Transcriptome Sequencing on Treatment of Kidney Deficiency and Blood Stasis-thin Endometrium in Rats with Bushen Huoxue Prescription Through Enema / 中国实验方剂学杂志

ObjectiveTo explore the mechanism of Bushen Huoxue enema in treating the rat model of kidney deficiency and blood stasis-thin endometrium （KDBS-TE） by transcriptome sequencing. MethodThe rat model of KDBS-TE was established by administration of tripterygium polyglycosides tablets combined with subcutaneous injection of adrenaline. The pathological changes of rat endometrium in each group were then observed. Three uterine tissue specimens from each of the blank group， model group， and Bushen Huoxue enema group were randomly selected for transcriptome sequencing. The differentially expressed circRNAs， lncRNAs， and miRNAs were screened， and the disease-related specific competitive endogenous RNA （ceRNA） regulatory network was constructed. Furthermore， the gene ontology （GO） functional annotation and the Kyoto Encyclopedia of Genes and Genomes （KEGG） pathway enrichment were performed for the mRNAs in the network. ResultCompared with the blank group， the model group showed endometrial dysplasia， decreased endometrial thickness and endometrial/total uterine wall thickness ratio （P<0.01）， and differential expression of 18 circRNAs， 410 lncRNAs， and 7 miRNAs. Compared with the model group， the enema and estradiol valerate groups showed improved endometrial morphology and increased endometrial thickness and ratio of endometrial to total uterine wall thickness （P<0.05）. In addition， 21 circRNAs， 518 lncRNAs， and 17 miRNAs were differentially expressed in the enema group. The disease-related specific circRNA-miRNA-mRNA regulatory network composed of 629 nodes and 664 edges contained 2 circRNAs， 34 miRNAs， and 593 mRNAs. The lncRNA-miRNA-mRNA regulatory network composed of 180 nodes and 212 edges contained 5 lncRNAs， 10 miRNAs， and 164 mRNAs. The mNRAs were mainly enriched in Hippo signaling pathway， autophagy-animal， axon guidance， etc. ConclusionBushen Huoxue enema can treat KDBS-TE in rats by regulating specific circRNAs， lncRNAs， and miRNAs in the uterus and the ceRNA network.

Construction of competitive endogenous RNA network mediated by lung ischemia-reperfusion core genes / 器官移植

Objective To analyze the core genes of lung ischemia-reperfusion injury and construct a competitive endogenous RNA (ceRNA) network. Methods Original data of GSE145989 were downloaded from the Gene Expression Omnibus (GEO) database as the training set, and the GSE172222 and GSE9634 datasets were used as the validation sets, and the differentially-expressed genes (DEG) were identified. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed. Protein-protein interaction (PPI) network was constructed, and the core genes were screened, and the diagnostic values of these core genes and the immune infiltration levels of immune cells were evaluated. The ceRNA network was constructed and validated. The targeted drugs based on ceRNA network were assessed. Results A total of 179 DEG were identified, including 61 down-regulated and 118 up-regulated genes. GO analysis showed that DEGs were associated with multiple biological processes, such as cell migration, differentiation and regulation, etc. They were correlated with cell components, such as vesicle membrane, serosa and membrane raft, etc. They were also associated with multiple molecular functions, such as chemokine receptor, G protein-coupled receptor, immune receptor activity and antigen binding, etc. KEGG pathway enrichment analysis revealed that DEG were involved in tumor necrosis factor (TNF), Wnt, interleukin (IL)-17 and nuclear factor (NF)-κB signaling pathways, etc. PPI network suggested that CD8A, IL2RG, STAT1, CD3G and SYK were the core genes of lung ischemia-reperfusion injury. The ceRNA network prompted that miR-146a-3p, miR-28-5p and miR-593-3p were related to the expression level of CD3G. The miR-149-3p, miR-342-5p, miR-873-5p and miR-491-5p were correlated with the expression level of IL-2RG. The miR-194-3p, miR-512-3p, miR-377-3p and miR-590-3p were associated with the expression level of SYK. The miR-590-3p and miR-875-3p were related to the expression level of CD8A. The miR-143-5p, miR-1231, miR-590-3p and miR-875-3p were associated with the expression level of STAT1. There were 13 targeted drugs for CD3G, 4 targeted drugs for IL-2RG, 28 targeted drugs for SYK and 3 targeted drugs for lncRNA MUC2. No targeted drugs were identified for CD8A, STAT1 and other ceRNA network genes. Conclusions CD8A, IL2RG, STAT1, CD3G and SYK are the core genes of lung ischemia-reperfusion injury. The research and analysis of these core genes probably contribute to the diagnosis of lung ischemia-reperfusion injury and providing novel research ideas and therapeutic targets.

