Transcriptom analysis revealed regulation of dexamethasone induced microRNAs in chicken thymus

miR-214-PTEN pathway is a potential mechanism for stress-induced immunosuppression affecting chicken immune response to avian influenza virus vaccine

Stress-induced immunosuppression (SIIS) is one of common problems in the intensive poultry industry, affecting the effect of vaccine immunization and leading to high incidences of diseases. In this study, the expression characteristics and regulatory mechanisms of miR-214 in the processes of SIIS and its influence on the immune response to avian influenza virus (AIV) vaccine in chicken were explored. The qRT-PCR results showed that serum circulating miR-214 was significantly differentially expressed (especially on 2, 5, and 28 days post immunization (dpi)) in the processes, so had the potential as a molecular marker. MiR-214 expressions from multiple tissues were closely associated with the changes in circulating miR-214 expression levels. MiR-214-PTEN regulatory network was a potential key regulatory mechanism for the heart, bursa of Fabricius, and glandular stomach to participate in the process of SIIS affecting AIV immune response. This study can provide references for further understanding of stress affecting immune response.

Circular RNA circAKIRIN2 participates in the process of stress-induced immunosuppression affecting immune response to infectious bursal disease virus vaccine in chicken

At present, stress-induced immunosuppression is still a hidden threat that leads to immunization failure and outbreaks of poultry diseases, and causes huge economic losses to the modern poultry industry. However, the molecular mechanisms of stress-induced immunosuppression affecting viral vaccine immunity are still poorly understood. Here, we identified circAKIRIN2 as a conserved circular transcript in chicken, and explored its expression patterns in different immune states by quantitative real-time PCR (qRT-PCR), then conducted bioinformatics analysis. The results showed that circAKIRIN2 actively participated in the process of stress-induced immunosuppression affecting the immune response to infectious bursal disease virus (IBDV) vaccine. The key time points for circAKIRIN2 involving in the process were 2 day post immunization (dpi), 5 dpi, and 28 dpi, especially at the acquired immune stage. The important tissues that responded to the process included the heart, liver, and lung, all of which changed significantly. In addition, circAKIRIN2 as a competing endogenous RNA (ceRNA) sponging zinc finger and BTB domain containing 20 (ZBTB20) was a potential molecular mechanism for regulating immune functions in the process. In conclusion, circAKIRIN2 is a key regulatory factor for stress-induced immunosuppression affecting the IBDV vaccine immune response, and this study can provide a new perspective for exploring the molecular regulatory mechanisms of stress-induced immunosuppression affecting immune response.

Integrated analysis of mRNA and microRNA expression pattern reveals differential transcriptome signatures in RIPK2 over-expressing chicken macrophages infected with avian pathogenic E. coli

1. As RIPK2 (receptor interacting serine/threonine kinase 2) has been shown to to alleviate excessive inflammatory responses, the following study conducted a systematic and in-depth analysis of the mRNA-seq and miRNA-seq data from chicken macrophages with/without over-expression of RIPK2 (oeRIPK2) combined with/without avian pathogenic E. coli (APEC) infection to identify the miRNA-mRNA interaction network and potential signalling pathways involved.2. A total of 9,201 differentially expressed (DE) mRNAs and 300 DE miRNA were identified in both oeRIPK2+APEC vs. APEC and oeRIPK2 vs. the wild-type (WT). Moreover, 4,269 instances of co-expression between miRNAs and mRNAs were seen involving 1,652 DE mRNAs and 164 DE miRNAs.3. Functional analysis of the DE mRNAs in the miRNA-mRNA interaction network showed that 223 biological processes and five KEGG pathways were significantly enriched in the two comparisons. In total, 128 pairs of miRNA-mRNA interactions were involved in the identified MAPK signalling pathway and focal adhesion immune related pathways.4. Significantly, these screened miRNAs (gga-miR-222b-5p and gga-miR-214) and their target genes were highly correlated with APEC infection and RIPK2. These recognised key genes, miRNA and the overall miRNA-mRNA regulatory network, enables better understanding of the molecular mechanism of host response to APEC infection, especially related to RIPK2.

Role of microRNA-34b-5p in cancer and injury: how does it work?

