Microarray gene expression profiling and bioinformatics analysis of premature ovarian failure in a rat model

The aim of the present study was to identify differentially expressed genes (DEGs) and their related functions and pathways of major burn injuries, and to prevent the occurrence of complications. The expression profiling of E-GEOD-37069 was downloaded from ArrayExpress Archive. The DEGs of major burn injuries were identified. Gene Ontology (GO) and Kyoto Encyclopedia of Gene and Genomes (KEGG) functional enrichment analysis were then performed for the DEGs. Based on the KEGG database, a pathway relationship network was constructed, and DEGs in significant GO terms and pathways were investigated. Gene signal network and gene co-expression network of these inserted DEGs were constructed. A total of 3,328 DEGs of major burn injuries were identified, including 1,337 up- and 1,991 downregulated DEGs. These DEGs were mainly enriched into various GO terms, including transcription, DNA-dependent, signal transduction and blood coagulation. Moreover, they were also enriched into different pathways, such as hematopoietic cell lineage, metabolic pathway and chemokine signaling pathway. The pathway relationship network was constructed with 72 nodes. The MAPK signaling pathway was the hub node. Based on the same gene symbol, 702 DEGs were obtained, identified in both GO terms and pathways. Finally, the gene signaling network and gene co-expression network were constructed with 391 and 128 nodes, respectively. These identified DEGs, including GNB2, LILRA2, ARRB2 and ARHGEF2, may be potential key genes involved in the treatment of major burn injuries and prevention of complications.

ABSTRACTObjective: Chordoma is a rare tumor with a certain rate of distant metastasis. Skull base and sacrum are the two most common origin sites. This study tends to identify key differentially expressed genes (DEGs) between classical clival and sacral chordomas, provide new targets for future treatment options of chordomas.Methods: The gene expression profiles of GSE95084 and GSE68497 were downloaded from Gene Expression Omnibus database and were analyzed using the limma R package. Function and enrichment analyses of DEGs were performed based on DAVID Database. Protein–protein interaction (PPI) network was constructed using the Cytoscape based on the data collected from STRING online datasets. Hub genes selection and modules analyses of the PPI network were conducted by plugin cytoHubba and MCODE of Cytoscape software, respectively.Result: In total, 728 genes, including 363 up-regulated genes and 365 down-regulated genes were selected as DEGs. Notably, GO analysis showed that both up-regulated and down-regulated DEGs were mainly involved in cell component such as an integral component of the membrane, plasma membrane and extracellular exosome. DEGs were mainly enriched in pathways like Pathways in cancer, PI3K-Akt signaling pathway, Cytokine-cytokine receptor interaction. FYN, ITGB3, ACTN2 and IGF1 were identified as hub genes and they were all involved in focal adhesion signaling pathway. Furthermore, five significant network modules were obtained from the PPI network.Conclusion: This study helps to further understand the molecular characteristics of classic chordomas of two distinct sites. Hub genes FYN, ITGB3, ACTN2, and IGF1, as well as focal adhesion signaling pathway, would be new targets for future treatment options of chordomas.