CeRNA interaction network and immune manifestation of ferroptosis-related signature genes in rheumatoid arthritis / 中国组织工程研究

BACKGROUND:Ferroptosis-related genes have been found to play an important role in the pathogenesis of rheumatoid arthritis.However,there is currently a lack of immune expression of ferroptosis-related signature genes in rheumatoid arthritis and the construction of competing endogenous RNA(CeRNA)interaction networks.Machine learning,as a powerful signature gene selection algorithm based on bioinformatics,can more accurately identify ferroptosis-related signature genes that dominate the pathogenesis of rheumatoid arthritis. OBJECTIVE:To screen ferroptosis-related signature genes in rheumatoid arthritis using bioinformatics and machine learning methods,and to analyze the correlation between ferroptosis-related signature genes and immune infiltration and the construction of CeRNA network of ferroptosis-related signature genes. METHODS:Rheumatoid arthritis-related microarrays were obtained from the GEO database,and ferroptosis-related genes and their differential gene expression were extracted using R language.The differentially expressed genes were screened using machine learning methods.The LASSO regression and SVM-RFE methods were used for signature gene screening,and the genes filtered by both were re-intersected to finally obtain the signature genes in rheumatoid arthritis.Receiver operating characteristic curves were used to assess the accuracy of the screened signature genes for disease diagnosis.Immune infiltration of rheumatoid arthritis and normal synovial tissues was analyzed using the CIBERSORT algorithm,and the correlation between the signature genes and immune cells was analyzed.Finally,the CeRNA network of ferroptosis-related signature genes for rheumatoid arthritis was constructed and the disease signature genes were validated. RESULTS AND CONCLUSION:A total of 150 ferroptosis-related genes in rheumatoid arthritis were obtained,including 55 up-regulated genes and 95 down-regulated genes.GO and KEGG enrichment analyses identified 18 GO significantly correlated entries and 30 KEGG entries respectively,mainly involving metal ion homeostasis,ferric ion homeostasis and oxidative stress response.Machine learning analysis finally identified disease signature genes GABARAPL1 and SAT1.GSEA analysis found that adipocytokine signaling pathway,drug metabolism cytochrome P450,fatty acid metabolism,PPAR signaling pathway,tyrosine metabolism were mainly concentrated when GABARAPL1 was highly expressed,and chemokine signaling pathway,intestinal immune network on IGA production were mainly concentrated when SAT1 was highly expressed.Immune infiltration analysis found that nine immune cells were significantly different in rheumatoid arthritis and normal synovial tissues,in which plasma cells,T-cell CD8,and T-cell follicular helper were highly expressed and the rest were lowly expressed in the disease group.Single gene and immune cell correlation analysis found that GABARAPL1 was positively correlated with dendritic resting cells,activated NK cells,and macrophage M1,with the most significant correlation with dendritic resting cells,while SAT1 was positively correlated with T cell CD4 and γδ T cells and negatively correlated with NK resting cells.GSVA analysis found that SAT1 was upregulated in ascorbic acid and aldehyde metabolism,while downregulated in B-cell receptor signaling pathway,Toll-like receptor signaling pathway,T-cell receptor signaling pathway,and natural killer cell-mediated cytotoxicity.GABARAPL1 showed a down-regulation trend in PPAR signaling pathway,metabolism of nicotinate and nicotinamide,tryptophan metabolism,fatty acid metabolism,and steroid biosynthesis.Sixty long non-code RNAs may play a key role in the development of rheumatoid arthritis.To conclude,the occurrence of rheumatoid arthritis is significantly correlated with the abnormal expression of rheumatoid arthritis-induced ferroptosis-related signature genes,and the signature genes induce disease development via relevant signaling pathways.By analyzing rheumatoid arthritis-related long non-code RNAs-mediated ceRNA networks,potential therapeutic targets and signaling pathways can be identified to further elucidate its pathogenesis and provide a reference basis for subsequent experimental studies.

Mechanisms of long non-coding RNA in osteoarthritis and traditional Chinese medicine intervention / 中国组织工程研究

BACKGROUND:The etiology of osteoarthritis is varied and its pathogenesis is still unclear.As bioinformatics has been deepening in recent years,increasing studies have found that the aberrant expression of long non-coding RNAs(lncRNAs)and microRNAs(miRNAs)in joint tissues may mediate the downstream signaling pathways involved in the development of osteoarthritis. OBJECTIVE:To review the mechanism of lncRNA in the development of osteoarthritis and the therapeutic effects of monomers and active compounds derived from traditional Chinese medicine that modulate lncRNA and downstream signaling pathways in osteoarthritis. METHODS:We searched CNKI,WanFang,VIP,and PubMed using the search terms of"long non-coding RNA,knee osteoarthritis,miRNA,chondrocytes,signaling pathway,and traditional Chinese medicine"in Chinese and English,respectively.The search time was from the inception of each database to March 2023.A total of 61 articles were included according to the inclusion and exclusion criteria. RESULTS AND CONCLUSION:The pathogenesis of knee osteoarthritis involves a complex molecular regulatory network,including aberrant expression of lncRNAs and miRNAs in cartilage tissues,which may lead to apoptosis of chondrocytes,degradation of cartilage extracellular matrix,and production of large amounts of pro-inflammatory cytokines.These changes interact with each other to cause degeneration of articular cartilage and progression of osteoarthritis.Therefore,further in-depth studies are needed to reveal the fine mechanisms of the molecular regulatory network.The mechanism of traditional Chinese medicine in the treatment of osteoarthritis mainly focuses on regulating the expression of lncRNA and miRNA,thereby alleviating chondrocyte apoptosis and extracellular matrix degradation,promoting cell proliferation,and slowing down the development of osteoarthritis.