MicroRNAs (miRNAs or miRs) are a class of noncoding single-stranded RNAs that can regulate gene expression by binding to the untranslated sequences at the 3 ' end of messenger RNAs. The microRNA-34 family is dysregulated in various human diseases. It is considered as a tumor-suppressive microRNA because of its synergistic effect with the well-known tumor suppressor p53. As a member of the miRNA-34 family, miR-34b-5p serves as a powerful regulator of a suite of cellular activities, including cell growth, multiplication, development, differentiation, and apoptosis. It promotes or represses disease occurrence and progression by participating in some important signaling pathways. This review aimed to provide an overview and update on the differential expression and function of miR-34b-5p in pathophysiologic processes, especially cancer and injury. Additionally, miR-34b-5p-mediated clinical trials have indicated promising consequences for the therapies of carcinomatosis and injury. With the application of the first tumor-targeted microRNA drug based on miR-34a mimics, it can be inferred that miR-34b-5p may become a crucial factor in the therapy of various diseases. However, further studies on miR-34b-5p should shed light on its involvement in disease pathogenesis and treatment options.

Stress-Induced Immunosuppression Affects Immune Response to Newcastle Disease Virus Vaccine via Circulating miRNAs

Simple Summary

Circulating miRNAs play important roles in immune response and stress-induced immunosuppression, but the function and mechanism of stress-induced immunosuppression affecting the NDV vaccine immune response remain unknown. In our study, key timepoints, functions, mechanisms, and potential biomarkers of circulating miRNAs involved in immune response and immunosuppression were discovered, providing a theoretical basis for studying the roles of circulating miRNAs in immune regulation.

Abstract

Studies have shown that circulating microRNAs (miRNAs) are important players in the immune response and stress-induced immunosuppression. However, the function and mechanism of stress-induced immunosuppression affecting the immune response to the Newcastle disease virus (NDV) vaccine remain largely unknown. This study analyzed the changes of 15 NDV-related circulating miRNAs at different immune stages by qRT-PCR, aiming to explore the key timepoints, potential biomarkers, and mechanisms for the functional regulation of candidate circulating miRNAs under immunosuppressed conditions. The results showed that stress-induced immunosuppression induced differential expressions of the candidate circulating miRNAs, especially at 2 days post immunization (dpi), 14 dpi, and 28 dpi. In addition, stress-induced immunosuppression significantly affected the immune response to NDV vaccine, which was manifested by significant changes in candidate circulating miRNAs at 2 dpi, 5 dpi, and 21 dpi. The featured expressions of candidate circulating miRNAs indicated their potential application as biomarkers in immunity and immunosuppression. Bioinformatics analysis revealed that the candidate circulating miRNAs possibly regulated immune function through key targeted genes, such as Mg²⁺/Mn²⁺-dependent 1A (PPM1A) and Nemo-like kinase (NLK), in the MAPK signaling pathway. This study provides a theoretical reference for studying the function and mechanism of circulating miRNAs in immune regulation.

Non-Targeted Metabolomic Analysis of Chicken Kidneys in Response to Coronavirus IBV Infection Under Stress Induced by Dexamethasone

Stress in poultry can lead to changes in body metabolism and immunity, which can increase susceptibility to infectious diseases. However, knowledge regarding chicken responses to viral infection under stress is limited. Dexamethasone (Dex) is a synthetic glucocorticoid similar to that secreted by animals under stress conditions, and has been widely used to induce stress in chickens. Herein, we established a stress model in 7-day-old chickens injected with Dex to elucidate the effects of stress on IBV replication in the kidneys. The metabolic changes, immune status and growth of the chickens under stress conditions were comprehensively evaluated. Furthermore, the metabolic profile, weight gain, viral load, serum cholesterol levels, cytokines and peripheral blood lymphocyte ratio were compared in chickens treated with Dex and infected with IBV. An LC-MS/MS-based metabolomics method was used to examine differentially enriched metabolites in the kidneys. A total of 113 metabolites whose abundance was altered after Dex treatment were identified, most of which were lipids and lipid-like molecules. The principal metabolic alterations in chicken kidneys caused by IBV infection included fatty acid, valine, leucine and isoleucine metabolism. Dex treatment before and after IBV infection mainly affected the host’s tryptophan, phenylalanine, amino sugar and nucleotide sugar metabolism. In addition, Dex led to up-regulation of serum cholesterol levels and renal viral load in chickens, and to the inhibition of weight gain, peripheral blood lymphocytes and IL-6 production. We also confirmed that the exogenous cholesterol in DF-1 cells promoted the replication of IBV. However, whether the increase in viral load in kidney tissue is associated with the up-regulation of cholesterol levels induced by Dex must be demonstrated in future experiments. In conclusion, chick growth and immune function were significantly inhibited by Dex. Host cholesterol metabolism and the response to IBV infection are regulated by Dex. This study provides valuable insights into the molecular regulatory mechanisms in poultry stress, and should support further research on the intrinsic link between cholesterol metabolism and IBV replication under stress conditions.

