Objectives:Despite the considerable regenerative capacity exhibited by adipose-derived mesenchymal stem cells(ASCs),their genetic and molecular mechanisms remain incompletely understood.Methods:In this study,we analyz...Objectives:Despite the considerable regenerative capacity exhibited by adipose-derived mesenchymal stem cells(ASCs),their genetic and molecular mechanisms remain incompletely understood.Methods:In this study,we analyzed the global gene expression profile of adipose-derived mesenchymal stem cells(ASCs)using microarray analysis and compared it with stromal vascular fraction(SVF)cells.Results:Microarray analysis revealed that ASCs express elevated levels of genes related to the extracellular matrix(ECM;extracellular matrix)and collagen,which are critical components of tissue remodeling and wound healing.Additionally,genes associated with cell growth,differentiation,motility,and plasticity were highly expressed.When compared to stromal vascular fraction(SVF)cells,ASCs demonstrated enrichment of genes involved in anti-inflammatory responses,immune modulation,tissue repair,cell adhesion,and migration processes.Gene Set Enrichment Analysis(GSEA;Gene Set Enrichment Analysis)showed activation of pathways related to angiogenesis,such as vascular endothelial growth factor(VEGF),Integrin,Wnt signaling pathways,transforming growth factor-beta(TGF-β),extracellular matrix(ECM),and matrix metalloproteinase(MMP),highlighting the significant angiogenic potential of ASCs.Gene Ontology(GO;Gene Ontology)analysis further linked ASCs to biological processes associated with the regulation of cell proliferation and muscle cell differentiation.Conclusion:These findings collectively underscore the suitability of adipose-derived mesenchymal stem cells(ASCs)as a promising candidate for regenerative medicine,particularly in applications involving tissue repair,immune modulation,and promotion of angiogenesis.展开更多
The emergence of a huge volume of "omics" data enables a computational approach to the investigation of the biology of cancer. The cancer informatics approach is a useful supplement to the traditional experi...The emergence of a huge volume of "omics" data enables a computational approach to the investigation of the biology of cancer. The cancer informatics approach is a useful supplement to the traditional experimental approach. I reviewed several reports that used a bioinformatics approach to analyze the associations among aging, stem cells, and cancer by microarray gene expression profiling. The high expression of aging- or human embryonic stem cell-related molecules in cancer suggests that certain important mechanisms are commonly underlying aging, stem cells, and cancer. These mechanisms are involved in cell cycle regulation, metabolic process, DNA damage response, apoptosis, p53 signaling pathway, immune/inflammatory response, and other processes, suggesting that cancer is a developmental and evolutional disease that is strongly related to aging. Moreover, these mechanisms demonstrate that the initiation, proliferation, and metastasis of cancer are associated with the deregulation of stem cells. These findings provide insights into the biology of cancer. Certainly, the findings that are obtained by the informatics approach should be justified by experimental validation. This review also noted that next-generation sequencing data provide enriched sources for cancer informatics study.展开更多
AIM： To investigate the mechanism of fibroblast cell proliferation stimulated by the Opisthorchis viverrini excretory/secretory （ES） product. METHODS： NIH-3T3, mouse fibroblast cells were treated with O. viverrini...AIM： To investigate the mechanism of fibroblast cell proliferation stimulated by the Opisthorchis viverrini excretory/secretory （ES） product. METHODS： NIH-3T3, mouse fibroblast cells were treated with O. viverrini ES product by non-contact co-cultured with the adult parasites. Total RNA from NIH-3T3 treated and untreated with O. viverrini was extracted, reverse transcribed and hybridized with the mouse 15K complementary DNA （cDNA） array. The result was analyzed by ArrayVision version 5 and GeneSpring version 5 softwares. After normalization, the ratios of gene expression of parasite treated to untreated NIH-3T3 cells of 2-and more-fold upregulated was defined as the differentially expressed genes. The expression levels of the signal transduction genes were validated by semiquantitative SYBR-based real-time RT-PCR. RESULTS： Among a total of 15 000 genes/ESTs, 239 genes with established cell proliferation-related function were 2 fold-and more-up-regulated by O. viverrini ES product compared to those in cells without exposure to the parasitic product. These genes were classified into groups including energy and