Search

Genetic variation is one of the important factors leading to the incidence and development of cancer. Copy number variation is an important source of genetic diversity， which can be expressed as gene amplification or deletion in structure， and is related to the occurrence and development of different tumors. High-throughput sequencing and gene chip technology can be adopted to detect the variation of copy number， and provide relevant information about tumor molecular characteristics， prognosis and treatment， which is conducive to more accurate diagnosis and treatment decisions for patients in clinical practice. Ovarian cancer is one of the female reproductive system diseases with the highest mortality rate. Understanding its pathogenesis is of significance for improving the survival rate of ovarian cancer. At present， the specific role and mechanism of copy number variation in ovarian cancer are still unclear. In this article， relevant copy number variation in ovarian cancer was reviewed based on the existing research results， aiming to provide novel ideas and methods for the prevention， diagnosis and treatment of ovarian cancer.

Objective To explore the development method of coronavirus gene chip, and to establish a method for rapid qualitative detection of nucleic acids of 7 coronaviruses and 2 influenza viruses in respiratory infection samples such as human throat swabs, sputum, and alveolar lavage fluid. Methods According to the gene sequences of 10 kinds of respiratory infection viruses published on the Internet, the corresponding primers and probe sequences were designed.After screening and verification by agarose gel electrophoresis, the probes were spotted on the aldehyde base modified substrate, completed the detection chip fabrication. Results The PCR amplification product was diluted by 10-fold serial dilution method and then detected by gene chip.The results showed that the lowest detection concentration that could form hybridization spots was 103copies/mL. Conclusion The developed coronavirus gene chip has good specificity and sensitivity, and can be used for simultaneous high-throughput and rapid detection of SARS-CoV-2 and other respiratory viruses.

Presently, onychomycosis is one of the major global public health issues. The diagnosis of onychomycosis relies on typical clinical signs, mycological examination (fungal microscopy, culture) and pathological analysis. The traditional methods are difficult to precisely and rapidly identify fungal species. Emerging technologies, such as PCR-based molecular identification, gene chip, LAMP, MALDI-TOF MS and spectroscopy, exhibit advantages of rapidity, simplicity and accuracy, and overcome the limitations of traditional methods. This paper summarizes the advantages and disadvantages of traditional and modern methods for mycological detection in order to facilitate the development of new detection methods.

Abstract Background Cadmium (Cd) exposure has been found to have detrimental effects on the development of the central nervous system and cognitive ability in children. However, there is ongoing debate regarding the impact of maternal Cd exposure on the cognitive ability of offspring. In this study, we aimed to investigate the mechanisms underlying the influence of maternal Cd exposure on the cognitive ability of offspring rats. Methods Here, we constructed a model of cadmium poisoning in first-generation rats through gavage. The cognitive and memory abilities of its offspring were evaluated by water maze experiment. Then, we used the gene chip to find out the key genes, and we performed qRT-PCR detection of these genes. Subsequently, enrichment analysis was employed to identify pathways. Finally, we constructed a co-expression network consisting of LncRNAs and mRNAs to elucidate the biological functions and regulatory mechanisms of LncRNAs. Results The results of the water maze trial demonstrated that the offspring of rats exposed to cadmium in the first generation had reduced cognitive and memory abilities. Through an analysis of gene expression in the hippocampus of the cadmium-treated rats' offspring and the control group, we identified a correlation between the islet secretion pathway and the cognitive impairment observed in the offspring. Utilizing various algorithms, we identified Cpa1 and Prss1 as potential key genes associated with the cognitive impairment caused by cadmium. The results of qRT-PCR demonstrated a decrease in the expression levels of these genes in the hippocampus of the cadmium-treated rats’ offspring. In addition, in the co-expression network, we observed that Cpa1 was co-expressed with 11 LncRNAs, while Prss1 was associated with 4 unexplored LncRNAs. Furthermore, we conducted an analysis to examine the relationship between Cpa1, Prss1-related transcription factors, and LncRNAs. Conclusion Overall, this study provides novel insights into the molecular effects of first generation Cd exposure on the cognitive ability of offspring. The target genes and signaling pathways investigated in this study could serve as potential targets for improving neurodevelopment and cognitive ability in children.

In humans particularly in children, adenovirus is one of the most common viruses that cause respiratory illnesses. Knowing how to detect adenovirus proficiently and rapidly will help reinforce surveillance of adenovirus infections, detect epidemic situations in real-time, and understand the trend of virus epidemics, which will allow effective actions to be taken quickly. The rapid detection of antiviral antibodies or viral antigens in clinical samples can be achieved by molecular diagnostic techniques like PCR, Real-Time PCR, LAMP, mPCR-RLB, PCR-ELISA, Tem-PCR, Gene Chip, and so on. Some of the molecular diagnostic methods are relatively economical, exceedingly sensitive and explicit. There are several commercially accessible molecular diagnostic techniques that enable their use in clinical laboratories all over the world. In this review, the principles, characteristics, and applications of molecular biology surveillance methods commonly used in labs and clinics for the detection of human adenoviruses are examined and highlighted.

Objective: To investigate the pharmacological action and mechanism of cholic acid derivatives in traditional Chinese medicine (TCM) based on the regulation of gene expression. Methods: Genome-wide gene expression profiles of Michigan Cancer Foundation-7 (MCF-7) cells treated with or without 4 cholic acid derivatives were detected by gene chip technology. Similarities in upregulated and downregulated genes were analyzed using the Connectivity Map (CMap) database. The affinity between cholic acid derivatives and the potential target was confirmed by molecular docking. The cholic acid derivative-regulated pathway enrichment analysis was performed by the STRING database, and the potential pathway was confirmed by in vitro experiments on MD Anderson-Metastatic Breast-231 (MDA-MB-231) cells. Results: Compared with the reference genome in the CMap database, the gene expression profiles of cholic acid derivatives were similar to those of antipsychotic, anticancer, anti-inflammatory, and anti-infective drugs. Among them, 4 derivatives were associated with antianxiety drugs, and molecular docking results showed that these compounds may act by binding to the ligand-binding site of gamma-aminobutyric acid (GABA) receptors. Moreover, the cytoskeletal pathway is one of the pathways enriched in the derivatives. Of them, ursodeoxycholic acid showed significant inhibitory activity on the cytoskeleton formation of MDA-MB-231 cells. Conclusion: The gene expression detection method, combined with CMap and pathway enrichment analysis, could be used to study the mechanism of the active ingredients of TCM. In addition, our research showed that cholic acid derivatives have a potential affinity for membrane receptors, where they can exert anxiolytic activity by modulating opioid receptor, GABA receptor, and dopamine receptor. Moreover, ursodeoxycholic and chenodeoxycholic acid inhibit cytoskeleton formation, probably by acting on membrane proteins to activate the corresponding cytoskeletal pathways.