Comparative analysis of the exosomal contents of DF-1 cells infected by ALV-J

Exploration of the abnormal expression of exosomal molecules during the infection of avian leukosis virus subgroup J (ALV-J) is essential to provide a deeper understanding of the exosome's role in the viral pathogenesis involved. The study aimed to investigate the differentially expressed proteins and miRNAs of the exosomes derived from DF-1 cells infected by ALV-J, their gene function and involved signal pathways. We isolated exosomes from DF-1 cells infected by ALV-J. The differentially expressed proteins and miRNAs of the exosomes were determined by proteomics and transcription detection technology. A Gene Ontology (GO) analysis and a Kyoto Encyclopedia of Genes and Genomes (KEGG) signal pathway analysis identified the miRNAs target genes and the signal pathways regulated by the different proteins or/and miRNAs. A total of 116 proteins (58 upregulated and 58 downregulated) and 3 miRNAs (all upregulated) were determined. These proteins were involved in 155 signal pathways, in which the highest number of proteins involved in the cancer pathway was (up to) seven. The target genes of the miRNAs were involved in 3 signal pathways. Both the proteins and target genes of the miRNAs were involved in the Ribosome pathway and ECM-receptor interaction pathway. The results suggested that the ALV-J infection changed the proteins and miRNAs of the exosomes significantly.

Stress-induced immunosuppression increases levels of certain circulating miRNAs and affects the immune response to an infectious bursal disease virus vaccine in chickens

Stress-induced immunosuppression can affect the immune effect of vaccine. However, the mechanism of stress-induced immunosuppression affecting immune response to infectious bursal disease virus (IBDV) vaccine in chicken is still unclear. In this study, thirteen IBDV related circulating miRNAs were selected to study their expressions, possible functions and mechanisms in dexamethasone (Dex)-induced immunosuppressed chicken vaccinated with IBDV attenuated vaccine. The experiment aimed to explore the relationship between the expressions of IBDV related circulating miRNAs and stress-induced immunosuppression. The quantitative real-time PCR (qRT-PCR) results showed that Dex-induced immunosuppression could induce the differential expressions of the candidate serum circulating miRNAs, especially on the 2nd, 5th, 7th and 28th day after dexamethasone treatment. Dex-induced immunosuppression could affect the immune response to the IBDV vaccine, which was possibly achieved by partially regulating the differential expressions of the IBDV related circulating miRNAs. Bioinformatics analysis showed that the candidate miRNAs could regulate the immune function mainly through targeting genes (such as CREB1 and MAPK1) in TGF-β and MAPK signaling pathways. This study can provide a preliminary reference for further studying the function and mechanism of circulating miRNAs in immune regulation.

Runs of homozygosity analysis reveals population characteristics of yellow-feathered chickens using re-sequencing data

1. To evaluate the inbreeding of yellow-feathered chickens (YFCs) and identify genes related to their unique characteristics, whole-genome re-sequencing data were applied to detect runs of homozygosity (ROH) in the genomes of ten YFC breeds. The number, length, distribution of ROH, and inbreeding coefficient in different YFC populations were calculated. Genomic regions with high frequency in ROH were annotated.2. In total, 25,547 ROH with an average length of 335 kb were detected, with most being <1 Mb. The domination of short ROH reflected the long breeding history of this chicken. The number, length, frequency, and distribution of ROH varied among chicken populations, and high genetic diversity was maintained.3. Numerous genes related to YFC characteristics were identified in the high-frequency ROH regions. Among these, IFNA, IFNB, IL11RA, IL22RA1, IFNLR1, and TRIF genes were involved in disease resistance. The AMY, G6PC, SDHB, GCNT4, and ACO genes were associated with energy material metabolism; and FABPL, AQP7, ACAA2, and RYR2 were related to meat quality and flavour. The KITLG, CREB3, RYR2, and LGR4 genes, related to pigmentation, were detected.4. This ROH-based inbreeding evaluation laid the foundation for breeding and conservation of YFC populations, and the candidate genes identified can be used for marker-assisted selection.