metabolism, signal transduction, protein synthesis and translation, matrix and structural protein, transcription control, cell cycle and DNA replication. Moreover, the expressions of serinethreonine kinase receptor, receptor tyrosine kinase and collagen production-related genes were up-regulated by O.viverrini ES product, The expression level of signal transduction genes, pkC, pdgfra, jak 1, eps 8, tgfβ 1/4,strap and h ras measured by real-time RT-PCR confirmed their expression levels to those obtained from cDNA array. However, only the up-regulated expression of pkC,eps 8 and tgfβ3 1/4 which are the downstream signaling molecules of either epidermal growth factor （EGF） or transforming growth factor-β （TGF-β） showed statistical significance （P 〈 0.05）.CONCLUSION： O. viverrini ES product stimulates the significant changes of gene expression in several functional categories and these mainly include transcripts related to cell proliferation. The TGF-β and EGF signal transduction pathways are indicated as the possible pathways of O. viverrini-driven cell proliferation.展开更多
Objective: Ajoene, a major compound extracted from crashed garlic, has been shown to have antitumor, antimycotic, antimicrobial, antimutagenic functions in vivo or in vitro and treated as a potential antitumor drug. H...Objective: Ajoene, a major compound extracted from crashed garlic, has been shown to have antitumor, antimycotic, antimicrobial, antimutagenic functions in vivo or in vitro and treated as a potential antitumor drug. However, the molecular mechanisms underlying the tumor cytotoxicity of ajoene and even garlic substances are poorly defined. In the present study, we aimed to generate gene expression profiles of HL-60 cell treated by ajoene. Methods: A cDNA microarray presenting 2400 of genes amplified from human leukocyte cDNA library was constructed and the gene expression profiles of HL-60 cell induced by ajoene were generated. Results: After data analysis, 28 differentially expressed genes were identified and sequenced. These genes include 21 known genes and 7 ESTs. Most of the known genes are related to cell apoptosis, such as secretory granule (PRG1), beta-2 microglobulin (B2M), 16S ribosomal RNA gene and ribosomal protein S12. Several genes are related to cell differentiation, including the genes similar to H3 histone and ribosomal protein L31. Northern blot analysis was used to verify and quantify the expression of selected genes. Conclusion: Ajoene can induce HL-60 cell apoptosis significantly and may play a role in differentiation. cDNA microarray technology can be a valuable tool to gain insight into molecular events of pharmacological mechanism of herbal medicine.展开更多
Objective: To establish gene expression profiles associated with malignant progression of ganglioglioma. Methods: The primary and two recurrent glioma specimens were collected intraoperatively from the same patient wh...Objective: To establish gene expression profiles associated with malignant progression of ganglioglioma. Methods: The primary and two recurrent glioma specimens were collected intraoperatively from the same patient who experienced tumor transformation into anaplastic astrocytoma and glioblastoma multiform for the first and second recurrence respectively. Gene expression was assayed through cDNA array and bioinformatics analysis. Results: A total of 197 differentially expressed genes with differential ratio value more than 3 compared with normal brain tissue were obtained. Among 109 functionally denned genes, those associated with development ranked the first by frequency, followed by genes associated with metabolism, differentiation, signal transduction and so on. As a result of cluster analysis among 368 genes, eleven genes were up regulated with malignant progression, while six genes were down regulated. Conclusion: Gene expression profiles associated with malignant progression of glioma were successfully established, which provides a powerful tool for research on molecular mechanisms of malignant progression of gliomas.展开更多
<i><span style="font-family:Verdana;"><i>Diabetes mellitus</i></span><i></i></i><span style="font-family:Verdana;"> is a chronic disease that i...<i><span style="font-family:Verdana;"><i>Diabetes mellitus</i></span><i></i></i><span style="font-family:Verdana;"> is a chronic disease that impacts the homeostasis of blood sugar levels caused by loss or defect of insulin-producing β-cells in the Islets of Langerhans.