Synovial sarcoma (SS) is a highly aggressive soft tissue tumor with high risk of local recurrence and metastasis. However, the mechanisms underlying SS metastasis are still largely unclear. The purpose of this study is to screen metastasis-associated biomarkers in SS by integrated bioinformatics analysis. Two mRNA datasets (GSE40018 and GSE40021) were selected to analyze the differentially expressed genes (DEGs). Using the Database for Annotation, Visualization and Integrated Discovery (DAVID) and gene set enrichment analysis (GSEA), functional and pathway enrichment analyses were performed for DEGs. Then, the protein-protein interaction (PPI) network was constructed via the Search Tool for the Retrieval of Interacting Genes (STRING) database. The module analysis of the PPI network and hub genes validation were performed using Cytoscape software. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the hub genes were performed using WEB-based GEne SeT AnaLysis Toolkit (WebGestalt). The expression levels and survival analysis of hub genes were further assessed through Gene Expression Profiling Interactive Analysis (GEPIA) and the Kaplan-Meier plotter database. In total, 213 overlapping DEGs were identified, of which 109 were upregulated and 104 were downregulated. GO analysis revealed that the DEGs were predominantly involved in mitosis and cell division. KEGG pathways analysis demonstrated that most DEGs were significantly enriched in cell cycle pathway. GSEA revealed that the DEGs were mainly enriched in oocyte meiosis, cell cycle and DNA replication pathways. A key module was identified and 10 hub genes (CENPF, KIF11, KIF23, TTK, MKI67, TOP2A, CDC45, MELK, AURKB, and BUB1) were screened out. The expression and survival analysis disclosed that the 10 hub genes were upregulated in SS patients and could result in significantly reduced survival. Our study identified a series of metastasis-associated biomarkers involved in the progression of SS, and may provide novel therapeutic targets for SS metastasis.

Aims: Valosin-containing protein (VCP) participates in signaling pathways essential for cell homeostasis in multiple tissues, yet its role in mammalian heart remains largely unknown. Our recent studies showed that overexpression of VCP protects cardiomyocytes from stress- induced cell death in both in vitro and in vivo , however, it is unknown which target genes and pathways are regulated by VCP through which the heart may be protected from stress-induced injury. Here we provided the first in vivo evidence of the VCP-regulated target genes by microarray gene expression profiling in a transgenic mouse model. Methods and results: We generated a transgenic (TG) mouse that over-expressed 3.5 fold VCP specifically in the heart. Total RNA extracted from the heart tissues from both adult VCP TG and their litter-matched wild type (WT) mice (N=4/group) was assayed by using Affymetrix Mouse Genome 430 2.0 Array, which interrogates over 39,000 transcripts. Differentially expressed genes (DEGs) were defined by p-value ≤ 0.05 and FC (fold change) ≥ 1.5, and totally 581 DEGs were identified between VCP TG and WT. Applying a more stringent criteria (FDR ≤ 0.05 and FC ≥ 1.5), we identified 21 upregulated and 28 downregulated genes in VCP TG mouse hearts compared to WT. Among the top DEGs, there is a significant up-regulation in the genes regulating the stress response and oxidation in VCP TG versus WT, such as a kinase interacting protein by 2.6 folds which is a key regulator of cardiac stress; glutathione peroxidase 1 by 2.2 folds which is an antioxidant enzyme and anti-apoptotic mediators: protein kinase C delta by 2.3 folds and B-cell lymphoma 2 by 2.7 folds. VCP TG mice also exhibits an upregulation in the genes involved in cellular structure and contractility, e.g., alpha 1 actin by 3.3 folds, myosin light chain 9 by 8.2 folds and Tropomyosin 2 by 4.5 folds which is a gene regulating the binding of myosin and actin. Other DEGs include the upregulated-genes regulating cellular amino acid metabolism such as pterin-4 alpha-carbinolamine dehydratase by 9.7folds, phosphatidic acid phosphatase 2c by 3.4 folds and sortilin 1 by 2.4 folds. Conclusion: Significant difference of gene regulation exists between VCP TG and WT in the heart, which may be the mechanism of VCP-mediated cardiac protection.