Expression and significance of lncRNA SNHG25 in prostate cancer based on the TCGA database / 现代泌尿外科杂志

【Objective】 To analyze the expression of lncRNA SNHG25 in prostate cancer and its significance, so as to explore the biomarkers and potential therapeutic targets for the diagnosis and prognosis of this disease. 【Methods】 Based on the TCGA database, differential, survival, and clinical correlation analyses of SNHG25 were performed.SNHG25 expression in prostate cancer was analyzed in the UALCAN database to determine its relationship with the clinical and pathological characteristics.The lncRNA-miRNA-mRNA correlation analysis was performed.The relevant ceRNA regulatory network was constructed.Prostate cancer samples were divided into high and low SNHG25 expression groups, and differential SNHG25 related genes were filtered and then enriched. 【Results】 SNHG25 expression was significantly upregulated in prostate cancer specimens compared to normal prostate specimens (P0.05).Regulatory networks of SNHG25/miR-330-3p/DLX1 and RPL22L1 were constructed. 【Conclusion】 SNHG25 is highly expressed in prostate cancer tissues and correlated with poor prognosis.SNHG25 expression does not significantly correlate with age, T-stage, N-stage, and Gleason score.SNHG25/miR-330-3p/DLX1 and RPL22L1 regulatory networks may play an important role in the development of prostate cancer.SNHG25 may become a biomarker and potential therapeutic target for prostate cancer.

lncRNA-mediated ceRNA network molecular mechanisms on ischemic stroke / 中国康复医学杂志

Objective:To construct the regulatory network of competitive endogenous RNA(ceRNA)and explore the mo-lecular mechanism of ischemic stroke(IS)by using bioinformatic analysis to screen the differentially-expressed genes. Method:The expression profiles of miRNA,mRNA and lncRNA in IS were downloaded from the NCBI GEO database.Differentially-expressed miRNAs,lncRNAs,and mRNAs were identified by the limma package in R software.The prediction of the relationship of lncRNA-miRNA and miRNA-mRNA were performed by starBase,miRDB and miRwalk databases.The results of prediction and differential analysis were taken to inter-sect and screened out differentially-expressed target mRNA(DETmRNAs),Kyoto Encyclopedia of Genes and Genomes(KEGG)and gene ontology(GO)enrichment analysis was performed by using the DAVID database.The protein-protein interaction(PPI)network was constructed by using the STRING database and the core tar-get genes in the network were identified by Cytoscape software. Result:A total of 20 differentially-expressed miRNAs,1512 lncRNAs,and 278 mRNAs were identified,and a ceRNA network was successfully constructed with the interactions of 5 lncRNAs-6 miRNAs-102 mRNAs in IS.The 285 DETmRNAs functions are mostly involved in the biological process such as chromatin organization,negative regulation of phosphoprotein phosphatase activity,or cell cycle.KEGG mainly enriched the signaling pathway including leukocyte trans-endothelial migration and platelet activation.The top 10 core genes were CREB1,MAPK1,GSK3B,SP1,PIK3R1,NR3C1,NCOR1,NFATC1,SETD2,and NSD1. Conclusion:The construction of the ceRNA network can help to further understand the molecular mechanism of IS and screen potential biomarkers,providing clues to further define rehabilitation targets and develop reha-bilitation strategies.

CircUBE2D2 regulates HMGB1 through miR-885-5p to promote ovarian cancer malignancy

Abstract Background The newly discovered CircUBE2D2 has been shown to abnormally upregulate and promote cancer progression in a variety of cancers. The present study explored circUBE2D2 (hsa_circ_0005728) in Ovarian Cancer (OC) progression. Methods CircUBE2D2, miR-885-5p, and HMGB1 were examined by RT-qPCR or WB. SKOV-3 cell functions (including cell viability, apoptosis, migration, and invasion) were validated using the CCK-8, flow cytometry, scratch assay, and transwell assay, respectively. The direct relationship between miR-885-5p and circUBE2D2 or HMGB1 was confirmed by a dual-luciferase reporter and RNA pull-down analysis. circUBE2D2′s role in vivo tumor xenograft experiment was further probed. Results OC tissue and cell lines had higher circUBE2D2 and HMGB1 and lower miR-885-5p. Mechanically, CircUBE2D2 shared a binding relation with miR-885-5p, while miR-885-5p can directly target HMGB1. Eliminating circUBE2D2 or miR-885-5p induction inhibited OC cell activities. However, these functions were relieved by down-regulating miR-885-5p or HMGB1 induction. Furthermore, circUBE2D2 knockout reduced tumor growth. Conclusion CircUBE2D2 regulates the expression of HMGB1 by acting as a sponge of ceRNA as miR-885-5p, thereby promoting the control of OC cell proliferation and migration and inhibiting cell apoptosis. Targeting CircUBE2D2 could serve as a new potential treatment strategy for OC.