</span> <i><span color:black;"=""><span style="font-family:Verdana;"><i>Type 1 diabetes</i></span><i></i></span></i><span style="font-family:Verdana;"> (</span><i><i></i><i><span style="font-family:Verdana;">T1D</span></i><i></i></i><span style="font-family:Verdana;">)</span><i><span color:black;"=""> </span></i><span style="font-family:Verdana;">is caused by auto-immune mediated destruction of β-cells,</span> <span color:black;"=""><span style="font-family:Verdana;">whereas in </span><i><i></i><i><span style="font-family:Verdana;">T2D</span></i><i></i></i></span><span style="font-family:Verdana;">, insulin is produced but used inefficiently.</span><span color:black;"=""> <i><i></i><i><span style="font-family:Verdana;">T2D</span></i><i></i></i></span><span style="font-family:Verdana;"> accounts for 90% of people with diabetes worldwide (</span><i><i></i><i><span style="font-family:Verdana;">WHO</span></i><i></i></i><i> </i><span style="font-family:Verdana;">1999)</span><span style="font-family:Verdana;"> and is</span> <span style="font-family:Verdana;">the fastest increasing disease worldwide (</span><span style="font-family:Verdana;"><a href="https://diabetesatlas.org/en/" target="_blank">https://diabetesatlas.org/en/</a></span><span style="font-family:Verdana;">)</span><span color:black;"=""><span style="font-family:Verdana;">. For an improved understanding of the pathomechanism of diabetes, profound knowledge of pancreas organogenesis and the associated gene regulatory networks is required. Therefore, we dissected and profiled the pancreatic endodermal and non-endodermal compartment between the embryonic stages (E) 12.5 and E 15.5 when progenitor cells commit to their different pancreatic lineages. Our associated study mined the global mRNA expression profile to increase the understanding of the secondary transition, endodermal-non-endodermal tissue interaction, and diabetic-related gene regulation. Furthermore, we validated 635 regulated pancreatic genes using the publicly available </span><i><i></i><i><span style="font-family:Verdana;">GenePaint.org</span></i><span color:black;"=""><span style="font-family:Verdana;">, respective </span><i><span style="font-family:Verdana;">gp3.mpg.de</span></i></span><i></i></i></span><span style="font-family:Verdana;"> to evaluate genes associated with genetic variants in Single-nucleotide polymorphism (SNP) related to </span><i><i></i><i><span style="font-family:Verdana;">T2D</span></i><i></i></i><span style="font-family:Verdana;">.</span>展开更多
Background:With growing interest in space exploration,understanding microgravity’s impact on human health is essential.This study aims to investigate gene expression changes and migration and invasion potential infive...Background:With growing interest in space exploration,understanding microgravity’s impact on human health is essential.This study aims to investigate gene expression changes and migration and invasion potential infive thyroid-related cell lines cultured under simulated microgravity.Methods:Five thyroid-related cell lines—normal thyrocytes(Nthy-ori 3-1),papillary thyroid cancer(PTC)cells(SNU-790,TPC-1),poorly differentiated thyroid cancer cell(BCPAP),and anaplastic thyroid cancer cell(SNU-80)—were cultured under simulated microgravity(10-3 g)using a clinostat.Differentially expressed genes(DEGs)were analyzed using cDNA microarray,followed by functional annotation and assessment of aggressiveness via Transwell migration and invasion assays.Results:DEG analysis under simulated microgravity revealed distinct gene expression profiles by gravity condition,with 2980 DEGs in SNU-790,1033 in BCPAP,562 in TPC-1,477 in Nthy-ori 3-1,and 246 in SNU-80,as confirmed by hierarchical clustering.In PTC cell lines(SNU-790,TPC-1),G2–M phase–related genes were upregulated.In non-PTC cell lines(BCPAP,SNU-80),genes associated with innate immune response,Toll-like receptor signaling,were upregulated,whereas Hypoxia-Inducible Factor 1-alpha(HIF-1α)signaling-related genes were downregulated.Additionally,under simulated microgravity,significant migration was observed in SNU-790(3×104 cells)and BCPAP(2×104 and 3×104),while significant invasion occurred in SNU-790,Nthy-ori 3-1,and BCPAP at a seeding density of 2×104.Other conditions showed no significant differences.Conclusion:This study comprehensively evaluates the effects of simulated microgravity using a diverse panel of thyroid-related cell lines.Thesefindings provide valuable insight into how microgravity could influence cancer biology,emphasizing the importance of further research on cancer behavior in space environments and its implications for human health during long-term space missions.展开更多