Abstract Background Classical swine fever (CSF), African swine fever (ASF), and atypical porcine pestivirus (APPV) are acute, virulent, and contagious viral diseases currently hampering the pig industry in China, which result in mummification or stillbirths in piglets and mortality in pigs. Diagnostic assays for the differentiation of infection and vaccination of CSFV, in addition to the detection of ASFV and APPV, are urgently required for better prevention, control, and elimination of these viral diseases in China. Methods A quadruple PCR-based gene microarray assay was developed in this study to simultaneously detect wild-type and vaccine CSFV strains, ASFV and APPV according to their conserved regions. Forty-two laboratory-confirmed samples, including positive samples of 10 other swine viral diseases, were tested using this assay to confirm its high specificity. Results This assay's limit of detections (LODs) for the wild-type and vaccine CSFV were 6.98 and 6.92 copies/µL. LODs for ASFV and APPV were 2.56 × 10 and 1.80 × 10 copies/µL, respectively. When compared with standard RT-PCR or qPCR for CSFV (GB/T 26875–2018), ASFV (MARR issue No.172), or APPV (CN108611442A) using 219 clinical samples, the coincidence was 100%. The results showed that this assay with high sensitivity could specifically distinguish ASFV, APPV, and CSFV, including CSFV infection and immunization. Conclusion This assay provides a practical, simple, economic, and reliable test for the rapid detection and accurate diagnosis of the three viruses and may have good prospects for application in an epidemiological investigation, prevention, and control and elimination of these three diseases.

Abstract Objective To detect differentially expressed genes in patients with neonatal necrotizing enterocolitis (NEC) by bioinformatics methods and to provide new ideas and research directions for the prevention, early diagnosis and treatment of NEC. Methods Gene chip data were downloaded from the Gene Expression Omnibus database. The genes that were differentially expressed in NEC compared with normal intestinal tissues were screened with GEO2R. The functions, pathway enrichment and protein interactions of these genes were analyzed with DAVID and STRING. Then, the core network genes and significant protein interaction modules were detected using Cytoscape software. Results Overall, a total of 236 differentially expressed genes were detected, including 225 upregulated genes and 11 downregulated genes, and GO and KEGG enrichment analyses were performed. The results indicated that the upregulated differentially expressed genes were related to the dimerization activity of proteins, while the downregulated differentially expressed genes were related to the activity of cholesterol transporters. KEGG enrichment analysis revealed that the differentially expressed genes were significantly concentrated in metabolism, fat digestion and absorption pathways. Through STRING analysis, 9 key genes in the protein network interaction map were identified: EPCAM, CDH1, CFTR, IL-6, APOB, APOC3, APOA4, SLC2A and NR1H4. Conclusion Metabolic pathways and biological processes may play important roles in the development of NEC. The screening of possible core targets by bioinformatics is helpful in clarifying the pathogenesis of NEC at the gene level and in providing references for further research.

Background: Integrin subunit α -v (ITGAV) has been demonstrated to be dysregulated and involved in cancer promotion processes in a variety of cancers, but studies on nasopharyngeal carcinoma (NPC) have been limited. Our study aimed to comprehensively assess the expression level and potential mechanisms of ITGAV in NPC. Results: A total of 13 mRNA expression datasets and internal tissue microarrays were included. ITGAV protein and mRNA were overexpressed in NPC. The pathways of upregulated genes positively related to ITGAV in NPC were analyzed, and the PI3K−Akt signaling pathway, cell cycle, and human papillomavirus infections were most significantly enriched. The protein–protein interaction network was constructed for the genes enriched in these pathways, and the corresponding hub genes were obtained. Among them, breast cancer susceptibility gene 1 (BRCA1) was predicted to be a transcription factor of ITGAV via the Cistrome DB Toolkit, which was also confirmed by ChIP-seq information and correlation calculations. Conclusions: ITGAV is overexpressed in NPC and can regulate BRCA1 to participate in the cancer process. ITGAV serves as a potential therapeutic target in NPC patients.How to cite: Huang S-W, Luo J-Y, Qin L-T, et al. Upregulation of ITGAV and the underlying mechanisms in nasopharyngeal carcinoma. Electron J Biotechnol 2022;60. https://doi.org/10.1016/j.ejbt.2022.09.002.

Background: Leucine zipper protein 2 (LUZP2) is a vital gene encoding leucine zipper protein. It is of great importance in the incidence and progress of several human cancers. However, little is known about the role and clinical effects of LUZP2 in prostate cancer (PCa). Therefore, it is crucial to unravel the clinicopathological value of LUZP2 in PCa. In all, 1467 PCa and 549 non-prostate cancer (non-PCa) prostate samples were collected from mRNA chip and RNA-sequencing datasets. The protein levels of LUZP2 were verified in 91 prostate gland tissues by in-house immunohistochemistry (IHC). The standardized mean difference (SMD) was calculated to analyze LUZP2 expression. Survival analysis was also conducted to explore the prognostic significance of LUZP2 in PCa. R software was employed to identify the upregulated differently expressed genes (up-DEGs) and coexpressed genes (CEGs) of LUZP2. Additionally, we explored the prospective molecular mechanism of CEGs of LUZP2 through GO and KEGG pathway analyses. Results: Compared with non-PCa, LUZP2 showed predominantly higher expression in PCa (SMD = 1.05, AUC = 0.88). IHC indicated the protein expression level of LUZP2 was consistently upregulated in PCa tissues (SMD = 2.23, 95%CI: 1.67–2.79). LUZP2 upregulation had an AUC of 0.88 (95%CI: 0.85–0.90) to distinguish PCa from non-PCa tissues. KEGG pathway analysis showed that the pathways of amino sugar and nucleoside sugar metabolism were chiefly enriched with the LUZP2 CEGs in PCa. Conclusion:: LUZP2 upregulation might play a promoting function in the occurrence of PCa.How to cite: Li S-H, Yang Y-P, He R-Q, et al. Comprehensive expression analysis reveals upregulated LUZP2 in prostate cancer tissues. Electron J Biotechnol 2022;59. https://doi.org/10.1016/j.ejbt.2022.06.001