Analysis of gene expression profile and construction of ceRNA regulatory network after DENV-2 infection with HUVECs / 西安交通大学学报(医学版)

【Objective】 To establish a co-expression lncRNA-mRNA ceRNA network and explore the potential molecular mechanism of lncRNA in dengue fever. 【Methods】 DENV-2-infected and normal pHUVEC were sequenced and screened for differentially expressed lncRNA and mRNA by gene microarray technology. Differentially expressed mRNA was analyzed by protein-protein interaction (PPI), and significantly related co-expressed lncRNA-mRNA was screened by Pearson’s correlation coefficient. The microRNA (miRNA) that bound to co-expressed lncRNA-mRNA was predicted by the database. The ceRNA network of co-expressed lncRNA-mRNA was constructed by Cytoscape software. Finally differentially expressed mRNAs and co-expressed lncRNA-mRNA were analyzed by GO and KEGG enrichment, and co-expressed lncRNA-mRNA was verified by RT-qPCR. 【Results】 At 48 h and 72 h after infection, 105 and 51 differentially expressed mRNAs were obtained, respectively, while 59 and 29 differentially expressed lncRNAs were obtained, respectively. Furthermore, at the two time intervals, there were 10 differential mRNAs and 5 differential lncRNAs, respectively. PPI analysis of differential mRNAs showed that isocratic values of interleukin 6 (IL6), interferon-induced protein with tetratricopeptide repeats 2 (IFIT2), and 2’-5’-oligoadenylate synthetase 2 (OAS2) were relatively high. The pairing results of lncRNA-mRNA co-expression analysis with the highest correlation coefficients at 48 h and 72 h after infection were XLOC_001966-SMTNL1 and XLOC_001966-ESR2, respectively. According to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, the functions of differentially expressed mRNA and co-expressed lncRNA-mRNA were mainly involved in virus epidemic prevention response, immune response, and signal transduction, as well as the Janus kinase (JAK)-signal transducer and activator of transcription (STAT) signaling pathway, type I interferon, and cytokine receptor interaction. RT-qPCR revealed that lncRNA XLOC-I2-8991 was upregulated in the co-expressed lncRNA-mRNA, whereas all the other lncRNA and mRNA were downregulated. 【Conclusion】 This study initially revealed the potential lncRNA-mRNA co-expression network during dengue virus infection, and found that co-expressed lncRNA-mRNA was mainly enriched in the immune regulation and signal transduction pathways during virus infection. The findings will help further exploration into the infection mechanism of DENV-2.

Circular RNA ame_circ_000115 regulates expression of genes in larval gusts of Apis mellifera ligustica stressed by Ascosphaera apis / 生物工程学报

Circular RNAs (circRNAs) are a new class of non-coding RNAs, which have been confirmed to regulate insect gene expression and immune response through multiple manners such as competing endogenous RNA (ceRNA) regulatory network. Currently, function of circRNA in honey bee immune response remains unclear. In this study, PCR and Sanger sequencing were performed to validate the back splicing (BS) site of ame_circ_000115 (in short ac115). RT-qPCR was used to detect the expression profile of ac115 in larval guts of Apis mellifera ligustica stressed by Ascosphaera apis. Dual-luciferase reporter gene assay was conducted to verify the binding relationship between ac115 and ame-miR-13b. Interference of ac115 in larval guts was carried out by feeding specific siRNA, followed by determination of the effect of ac115 interference on expression of six genes relevant to host immune response. The results confirmed the existence of BS site within ac115. Compared with the un-inoculated group, the expression of ac115 in 4-day-old larval gut of the A. apis-inoculated group was up-regulated with extreme significance (P < 0.000 1), while that in 5- and 6-day-old larval guts were significantly up-regulated (P < 0.05). The brightness of specific band for ac115 in 4-, 5- and 6-day-old larval guts of the siRNA-circ_000115-fed group gradually became weak, whereas that of the siRNA-scrambl-fed group was pretty high without obvious variation. Compared with that of the siRNA-scramble-fed group, the expression of ac115 in 4-day-old larval gut of the siRNA-circ_000115-fed group was significantly down-regulated (P < 0.05), whereas that of the 5- and 6-day-old larval guts were down-regulated with extreme significance (P < 0.001). Ame-miR-13b was truly existed and expressed in A. m. ligustica larval guts, and there was true binding relationship between ac115 and ame-miR-13b. Compared with that of the siRNA-scramble-fed group, the expression of antimicrobial peptide genes hymenoptaecin and abaecin in 6-day-old larval gut of the siRNA-circ_000115-fed group was significantly up-regulated (P < 0.05), while that of ecdysone receptor (Ecr) was down-regulated with extreme significance (P < 0.01). These results indicate that ac115 is truly expressed in A. m. ligustica larval guts, BS site truly exists within ac115, and effective interference of ac115 in A. m. ligustica larval guts can be achieved via feeding siRNA. Moreover, ac115 potentially regulates Ecr expression through adsorption of ame-miR-13b and expression of hymenoptaecin and abaecin using a non-ceRNA manner, further participating in host stress-response.

