Messenger RNA Expression Profiles Research Articles

Expression and Function of Long Non-coding RNA in Endemic Cretinism.

Endemic cretinism (EC) is one of the most severe iodine deficiency disorders, leading to typical symptoms such as neurodevelopmental impairments or mental deficits. In addition to environmental factors, the pathogenesis of its genetic contribution remains unclear. The study revealed the differential expression profiles of long non-coding RNA(lncRNA) and messenger RNA(mRNA) based on high-throughput RNA-seq. GO and KEGG analyses were used to annotate the function and pathway of differentially expressed (DE) mRNA and co-expressed mRNA. The protein-protein interaction(PPI) network was established. The expression levels of three lncRNAs and six mRNAs were validated by quantitative real-time PCR analysis (qRT-PCR) and subjected to correlation analysis.Compared to controls, a total of 864 lncRNAs and 393 mRNAs were differentially expressed. The PPI network had 149 nodes and 238 edges, and three key protein-coding genes were observed.Levels of LINC01220 and target mRNA IDO1 were statistically elevated in EC patients.Differentially expressed lncRNA may be a new potential player in EC. LINC01220 and IDO1 might interact with each other to participate in EC. The biological process of regulation of postsynaptic membrane potential and the Rap1 signaling pathway might exert a regulating role in the pathophysiological process of EC. Our findings could provide more theoretical and experimental evidence for investigating the pathophysiological mechanisms of EC.

LncRNA CBR3-AS1 is associated with the BCR::ABL1 kinase independent mechanism of tyrosine kinase inhibitor (TKI) resistance in chronic myeloid leukemia patients.

It is difficult for chronic myeloid leukemia (CML) patients with BCR::ABL1 independent drug resistance to achieve optimal efficacy. The aim of this study is to investigate the BCR::ABL1 kinase independent mechanism of tyrosine kinase inhibitor (TKI) resistance in CML patients to develop targeted therapeutic strategy. Herein, we analyzed the long non-coding RNA (lncRNA) and messenger RNA (mRNA) expression profiles of patients who achieved sustained deep molecular response (DMR) after TKI treatment and patients with non-DMR using RNA-seqencing. Furthermore, the differentially expressed lncRNAs and mRNAs were identified. The expression of chosen lncRNA was validated in an expanded cohort, and bioinformatics analysis was performed to analyze the function of selected mRNA. LncRNA data analysis indicated the diversity lncRNA profiles among healthy individuals, CML patients with non-DMR, and CML patients with DMR. Differential expression analysis and Veen plot of up-regulated lncRNAs in patients with non-DMR (compared with healthy individuals) and down-regulated lncRNAs in patients with DMR (compared to patients with non-DMR) revealed that lncRNA CBR3-AS1 overexpression might be related to BCR::ABL1 independent TKI resistance of CML patients. The expression of CBR3-AS1 was then verified in an expanded cohort, suggesting that, compared with control group, there was no statistical difference of CBR3-AS1 expression in DMR group, whereas, CBR3-AS1 was up-regulated in non-DMR group. Moreover, the mRNA data analysis of RNA-sequencing was performed. We considered genes that up-regulated in non-DMR group (compared with control group), down-regulated in DMR group (compared with non-DMR group), showed no statistical difference between control and DMR group as the potential genes that associated with TKI resistance of CML patients. A total of 55 corresponding mRNAs were obtained including KCNA6, a target gene of CBR3-AS1. Further bioinformatics analysis showed that the major interacted genes of KCNA6 were enriched in several resistance-associated pathways including interleukin -17 signaling pathway and cyclic adenosine monophosphate signaling pathway. In conclusion, this work indicates that CBR3-AS1 might be involved in BCR::ABL1 independent TKI resistance of CML patients through targeting KCNA6, providing a novel target for intervention treatment of CML patients with BCR::ABL1 independent TKI resistance.

Transcriptome analysis of adipose tissue in grazing cattle: Identifying key regulators of fat metabolism.

The taste and tenderness of meat are the main determinants of carcass quality in many countries. This study aimed to discuss the mechanisms of intramuscular fat deposition in grazing and house-breeding cattle. We performed transcriptome analysis to characterize messenger RNA and microRNA (miRNA) expression profiles. A total of 456 and 66 differentially expressed genes (DEGs) and differentially expressed (DE) miRNAs were identified in the adipose tissue of grazing and house-breeding cattle. Kyoto Encyclopedia of Genes and Genomes pathway analysis identified the association of DEGs with fatty acid metabolism, fatty acid degradation, peroxisome proliferator-activated receptors signaling pathway, adenosine monophosphate-activated protein kinase signaling pathway, adipocytokine signaling pathway, and the association of DE miRNAs with mitogen-activated protein kinase signaling pathway. Apolipoprotein L domain containing 1, pyruvate dehydrogenase kinase 4, and sphingosine-1-phosphate lyase 1 genes may be the key regulators of fat metabolism in grazing cattle. Finally, we found that miR-211 and miR-331-5p were negatively correlated with the elongation of very long-chain fatty acids protein 6 (ELOVL6), and miR-331-5p might be the new regulator involved in fat metabolism. The results indicated that ELOVL6 participated in various functions and pathways related to fat metabolism. Meanwhile, miR-331-5p, as a new regulator, might play an essential role in this process. Our findings laid a more in-depth and systematic research foundation for the formation mechanism and characteristics of adipose tissue in grazing cattle.

