the groundwork for future research on the pathogenesis of IFNLR1-associated hearing loss.

DUSP6 inhibits the proliferation of hair follicle stem cells (HFSCs) in vitro

RNA-seq has shown that the DUSP6 and MAPK signaling pathways are associated with the production of high-quality brush hair (type III hair) in Yangtze River Delta white goats. However, there are few reports on the regulatory effects of DUSP6 expression on hair follicle stem cells (HFSCs) and cellular processes, as well as the underlying mechanism. Here, we investigated the effect of DUSP6 level in HFSCs and the molecular mechanism underlying the functional regulation of HFSCs by DUSP6. Overexpression of DUSP6 significantly suppressed the proliferation of HFSCs by inducing cell cycle arrest in the G1 phase and by promoting apoptosis. Transcriptome analysis revealed a total of 217 differentially expressed genes between DUSP6-overexpressing and control HFSCs, of which 33 (15.2%) were upregulated in DUSP6-overexpressing cells. The two pathways with the most significant enrichment of differentially expressed genes were the TNF signaling pathway and cytokine-cytokine receptor interaction pathway, and the significantly enriched terms in the GO enrichment analysis involved cell attachment and cytokines. These results indicate that DUSP6 can function as an inhibitory factor in HFSCs through the induction of cell cycle arrest in the G1 phase and can promote apoptosis by mediating crosstalk among several pathways and cytokines. Highlights We constructed DUSP6 overexpression vectors to detect mRNA and protein expression levels related to high-quality brush hair in MAPK signaling pathway. We found that high expression level of DUSP6 can inhibit the proliferation of hair follicle stem cells (HFSCs) and promote cell apoptosis of HFSCs. DUSP6 may be involved in the growth regulation of HFSCs like Other studies in cancer, tumors by regulating the expression of cytokines, changing the transmission of signals between cells, activating or suppressing immune-related pathways.

Immunotoxicity and uterine transcriptome analysis of the effect of zearalenone (ZEA) in sows during the embryo attachment period

Zearalenone is a mycotoxin and a pollutant that is commonly found in crops. Once ingested, ZEA can cause disturbances in the immune system and produce immunotoxicity. However, there is little research on the effect of ZEA exposure on the relationship between immune regulation and embryo implantation in the uteri of sows. Embryo implantation relies upon the fact that the relationship between the maternal and fetal immune systems is balanced. This balance is provided by the joint regulation of immune organs, cytokines, and uterine immunity. In this study, we investigated 20 sows with an initial weight of 100.00 ± 5.00 kg and 200 days in age. The sows were fed with diets containing ZEA at concentrations of 0 mg/kg, 1 mg/kg, 2 mg/kg, and 10 mg/kg, respectively, from 8 to 14 days of gestation. We studied immunotoxicity and the uterine transcriptomics associated with the effect of ZEA in sows during embryo attachment. Following ZEA treatment, serum biochemical analysis and RT-qPCR were used to detect the concentration and mRNA expression levels of immunoglobulin IgA, IgG, and IgM, in the serum and spleen, respectively. The same analysis was carried out for a range of cytokines in the serum and spleen: IL-1, IL-2, IL-6, IL-10, and TNF. Uterine transcriptome analysis revealed 75, 215, and 81 genes that were differentially expressed in the 0 mg/kg vs 1 mg/kg treatment, 0 mg/kg vs 10 mg/kg treatment, and 1 mg/kg vs 10 mg/kg treatment, respectively. GO terms analysis showed that the up-regulated genes related to the immune system were highly expressed. KEGG pathway analysis further revealed the importance of several metabolic pathways, including drug metabolism-cytochrome P450, the cytokine-cytokine receptor interaction pathway, and calcium signaling pathways. The differentially expressed genes were confirmed by quantitative real-time PCR. These findings expand our understanding of the gene expression profiles and signaling pathways associated with the immune response to ZEA exposure in sows during the embryo implantation window. This study provides valuable information for clarifying the molecular mechanism of ZEA's immunotoxicity to early pregnant sows in the future.