Expression of hsa-miR-422a in hypertrophic scars: a bioinformatics analysis / 中华医学美学美容杂志

Objective:To evaluate the expression level of hsa-miR-422a in hypertrophic scars and to identify the target genes of hsa-miR-422a along with their biological functions using bioinformatics approaches.Methods:From June 2020 to December 2020, tissue samples of 3 hypertrophic scar and 3 normal skin were collected from patients (3 males, 3 females, aged 20-42 years) in Department of Plastic and Reconstructive Surgery, Shanghai Ninth People′s Hospital, Shanghai Jiaotong University School of Medicine. Primary fibroblasts were isolated and cultured. Real-time quantitative PCR was performed to quantify the expression of hsa-miR-422a. To construct a ceRNA network, starbase and Target Scandata bases were utilized to predict genes as well as long noncoding RNAs (lncRNAs) that may sponge hsa-miR-422a. GO and KEGG pathway enrichment analyses were conducted on the target genes of hsa-miR-422a; protein-protein interaction (PPI) networks were constructed to identify the hub genes whose functions were predicted by functional enrichment analyses. The expression of hub genes was validated through real-time quantitative PCR in hypertrophic scars.Results:The expression of hsa-miR-422a was significantly lower in the hypertrophic scar tissue samples and fibroblasts compared to that in the normal skin ( P<0.05). 133 target genes as well as 1033 lncRNAs were predicted by starBase and TargetScandata bases and used to construct an hsa-miR-422a-centered ceRNA network. PPI networks of the target genes revealed 10 hub genes, including MAPK1, GRB2, and IGF1R, which were discovered to be related to protein serine/threonine/tyrosine kinase activity, ubiquitin protein ligase binding, fibroblast growth factor receptor signaling pathway, muscle cell proliferation, and many others; besides, they may be involved in FoxO, mTOR, Toll-like receptor, Ras, MAPK, PI3K-Akt signaling pathways and signaling pathways regulating pluripotency of stem cells. Three hub genes (MAPK1, GRB2, and IGF1R) were significantly upregulated in hypertrophic scars ( P<0.05). Conclusions:hsa-miR-422a is significantly downregulated in the hypertrophic scars and may target hub genes such as MAPK1 in ceRNA networks, ultimately modulating hypertrophic scar formation.

Construction of CeRNA network of differential LncRNAs in THP-1 cells infected by Dengue virus type Ⅲ and its antibody dependent enhancement / 中国生物制品学杂志

@#ObjectiveTo establish models of Dengue virus type Ⅲ（DENV-3,DV-3）infection and antibody dependent enhancement(ADE)infection at the acute monocytic leukemia cells(THP-1),investigate the differential expression of long non-coding RNAs(LncRNAs),map the competitive endogenous RNA(CeRNA)regulatory network and predict the translation function of LncRNAs.MethodsThe culture supernatant was harvested 6 d after C6/36 cells were infected with DENV-3,the virus titer was determined by CCID50,and the type and full-length genome amplification were identified by PCR;The DENV-3 standard plasmid was amplified,identified by PCR,and the standard curve was drawn;THP-1 cells were divided into negative control group(THP-1),direct infection group(DV-3),ADE group and blank control group[1640(-)]. After 48 h of infection,the total RNA was extracted and the copy number of intracellular virus nucleic acid was measured;Through the whole transcriptome sequencing technology,the CeRNA regulatory network was constructed for the top five up-regulated and down-regulated LncRNAs in THP-1 vs DENV3,THP-1 vs ADE,DENV3 vs ADE groups,and the functions of their coding proteins were analyzed.ResultsC6/36 cells infected with DENV-3 for 3 d showed obvious cell fusion,vacuoles and abscission;The virus had a titer of about 1. 0 × 104. 64PFU/mL and was identified as DENV-3 by PCR specific primers,of which the complete gene sequence was obtained;The number of viral nucleic acid copies in ADE group was significantly higher than those in DV-3 group and blank control group;In THP-1 vs DENV-3,the expression of cytohesin interacting protein(CYTIP)was predicted to be up-regulated;In THP-1 vs ADE,the expression of kinesin family5A(KIF5A)was predicted to be down-regulated;In DENV-3 vs ADE,the expression of cluster differentiation antigen 9(CD9)and insulin like growth factor 2(IGF2)was predicted to be up-regulated. All of these differential LncRNAs had open reading frames(ORFs). Except Lnc-SH3BP1 and Lnc-RPL41,all of the other LncRNAs had internal ribosome binding site(IRES).ConclusionIn DENV-3 infection of THP-1 cells and ADE infection mediated by DENV-3,the expression of LncRNAs has changed significantly,and may regulate the process of infection through a variety of biological functions,which is helpful for a deeper understanding of the mechanism of ADE infection.