The present study aimed to reveal the potential genes associated with the pathogenesis of intervertebral disc degeneration (IDD) by analyzing microarray data using bioinformatics. Gene expression profiles of two regions of the intervertebral disc were compared between patients with IDD and controls. GSE70362 containing two groups of gene expression profiles, 16 nucleus pulposus (NP) samples from patients with IDD and 8 from controls, and 16 annulus fibrosus (AF) samples from patients with IDD and 8 from controls, was downloaded from the Gene Expression Omnibus database. A total of 93 and 114 differentially expressed genes (DEGs) were identified in NP and AF samples, respectively, using a limma software package for the R programming environment. Gene Ontology (GO) function enrichment analysis was performed to identify the associated biological functions of DEGs in IDD, which indicated that the DEGs may be involved in various processes, including cell adhesion, biological adhesion and extracellular matrix organization. Pathway enrichment analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) demonstrated that the identified DEGs were potentially involved in focal adhesion and the p53 signaling pathway. Further analysis revealed that there were 35 common DEGs observed between the two regions (NP and AF), which may be further regulated by 6 clusters of microRNAs (miRNAs) retrieved with WebGestalt. The genes in the DEG-miRNA regulatory network were annotated using GO function and KEGG pathway enrichment analysis, among which extracellular matrix organization was the most significant disrupted biological process and focal adhesion was the most significant dysregulated pathway. In addition, the result of protein-protein interaction network modules demonstrated the involvement of inflammatory cytokine interferon signaling in IDD. These findings may not only advance the understanding of the pathogenesis of IDD, but also identify novel potential biomarkers for this disease.

To compare fracture healing therapies, the gene expression profiles of rat fracture samples treated with nail and plate fixation were analyzed at 1 day, 3 days, 1 week, 2 weeks, 4 weeks, and 6 weeks after surgery. The gene expression profiles GSE1685, which include 19 samples, were downloaded from the Gene Expression Omnibus database. After preprocessing, the gene expression profiles were subjected to time series analysis using the Short Time-series Expression Miner software, and the significantly differentially expressed gene (DEG) sets were selected. Further, the distributions of those DEG sets on the corresponding chromosomes were identified using the functional classification tool. Finally, the DEGs were subjected to function and pathway enrichment analysis. DEG analysis indicated that the number of DEGs (854 genes) from nail fixation was significantly lower than that of DEGs (1029 genes) from plate fixation. The DEGs were mainly enriched in cell proliferation, cellular localization, and response to wounding functions. Several critical DEGs expressed during the fracture healing process were screened, and 2 common pathways were enriched for the DEGs in the nail fixation and plate fixation. These DEGs and pathways may be potential targets or predictive markers during fracture healing.

The main aim of this study was to investigate the use of Attenuated Total Reflection Fourier Transform Infrared Spectroscopy (ATR FTIR) and selected chemometric methods to classify eggs in terms of the laying hen farming method, as well as to identify changes in the individual egg compositions during storage. In total, 50 eggs were used for the study; 10 eggs per classes: 0, 1, 2, 3 and rural. Eggs were stored by 29 days period, which was divided on the 10 measuring days in which one egg from each class was tested by recording two FTIR spectra for the shell, albumen and egg yolk. The chemometric analysis, including Hierarchical Cluster Analysis (HCA) and the Principal Component Analysis (PCA), was performed based on the recorded FTIR spectra. Changes in chemical composition during the experiment in individual egg elements were analyzed. Furthermore, by analyzing the graphs (HCA and PCA) obtained by the chemometric analysis, it was noted that the largest changes in the chemical composition of eggs occurred in the shell and yolk, while in the albumen it was less insignificant. The chemometric analysis of the recorded spectra also showed that combination of chemometric methods and FTIR spectroscopy can potentially be used to develop a non-destructive method for classifying eggs in terms of the hen culture method and to monitor of their freshness.

Network and experimental pharmacology on mechanism of Si-Wu-tang improving ovarian function in a mouse model of premature ovarian failure induced by cyclophosphamide