Objective: To analyze the differential gene expression profile of serum exosomes in patients with acute cerebral infarction (ACI) and clarify the changes in gene expression related to cerebral infarction injury and the potential serum markers. Methods: Four patients with ACI and five healthy people were enrolled in the Phase Ⅰ study. After serum isolation from peripheral blood, exosomes were extracted with exosomes kits, high-throughput detection of mRNA was performed with gene chips, and differentially expressed mRNAs were screened. Gene Ontology (GO) functional analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed simultaneously. Furthermore, real-time polymerase chain reaction (qRT-PCR) was used to verify the expression levels of the screened differential mRNAs in the serum exosomes collected in Phase Ⅱ from 32 patients each in the ACI case and normal control groups. Results: In the Phase Ⅰ study, there were 248 differentially expressed mRNAs (fold change ≥ 2.0, P < 0.05) among five patients in the normal control group and four patients in the case group, of which the expression of 242 was upregulated and that of six was downregulated. The results of GO functional enrichment analysis mainly included behavior regulation, cell connection, and antioxidant activity. The results of KEGG pathway enrichment analysis mainly included ribosomes, proteasomes, oxytocin signaling pathways, and oxidative phosphorylation. After researching and screening based on relevant literature, it was found that among the genes with significant differential expression, H3F3B mRNA may be associated with and might play an important role in ACI. The qRT-PCR method was used to detect the H3F3B mRNA expression in serum exosomes of 32 patients each in the normal control and case groups in Phase Ⅱ; the expression was significantly higher in serum exosomes of the case group than in those of the normal control group (P < 0.001). H3F3B mRNA expression in serum exosomes of the case group positively correlated with age, the National Institutes of Health Stroke Scale (NIHSS) score, and the maximum infarct size (P < 0.05). Conclusion: ACI can lead to changes in the serum exosomes mRNA expression profile, which may be closely related to the occurrence, development, and prognosis of this condition. These findings will provide direction for research on the molecular mechanism, diagnostic markers, and therapeutic targets of ACI.

Purpose: To examine the differences in gene expression between ruptured and non-ruptured nucleus pulposus tissues of the intervertebral discs using gene chip technology.Methods: A total of 8 patients with nucleus pulposus from a lumbar disc herniation (LDH) undergoing discectomy in our hospital were selected, including 4 ruptured and 4 non-ruptured herniated nucleus pulposus cases. Total RNA was extracted from cells by using TRIzol reagent. Nucleus pulposus cDNA probes of the two groups were obtained by the single marker method and hybridized with a human gene expression profiling chip (Agilent). The fluorescence signal images were scanned by a laser, and the obtained genes were analyzed by bioinformatics.Results: There were 75 differentially expressed genes with more than 2-fold-changes, of which 56 were up-regulated and 19 were down-regulated. The differential expression of THSD7A, which was up-regulated 18 times, was the most significant, followed by CCL5, AQP3 and SDC4.Conclusion: THSD7A can be used as a characteristic differentially expressed gene in human ruptured nucleus pulposus. Moreover, CCL5, AQP3 and SDC4 may improve the chemotaxis of stem cell migration for self-healing of damaged disc tissue, increase water uptake by nucleus accumbens cells, and inhibit the inflammatory response, thus delaying the process of intervertebral disc degeneration.

Gastrointestinal stromal tumors (GISTs) are common ICC precursor sarcomas, which are considered to be a potential malignant mesenchymal tumor driven by specific KIT or PDGFRA signals in the gastrointestinal tract. The standard treatment for GIST without metastasis is surgical resection. GIST with metastasis is usually treated with tyrosine kinase inhibitors (TKIs) only but cannot be cured. The TKI imatinib is the main drug of GIST drug therapy. In adjuvant therapy, the duration of imatinib adjuvant therapy is 3 years. It has been proved that imatinib can improve the overall survival time (OS). However, many GIST patients develop drug resistance due to the long-term use of imatinib. We were forced to look for new strategies to treat GIST. The purpose of the current academic work is to study the drug-resistant genes of imatinib and their potential mechanisms. A total of 897 differentially expressed genes (DEGs) were found between imatinib-sensitive cell line GIST882 and imatinib-resistant cell line GIST430 by RNA sequencing (RNA-seq). After analyzing the DEGs, 10 top genes were selected (NDN, FABP4, COL4A1, COLEC11, MEG3, EPHA3, EDN3, LMO3, RGS4, and CRISP2). These genes were analyzed by RT-PCR, and it was confirmed that the expression trend of FABP4, COL4A1, and RGS4 in different imatinib-resistant cell lines was in accord with the GEO database. It is suggested that these genes may play a potential role in the clinical diagnosis and treatment of imatinib resistance in GIST.

Objective: Network pharmacology was utilized to explore the mechanism of Guanxinning (GXN) tablet for the treatment of stable coronary artery disease (SCAD). Materials and Methods: First, active ingredients and therapeutic targets were predicted by databases and gene chip. Then, we constructed the compound-target (C-T) network and target-disease (T-D) network to screen hub compounds and therapeutic targets based on contribution index (CI), degree, closeness, betweenness, and coreness in the networks. Enrichment analysis was performed on hub therapeutic targets, and finally, the verification of hub ingredients and hub therapeutic targets was performed through molecular docking. Results: With “oral bioavailability ≥30%, druglikeness ≥0.18, and half-life ≥4 h” as screening conditions, 58 active ingredients were obtained. Seven hundred and seventeen compound targets and 636 SCAD targets were retrieved using databases and gene chip, and the intersection of both (139 targets) was defined as therapeutic targets. According to CI, degree, betweenness, closeness, and coreness, 2 hub compounds and 13 hub therapeutic targets were chosen from the C-T network and T-D network, respectively. The Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis indicated that GXN treated SCAD from several aspects including inflammatory reaction, oxidative stress, nutritional metabolism, blood pressure regulation, ventricular remodeling, vascular smooth muscle proliferation, angiogenesis, and platelet aggregation. Tissue enrichment analysis revealed that the therapeutic targets were enriched in multiple organs and tissues. The excellent binding force between the hub compounds and hub therapeutic targets was verified by molecular docking. Conclusions: The treatment of SCAD by GXN has the characteristics of multiple ingredients, multiple targets, and multiple approaches. Consequently, it may theoretically treat SCAD from multiple angles and levels.