Chr9∶52042693|52047844⁃miR⁃351⁃5p⁃Pten Is Involved in the Development and Progression of Obstructive Sleep Apnea Syndrome through a ceRNA Mechanism / 中国生物化学与分子生物学报

Intermittent hypoxia (IH) is an important pathophysiological feature of obstructive sleep apnea (OSA), but its molecular mechanism is still unclear. We aim to investigate the role of endogenous competing endogenous RNA (ceRNA) regulatory network in the development of IH in OSA rats. An intermittent hypoxic rat model of OSA was constructed by hypoxic and reoxygenation cycles. CircRNAs and mRNAs were detected in rat bronchial tissues, and 230 up-regulated and 181 down-regulated circRNAs and 1238 up-regulated and 608 down-regulated mRNAs were analyzed and screened. The results of Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of the differential circRNAs and mRNAs suggested that they were mainly associated with metabolic pathways and PI3K-Akt signaling pathways. The key circRNAs (the top six circRNAs with the largest differences) were further validated by quantitative real-time polymerase chain reaction (qRT-PCR), chr9:52042693| 52047844 and chr4: 64889575|64899587 were expressed in bronchial tissues consistent with the sequencing results, which were used to further construct the ceRNA regulatory network. Four potential ceRNA regulatory networks were identified by TargetScan and miRanda database, combined with the results of differential circRNA and mRNA. The expression of molecules in the four potential ceRNA regulatory networks was detected by qRT-PCR in bronchial and lung tissues, and the results suggested that the expression of this regulatory network, chr9:52042693|52047844-miR-351-5p-Pten, was consistent with the sequencing results. The findings indicate that chr9:52042693 | 52047844-miR-351-5p-Pten may be involved in the development and progression of obstructive sleep apnea syndrome through a ceRNA mechanism.

Differential expression of cyclic RNA in peripheral blood mononuclear cells of patients with rheumatoid arthritis / 中华风湿病学杂志

Objective:To investigate the differences in the expression profiles of cyclic RNA (circRNA) in peripheral blood mononuclear cells (PBMCs) of rheumatoid arthritis (RA) and its clinical significance.Methods:Venous blood were collected from 4 patients with RA (group T) and 4 healthy subjects (group C). The expression profiles of circRNA in PBMCs of the two groups were detected by Arraystar circRNA microarray, and the differentially expressed circRNA was analyzed by clustering analysis. The binding sites for interaction between differentially expressed circRNA and miRNA were predicted, and functional analysis such as geneontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was performed. quantitative real-time polymerase chain reaction (RT-qPCR) was used to verify the expression of partially differentially expressed circRNA in the two groups of PBMCs, and a circRNA-miRNA-mRNA regulatory network (ceRNA network) was constructed for the target circRNA with significantly differential expression. A receiver operating characteristic curve [receiver operating characteristic curve (ROC)] was established to analyze the potential diagnostic value of target circRNA. SPSS Statistics 23.0 and Graphpad Prism 8.0 were used to analyze the data, and the independent t test was used to analyze the difference between the two groups. Results:① Microarray results showed that, compared with group C, a total of 399 [fold of difference (FC)>1.5, and P<0.05] circRNA were abnormally expressed in PBMCs of group T; including 149 up-regulated and 250 down-regulated. ② Bioinformatics analysis: The prediction of the binding site of circRNA and miRNA suggested that the differentially expressed circRNA in RA might affect the inflammatory response by targeting miR-140-5p, miR-338-5p, and miR-9-5p. GO analysis showed that the differentially expressed circRNA was mainly involved in the intimal-binding organelles, protein metabolism and binding, etc. KEGG pathway analysis showed that most of the involved pathways were related to infection and human immune dysregulation. ③ The results of multi-sample RT-qPCR validation showed that the expression level of hsa_circRNA_009012 in group T was significantly higher than that in group C ( t=-4.417, P<0.01), the expression level of hsa_circRNA_101328 was significantly lower than that in group C ( t=-1.042, P<0.01), and the expression of hsa_circRNA_058230 had no significant change ( t=4.691, P>0.05). ④ ROC curve analysis indicated that hsa_circRNA_009012 had potential value in the diagnosis of RA [area under curve=0.96]. Conclusion:The expression of circRNA in PBMCs of patients with RA is imbalanced, and it may participate in the regulation of the development of RA. Among them, hsa_circRNA_009012 is expected to become a new biological marker for the diagnosis and treatment of RA.

Research Progress on Roles of lncRNA as ceRNA in EMT of Gastric Cancer / 肿瘤防治研究

Gastric cancer is one of the most common malignant tumors in the world, and EMT plays a key role in the development and metastasis of gastric cancer. The regulation of EMT is a complex network. Transcription factors such as SNAIL/SLUG, Twist1/2 and ZEB1/2 play an important induction role in the process of tumor EMT. In addition, the regulation of EMT is related to the participation of cytokines and miRNAs (such as miR-200 family). In recent years, with the deepening studies on non-coding RNAs, researchers discovered that ceRNA networks, involving lncRNA, circRNA, miRNA, mRNA and other RNA molecules, can extensively regulate the proliferation and metastasis of tumor cells, and are closely related to EMT. This paper reviews the role and molecular mechanism of lncRNA as ceRNA in EMT of gastric cancer, to deepen the understanding of ceRNA network in gastric cancer and other malignant tumors.