Pathways relevant to Alzheimer’s disease are identified during proinflammatory activation from a microglial model derived from human monocytes

Microglia are the primary immune cells of the central nervous system. These immune cells play a crucial role in maintaining the brain homeostasis. Neuroinflammation, usually mediated by microglial activation, is a common feature of many neurodegenerative disorders, such as Alzheimer's disease (AD). Understanding the microglial proteome during their activation will provide insights into the mechanisms of how genes and pathways maintain brain homeostasis or contribute to disease progression.In this study, we first generated the in vitro microglia-like cells (iMGCs) that were induced from peripheral monocytes of three individuals. We then activated the iMGCs into an M1 (pro-inflammatory) state with lipopolysaccharide (LPS) treatment. We then conducted comprehensive proteomics analysis to determine gene and pathway regulations during the LPS-treated M1 microglial activation via data-independent acquisition mass spectrometry.Not surprisingly, we found that the LPS-treated microglia upregulated genes were enriched in cytokine-cytokine receptor interaction or chemokine signaling pathway (IL-1β, IL-6, CXCL family), TNF-α signaling pathway (TRAF1, TNFAIP6, PTGS2), or NF-ƙB (NF-ƙB2) pathway. We also found that TNF-α, NF-ƙB1, RELA, and IL-1β were likely to function as the upstream regulators during the microglial activation. More interestingly, our data indicated that M1 microglia activation underwent significant changes in biological processes, including neuroinflammatory response, regulation of signaling receptor activity, and glial cell activation.Therefore, our study indicated that a human monocyte-derived microglia model treated with a pro-inflammatory agent such as LPS could provide microglia-specific regulations during M1 activation and further identify disease-relevant genes, biological processes, or pathways. The study implements that the microglial model can be used in clinical studies for new biomarker or drug discovery for many neuroinflammatory disorders, including AD. Further studies with this microglial model in AD patients are warranty to verify our finding.

Th17 cell differentiation induced by cytopathogenic biotype BVDV-2 in bovine PBLCs

BackgroundBovine viral diarrhea virus (BVDV) is a major pathogen that causes bovine viral diarrhea/mucosal disease (BVD-MD), which has become a global infectious disease due to its wide spread and the lack of effective treatment. The process of BVDV infection is complex. Once infected, host immune cells are activated and modulated. As a major immune cell, peripheral blood lymphocyte cells (PBLCs) are the primary target of BVDV. In order to further understand the mechanism of BVDV- host interaction, the expression profiles of host lymphocytes mRNAs associated with BVDV infection were investigated by transcriptomic sequencing analysis.ResultsThe transcriptomic sequencing analysis was performed on bovine PBLCs infected with CP BVDV-2 GS2018 after 12 h of infection. Gene expression profiling demonstrated that 1052 genes were differentially expressed in GS2018 infected PBLCs compared with the control group. Of these genes, 485 genes were up-regulated and 567 were down-regulated. The 19 differential expressed genes (DEGs) were selected for validation using quantitative real-time PCR and the results were consistent with the results of RNA-Seq. Gene ontology enrichment and KEGG pathway analysis showed that 1052 DEGs were significantly enriched in 16 pathways, including cytokine-cytokine receptor interaction, IL17, PI3K-Akt, MAPK and TNF signaling pathway. PPI network analysis showed that IL17A, IFN-γ and TNF-α interacted with various proteins and may play crucial roles in BVDV-2 infection. Of note, we confirmed that GS2018 induced Th17 cell differentiation in PBLCs and persistently increased the expression levels of IL17A. In turn, the replication of GS2018 was inhibited by IL17A.ConclusionIn this study, the transcription changes of DEGs related to host immune responses in bovine PBLCs were caused by CP BVDV-2 infection. In particular, the effector molecules IL17A of Th17 cells were significantly up-regulated, which inhibited viral replication. These results will contribute to exploration and further understanding of the host immune response mechanism and interaction between host and BVDV-2.