Circulating miRNA’s biomarkers for early detection of hepatocellular carcinoma in Egyptian patients based on machine learning algorithms

Liver cancer, which ranks sixth globally and third in cancer-related deaths, is caused by chronic liver disorders and a variety of risk factors. Despite therapeutic improvements, the prognosis for Hepatocellular Carcinoma (HCC) remains poor, with a 5-year survival rate for advanced cases of less than 12%. Although there is a noticeable decrease in the frequency of cases, liver cancer remains a significant worldwide health concern, with estimates surpassing one million cases by 2025. The prevalence of HCC has increased in Egypt, and it includes several neoplasms with distinctive messenger RNA (mRNA) and microRNA (miRNA) expression profiles. In HCC patients, certain miRNAs, such as miRNA-483-5P and miRNA-21, are upregulated, whereas miRNA-155 is elevated in HCV-infected people, encouraging hepatocyte proliferation. Short noncoding RNAs called miRNAs in circulation have the potential as HCC diagnostic and prognostic markers. This paper proposed a model for examining circulating miRNAs as diagnostic and predictive markers for HCC in Egyptian patients and their clinical and pathological characteristics. The proposed HCC detection model consists of three main phases: data preprocessing phase, feature selection based on the proposed Binary African Vulture Optimization Algorithm (BAVO) phase, and finally, classification as well as cross-validation phase. The first phase namely the data preprocessing phase tackle the main problems associated with the adopted datasets. In the feature selection based on the proposed BAVO algorithm phase, a new binary version of the BAVO swarm-based algorithm is introduced to select the relevant markers for HCC. Finally, in the last phase, namely the classification and cross-validation phase, the support vector machine and k-folds cross-validation method are utilized. The proposed model is evaluated on three studies on Egyptians who had HCC. A comparison between the proposed model and traditional statistical studies is reported to demonstrate the superiority of using the machine learning model for evaluating circulating miRNAs as diagnostic markers of HCC. The specificity and sensitivity for differentiation of HCC cases in comparison with the statistical-based method for the first study were 98% against 88% and 99% versus 92%, respectively. The second study revealed the sensitivity and specificity were 97.78% against 90% and 98.89% versus 92.5%, respectively. The third study reported 83.2% against 88.8% and 95.80% versus 92.4%, respectively. Additionally, the results show that circulating miRNA-483-5p, 21, and 155 may be potential new prognostic and early diagnostic biomarkers for HCC.

Comprehensive Analysis of circRNA, lncRNA, miRNA and mRNA Expression Profiles and Their Competing Endogenous RNA Networks in Hepatitis B Virus-Related Hepatocellular Carcinoma.

Pursuing knowledge about circular RNA (circRNA), long non-coding RNA (lncRNA), microRNA (miRNA), and messenger RNA (mRNA) expression profiles and their competing endogenous RNA (ceRNA) networks in hepatitis B virus-related hepatocellular carcinoma (HBV-related HCC) was the focus of this research. Expression patterns of circRNAs, lncRNAs, miRNAs, and mRNAs were searched for in relation to HBV-related HCC using whole-transcriptome sequencing. The expression levels of chosen circRNA, lncRNA, miRNA, and mRNA were analyzed using quantitative reverse transcription-polymerase chain reaction (qRT-PCR). The potential connections and roles of ceRNA were deduced via bioinformatics research. The sum of 284 circRNAs, 2,927 lncRNAs, 693 miRNAs, and 5566 mRNAs were discovered to be expressed at considerably different levels in HBV-related HCC tissue and adjacent normal tissue. And the most significantly up- and down-regulated circRNAs, lncRNAs, miRNAs, and mRNAs were verified in HBV-related HCC by qRT-PCR. The circRNA/miRNA/mRNA and lncRNA/miRNA/mRNA networks of HBV-related HCC were established, and the ceRNA regulatory networks revealed the gene expression mechanisms controlled by ncRNAs. Collectively, we revealed the contribution of various circRNA, lncRNA, miRNA, and mRNA expression profiles and identified their ceRNA regulatory networks in HBV-related HCC, providing a theoretical basis for further exploration.