Immune function of miR-214 and its application prospects as molecular marker

MicroRNAs are a class of evolutionary conserved non-coding small RNAs that play key regulatory roles at the post-transcriptional level. In recent years, studies have shown that miR-214 plays an important role in regulating several biological processes such as cell proliferation and differentiation, tumorigenesis, inflammation and immunity, and it has become a hotspot in the miRNA field. In this review, the regulatory functions of miR-214 in the proliferation, differentiation and functional activities of immune-related cells, such as dendritic cells, T cells and NK cells, were briefly reviewed. Also, the mechanisms of miR-214 involved in tumor immunity, inflammatory regulation and antivirus were discussed. Finally, the value and application prospects of miR-214 as a molecular marker in inflammation and tumor related diseases were analyzed briefly. We hope it can provide reference for further study on the mechanism and application of miR-214.

A functional polymorphism of inhibin alpha subunit at miR-181b-1-3p-binding site regulates proliferation and apoptosis of chicken ovarian granular cells

INHA, the gene encoding the inhibin alpha subunit, was involved in folliculogenesis in mammals, but no study was reported for its working pathway in birds. Here we hypothesize that gene polymorphism in INHA 3'UTR might influence miRNAs binding efficiency and further affect the function of this gene. Thus, we investigated the association between the 3'UTR single-nucleotide polymorphisms (SNPs) in INHA and the laying performance in chickens and further explore their possible molecular cascades in granulosa cells (GC). Five SNPs were detected in Tianfu green-shell layers and g. 22,178,975 G > A was significantly associated with total egg numbers at the age of 300 days (EN, n = 286). Birds carrying the AA genotype laid more EN than those with GG (P < 0.05). The allele transition from G to A in the 3'UTR of INHA gene destroyed a binding site which was targeted by miR-181b-1-3p. The expression abundances of INHA mRNA increased firstly and then decreased with follicle growing, and reached the top in the sixth largest pre-ovulation follicle, whereas miR-181b-1-3p levels in chicken pre-hierarchical follicles had the contrary tendency. Further studies indicated that high levels of miR-181b-1-3p increased apoptosis and reduced GC proliferation while miR-181b-1-3p inhibitors decreased apoptosis and promoted GC proliferation. Additionally, depression of INHA increased apoptosis and reduced GC proliferation via a caspase-3-dependent mitochondrial pathway. Generally, the mutation in INHA 3'UTR was tightly correlated with egg production in chickens, and blocked a binding site of miR-181b-1-3p. miR-181b-1-3p inhibited GC proliferation and promoted apoptosis by targeting INHA.

Genomic variations and signatures of selection in Wuhua yellow chicken

Wuhua yellow chicken (WHYC) is an important traditional yellow-feathered chicken from China, which is characterized by its white tail feathers, white flight feathers, and strong disease resistance. However, the genomic basis of these unique traits associated with WHYC is poorly understood. In this study, whole-genome resequencing was performed with an average coverage of 20.77-fold to investigate heritable variation and identify selection signals in WHYC. Reads were mapped onto the chicken reference genome (Galgal5) with a coverage of 85.95%. After quality control, 11,953,471 single nucleotide polymorphisms and 1,069,574 insertion/deletions were obtained. In addition, 41,408 structural variants and 33,278 copy number variants were found. Comparative genomic analysis of WHYC and other yellow-feathered chicken breeds showed that selected regions were enriched in genes involved in transport and catabolism, immune system, infectious diseases, signal transduction, and signaling molecules and interactions. Several genes associated with disease resistance were also identified, including IFNA, IFNB, CD86, IL18, IL11RA, VEGFC, and ATG10. Furthermore, our results suggest that PMEL and TYRP1 may contribute to the white feather coloring in WHYC. These findings can improve our understanding of the genetic characteristics of WHYC and may contribute to future breed improvement.

Identification of genes related to dexamethasone-induced immunosuppression in chicken thymus using transcriptome analysis