The tumor microenvironment (TME) has been shown to be involved in angiogenesis, tumor metastasis, and immune response, thereby affecting the treatment and prognosis of patients. This study aims to identify genes that are dysregulated in the TME of patients with colon adenocarcinoma (COAD) and to evaluate their prognostic value based on RNA omics data. We obtained 512 COAD samples from the Cancer Genome Atlas (TCGA) database and 579 COAD patients from the independent dataset (GSE39582) in the Gene Expression Omnibus (GEO) database. The immune/stromal/ESTIMATE score of each patient based on their gene expression was calculated using the ESTIMATE algorithm. Kaplan–Meier survival analysis, Cox regression analysis, gene functional enrichment analysis, and protein–protein interaction (PPI) network analysis were performed. We found that immune and stromal scores were significantly correlated with COAD patients’ overall survival (log rank p < 0.05). By comparing the high immune/stromal score group with the low score group, we identified 688 intersection differentially expressed genes (DEGs) from the TCGA dataset (663 upregulated and 25 downregulated). The functional enrichment analysis of intersection DEGs showed that they were mainly enriched in the immune process, cell migration, cell motility, Toll-like receptor signaling pathway, and PI3K-Akt signaling pathway. The hub genes were revealed by PPI network analysis. Through Kaplan–Meier and Cox analysis, four TME-related genes that were significantly related to the prognosis of COAD patients were verified in GSE39582. In addition, we uncovered the relationship between the four prognostic genes and immune cells in COAD. In conclusion, based on the RNA expression profiles of 1091 COAD patients, we screened four genes that can predict prognosis from the TME, which may serve as candidate prognostic biomarkers for COAD.

Study question Can Biosilk be used as scaffold for establishing a 3D-culture system to support attachment and growth of primary cells derived from adult ovarian biopsies? Summary answer The use of recombinant spider silk-based scaffold allowed the formation of 3D-structured ovarioids from both cortex and medulla isolated from 5 different patients. What is known already Fertility in women is adversely affected by several factors, such as age, environmental pollutants and diseases requiring gonadotoxic treatments. Understanding ovarian cell composition and organization may pave the way to novel fertility preservation methods with the ultimate goal of being applied to clinics. So far, there are no clinically established methods for in vitro growth and maturation of human ovarian follicles leading to mature competent oocytes. Therefore, exploring new 3D-culture systems for in vitro reconstruction of ovarian somatic cell niche could lead to development of novel tools to support growth of patient-specific follicles. Study design, size, duration Ovarian tissue was collected from gender reassignment patients (GRP) after informed written consent at Karolinska University Hospital Huddinge from 2019 to 2022. After separation of cortex and medulla, the samples were mechanically and enzymatically dissociated into single-cell suspensions and used to evaluate 3D- and 2D-culture methods. Freshly fixed biopsies from cortex and medulla (3x3x1 mm3) were used as control for the transcriptomic analysis and RNA-FISH assay. Participants/materials, setting, methods Tissue was obtained from five patients aged 23-31 years. Dissociated primary somatic cells seeded on Biosilk-foam scaffolds were kept in culture for 2 weeks, followed by detachment, equal division of the foams and suspension culture for additional 4 weeks (BioSilk-Ovarioids, BSO). BSOs were harvested in PFA and RNAlater (n = 6/patient, respectively) for morphological and transcriptomic analysis. Protein ZO1, and cell type-specific marker genes (AMHR2, PDGFRa, CLDN5, GJA4) were evaluated via immunodetection and RNA-FISH assay, respectively. Main results and the role of chance The sizes of BSOs from both cortex and medulla ranged between 0.5-1 mm at the end of the culture, appearing highly compacted under optical microscope. HE-stained BSO sections revealed that cells were distributed throughout the foams, showing good attachment and distribution. Marker genes were selected for specific cell types [AMHR2-granulosa, PDGFRa-stroma, CLDN5-endothelial, GJA4-perivascular cells (Wagner et al. 2020)] and used to study the representation of different somatic cells in the BSOs. The RNA-FISH analysis confirmed the presence of all cell type-specific marker genes, with predominating presence of stromal cells (PDGFRa). Newly formed ZO1-specific gap junctions were detected in both cortex- and medulla-derived BSOs, appearing mainly in the outer part of the structures. Interestingly, cell layers surrounding the original Biosilk scaffold were observed, especially in medulla-BSOs. Transcriptomic profiling of the samples showed clear separation to three main clusters by principal component analysis: freshly fixed tissue, 2D-cultures, and BSO. Moreover, clustering analysis of differentially expressed genes (DEGs) showed the presence of gene clusters in fresh tissues affected by both 3D/2D-cultures. Further analyses will focus on identification of significantly affected gene ontologies and pathways, which will further guide the optimization of the BSO culture system. Limitations, reasons for caution The tissue was derived from GRPs who always receive androgen treatments prior to surgery. As hormonal treatment may affect the ovarian environment, further trials with untreated patient samples will be needed to generalize the model to fertility preservation patients. Wider implications of the findings The establishment and development of the BSO 3D-culture system may enable the construction of patient-specific clinically significant tools for in vitro folliculogenesis. This would open new avenues for fertility restoration in patients who cannot receive auto-transplants and treatment of infertility in premature ovarian insufficiency if residual follicles remain in tissue. Trial registration number Not applicable