Integrated analysis of microRNA and messenger RNA expression profiles reveals functional microRNA in infectious bovine rhinotracheitis virus-induced mitochondrial damage in Madin-Darby bovine kidney cells

BackgroundStudies have confirmed that Infectious bovine rhinotracheitis virus (IBRV) infection induces mitochondrial damage. MicroRNAs (miRNAs) are a class of noncoding RNA molecules, which are involved in various biological processes and pathological changes associated with mitochondrial damage. It is currently unclear whether miRNAs participate in IBRV-induced mitochondrial damage in Madin-Darby bovine kidney (MDBK) cells.ResultsIn the present study, we used high-throughput sequencing technology, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis to screen for mitochondria-related miRNAs and messenger RNAs (mRNAs). In total, 279 differentially expressed miRNAs and 832 differentially expressed mRNAs were identified in 6 hours (IBRV1) versus 24 hours (IBRV2) after IBRV infection in MDBK cells. GO and KEGG enrichment analysis revealed that 42 differentially expressed mRNAs and 348 target genes of differentially expressed miRNAs were correlated with mitochondrial damage, and the miRNA-mitochondria-related target genes regulatory network was constructed to elucidate their potential regulatory relationships. Among the 10 differentially expressed miRNAs, 8 showed expression patterns consistent with the high-throughput sequencing results. Functional validation results showed that overexpression of miR-10a and miR-182 aggravated mitochondrial damage, while inhibition of miR-10a and miR-182 alleviated mitochondrial damage.ConclusionsThis study not only revealed the expression changes of miRNAs and mRNAs in IBRV-infected MDBK cells, but also revealed possible biological regulatory relationship between them. MiR-10a and miR-182 may have the potential to be developed as biomarkers for the diagnosis and treatment of IBRV. Together, Together, these data and analyses provide additional insights into the roles of miRNA and mRNA in IBRV-induced mitochondria damage

Prediction of Prognostic Features Based on Neutrophil-Related Genes for Lung Squamous Cell Carcinoma Reveals Immune Landscape and Drug Candidates.

Background: Since to the prognosis of lung squamous cell carcinoma is generally poor, there is an urgent need to innovate new prognostic biomarkers and therapeutic targets to improve patient outcomes. Objectives: Our goal was to develop a novel multi-gene prognostic model linked to neutrophils for predicting lung squamous cell carcinoma prognosis. Methods: We utilized messenger RNA expression profiles and relevant clinical data of lung squamous cell carcinoma patients from the Cancer Genome Atlas database. Through K-means clustering, least absolute shrinkage and selection operator regression, and univariate/multivariate Cox regression analyses, we identified 12 neutrophil-related genes strongly related to patient survival and constructed a prognostic model. We verified the stability of the model in the Cancer Genome Atlas database and gene expression omnibus validation set, demonstrating the robust predictive performance of the model. Results: Immunoinfiltration analysis revealed remarkably elevated levels of infiltration for natural killer cells resting and monocytes in the high-risk group compared to the low-risk group, while macrophages had considerably lower infiltration in the high risk group. Most immune checkpoint genes, including programmed cell death protein 1 and cytotoxic T-lymphocyte-associated antigen 4, exhibited high expression levels in the high risk group. Tumor immune dysfunction and exclusion scores and immunophenoscore results suggested a potential inclination toward immunotherapy in the "RIC" version V2 revised high risk group. Moreover, prediction results from the CellMiner database revealed great correlations between drug sensitivity (e.g., Vinorelbine and PKI-587) and prognostic genes. Conclusion: Overall, our study established a reliable prognostic risk model that possessed significant value in predicting the overall survival of lung squamous cell carcinoma patients and may guide personalized treatment strategies. (Rev Invest Clin. 2024;76(2):116-31).

Gene expression of Postn and FGF7 in canine chordae tendineae and their effects on flexor tenocyte biology.

Chordae tendineae, referred to as heart tendinous cords, act as tendons connecting the papillary muscles to the valves in the heart. Their role is analogous to tendons in the musculoskeletal system. Despite being exposed to millions of cyclic tensile stretches over a human's lifetime, chordae tendineae rarely suffer from overuse injuries. On the other hand, musculoskeletal tendinopathy is very common and remains challenging in clinical treatment. The objective of this study was to investigate the mechanism behind the remarkable durability and resistance to overuse injuries of chordae tendineae, as well as to explore their effects on flexor tenocyte biology. The messenger RNAexpression profiles of chordae tendineae were analyzed using RNA sequencing and verified by quantitative reverse transcription polymerase chain reaction and immunohistochemistry. Interestingly, we found that periostin (Postn) and fibroblast growth factor 7 (FGF7) were expressed at significantly higher levels in chordae tendineae, compared to flexor tendons. We further treated flexor tenocytes in vitro with periostin and FGF7 to examine their effects on the proliferation, migration, apoptosis, and tendon-related gene expression of flexor tenocytes. The results displayed enhanced cell proliferation ability at an early stage and an antiapoptotic effect on tenocytes, while treated with periostin and/or FGF7 proteins. Furthermore, there was a trend of promoted tenocyte migration capability. These findings indicated that Postn and FGF7 may represent novel cytokines to target flexor tendon healing. Clinical significance: The preliminary discovery leads to a novel idea for treating tendinopathy in the musculoskeletal system using specific molecules identified from chordae tendineae.