Abstract Background Hepatocellular carcinoma (HCC) remains one of the most common cancers worldwide and tends to be detected at an advanced stage. More effective biomarkers for HCC screening and prognosis assessment are needed and the mechanisms of HCC require further exploration. The role of MAOA in HCC has not been intensively investigated. Methods In‐house tissue microarrays, genechips, and RNAsequencing datasets were integrated to explore the expression status and the clinical value of MAOA in HCC. Immunohistochemical staining was utilized to determine MAOA protein expression. Intersection genes of MAOA related co‐expressed genes and differentially expressed genes were obtained to perform functional enrichment analyses. In vivo experiment was conducted to study the impact of traditional Chinese medicine nitidine chloride (NC) on MAOA in HCC. Results MAOA was downregulated and possessed an excellent discriminatory capability in HCC patients. Decreased MAOA correlated with poor prognosis in HCC patients. Downregulated MAOA protein was relevant to an advanced TNM stage in HCC patients. Co‐expressed genes that positively related to MAOA were clustered in chemical carcinogenesis, where CYP2E1 was identified as the hub gene. In vivo experiment showed that nitidine chloride significantly upregulated MAOA in a nude mouse HCC model. Conclusions A decreased MAOA level is not only correlated with aggressive behaviors in males but also serves as a promising biomarker for the diagnosis and prognosis of HCC patients. Moreover, MAOA may play a role in AFB1 toxic transformation through its synergistic action with co‐expressed genes, especially CYP3A4. MAOA also serves as a potential therapy target of NC in HCC patients.

Background: The systems pharmacology approach is a target prediction model for traditional Chinese medicine and has been used increasingly in recent years. However, the accuracy of this model to other prediction models is yet to be established.Objective: To compare the systems pharmacology modelwithexperimental gene chip technology by using these models to predict targets of a traditional Chinese medicine formulain the treatment of primary liver cancer.Methods: Systems pharmacology and gene chip target predictions were performed for the traditional Chinese medicine formula ZhenzhuXiaojiTang (ZZXJT). A third square alignment was performed with molecular docking.Results: Identification of systems pharmacology accounted for 17% of targets, whilegene chip-predicted outcomes accounted for 19%.Molecular docking showed that the top ten targets (excludingcommon targets) of the system pharmacology model had better binding free energies than the gene chip model using twocommon targets as a benchmark. For both models, the core drugs predictions were more consistent than the core small molecules predictions.Conclusion:In this study, the identified targets of systems pharmacology weredissimilar to those identified by gene chip technology; whereas the core drug and small molecule predictions were similar.

Background Immediate early response 3 (IER3) is correlated to the prognosis of several cancers, but the precise mechanisms underlying the regulation by IER3 of the occurrence and development of hepatocellular carcinoma (HCC) remain unknown. Methods The expression level of IER3 was examined by using in-house immunohistochemistry (IHC), public gene chip, and public RNA-sequencing (RNA-seq). The standardized mean difference (SMD) was calculated to compare the expression levels of IER3 between HCC patients and controls. The summary receiver operating characteristics (sROC) was plotted to comprehensively understand the discriminatory capability of IER3 between HCC and non-HCC group. The Kaplan–Meier curves and the combined hazard ratios (HRs) were used to determine the prognostic value of IER3 in HCC. Moreover, differentially expressed genes (DEGs) and co-expression genes (CEGs) were used to explored the molecular mechanisms of IER3 underlying HCC. hTFtarget was used to predict the transcription factors (TFs) of IER3. The binding site of TFs and the IER3 promoter region was forecasted using the JASPAR website. The relevant ChIP-seq data were used to determine whether TF peaks were present in the IER3 transcription initiation. Results A significantly increased expression of IER3 protein was found in HCC tissue relative to non-HCC tissue as detected by IHC (p

Abstract Background To investigate the species distribution of non-tuberculous mycobacteria (NTM) among tuberculosis (TB) specimens collected from January 2013 to December 2018 at Peking Union Medical Hospital (Beijing), China. NTM species identification was carried out by DNA microarray chip. Results Mycobacterial species were detected in 1514 specimens from 1508 patients, among which NTM accounted for 37.3% (565/1514), increasing from a proportion of 15.6% in 2013 to 46.1% in 2018 (P

Psoriasis is chronic skin disease and an important health concern. Traditional Chinese Medicine (TCM) has shown great promise in the treatment of psoriasis. However, the correlation between TCM Syndromes and genomics of psoriasis has not been evaluated. Here, we analyzed gene expression profiling of monocytes from psoriasis vulgaris patients with different TCM syndrome types to reveal the molecular basis of different psoriasis syndromes. Of the 62 cases of psoriasis vulgaris recruited, 16, 23, and 23 cases were of blood-heat syndrome, blood stasis syndrome, and blood-dryness syndrome, respectively; 10 healthy controls were recruited as controls. Affymertix’s Gene Chip ®clariom D gene chip was used to detect the gene expression profile of peripheral blood monocytes collected from recruited individuals. Compared with the healthy control group, 1570 genes were up-regulated and 977 genes were down-regulated in the psoriasis vulgaris patients group; 798 genes and 108 genes were up- and down-regulated in the blood-heat syndrome group respectively; 319 and 433 genes were up- and down-regulated in the blood-dryness syndrome group, respectively; and 502 and 179 genes were up-and down-regulated in the blood-stasis syndrome group. Our analyses indicated not only common differential genes and pathways between psoriasis syndrome groups and healthy controls, but also syndrome-specific genes and pathways. The results of this study link the three syndromes at the gene level and will be useful for clarifying the molecular basis of TCM syndromes of psoriasis.Clinical Trial Registration: (http://www.chictr.org.cn/showproj.aspx?proj=4390), identifier (ChiCTR-TRC-14005185).