Infection with different viruses threatens the health of animals in the livestock and poultry industry.Immunopotentia-tors can increase natural immunity and vaccination efficacy;however,most are expensive chemical and...Infection with different viruses threatens the health of animals in the livestock and poultry industry.Immunopotentia-tors can increase natural immunity and vaccination efficacy;however,most are expensive chemical and biological compounds with questionable safety.Traditional Chinese medicines(TCMs)such as Yupingfeng(YPF),a well-known immunomodulatory remedy,provide healthy alternatives to such agents.The aim of this study was to examine the therapeutic properties of Qi-Gen powder(QG)and compare them with those of YPF.The immune organ index,cytokine levels,and other indicators were utilized to evaluate the effects of QG in an immunosuppression mouse model.QG was further assessed for its ability to enhance vaccine effectiveness in chickens immunized for Newcastle disease virus(NDV).Potential therapeutic mechanisms and targets of QG were examined in the breast cancer cell line MCF-7 using microarray technology combined with the TCM systems pharmacology database of known targets.Compared with model controls,QG improved immunological function,outperforming YPF in mice.QG also enhanced the immunological response to NDV vaccine in immune organs and increased feed intake of chickens.Further research is needed to validate the link between the PI3K/Akt/GSK-3 pathway and the immune-boosting effects of QG.展开更多
AIM： To compare gene expression profiles of pancreatic adenocarcinoma tissue specimens, human pancreatic and colon adenocarcinoma and leukemia cell lines and normal pancreas samples in order to distinguish differenti...AIM： To compare gene expression profiles of pancreatic adenocarcinoma tissue specimens, human pancreatic and colon adenocarcinoma and leukemia cell lines and normal pancreas samples in order to distinguish differentially expressed genes and to validate the differential expression of a subset of genes by quantitative real-time RT-PCR （RT-QPCR） in endoscopic ultrasound-guided fine needle aspiration （EUS-guided FNA） specimens.METHODS： Commercially dedicated cancer cDNA macroarrays （Atlas Human Cancer 1.2） containing 1176 genes were used. Different statistical approaches （hierarchical clustering, principal component analysis （PCA） and SAM） were used to analyze the expression data. RT-QPCR and immunohistochemical studies were used for validation of results.RESULTS： RT-QPCR validated the increased expression of LCN2 （lipocalin 2） and for the first time PLAT （tissue-type plasminogen activator or tPA） in malignant pancreas as compared with normal pancreas. Immunohistochemical analysis confirmed the increased expression of LCN2 protein localized in epithelial cells of ducts invaded by carcinoma. The analysis of PLAT and LCN2 transcripts in 12 samples obtained through EUS-guided FNA from patients with pancreatic adenocarcinoma showed significantly increased expression levels in comparison with those found in normal tissues, indicating that a sufficient amount of high quality RNA can be obtained with this technique.CONCLUSION： Expression profiling is a useful method to identify biomarkers and potential target genes. Molecular analysis of EUS-guided FNA samples in pancreatic cancer appears as a valuable strategy for the diagnosis of pancreatic adenocarcinomas.展开更多
Background Early stage （FIGO stage Ⅰ-Ⅱ） endometrioid endometrial adenocarcinoma （EEA） is very common in clinical practice.However,patients with the early stage EEA show various clinical behaviors due to biologic...Background Early stage （FIGO stage Ⅰ-Ⅱ） endometrioid endometrial adenocarcinoma （EEA） is very common in clinical practice.However,patients with the early stage EEA show various clinical behaviors due to biological heterogeneity.Hence,we aimed to discover distinct classes of tumors based on gene expression profiling,and analyze whether the molecular classification correlated with the histopathological stages or other clinical parameters.Methods Hierarchical clustering was performed for class discovery in 28 eady stage EEA samples using a special cDNA microarray chip containing 492 genes designed for endometrial cancer.Correlations between clinicopathologic parameters and our classification were analyzed.And the significance analysis of microarrays （SAM） array was used to identify the signature genes according to the tumor grade and myometrial invasion.Results Three tumor subtypes （subtypes Ⅰ,Ⅱ and Ⅲ） were identified by hierarchical clustering,each subtype had different clinicopathological factors,such as tumor grade,myometrial invasion status,and FIGO stage.Moreover,SAM analysis showed 34 up-regulated genes in high grade tumors,and 38 up-regulated genes and 1 down-regulated in deep myometrial invasive tumors.The overlap genes between these two high-risk factors were markedly up-regulated in subtype Ⅰ,but down-regulated in subtype Ⅲ.Conclusion We have identified novel molecular subtypes in early stage EEA.Differential gene signatures characterize each tumor subtype,which could be used for recognizing the tumor risk and providing a basis for further treatment stratification.展开更多