Transcriptomic Profiling to Understand Inhibitor Development in Previously Untreated Patients with Severe Hemophilia a

Background: When starting treatment with factor VIII (FVIII) concentrate in individuals with severe hemophilia A, minimizing the risk of FVIII inhibitor development is an important concern for clinicians, patients and their families. Despite increased understanding of some of the genetic and environmental risk factors for inhibitor formation from epidemiological studies, identification of previously untreated patients (PUPs) at risk of developing inhibitors remains a challenge. Prediction of inhibitor development may help optimize care in PUPs with hemophilia A. RNA sequencing (RNA-Seq) with next-generation sequencing (NGS) could be used to investigate the underlying mechanisms of inhibitor development. Aims: Toevaluate peripheral blood transcriptomic profiles prior to and during early FVIII treatment in severe hemophilia A patients who did or did not develop inhibitors to simoctocog alfain the prospective NuProtect study. Methods: The NuProtect study (NCT01712438; EudraCT 2012-002554-23) was a multicenter, multinational, open-label, non-controlled, phase III study that enrolled male PUPs with severe hemophilia A (FVIII:C <1%) of any age and ethnicity. Patients received simoctocog alfa for prophylaxis or on-demand treatment, as well as for surgical prophylaxis. RNA-Seq was performed on blood samples collected from baseline and every 3-4 exposure days (ED) up to 20 EDs or until inhibitor development to assess messenger RNA (mRNA) expression profiles. Bioinformatics analyses were performed for the following timepoints: baseline, early treatment and a later timepoint on treatment. Principal component analysis (PCA) was performed to identify differences in global mRNA expression profiles between inhibitor and non-inhibitor patients. Gene ontology (GO) analyses were performed to detect differences in GO clusters between inhibitor and non-inhibitor patients. Results: Within this first analysis of the full dataset, transcriptomic profiles from 78 of 108 severe hemophilia A PUPs were analyzed (inhibitors n=22, non-inhibitors n=56). Median (range) age at ED1 was 13 (0.5-146) months; 44.9% of patients had the intron 22 inversion F8 gene mutation. Although the PCA indicated no strong global signal for differential expression profiles between non-inhibitor and inhibitor patients, GO analyses demonstrated differences between these patient groups. Inhibitor patients demonstrated increased gene expression of metabolic processes (GO:0008152) and cellular processes (GO:0009987) at baseline. Upregulation of immune system processes (GO:0002376) was seen in inhibitor patients at the early timepoint compared with non-inhibitor patients. Expression of ribosomal proteins, including RPL17 and RPS8 were significantly upregulated at baseline in inhibitor patients (p<0.05). Inhibitor patients further demonstrated upregulation of proteins involved in adaptive immune responses: IGHV1-69-2 at all timepoints (p<0.01) and IGHV2-70D at baseline and the early timepoint (p<0.01) compared with non-inhibitor patients. Upregulation of the B-cell related factors DPP4 at baseline and the early timepoint (p<0.05) and CD20 at the late timepoint (p<0.05) was observed in inhibitor patients compared with non-inhibitor patients. Conclusion: Differential transcriptomic profiles were seen in severe hemophilia A patients who developed inhibitors compared with those who do not, even before commencing FVIII treatment. Inhibitor patients demonstrated alterations in ribosomal protein expression that could disrupt protein synthesis efficiency, protein folding and quality control processes, and trigger cellular stress responses. Inhibitor patients also showed an upregulation of B-cell mediated factors involved in adaptive immune mechanisms. Additional analyses are ongoing to evaluate dynamic changes in gene expression during commencement of FVIII replacement to further identify patients at risk of inhibitor development.

Bioinformatics and functional experiments reveal that MRC2 inhibits atrial fibrillation via the PPAR signaling pathway.