Clinical studies have shown similarities in the genetic background and biological functional characteristics between Hashimoto’s thyroiditis (HT) and papillary thyroid carcinoma (PTC), and that HT may increase risks of PTC. Here, we set to determine the gene expression specificity of HT and PTC by screening related genes or co-expressed genes and exploring their genetic correlation. Referencing the Oncomine database, HT-related genes were discovered to be expressed in many different types of thyroid cancer, such as TSHR that is highly expressed in thyroid cancer. An in-depth genetic analysis and verification of 35 cancer and paracancerous tissue pairs from patients with thyroid cancer, and 35 tissues and blood cells pairs from patients with Hashimoto’s thyroiditis was conducted. Gene chip technology research showed that TSHR, BACH2, FOXE1, RNASET2, CTLA4, PTPN22, IL2RA and other HT-related genes were all expressed in PTC, in which TSHR was significantly over-expressed in PTC patients sensitive to radioactive iodine therapy, while BACH2 was significantly under-expressed in these patients. The biologically significant candidate Tag SNP highlighted from HT-related genes was screened by the high-throughput detection method. Somatic mutations in patients with HT and PTC were detected by target region capture technique, and 75 mutations were found in patients with HT and PTC. The upstream regulatory factors of the different genes shared by HT and PTC were analyzed based on Ingenuity Pathway Analysis (IPA), and it was found that HIF-1α and PD-L1 could be used as important upstream regulatory signal molecules. These results provide a basis for screening key diagnostic genes of PTC by highlighting the relationship between some HT-related genes and their polymorphisms in the pathogenesis of PTC.

Foodborne pathogens that enter the human food chain are a significant threat worldwide to human health. Timely and cost-effective detection of them became challenging for many countries that want to improve their detection and control of foodborne illness. We summarize simple, rapid, specific, and highly effective molecular technology that is used to detect and identify foodborne pathogens, including polymerase chain reaction, isothermal amplification, loop-mediated isothermal amplification, nucleic acid sequence-based amplification, as well as gene chip and gene probe technology. The principles of their operation, the research supporting their application, and the advantages and disadvantages of each technology are summarized.

β-Casomorphin is an opioid-like bioactive peptide derived from β-casein of milk that plays a crucial role in modulating animal’s feed intake, growth, nutrient utilization and immunity. However, the effect of β-casomorphin on lipid metabolism in chickens and its mechanism remain unclear. The aim of this study was to investigate the effects of β-casomorphin on fat deposition in broiler chickens and explore its mechanism of action. A total of 120 21-day-old Arbor Acres male broilers (747.94±8.85 g) was chosen and randomly divided into four groups with six replicates of five birds per replicate. Three groups of broilers were injected with 0.1, 0.5 or 1.0 mg/kg BW of β-casomorphin in 1 ml saline for 7 days, whereas the control group received 1 ml saline only. The results showed that subcutaneous administration of β-casomorphin to broiler chickens increased average daily gain, average daily feed intake and fat deposition, and decreased feed : gain ratio (P

This study explored the possible bioactive ingredients and target protein of Rostellularia procumbens (L.) Nees. The results of optical turbidimetry revealed that the ethyl acetate extraction obtained from R. procumbens (L.) Nees could inhibit platelet aggregation. Gene chip was used to investigate differentially expressed genes. According to the results of the gene chip, the targets of compounds isolated from the ethyl acetate extraction were predicted by network pharmacology. Computational studies revealed that chinensinaphthol methyl ether and neojusticin B may target the integrin αIIbβ3 protein. The results of Prometheus NT.48 and microscale thermophoresis suggested that the molecular interactions between the two compounds with purified integrin αIIbβ3 protein in the optimal test conditions were coherent with the docking results. To our best knowledge, this is the first report to state that chinensinaphthol methyl ether and neojusticin B target the integrin αIIbβ3 protein.

The incidence of obesity has increased significantly on account of the alterations of living habits, especially changes in eating habits. In this study, we investigated the effect of octacosanol on lipid lowering and its molecular mechanism. High-fat diet (HFD)-induced obesity mouse model was used in the study. Thirty C57BL/6J mice were divided into control, HFD, and HFD+Oct groups randomly, and every group included ten mice. The mice of HFD+Oct group were intragastrically administrated 100 mg/kg/day of octacosanol. After 10 weeks for treatment, our results indicated that octacosanol supplementation decreased the body, liver, and adipose tissues weight of HFD mice; levels of TC, TG, and LDL-c were reduced in the plasma of HFD mice; and level of HDL-c were increased. H&E staining indicated that octacosanol supplementation reduces the size of fat droplets of hepatic tissues and adipose cells comparing with the HFD group. Gene chip analysis found that octacosanol regulated 72 genes involved in lipid metabolism in the tissues of liver comparing to the HFD group. IPA pathway network analysis indicated that PPAR and AMPK may play a pivotal role in the lipid-lowering function of octacosanol. Real-time quantitative PCR and Western blot showed that the octacosanol supplementation caused change of expression levels of AMPK, PPARs, FASN, ACC, SREBP-1c, and SIRT1, which were closely related to lipid metabolism. Taken together, our results suggest that octacosanol supplementation exerts a lipid-decreasing effect in the HFD-fed mice through modulating the lipid metabolism-related signal pathway.