Aims In individuals with focal segmental glomerulosclerosis, identify the important differentially expressed genes (DEGs) relative to healthy control, in kidney tissue samples (glomeruli and tubulointerstitium tissue) and examine their probable role in the molecular mechanism and pathogenesis process of disease. Methods From the Gene Expression Omnibus (GEO) database, raw microarray data generated from kidney tissues from focal segmental glomerulosclerosis patients, and healthy controls patients (GSE121233, GSE125779, GSE129973) were retrieved. Transcription analysis console 4.0 was used to identify DEGs. FUNRICH (Functional enrichment analysis tools) and Enrichr were used to perform functional gene enrichment analysis. Then, Search Tool for Retrieval Interacting Genes (STRING) 10.0 for PPI analysis and cyto scape's for network visualization was used. Further hub genes were identified using the cytohubbaalogorithm plug-in. Then KEGG and REACTOME databases were integrated with Shiny Go and FUNRICH to perform pathway analysis. We used GSEA analysis and associated pathway enrichment by metascape analysis utilizing the molecular complex identification (MCODE) algorithm to discover densely linked network components to further elucidate the likely mechanism of action of related genes in FSGS. The MCODE networks identified for individual gene lists have been gathered. Pathway and process enrichment analysis has been applied to each MCODE component independently, and the three best-scoring terms by p-value have been retained as the functional description of the corresponding components, shown in the tables underneath corresponding network plots further cross validation was done by ORA (over representation analysis) for the commonly (up-regulated) genes including hubgene from all three datasets was done by webgestalt. Finally, we check the raw expression level of all up regulated DEGs, including hub genes, in one main data set (GSE121233) and one validation dataset (GSE129973) to validate the expression of genes identified. We also checked the gene expression level in ERCB (RNA-seq) datasets for various kidney diseases with diabetes including FSGS and other demographic parameters such as GFR and proteinuria, as well as gene expression in gender by using nephroseq. Results 85 DEGs were co-expressed in the three datasets, out of which 16 genes were up-regulated and 69 genes were down regulated in FSGS. DEGs are mostly involved in extracellular matrix organization (biological process), extracellular matrix proteoglycans and integrins cell surface interaction (biological pathways). Protein–protein interaction (PPI) network of 16 upregulated degs in FSGS, identified 43 co expressed genes out of which 20 genes as hub gene where identified by cytohubba, four high ranked hubgenes with greater degree of interaction were (Fibronectin-1, Complement C3 & collagen, type IV, alpha 1, Integrin β6). Metascape analysis results suggests extracellular matrix organization and the genes involved to regulated this biological process are (COL4A1, FN1, ITGB6, LUM, ADAMTS1) shows highest interactions with ECM proteoglycans regulated by genes (COL4A1, FN1, ITGB6, LUM) and integrin mediated signaling pathways regulated by genes (COL4A1, FN1, ITGB6, LUM, ADAMTS1) with enrichment score 134 and 120 with p value p<0.01 and z score 21 and 14. Over representation analysis suggests FN1, C3, ITGB6, COL4A1, C7 and LUMgene is enriched in above stated pathways identified with enrichment ratio more than 50% with p value P<0.0001, GSEA suggests higher expression of genes in these pathways. Three datasets showed the same expression in average as well as raw signals, of upregulated genes including hub gene (LUM,ABCG1, ADAMTS1, C3, MIR4521, PIGR, FN1, COL4A1, MYOF, ITGB6, CLDN1, REN, CDH6, C7, HAVCR1, NR1D1) further each identified genes are checked in nephroseq database at RNA-seq levels for different demographics and other diabetes associated diseases, shown by box plot and bar graph as in our bioinformatics analysis. Conclusion In FSGS, bioinformatics analysis revealed 16 upregulated genes, including 11 crucial genes (HAVCR1, COL4A1, ABCG1, C3, ITGB6, LUM, MYOF, PIGR, C7, FN1, ADAMTS1) and 4 hub-genes (FN1, C3, ITGB6, COL4A1) with high rank and high degree of interaction from three FSGS datasets included in the study, indicating their involvement in FSGS pathways and suggesting they could be potential targets in the disease molecular mechanism.