Atrial fibrillation (AF) is a prevalent cardiac arrhythmia that requires improved clinical markers to increase diagnostic accuracy and provide insight into its pathogenesis. Although some biomarkers are available, new ones need to be discovered to better capture the complex physiology of AF. However, their limitations are still not fully addressed. Bioinformatics and functional studies can help find new clinical markers and improve the understanding of AF, meeting the need for early diagnosis and individualized treatment. To identify AF-related differentially expressed genes (DEGs), We applied the messenger RNA (mRNA) expression profile retrieved in Series Matrix File format from the GSE143924 microarray dataset obtained from the Gene Expression Omnibus (GEO) database, and then used weighted gene co-expression network analysis (WGCNA) to identify the overlapping genes. These genes were analyzed by enrichment analysis, expression analysis and others to obtain the hub gene. Additionally, the potential signaling pathway of hub gene in AF was explored and verified by functional experiments, like quantitative real-time polymerase chain reaction (qRT-PCR), cell counting kit-8 (CCK-8), flow cytometry, and Western blotting (WB) assay. From the GSE143924 data (410 DEGs) and tan module (57 genes), 10 overlapping genes were identified. A central down-regulated gene in AF, MRC2, was identified through bioinformatics analysis. based on these results, it was hypothesized that the PPAR signaling pathway is related to the mechanism of action of MRC2 in AF. Moreover, over-MRC2 markedly reduced the growth speed of angiotensin II (Ang II)-induced human cardiac fibroblasts (HCFs) and increased apoptosis. Conversely, knockdown of MRC2 promoted HCFs cell proliferation number. Additionally, MRC2 over-expression increased the protein expression level of PPARα, PPARγ, CPT-1, and SIRT3 in Ang II-induced HCFs. While meeting the need for new biomarkers in the diagnosis and prognosis of AF, this study reveals the inherent limitations of current biomarkers. We identified MRC2 as a key player as an inhibitory gene in AF, highlighting its role in suppressing AF progression through the PPAR signaling pathway. MRC2 may not only serve as a diagnostic indicator, but also as a promising therapeutic target for patients with AF, which is expected to be applied in clinical practice and open up new avenues for individualized interventions.

A new ferroptosis-related signature model including messenger RNAs and long non-coding RNAs predicts the prognosis of gastric cancer patients.

Gastric cancer (GC) is among the most malignant tumor types, which causes heavy healthy and economic burden to the people and societies all around the world. Establishment of an effective set of prognostic marker will benefit a lot to the treatment of GC patients clinically. Ferroptosis is a newly identified regulated cell death modality, with tight relevance with GC development. However, its application in the prognosis of GC has not been studied in detail. Deregulated messenger RNA (mRNA) and long non-coding RNA (lncRNA) expression profile in tumor can serve as novel prognostic marker for predicting the survival and cancer relapse in patients. We downloaded ferroptosis-related gene expression microarray data, clinicopathologic information and a list of 259 ferroptosis-related genes from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), and Ferroptosis database, respectively. Then, correlation analysis, univariate and multivariate Cox regression analysis were used to construct a novel prognostic model for GC. Then, we validated the model in the GEO datasets. Finally, we evaluated the differences in immune microenvironment between high- and low-risk groups. We utilized the ferroptosis-related mRNA and lncRNA profile to successfully construct a prognostic model (incorporating 2 mRNAs and 15 lncRNAs) in GC. Our model, integrating diverse clinical traits and critical factors of GC, showed desirable efficacy in the prognosis of GC patients. This model also manifested effectively in validation by using external patients' data. Our study developed a novel ferroptosis-related signature to predict the prognosis of gastric cancer patients. The ferroptosis-related signature had a favorable predictive ability. This model may greatly boost the treatment of GC patients in clinical practice.

Transcriptome-wide association study reveals candidate causal genes for lumbar spinal stenosis.

Lumbar spinal stenosis (LSS) is a common skeletal system disease that has been partly attributed to genetic variation. However, the correlation between genetic variation and pathological changes in LSS is insufficient, and it is difficult to provide a reference for the early diagnosis and treatment of the disease. We conducted a transcriptome-wide association study (TWAS) of spinal canal stenosis by integrating genome-wide association study summary statistics (including 661 cases and 178,065 controls) derived from Biobank Japan, and pre-computed gene expression weights of skeletal muscle and whole blood implemented in FUSION software. To verify the TWAS results, the candidate genes were furthered compared with messenger RNA (mRNA) expression profiles of LSS to screen for common genes. Finally, Metascape software was used to perform enrichment analysis of the candidate genes and common genes. TWAS identified 295 genes with permutation p-values < 0.05 for skeletal muscle and 79 genes associated for the whole blood, such as RCHY1 (PTWAS = 0.001). Those genes were enriched in 112 gene ontology (GO) terms and five Kyoto Encyclopedia of Genes and Genomes pathways, such as 'chemical carcinogenesis - reactive oxygen species' (LogP value = -2.139). Further comparing the TWAS significant genes with the differentially expressed genes identified by mRNA expression profiles of LSS found 18 overlapped genes, such as interleukin 15 receptor subunit alpha (IL15RA) (PTWAS = 0.040, PmRNA = 0.010). Moreover, 71 common GO terms were detected for the enrichment results of TWAS and mRNA expression profiles, such as negative regulation of cell differentiation (LogP value = -2.811). This study revealed the genetic mechanism behind the pathological changes in LSS, and may provide novel insights for the early diagnosis and intervention of LSS.