Abstract Background With the widespread use of rifampicin and isoniazid, bacterial resistance has become a growing problem. Additionally, the lack of relevant baseline information for the frequency of drug-resistant tuberculosis (TB) gene mutations is a critical issue, and the incidence of this infection in the city of Changchun has not investigated to date. However, compared with the slow traditional methods of drug susceptibility testing, recently developed detection methods, such as rifampicin and isoniazid resistance-related gene chip techniques, allow for rapid, easy detection and simultaneous testing for mutation frequency and drug resistance. Methods In this study, the rifampicin and isoniazid resistance-related gene mutation chip method was employed for an epidemiological investigation. To assess the gene mutation characteristics of drug-resistant TB and evaluate the chip method, we tested 2143 clinical specimens from patients from the infectious diseases hospital of Changchun city from January to December 2016. The drug sensitivity test method was used as the reference standard. Results The following mutation frequencies of sites in the rifampicin resistance gene rpoB were found: Ser531Leu (52.6%), His526Tyr (12.3%), and Leu511Pro (8.8%). The multidrug-resistance (MDR)-TB mutation frequency was 34.7% for rpoB Ser531Leu and katG Ser315Thr, 26.4% for rpoB Ser531Leu and inhA promoter − 15 (C → T), and 10.7% for rpoB His526Tyr and katG Ser315Thr. In addition, drug susceptibility testing served as a reference standard. In previously treated clinical cases, the sensitivity and specificity of GeneChip were 83.1 and 98.7% for rifampicin resistance, 79.9 and 99.6% for isoniazid resistance, and 74.1 and 99.8% for MDR-TB. Conclusions Our experimental results show that the chip method is accurate and reliable; it can be used to detect the type of drug-resistant gene mutation in clinical specimens. Moreover, this study can be used as a reference for future research on TB resistance baselines.

Abstract Background Long non-coding RNAs (lncRNAs) play an important role in tumorigenesis. Vocal cord leukoplakia is a precancerous lesion in otolaryngological practice. Till now, the expression patterns and functions of lncRNAs in vocal cord leukoplakia have not been well understood. In this study, we used microarrays to investigate the aberrantly expressed lncRNAs and mRNAs in vocal cord leukoplakia and adjacent non-neoplastic tissues. Methods Gene Ontology and pathway analyses were performed to determine the significant function and pathways of the differentially expressed mRNAs. qRT-PCR was performed to further validate the expression of selected lncRNAs and mRNAs in vocal cord leukoplakia. Results Our study identified 170 differentially expressed lncRNAs and 99 differentially expressed mRNAs, including 142 up-regulated lncRNAs and 28 down-regulated lncRNAs, and 54 up-regulated mRNAs and 45 down-regulated mRNAs. Among these, XLOC_000605 and DLX6-AS1 were the most aberrantly expressed lncRNAs. Furthermore, we identified an antisense lncRNA (LOC100506801), an enhancer-like lncRNA (AK057351) and three long intergenetic noncoding RNAs including XLOC_008001, XLOC_011989 and XLOC_007341. Conclusions Our results revealed that many lncRNAs were differentially expressed between vocal cord leukoplakia tissues and normal tissue, suggesting that they may play a key role in vocal cord leukoplakia tumorigenesis.

Objective: To construct gene co-occurrence network of hypertension and liver-fire hyperactivity syndrome, to investigate the biological basis of hypertension and liver-fire hyperactivity syndrome and the characteristics of the molecular network from gene level. Materials and Methods: Applying GenCLip 2.0 online platform to retrieve the up-to-date literature referred to essential hypertension from PubMed database, cluster the abnormal expression of essential hypertension-related genes and analyze their function, combining Kyoto encyclopedia of genes and genomes-pathway analysis to investigate the closely related genes and the signaling molecules. Based on the genes closely related to hypertension, standard diagnostic symptoms of liver-fire hyperactivity were used as keywords to conduct hypertension liver-fire hyperactivity-related gene cluster analysis. Results: The top 1000 genes of essential hypertension were retrieved from GenCLip 2.0 online platform, which mainly clustered in the regulation of ambulatory blood pressure, regulation of renin-angiotensin-aldosterone system (RAAS), and sympathetic nervous system activity, as well as endothelial dysfunction; the closely related genes of hypertension with liver-fire hyperactivity are related to RAAS, gene REN, angiotensin converting enzyme, angiotensinogen, and cytochrome P450 family CYP2D6. Conclusion: A combination of literature mining and data mining can construct the gene network of hypertension and the syndrome-related genes, which provides a new method for the study of the biological basis of hypertension from the genetic level.

Abstract Background Chronic myelogenous leukemia (CML) is a myeloproliferative neoplasm that arises from the acquisition of constitutively active BCR‐ABL tyrosine kinase in hematopoietic stem cells. The persistence of bone marrow leukemia stem cells (LSCs) is the main cause of TKI resistance and CML relapse. Therefore, finding a key target or pathway to selectively target LSCs is of great significance for the thorough treatment of CML. Methods In this study, we aimed to identify key microRNAs, microRNA targets and pathways for the treatment of CML LSCs by integrating analyses of three microarray data profiles. We identified 51 differentially expressed microRNAs through integrated analysis of GSE90773 and performed functional gene predictions for microRNAs. Then, GSE11889 and GSE11675 were integrated to obtain differentially expressed genes (DEGs), and the overlapping DEGs were used as models to identify predictive functional genes. Finally, we identified 116 predictive functional genes. Clustering and significant enrichment analysis of 116 genes was based on function and signaling pathways. Subsequently, a protein interaction network was constructed, and module analysis and topology analysis were performed on the network. Results A total of 11 key candidate targets and 33 corresponding microRNAs were identified. The key pathways were mainly concentrated on the PI3K/AKT, Ras, JAK/STAT, FoxO and Notch signaling pathways. We also found that LSCs negatively regulated endogenous and exogenous apoptotic pathways to escape from apoptosis. Conclusion We identified key candidate targets and pathways for CML LSCs through bioinformatics methods, which improves our understanding of the molecular mechanisms of CML LSCs. These candidate genes and pathways may be therapeutic targets for CML LSCs.