Rheumatoid arthritis (RA) is one of the most prevalent chronic inflammatory and angiogenic diseases. The aim of this study was to evaluate the anti-inflammatory and anti-angiogenic activities in vitro of eight diterpenoids isolated from Daphne genkwa. LC-MS was used to identify diterpenes isolated from D. genkwa. The anti-inflammatory and anti-angiogenic activities of eight diterpenoids were evaluated on LPS-induced macrophage RAW264.7 cells and TNF-α-stimulated human umbilical vein endothelial cells (HUVECs) using hierarchical cluster analysis (HCA) and principal component analysis (PCA). The eight diterpenes isolated from D. genkwa were identified as yuanhuaphnin, isoyuanhuacine, 12-O-(2'E,4'E-decadienoyl)-4-hydroxyphorbol-13-acetyl, yuanhuagine, isoyuanhuadine, yuanhuadine, yuanhuaoate C and yuanhuacine. All the eight diterpenes significantly down-regulated the excessive secretion of TNF-α, IL-6, IL-1β and NO in LPS-induced RAW264.7 macrophages. However, only 12-O-(2'E,4'E-decadienoyl)-4-hydroxyphorbol-13-acetyl markedly reduced production of VEGF, MMP-3, ICAM and VCAM in TNF-α-stimulated HUVECs. HCA obtained 4 clusters, containing 12-O-(2'E,4'E-decadienoyl)-4-hydroxyphorbol-13-acetyl, isoyuanhuacine, isoyuanhuadine and five other compounds. PCA showed that the ranking of diterpenes sorted by efficacy from highest to lowest was 12-O-(2'E,4'E-decadienoyl)-4-hydroxyphorbol-13-acetyl, yuanhuaphnin, isoyuanhuacine, yuanhuacine, yuanhuaoate C, yuanhuagine, isoyuanhuadine, yuanhuadine. In conclusion, eight diterpenes isolated from D. genkwa showed different levels of activity in LPS-induced RAW264.7 cells and TNF-α-stimulated HUVECs. The comprehensive evaluation of activity by HCA and PCA indicated that of the eight diterpenes, 12-O-(2'E,4'E-decadienoyl)-4-hydroxyphorbol-13-acetyl was the best, and can be developed as a new drug for RA therapy.