Molecular Characterization of Immunoglobulin M (IgM) and Polymeric Immunoglobulin Receptor (pIgR) and Expression Response to Vibrio harveyi Challenge in Leopard Coral Grouper (Plectropomus leopardus)

Immunoglobulin M (IgM) is the primary antibody in fish, which is transported from epithelial cells into the external secretion system by polymeric immunoglobulin receptor (pIgR). In this study, the full length of IgM and pIgR complementary DNA sequences from leopard coral grouper (Plectropomus leopardus) was characterized, and their expression levels under Vibrio harveyi infection were studied. cDNA sequence analysis showed that the pl-IgM heavy chain cDNA contained an open reading frame (ORF) of 1797 bp encoding a polypeptide of 597 amino acids consisting of a signal peptide, a variable region, and 4 constant regions. pl-pIgR (1041 bp) encodes 346 amino acids with 2 Ig-like domains (ILDs). The expression levels of pl-IgM and pl-pIgR in healthy fish were mainly in the intestine and spleen of fish, which indicates the relationship between the mucosal-associated lymphoid tissue and system lymphoid tissue. Messenger RNA (mRNA) expression profiles of pl-IgM and pl-pIgR were significantly increased in the intestine, head kidney, spleen, and liver after V. harveyi infection. The cDNA sequences of two ILDs were cloned and expressed in Escherichia coli BL21 (DE3). The recombinant pl-pIgR protein had antibacterial function against V. harveyi and Vibrio alginolyticus at 200 ng/μl. Our results indicate that pl-IgM and pl-pIgR are involved in the mucosal-associated immune and systemic immune response in the antibacterial immunity of leopard coral grouper.

Comparative analysis of microRNA and messengerRNA expression profiles in plateau zokor testicular cells under reproductive suppression.

Reproductive suppression is an adaptive strategy that affects the success rate and reproductive efficiency in animals, which in turn affects population continuation and evolution. However, no studies on the miRNAs in testicular development and spermatogenesis regulatory mechanisms under reproductive suppression have been reported. In this study, the differentially expressed (DE) miRNAs, miRNA-mRNA interaction network and function of the plateau zokor testicular cells of non-breeders and breeders during the breeding season were comprehensively analyzed by transcriptomics. In total, 381 known and 94 novel miRNAs were determined. Compared with that in the breeders, 70 downregulated and 68 upregulated DE miRNAs were identified in the non-breeders. We predicted 1670 significant target mRNAs by analyzing the miRNA and mRNA expression profiles. According to the miRNA-mRNA interaction network, the target mRNAs of the DE miRNAs were related to testicular development and spermatogenesis. GO indicate that the target mRNAs were related to testicular development and spermatogenesis. KEGG indicate that pathways of target mRNAs enrichment related to testicular development, spermatogenesis, and energy metabolism. PROK2 was determined as the target mRNA of rno-miR-143-3p. Our study offers a basis for the regulatory mechanisms of miRNAs in testicular development and spermatogenesis in plateau zokor under reproductive suppression and offers a reference for reproductive regulation.

Sperm-borne microRNA-34c regulates maternal mRNA degradation and preimplantation embryonic development in mice

BackgroundStudies have shown that sperm-borne microRNAs (miRNAs) are involved in mammalian preimplantation embryonic development. In humans, spermatozoan miR-34c levels are correlated with in vitro fertilization outcomes, such as embryo quality and the clinical pregnancy and live birth rates. In rabbits and cows, miR-34c improves the developmental competence of embryos generated by somatic cell nuclear transfer. However, the mechanisms underlying the regulation of embryonic development by miR-34c remain unknown.MethodsFemale C57BL/6 mice (6–8 weeks old) were superovulated, and pronucleated zygotes were collected and microinjected with an miR-34c inhibitor or a negative-control RNA. The embryonic development of the microinjected zygotes was evaluated, and the messenger RNA (mRNA) expression profiles of the embryos at the two-cell, four-cell and blastocyst stages (five embryos per group) were determined by RNA sequencing analysis. Gene expression levels were verified by reverse transcription–quantitative polymerase chain reaction. Cluster analysis and heat map visualization were performed to detect differentially expressed mRNAs. Pathway and process enrichment analyses were performed using ontology resources. Differentially expressed mRNAs were systematically analyzed using the Search Tool for the Retrieval of Interacting Genes/Proteins database to determine their biological functions.ResultsEmbryonic developmental potential was significantly reduced in zygotes microinjected with the miR-34c inhibitor compared with those microinjected with a negative-control RNA. Two-cell stage embryos microinjected with an miR-34c inhibitor presented altered transcriptomic profiles, with upregulated expression of maternal miR-34c target mRNAs and classical maternal mRNAs. Differentially expressed transcripts were mainly of genes associated with lipid metabolism and cellular membrane function at the two-cell stage, with cell-cycle phase transition and energy metabolism at the four-cell stage; and with vesicle organization, lipid biosynthetic process and endomembrane system organization at the blastocyst stage. We also showed that genes related to preimplantation embryonic development, including Alkbh4, Sp1, Mapk14, Sin3a, Sdc1 and Laptm4b, were significantly downregulated after microinjection of an miR-34c inhibitor.ConclusionsSperm-borne miR-34c may regulate preimplantation embryonic development by affecting multiple biological processes, such as maternal mRNA degradation, cellular metabolism, cell proliferation and blastocyst implantation. Our data demonstrate the importance of sperm-derived miRNAs in the development of preimplantation embryos.