The molecular mechanism of stress-induced immunosuppression (SIS) in certain poultry immune organs is not completely clear. In this study, we constructed a stress immunosuppression model by selecting 180 healthy 7-day-old Gushi chickens and dividing them randomly into two groups: a D_T group and a B_T group. The D_T group was given dexamethasone, and the B_T group was given normal saline, according to the treatment method established and reported in our previous study. Thymus samples were subsequently taken from both groups. RNA-seq was used to sequence the transcriptomes of the thymus samples from both groups, and 1278 significant differentially expressed genes (DEGs) were obtained, of which 845 genes were up-regulated and 433 genes were down-regulated (padj<0.05, |FC| ≥ 2, FPKM>1). We identified immune-related gene ontology (GO) terms including immune system processes, immune system process regulation, and T cell activation. The results of KEGG (http: //www.kegg.jp) analysis showed that the DEGs are involved in a variety of immune-related pathways, such as cytokine-cytokine receptor interactions, Jak-STAT signaling pathways, and cell adhesion molecules (CAMs). The cytokine-cytokine receptor interaction pathway involves the DEGs CCR6, CCR5, CD40LG and FAS. The DEGs in the Jak-STAT signaling pathway were SPRY2, BCL2L1. These DEGS play an important role in cell apoptosis. CD40L, CD8, among other genes, are involved in the CAMs pathway. The results of this study add to existing data on the genomic study of stress affecting immune function, and provide a basis for further studies of the molecular mechanisms of stress-influenced immune function.

High expression of KITLG is a new hallmark activating the MAPK pathway in type A and AB thymoma

Background

KIT proto‐oncogene ligand (KITLG) is a pleiotropic factor which is found in diverse cancers and is involved in cell proliferation, differentiation, and survival. However, the value of KITLG in thymoma remains unclear.

Methods

A total of 121 thymoma samples from The Cancer Genome Atlas Thymoma (TCGA‐THYM) dataset were used to analyze KITLG related genome‐wide expression profiles, and microRNA profiles and methylation alterations and a GEO dataset‐GSE29695, including 37 samples was used as verification. For cell‐based studies, specific small interfering RNA targeting KITLG or a KITLG overexpression vector were used to clarify the changes of the MAPK pathway in an AB thymoma cell line Thy0517.

Results

Both datasets showed that high expression of KITLG was significantly associated with type A and AB thymoma. Through multiomic analysis of the TCGA‐THYM, it was found that with the high expression of KITLG, there were 220 upregulated and 72 downregulated genes at the mRNA level, 79 positive and 78 negative miRNAs, 28 hypermethylation and 163 hypomethylation regions. In the thymoma cell line Thy0517, it was found that the expression of GRB2 and the phosphorylation levels of BRAF, MEK1/2, and ERK1/2 in the MAPK pathway were positively correlated with the change in KITLG.

Conclusions

High expression of KITLG is a new hallmark of WHO type A and AB thymomas in which it might play a critical role through the activation of the MAPK signaling pathway. Additionally, it is hoped that KITLG will become a potential target for the diagnosis of type A and AB thymoma through further research in the future.

Key points

Significant findings of the study

KIT proto‐oncogene ligand (KITLG) is a new hallmark of type A and AB thymomas which induce a series of aberrant alteration of mRNA, miRNA and DNA methylation. The expression of KITLG is significantly higher in type A and AB than other subtypes of thymoma.

What this study adds

KITLG activated the MAPK signaling pathway to promote type A and AB thymoma which might be a potential diagnostic biomarker or target.

Identifying Hub Genes for Heat Tolerance in Water Buffalo (Bubalus bubalis) Using Transcriptome Data

Heat stress has a detrimental effect on the physiological and production performance of buffaloes. Elucidating the underlying mechanisms of heat stress is challenging, therefore identifying candidate genes is urgent and necessary. We evaluated the response of buffaloes (n = 30) to heat stress using the physiological parameters, ELISA indexes, and hematological parameters. We then performed mRNA and microRNA (miRNA) expression profiles analysis between heat tolerant (HT, n = 4) and non-heat tolerant (NHT, n = 4) buffaloes, as well as the specific modules, significant genes, and miRNAs related to the heat tolerance identified using the weighted gene co-expression network analysis (WGCNA). The results indicated that the buffaloes in HT had a significantly lower rectal temperature (RT) and respiratory rate (RR) and displayed a higher plasma heat shock protein (HSP70 and HSP90) and cortisol (COR) levels than those of NHT buffaloes. Differentially expressed analysis revealed a total of 753 differentially expressed genes (DEGs) and 16 differentially expressed miRNAs (DEmiRNAs) were identified between HT and NHT. Using the WGCNA analysis, these DEGs assigned into 5 modules, 4 of which were significantly correlation with the heat stress indexes. Interestingly, 158 DEGs associated with heat tolerance in the turquoise module were identified, 35 of which were found within the protein-protein interaction network. Several hub genes (IL18RAP, IL6R, CCR1, PPBP, IL1B, and IL1R1) were identified that significantly enriched in the Cytokine-cytokine receptor interaction. The findings may help further elucidate the underlying mechanisms of heat tolerance in buffaloes.