The present study explored the possible bioactive ingredients and target protein of Rostellularia procumbens (L.) Nees. Firstly, we found that the ethyl acetate extraction obtained from R. procumbens could inhibit platelet aggregation. Then, gene chip was used to investigate differentially expressed genes and blood absorption compounds were investigated using high performance liquid chromatography-mass spectrometry characterization (LC-MS). Depending on the results of gene chip and LC-MS, the targets of blood absorption compounds were predicted according to the reverse pharmacophore matching model. The platelet aggregation-related genes were discovered in databases, and antiplatelet aggregation-related gene targets were selected through comparison. The functions of target genes and related pathways were analyzed and screened using the DAVID database, and the network was constructed using Cytoscape software. We found that integrin αIIbβ3 had a highest degree, and it was almost the intersection of all pathways. Then, blood absorption compounds were screened by optical turbidimetry. Western blot (WB) revealed that justicidin B separated from the ethyl acetate fraction may inhibit the expression of integrin αIIbβ3 protein. For the first time, we used Prometheus NT.48 and MST to detect the stability of this membrane protein to optimize the buffer and studied the interaction of justicidin B with its target protein. To our best knowledge, this is the first report to state that justicidin B targets the integrin αIIbβ3 protein. We believe that our findings can provide a novel target protein for the further understanding of the mechanism of R. procumbens on platelet aggregation.

Atherosclerosis is the pathological basis of coronary artery disease (CAD) and causes high mortality. Thus, early detection is thought to be crucial in reducing the risk of CAD. Uncovering the mechanisms of the progression and regression of atherosclerosis will provide insights into discovering novel biomarkers to identify subjects at risk for CAD and improve prevention. We established atherosclerosis progression and regression in a rabbit model. Then, we extracted mRNA of the abdominal aorta from control, model and recovery groups to perform gene chip analysis. Candidate biomarkers were screened by large-scale gene analysis and validated in patients with CAD or with CAD recovery by ELISA. The differentially expressed genes in the progression and regression of atherosclerosis were mainly enriched in four clusters. Genes associated with inflammation and extracellular matrix were returned to normal or close-to-normal levels much earlier than genes associated with metabolism and sarcoplasmic proliferation, and they were maintained downregulated or upregulated after feeding a normal diet. We then selected four candidate biomarkers and found that lipoprotein lipase (LPL), bone morphogenetic protein 7 and somatostatin concentrations could indicate CAD diagnosis. In addition, LPL and macrophage cationic peptide 2 can be indicators of the prognosis of CAD. Molecular changes during the progression and regression of atherosclerosis in rabbits were revealed, and candidate regulators were identified. The identified factors could be used as novel biomarkers and targets for improving the diagnosis and prognosis of human CAD in the future.

Objective: To explore the targets, signal regulatory networks and mechanisms involved in Baixiangdan (BXD) capsule regulation of premenstrual dysphoric disorder (PMDD) at the gene transcription level, since the etiology and pathogenesis of PMDD are not well understood.Methods: The PMDD rat model was prepared using the resident-intruder paradigm. The rats were tested for aggressive behavior, and those with scores in the lowest 30% were used as controls, while rats with scores in the highest 30% were divided into a PMDD model group, BXD administration group and fluoxetine administration group, which were evaluated with open-field tests and aggressive behavior tests. We also analyzed gene expression profiles in the hippocampus for each group, and verified differential expression of genes by real-time PCR.Results: Before and after BXD or fluoxetine administration, scores in the open-field test exhibited no significant differences. The aggressive behavior of the PMDD model rats was improved to a degree after administration of both substances. Gene chip data indicated that 715 genes were differentially expressed in the control and BXD groups. Other group-to-group comparisons exhibited smaller numbers of differentially expressed genes. The effective targets of both drugs included the Htr2c, Cdh3, Serpinb1a, Ace, Trpv4, Cacna1a, Mapk13, Mapk8, Cyp2c13, and Htr1a genes. The results of real-time PCR tests were in accordance with the gene chip data. Based on the target genes and signaling pathway network analysis, we have elaborated the impact and likely mechanism of BXD in treating PMDD and premenstrual irritability.Conclusion: Our work contributes to the understanding of PMDD pathogenesis and the mechanisms of BXD treatment. We speculate that the differentially expressed genes could participate in neuroactive ligand-receptor interactions, mitogen-activated protein kinase, calcium, and gamma-aminobutyric acid signal transduction.

This study investigated the mechanisms controlling hair follicle development in the Rex rabbit. The Agilent rabbit gene expression microarray was used to determine differentially expressed genes in Rex rabbit foetuses with different wool densities. The expression patterns of selected differentially-expressed genes were further investigated by quantitative real-time PCR. Compared to low wool density rabbits, 1342 differentially expressed probes were identified in high wool density rabbits, including 950 upregulated probes and 392 downregulated probes. Gene ontology analysis revealed that the most upregulated differentially expressed probes belonged to receptors and the most downregulated differentially expressed probes belonged to DNA binding molecules. Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that the differentially expressed probes were mainly involved in the sonic hedgehog (Shh) and Eph signalling pathways. The results also suggest that transforming growth factor-beta 1, growth hormone receptor, and the keratin-associated protein 6.1 genes, as well as the Shh and Eph signalling pathways, may be involved in the regulation of hair follicle developmental in Rex rabbits.

Objective: A Tag Array chip was used to detect plasmids of different template concentration, and then analyzed for sensitivity and specificity. Drug resistance genes from tuberculosis clinical specimens were detected, giving comparative phenotypic resistance results to explore the feasibility and value of clinical applications.Methods: Twenty-four strains of Mycobacterium Tuberculosis (MTB) having sequence differences in extracted plasmids of mutant strains. The plasmid was diluted into different concentrations, and then was performed to analyze the sensitivity and specificity of the chip system. A total of 427 clinical specimens (including spinal tuberculosis and pulmonary tuberculosis) were collected from patients who came from seven hospitals. Design, optimization and preparation of the chip detection system, sequencing and phenotypic drug susceptibility results were analyzed to evaluate the sensitivity and specificity of the gene chip.Results: In the template, concentrations of 1 × 103 copies/μL and above were consistent with sequencing results in the mutant. The sensitivity and specificity in spine Tuberculosis specimen of rifampicin (RFP) were 94.40 and 92.86%; isoniazide (INH) were 92.37 and 87.50%; ethambutol (EMB) were 61.36 and 89.29%; fluoroquinolones (FQS) were 79.41 and 92.86%; streptomycin (SM) were 90.18 and 89.29%; second line drugs (SLD) were 77.61 and 83.93%. In Pulmonary Tuberculosis specimen, the sensitivity and specificity respectively were RFP: 92.74%; 93.75%; INH: 91.26%; 87.50%; EMB: 54.17%; 89.58%; FQS: 84.87%; 93.75%; SM: 86.73%; 85.42%; SLD: 80.9%; 91.67%. The RFP, INH, FQs and SM resistance genes was highly sensitive and specific: however, for detection of amikacin (AMK), capreomycin (CPM), kanamycin (KM), specificity was higher, but sensitivity was lower. Sensitivity for the detection of a mutation in the eis promoter region could be improved.Conclusion: Tag Array chip can achieve rapid, accurate detection of tuberculosis resistance, which has important clinical significance and feasibility.