Identification of new immune subtypes of renal injury associated with anti-neutrophil cytoplasmic antibody-associated vasculitis based on integrated bioinformatics analysis.

Background: Anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) is a systemic autoimmune disease that may lead to end-stage renal disease. However, few specifific biomarkers are available for AAV-related renal injury. The aim of this study was to identify important biomarkers and explore new immune subtypes of AAV-related renal injury. Methods: In this study, messenger RNA expression profiles for antibody-associated vasculitis and AAV-associated kidney injury were downloaded from the Gene Expression Omnibus database. Weighted gene co-expression network analysis (WGCNA) was performed to identify the most relevant module genes to AAV. Key module genes from WGCNA were then intersected with AAV- and nephropathy-related genes from the Genecards database to identify key genes for AAV-associated kidney injury. Subsequently, the expression of key genes was validated in independent datasets and the correlation of genes with clinical traits of kidney injury was verified by the Nephroseq database. Finally, non-negative matrix factorization (NMF) clustering was performed to identify the immune subtypes associated with the key genes. Results: Eight co-key genes (AGTR2, ANPTL2, BDKRB1, CSF2, FGA, IL1RAPL2, PCDH11Y, and PGR) were identifified, and validated the expression levels independent datasets. Receiver operating characteristic curve analysis revealed that these eight genes have major diagnostic value as potential biomarkers of AAV-related renal injury. Through our comprehensive gene enrichment analyses, we found that they are associated with immune-related pathways. NMF clustering of key genes identified two and three immune-related molecular subtypes in the glomerular and tubular data, respectively. A correlation analysis with prognostic data from the Nephroseq database indicated that the expression of co-key genes was positively co-related with the glomerular filtration rate. Discussion: Altogether, we identifified 8 valuable biomarkers that firmly correlate with the diagnosis and prognosis of AAV-related renal injury. These markers may help identify new immune subtypes for AAV-related renal injury.

Identification of autophagy-related genes and immune cell infiltration characteristics in sepsis via bioinformatic analysis.

Sepsis is a life-threatening disease with a high mortality in the intensive care unit (ICU), and autophagy plays an essential role in the development of sepsis. The purpose of this study was to identify potential autophagy-related genes in sepsis and their relationship with immune cell infiltration by bioinformatics analysis. The messenger RNA (mRNA) expression profile of the GSE28750 data set was collected from the Gene Expression Omnibus (GEO) database. The potential differentially expressed autophagy-related genes of sepsis were screened with the "limma" package in R (The Foundation for Statistical Computing). The hub genes were selected by weighted gene coexpression network analysis (WGCNA) networks with Cytoscape, and functional enrichment analysis was performed. The expression level and diagnostic value of the hub genes were validated by Wilcoxon test and receiver operating characteristic (ROC) curve analysis of the GSE95233 data set. The compositional patterns of immune cell infiltration in sepsis were estimated using the CIBERSORT algorithm. Spearman rank correlation analysis was used to associate the identified biomarkers with infiltrating immune cells. A competing endogenous (ceRNA) network was constructed to predict related noncoding RNAs of identified biomarkers with the miRWalk platform. In all, 80 differential autophagy-related genes were obtained. GABARAPL2, GAPDH, WDFY3, MAP1LC3B, DRAM1, WIPI1, and ULK3 were identified as hub genes and diagnostic biomarker groups for sepsis. In addition, 7 differentially infiltrated immune cells correlated with the hub autophagy-related genes were identified. The ceRNA network predicted 23 microRNAs and 122 long noncoding RNAs related to 5 hub autophagy-related genes. GABARAPL2, GAPDH, WDFY3, MAP1LC3B, DRAM1, WIPI1, and ULK3 may influence the development of sepsis and have a vital impact on sepsis immune regulation as autophagy-related genes.

Expression of Neurotensin and Its Receptors Along the Intestinal Tract in Type 2 Diabetes Patients and Healthy Controls.

Enteroendocrine N cells secrete neurotensin (NTS). NTS reduces food intake in rodents and may increase insulin release. In humans, postprandial NTS responses increase following Roux-en-Y gastric bypass, associating the hormone with the glucose- and body weight-lowering effects of these procedures. We looked at N cell density and mucosal messenger RNA (mRNA) expression profiles of NTS and NTS receptors in type 2 diabetes (T2D) patients and healthy controls. Using double-balloon enteroscopy, 12 patients with T2D and 12 sex-, age-, and body mass index-matched healthy controls had mucosa biopsies taken from the entire length of the small intestine (at 30-cm intervals) and from 7 anatomically well-defined locations in the large intestine. Biopsies were analyzed using immunohistochemistry and mRNA sequencing. N cell density and NTS mRNA expression gradually increased from the duodenum to the ileum, while negligible NTS-positive cells and NTS mRNA expression were observed in the large intestine. NTS receptor 1 and 2 mRNA expression were not detected, but sortilin, a single-pass transmembrane neuropeptide receptor of which NTS also is a ligand, was uniformly expressed in the intestines. Patients with T2D exhibited lower levels of NTS-positive cells and mRNA expression than healthy controls, but this was not statistically significant after adjusting for multiple testing. This unique intestinal mapping of N cell density and NTS expression shows increasing levels from the small intestine's proximal to distal end (without differences between patients with T2D and healthy controls), while negligible N-cells and NTS mRNA expression were observed in the large intestine. Sortilin was expressed throughout the intestines in both groups; no NTS receptor 1 or 2 mRNA expression were detected.