LncRNA-m18as1 competitively binds with miR-18a-5p to regulate follicle-stimulating hormone secretion through the Smad2/3 pathway in rat primary pituitary cells / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

Long noncoding RNAs (lncRNAs) are expressed in different species and different tissues, and perform different functions, but little is known about their involvement in the synthesis or secretion of follicle-stimulating hormone (FSH). In general, we have revealed lncRNA‍‒‍microRNA (miRNA)‍‒‍‍messenger RNA (mRNA) interactions that may play important roles in rat primary pituitary cells. In this study, a new lncRNA was identified for the first time. First, we analyzed the gene expression of lncRNA-m18as1 in different tissues and different stages by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and observed the localization of lncRNA-m18as1 with fluorescence in situ hybridization, which indicated that this lncRNA was distributed mainly in the cytoplasm. Next, we used RT-qPCR and enzyme-linked immunosorbent assay (ELISA) to analyze the regulation of FSH synthesis and secretion after overexpression or knockdown of lncRNA-m18as1 and found that lncRNA-m18as1 was positively correlated with FSH synthesis and secretion. In addition, mothers against decapentaplegic homolog 2 (Smad2) was highly expressed in our sequencing results. We also screened miR-18a-5p from our sequencing results as a miRNA that may bind to lncRNA-m18as1 and Smad2. We used RNA immunoprecipitation-qPCR (RIP-qPCR) and/or dual luciferase assays to confirm that lncRNA-m18as1 interacted with miR-18a-5p and miR-18a-5p interacted with Smad2. Fluorescence in situ hybridization (FISH) showed that lncRNA-m18as1 and miR-18a-5p were localized mainly in the cytoplasm. Finally, we determined the relationship among lncRNA-m18as1, miR-18a-5p, and the Smad2/3 pathway. Overall, we found that lncRNA-m18as1 acts as a molecular sponge of miR-18a-5p to regulate the synthesis and secretion of FSH through the Smad2/3 pathway.

Porcine Circular RNA Insulin-like Growth Factor 1 Receptor Promotes Adipocyte Differentiation / 中国生物化学与分子生物学报

Circular RNA (circRNA), as a competitive endogenous RNA (ceRNA), plays an importantrole in the regulation of cell differentiation. The purpose of this study was to identify and analyze porcinecircular RNA insulin-like growth factor 1 receptor (circIGF1R), explore its expression patterns, construct a ceRNA regulatory network related to circIGF1R, and explore the regulation of its ectopicexpression on adipogenic differentiation of mouse mesenchymal stem cells (C3H10T1 / 2) effect. Forwardand reverse PCR, Sanger sequencing, RNase R enzyme digestion tests, and qRT-PCR were used toverify that circIGF1R is a circRNA formed by the second exon of insulin-like growth factor 1 receptor(IGF1R). It was expressed in all tissues of pigs, and its expression level increased with age in adiposetissues. miRDB, TargetScan and miRWalk online software were used to predict circIGF1R target genes. RNAhybrid software was used for binding site prediction. DAVID bioinformatics functional analysissoftware was used to perform GO and KEGG enrichment analysis on candidate target genes. Cytoscapesoftware was used to construct the ceRNA network diagram. Based on the gene expression correlation andpredicted target relationship, the GO and KEGG enrichment analysis was drawn and the ceRNA networkwas constructed; the dual luciferase reporter gene test was used, and we found that circIGF1R andFABP4 can bind to ssc (Sus scrofa chromosome) -miR-133a-5p. The circIGF1R overexpression vectorwas successfully constructed and expressed in C3H10T1/ 2 cells. It was found that after overexpression ofcircIGF1R, the expression of key adipogenic regulatory factors CEBPa, CEBPß, FABP4 and PPAR? increased significantly(P<0. 01), and the number of lipid droplets increased significantly. The results ofthis study show that circIGF1R exists in pig adipose tissues, and may positively regulate the adipogenicdifferentiation of C3H10T1/ 2 cells through the ceRNA mechanism, which lays a theoretical foundation forfurther research on circIGF1R regulating the adipogenic differentiation of pig precursor intramuscularadipocytes.

Mechanism study of CeRNA regulatory network mediating malignant tumor phenotype / 国际肿瘤学杂志

Competing endogenous RNAs (CeRNAs) are crisscrossing regulatory networks. CeRNAs networks can mediate malignant tumor cell phenotypes, including proliferation and inhibition, autophagy, infinite growth, induction of angiogenesis and angiogenic mimicosis, immune escape, etc.. It is expected to provide new diagnostic markers and therapeutic targets for malignant tumors to master the regulation and function of CeRNAs mediated phenotype in malignant tumors.