Acute lung injury (ALI) is characterized by non-cardiogenic diffuse alveolar damage and often leads to a lethal consequence, particularly when hypoxia coexists. The treatment of ALI remains a challenge: pulmonary inflammation and hypoxia both contribute to its onset and progression and no effective prevention approach is available. Here, we aimed to investigate the underlying mechanism of hypoxia interaction with inflammation in ALI and to evaluate hypoxia-inducible factor 1 alpha (HIF-1α)—the crucial modulator in hypoxia—as a potential therapeutic target against ALI. First, we developed a novel ALI rat model induced by a combined low-dose of lipopolysaccharides (LPS) with acute hypoxia. Second, we used gene microarray analysis to evaluate the inflammatory profiles of bronchi alveolar lavage fluid cells of ALI rats. Third, we employed an alveolar macrophage cell line, NR8383 as an in vitro system together with a toll-like receptor 4 (TLR4) antagonist TAK-242, to verify our in vivo findings from ALI animals. Finally, we tested the therapeutic effects of HIF-1α augmentation against inflammation and hypoxia in ALI. We demonstrated that (i) LPS upregulated inflammatory genes, tumor necrosis factor alpha (TNF-α), interleukin-1 beta (IL-1β), and interleukin-6 (IL-6), in the alveolar macrophages of ALI rats, which were further enhanced when ALI combined with hypoxia; (ii) hypoxia exposure could further enhance the upregulation of alveolar macrophageal TLR4 that was noticed in LPS-induced inflammatory ALI, conversely, TLR4 antagonist TAK-242 could suppress the macrophageal expression of TLR4 and inflammatory cytokines, including TNF-α, IL-1β, and IL-6, suggesting that the TLR4 signaling pathway as a central link between inflammation and hypoxia in ALI; (iii) manipulation of HIF-1α in vitro could suppress TLR4 expression induced by combined LPS and hypoxia, via suppressing promoter activity of the TLR4 gene; (iv) preconditioning augmentation of HIF-1α in vivo by HIF hydroxylase inhibitor, DMOG excreted protection against inflammatory, and hypoxic processes in ALI. Together, we see that hypoxia can exacerbate inflammation in ALI via the activation of the TLR4 signaling pathway in alveolar macrophages and predispose impairment of the alveolar-capillary barrier in the development of ALI. Targeting HIF-1α can suppress TLR4 expression and macrophageal inflammation, suggesting the potential therapeutic and preventative value of HIF-1α/TLR4 crosstalk pathway in ALI.

Abstract China is the largest royal jelly producer and exporter in the world, and high royal jelly-yielding strains have been bred in the country for approximately three decades. However, information on the molecular mechanism underlying high royal jelly production is scarce. Here, a cDNA microarray was used to screen and identify differentially expressed genes (DEGs) to obtain an overview on the changes in gene expression levels between high and low royal jelly producing bees. We developed a honey bee gene chip that covered 11,689 genes, and this chip was hybridised with cDNA generated from RNA isolated from heads of nursing bees. A total of 369 DEGs were identified between high and low royal jelly producing bees. Amongst these DEGs, 201 (54.47%) genes were up-regulated, whereas 168 (45.53%) were down-regulated in high royal jelly-yielding bees. Gene ontology (GO) analyses showed that they are mainly involved in four key biological processes, and pathway analyses revealed that they belong to a total of 46 biological pathways. These results provide a genetic basis for further studies on the molecular mechanisms involved in high royal jelly production.

Abstract Background Epstain-Barr virus (EBV) can transform human B lymphocytes making them immortalized and inducing tumorigenic ability in vitro, but the molecular mechanisms remain unclear. The aim of the present study is to detect and analyze differentially expressed genes in two types of host cells, normal human lymphocytes and coupled EBV-transformed lymphoblasts in vitro using gene chips, and to screen the key regulatory genes of lymphocyte transformation induced by EB virus. Methods Fresh peripheral blood samples from seven healthy donors were collected. EBV was used to transform lymphocytes in vitro. Total RNA was extracted from 7 cases of the normal lymphocytes and transformed lymphoblasts respectively, marked with dihydroxyfluorane after reverse transcription, then hybridized with 4 × 44 K Agilent human whole genome microarray. LIMMA, String, Cytoscape and other softwares were used to screen and analyze differentially expressed genes. Real-time PCR was applied to verify the result of gene expression microarrays. Results There were 1745 differentially expressed genes that had been screened, including 917 up-regulated genes and 828 down-regulated genes. According to the results of Generank, String and Cytoscape analyses, 38 genes may be key controlled genes related to EBV-transformed lymphocytes, including 22 up-regulated genes(PLK1, E2F1, AURKB, CDK2, PLCG2, CD80, PIK3R3, CDC20, CDC6, AURKA, CENPA, BUB1B, NUP37, MAD2L1, BIRC5, CDC25A, CCNB1, RPA3, HJURP, KIF2C, CDK1, CDCA8) and 16 down-regulated genes(FYN, CD3D, CD4, CD3G, ZAP70, FOS, HCK, CD247, PRKCQ, ITK, LCP2, CXCL1, CD8A, ITGB5, VAV3, CXCR4), which primarily control biological processes such as cell cycle, mitosis, cytokine-cytokine pathway, immunity response and so on. Conclusions Human lymphocyte transformation induced by EB virus is a complicated process, involving multiple-genes and –pathways in virus-host interactions. Global gene expression profile analysis showed that EBV may transform human B lymphocytes by promoting cell cycle and mitosis, inhibiting cell apoptosis, hindering host immune function and secretion of cytokines.