Oral contraceptive pill (OCP) treatment alters the gene expression of intercellular adhesion molecule-1 (ICAM-1), tumor necrosis factor-α (TNF-α), monocyte chemoattractant protein-1 (MCP-1) and plasminogen activator inhibitor-1 (PAI-1) in polycystic ovary syndrome (PCOS) women compared to drug-naive PCOS women

BackgroundPolycystic ovary syndrome (PCOS) presents clinical symptoms of menstrual abnormalities, excessive hair growth (hirsutism), scalp hair loss, acne and infertility. Metabolic abnormalities such as obesity, insulin resistance, glucose intolerance and cardiovascular problems constitute an essential part of PCOS, all of which can have significant long-term health consequences. Low-grade chronic inflammation demonstrated by persistent moderately elevated serum levels of inflammatory and coagulatory markers plays a critical role in the pathogenesis of PCOS. Oral contraceptive pills (OCPs) constitute the mainstay of pharmacologic therapy for women with PCOS to regularize cyclicity and ameliorate androgen excess. On the other hand, OCP use is associated with various venous thromboembolic and proinflammatory events in the general population. PCOS women always carriers the increased lifetime risk of these events. The studies on the effect of OCPs on inflammatory, coagulation and metabolic parameters in PCOS are less robust. Therefore in this study, we investigated and compared the messenger RNA (mRNA) expression profiles of genes implicated in inflammatory and coagulation pathways between drug-naive and OCP-treated PCOS women. The selected genes include intercellular adhesion molecule-1 (ICAM-1), tumor necrosis factor-α (TNF-α), monocyte chemoattractant protein-1 (MCP-1) and plasminogen activator inhibitor-1 (PAI-1). Furthermore, the correlation between the selected markers and various metabolic indices in the OCP group has also been explored.MethodThe relative amounts of ICAM-1, TNF-α, MCP-1 and PAI-1 mRNA in peripheral blood mononuclear cells from 25 drug-naive PCOS subjects (controls) and 25 PCOS subjects who received OCPs containing 0.03 mg-ethinyl-estradiol and 0.15 mg-levonorgestrel for at least six months (cases) were estimated using real-time qPCR. The statistical interpretation was conducted using SPSS version 20.0 (SPSS, Inc, Chicago, IL), Epi Info version 2002 (Disease Control and Prevention Centres, Atlanta, GA) and GraphPad Prism 5 (GraphPad Software, La Jolla, CA) software.ResultSix months of OCP therapy enhanced the expression of inflammatory genes viz ICAM-1, TNF-α and MCP-1 mRNA in PCOS women by 2.54, 2.05 and 1.74 folds, respectively, in this study. However, PAI-1 mRNA in the OCP group showed no significant increase. Furthermore, in cases, ICAM-1 mRNA expression positively correlated with body mass index (BMI) (p = 0.01), fasting insulin (p = 0.01), insulin 2 h p = 0.02), glucose 2 h (p = 0.01) and triglycerides (p = 0.01). TNF-α mRNA expression positively correlated with fasting insulin (p = 0.0007). MCP-1 mRNA expression positively correlated with (BMI) (p = 0.002).ConclusionOCPs helped reduce clinical hyperandrogenism and regularise menstrual cycles in women with PCOS. However, OCP use was associated with increased fold expression of inflammatory markers which positively correlated with metabolic abnormalities.

MicroRNA and Messenger RNA Expression Profiles in Canine Mammary Gland Tumor.

Canine mammary gland tumor (CMT) is the most frequently diagnosed neoplasm in intact female dogs. As prognosis depends on the malignancy of tumors and metastasis levels, early and accurate diagnosis are crucial for prolongation of life expectancy. The genetic similarity of dogs with humans in addition to environmental and physiological similarities make them ideal models for the study of cancer. In this study, we analyzed differentially expressed microRNAs followed by RNA-Seq to investigate the alterations in mRNA levels based on the malignancy (benign, malignant) and the biopsy locations (tumors, surrounding normal tissues). We identified multiple breast cancer-related genes regardless of malignancy. We found cfa-miR-503 to be the only miRNA that showed altered expression in response to malignancy in CMTs. Although further validation is needed, cfa-miR-503 could be used as a potential diagnostic biomarker as well as a potential RNA-based anti-tumor drug in malignant CMTs.