Exploring the potential mechanism of Rhodomyrtus tomentosa (Ait.) Hassk fruit phenolic rich extract on ameliorating nonalcoholic fatty liver disease by integration of transcriptomics and metabolomics profiling

Nonalcoholic fatty liver disease (NAFLD), as the commonest form of chronic liver disease, is accompanied by liver oxidative stress and inflammatory responses. Rhodomyrtus tomentosa (Ait.) Hassk fruit phenolic rich extract (RTE) possesses multiple pharmacological effects in management of chronic diseases. In this study, the liver-protective effect of RTE on mice with high-fat-diet (HFD)-induced NAFLD was investigated for the first time, and the underlying molecular mechanism was explored via integration of transcriptomics and metabolomics. The results showed that RTE mitigated liver damage, which was evidenced by declined inflammatory cell infiltration in liver, decreased liver function markers, oxidative stress indexes, lipid profile levels and inflammatory cytokines levels. The differential metabolites by metabonomics illustrated supplementation of RTE affected metabolomics pathways including tryptophan metabolism, alanine, aspartate and glutamate metabolism, D-glutamine and D-glutamate metabolism, cysteine and methionine metabolism, arginine and proline metabolism, which are all involved in oxidative stress and inflammation. Furthermore, the five differential expression genes (DEGs) through liver transcriptomics were screened and recognized, namely Tnfrsf21, Ifit1, Inhbb, Mapk15 and Gadd45g, which revealed that HFD induced Cytokine-cytokine receptor interaction pathway, NF-κB signaling pathway NOD-like receptor pathway, TNF signaling pathway. Integrated analysis of transcriptomics and metabolomics confirmed the supplementation of RTE had significantly regulatory effects on the metabolic pathways involved in inflammatory responses. Additionally, RT-PCR and western blot authenticated RTE intervention regulated the mRNA levels of liver genes involved in inflammation response and inhibited the liver endotoxin-TLR4-NF-κB pathway triggered by HFD, thus alleviating NAFLD. Our findings strongly support the possibility that RTE can be regarded as a potential therapeutic method for obesity-associated NAFLD.

Splicing factor SRSF1 controls distinct molecular programs in regulatory and effector T cells implicated in systemic autoimmune disease

Systemic autoimmune diseases are characterized by hyperactive effector T cells (Teffs), aberrant cytokines and chemokines, and dysfunctional regulatory T cells (Tregs). We previously uncovered new roles for serine/arginine-rich splicing factor 1 (SRSF1) in the control of genes involved in T cell signaling and cytokine production in human T cells. SRSF1 levels are decreased in T cells from patients with systemic lupus erythematosus (SLE), and low levels correlate with severe disease. Moreover, T cell-conditional Srsf1-deficient mice recapitulate the autoimmune phenotype, exhibiting CD4 T cell hyperactivity, dysfunctional Tregs, systemic autoimmunity, and tissue inflammation. However, the role of SRSF1 in controlling molecular programs in Teffs and Tregs and how these pathways are implicated in autoimmunity is not known. Here, by comparative bioinformatics analysis, we demonstrate that SRSF1 controls largely distinct gene programs in Tregs and Teffs in vivo. SRSF1 regulates 189 differentially expressed genes (DEGs) unique to Tregs, 582 DEGs unique to Teffs, and 29 DEGs shared between both. Shared genes included IL-17A, IL-17F, CSF1, CXCL10, and CXCR4, and were highly enriched for inflammatory response and cytokine-cytokine receptor interaction pathways. SRSF1 controls distinct pathways in Tregs, which include chemokine signaling and immune cell differentiation, compared with pathways in Teffs, which include cytokine production, T cell homeostasis, and activation. We identified putative mRNA binding targets of SRSF1 which include CSF1, CXCL10, and IL-17F. Finally, comparisons with transcriptomics profiles from lupus-prone MRL/lpr mice reveal that SRSF1 controls genes and pathways implicated in autoimmune disease. The target genes of SRSF1 and putative binding targets we discovered, have known roles in systemic autoimmunity. Our findings suggest that SRSF1 controls distinct molecular pathways in Tregs and Teffs and aberrant SRSF1 levels may contribute to their dysfunction and immunopathogenesis of systemic autoimmune disease.