Objective To determine whether a periprosthetic joint infections (PJI) patient derived S. aureus is an appropriate candidate tool bacterium for studying the pathogenesis of S. aureus-induced PJI. Methods Whole genome sequencing data of ST1792 was obtained using the Illumina Hiseq platform of a Staphylocuccal. aureus(S. aureus) strain derived from a PJI prosthesis, and gene functional enrichment analysis based on gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) database was performed. Besides, its biofilm formation ability in drainage fluid, synovial fluid and human plasmin were compared to that in experimental cultures, in order to determine differences in biofilm forming ability in different environment. In addition, based on Illumina Hiseq platform, transcriptome analysis of the S. aureus in the three types of fluid above was performed to determine its gene expression profile and functional enrichment analysis of the differentially expressed genes was conducted through the GO and KEGG database. Finally, adaptability in different human fluid of the S. aureus was analyzed with the transcriptome profile and biofilm formation data. Results The genome of ST1792 consisted of 2 718 coding sequences, including main virulence encoding genes and regulation related genes. Functional enrichment showed no sign of significant missing or major recombination in the bacterial genome. The biofilm mass in plasmin was much higher than that in synovial fluid, both significantly higher than the biofilm mass in TSB. But the biofilm mass in drainage fluid was not statistically different from that in TSB. This revealed that the bacterial biofilm phenotype was significantly altered in PJI human fluid. Transcriptomics sequencing revealed that a huge number of genes were differentially expressed in drainage fluid, synovial fluid and human plasmin compared to TSB. Functional enrichment revealed that the bacterial gene expression profile was different in PJI human fluids, which showed the sophisticated adaptation of the bacterium to human fluid environment. Conclusion As a clinical S. aureus isolated from a PJI patient, ST1792 presents distinct phenotypes and adaptations in vivo, so it is a proper candidate for future studies in the pathogenesis of S. aureus induced PJI. Key words: Biofilms; Prosthesis-related infections; Staphylococcus aureus; Genomics

Coptis plants (Ranunculaceae) to have played an important role in the prevention and treatment human diseases in Chinese history. In this study, a multi-level strategy based on metabolic and molecular genetic methods was performed for the characterization of four Coptis herbs (C. chinensis, C. deltoidea, C. omeiensis and C. teeta) using high performance liquid chromatography-ultraviolet (HPLC-UV) and restriction site-associated DNA sequencing (RAD-seq) techniques. Protoberberine alkaloids including berberine, palmatine, coptisine, epiberberine, columbamine, jatrorrhizine, magnoflorine and groenlandicine in rhizomes were identified and determined based on the HPLC-UV method. Among them, berberine was demonstrated as the most abundant compound in these plants. RAD-seq was applied to discover single nucleotide polymorphisms (SNPs) data. A total of 44,747,016 reads were generated and 2,443,407 SNPs were identified in regarding to four plants. Additionally, with respect to complicated metabolic and SNP data, multivariable statistical methods of principal component analysis (PCA) and hierarchical cluster analysis (HCA) were successively applied to interpret the structure characteristics. The metabolic variation and genetic relationship among different Coptis plants were successfully illustrated based on data visualization. Summarily, this comprehensive strategy has been proven as a reliable and effective approach to characterize Coptis plants, which can provide additional information for their quality assessment.

A comparative analysis of gene expression profiles between early and advanced carotid atherosclerotic plaque was performed to identify key genes and pathways involved in the progression of carotid atherosclerotic plaque. Gene expression data set GSE28829 was downloaded from Gene Expression Omnibus, including 13 early and 16 advanced atherosclerotic plaque samples from human carotid. Differentially expressed genes (DEGs) were identified using the package limma of R. Principal component analysis was carried out for the DEGs with package rgl of R. A gene coexpression network was constructed with information from COXPRESdb and then visualized with Cytoscape. Functional enrichment analysis was performed with DAVID and pathway enrichment analysis was done with KEGG. A total of 319 DEGs were identified in the advanced atherosclerotic plaque samples compared with early atherosclerotic plaque samples, including 267 up-regulated genes and 52 down-regulated genes. In the gene coexpression network, TYRO protein tyrosine kinase binding protein was the hub gene with a degree of 23. Functional enrichment analysis and pathway enrichment analysis suggested that the immune response played a critical role in the progression of carotid atherosclerotic plaque. A number of key genes were revealed in carotid atherosclerotic plaque, and are potential biomarkers for diagnosis or treatment. These findings may also guide future research to better decipher the progression of atherosclerosis.