Potential mechanism of cisplatin resistance in non-small cell lung cancer A549 cells analyzed by the whole-transcriptome / 中国胸心血管外科临床杂志

@#Objective    To reveal the potential mechanism of cisplatin resistance in non-small cell lung cancer A549 cells by comparing the expression profiles of wild-type A549 cells and cisplatin-resistant A549 cells (A549/DPP) through whole transcriptome sequencing analysis. Methods    The cisplatin resistant A549 (A549/DDP) cell line was first established. Then, the whole-transcriptome analysis was conducted both on A549 and A549/DDP cells. Next, the differentially expressed RNAs of lncRNA-seq, circRNA-seq, and miRNA-seq data were identified, respectively, followed by functional enrichment analysis. Finally, a comprehensive analysis based on the whole transcriptome data was performed and the construction of the ceRNA network was carried out. Results    A total of 4 517 lncRNA, 123 circRNA, and 145 miRNA were differentially expressed in A549/DDP cells compared with the A549 cell line. These different RNAs were significantly enriched in cancer-related pathways. The ceRNA network contained 12 miRNAs, 4 circRNAs, 23 lncRNAs, and 9 mRNA nodes, of which hsa-miR-125a-5p and hsa-miR-125b-5p were important miRNAs based on the topological analysis. Conclusion    Tumor necrosis factor signaling pathway and p53 signaling pathway are involved in A549/DPP resistance. Hsa-miR-125a-5p and hsa-miR-125b-5p may be potential targets for reversing cisplatin resistance.

Effects of Competing Endogenous RNA on Proliferation and Differentiation of Skeletal Muscle Cells / 中国生物化学与分子生物学报

The skeletal muscle is an important part of the animal body, which is closely related to body movement, energy consumption, production performance and its development process is regulated by many factors. The molecular mechanism of skeletal muscle growth and development is not only closely related to animal husbandry production, but also provides a theoretical basis for the treatment of muscle dis-eases, such as amyotrophic muscular dystrophy, and so on. Non-coding RNA (ncRNA) is a kind of RNA without coding ability, in which circular RNA (circRNA), long non-coding RNA (lncRNA) and micro RNA (miRNA) have been proved to play an important role in the development of skeletal muscles. miR-NA can specifically bind to the 3′ untranslated region (3′ UTR) of the target gene through its seed se-quence, so as to inhibit the translation process of the target gene or directly degrade the target gene, and become a prominent participant in a variety of biological processes. Studies have shown that circRNA, ln-cRNA, pseudogenes and mRNA with miRNA response elements (MRE) can competitively combine miRNA to regulate gene expression, forming a competing endogenous RNA (ceRNA) regulatory network model. This hypothesis subverts the previous concept of unidirectional regulation of target genes by miRNA, and endows them with new biological functions in transcriptome, which is of great biological significance. In recent years, it has been found that ceRNA plays an important regulatory role in the growth and development of skeletal muscles. This paper reviews the role of miRNA, lncRNA and circRNA in the proliferation and differentiation of animal skeletal muscle cells, which is an important member of ceRNA mechanism, in order to broaden the research direction of skeletal muscle mechanism and provide new ideas for the development of animal husbandry and the treatment of muscle diseases.

The Long Non-coding RNA ILF3-AS1 Inhibited Proliferation of Cervical Cancer Cells Through the MiR-130a-3p/PTEN Axis / 中国生物化学与分子生物学报

ILF3 antisense RNA 1 (ILF3-AS1), the antisense RNA of interleukin enhancer binding factor 3 (ILF3), is a lncRNA located on chromosome 19p13. 2. ILF3-AS1 played a key role in the occurrence and development of a variety of tumors, but its role in cervical cancer had not been explored yet. Therefore, we first used TCGA and GTEx database to conduct bioinformatics analysis. The results suggested that ILF3-AS1 was down-regulated in cervical cancer tissues (P < 0. 001) and was associated with a good prognosis (P = 0. 045). The qRT-PCR experiment showed that expression of ILF3-AS1 in cervical cancer tissues and SiHa, HeLa, CaSki cervical cancer cell lines was lower than that in control groups. Subsequently, overexpressing of ILF3-AS1 can significantly inhibit the cancer cell viability and stimulate apoptosis (P<0. 001). Analysis using the Star Base v3. 0 database suggested that ILF3-AS1 can target miR-130a-3p; while miR-130a-3p may target PTEN. The qRT-PCR test showed that the expression of miR-130a-3p in cervical cancer was significantly higher than that in normal cervical tissues (P < 0. 01). The results of the luciferase reporter assay showed that ILF3-AS1 can specifically bind to miR-130a-3p (P<0. 01). After overexpression of ILF3-AS1 in HeLa cells, the expression of miR-130a-3p was significantly down-regulated (P < 0. 01). Co-transfection with pcDNA3. 1-ILF3-AS1 and miR-130a-3p mimics, the inhibitory effect of LF3-AS1 on cell proliferation can partially be reversed (P<0. 001). After HeLa cells overexpressed ILF3-AS1, the expression of phosphatase and tensin homolog deleted on chromosome ten (PTEN) mRNA (P < 0. 001) and proteins (P < 0. 001) significantly increased; when miR-130a-3p mimics was simultaneously used in HeLa cell, the increased expression of PTEN mRNA (P <0. 001) and proteins (P < 0. 001) was notably inhibited. In summary, ILF3-AS1 inhibited the proliferation of cervical cancer cells by sponging miR-130a-3p to regulate the expression of PTEN.