OBJECTIVE: To evaluate the clinical efficacy and safety of Shenzhu Guanxin recipe granules(参术冠心颗粒, SGR) in treating patients with intermediate coronary lesions(ICL), and to investigate the potential mechanism th...OBJECTIVE: To evaluate the clinical efficacy and safety of Shenzhu Guanxin recipe granules(参术冠心颗粒, SGR) in treating patients with intermediate coronary lesions(ICL), and to investigate the potential mechanism though a transcriptome sequencing approach. METHODS: ICL patients with Qi deficiency and phlegm stasis were adopted and randomly assigned to a case group or a control by random number generator in a 1∶1 randomization ratio to evaluate the clinical efficacy. RESULTS: There was no significant difference between the two groups in coronary computed tomography angiography related indexes in the two groups before and after intervention. Through the gene chip expression analysis, it is finally concluded that there are 355 differential mRNAs(190 up-regulated genes and 165 down regulated genes) when compared the SGR group and placebo group. Through protein-protein interaction network analysis of differentially expressed genes, 10 hub genes were finally obtained: CACNA2D2, CACNA2D3, DNAJC6, FGF12, SGSM2, CACNA1G, LRP6, KIF25, OXTR, UPB1. CONCLUSIONS: SGR combined with Western Medicine can be safely used to treat ICL patients with Qi deficiency and phlegm stasis. The possible mechanism of action and relevant gene loci and pathway were proposed.展开更多
Cysteine-rich polycomb-like(CPP)is a small gene family in plants,which plays key role in plant development and stress response.Although CPP transcription factors have been characterized in several other plant species,...Cysteine-rich polycomb-like(CPP)is a small gene family in plants,which plays key role in plant development and stress response.Although CPP transcription factors have been characterized in several other plant species,a genome-wide characterization of the CPP gene family has been absent in Camellia sinensis.In this study,we totally identified 7,8,and 8 non-redundant CsCPP genes in three published genomes,including Camellia sinensis var.assamica cv.Yunkang-10(CSA-YK10),Camellia sinensis var.sinensis cv.Biyun(CSS-BY)and Camellia sinensis var.sinensis cv.Shuchazao(CSS-SCZ).CPP proteins from tea tree and other plant species were classified into three groups,which were further divided into four subgroups based on phylogenetic relationships.Most CPP genes in the same subgroup had similar gene structures and conserved motifs.The cis-acting elements analysis indicated that CPP genes might be involved in plant growth,development and stress responses.Analysis of gene expression using qRT-PCR experiments validated that CPP genes exhibited different expression patterns across the examined tissues.All the genes were expressed differentially in a range of tissues,indicating that CPPs were involved in a range of developmental and physiological processes.This study has obtained new insights into the evolution and function of the CPP gene family in the growth and development of tea plants,and also provide candidate genes for further functional characterization in tea tree.展开更多
Objective: The effect of Chuanzhi Fang (ZGC) on the whole genome expression profile of RAW264.7 cells activated by lipopolysaccharide (LPS) was analyzed, and to explore the possible mechanism of action and core target...Objective: The effect of Chuanzhi Fang (ZGC) on the whole genome expression profile of RAW264.7 cells activated by lipopolysaccharide (LPS) was analyzed, and to explore the possible mechanism of action and core target of this formula on macrophage inflammatory injury at the overall level. Methods: A model of LPS-induced inflammation in RAW264.7 cells was constructed, and the effect of ZGC intervention on the genome-wide expression of inflammatory macrophages 3was examined by gene microarray technology, GO/KEGG enrichment analysis was performed for significantly differentially expressed genes among each group. Results: The results of genome-wide expression profiling microarray analysis showed that the ZGC intervention group upregulated the expression of 5 genes including C4bp and inhibited the expression of 22 genes including Mgat3, Psma6, and Siglecg relative to the LPS model group. KEGG signaling pathway analysis results showed that ZGC mainly acted through cytokine receptor interaction and the C-type lectin receptor signaling pathway. Conclusion: ZGC can interfere with the abnormal expression of 27 genes in inflammatory macrophages, and the related genes may exert corresponding anti-inflammatory effects by affecting cytokine receptor interactions, C-type lectin receptor signaling pathway, and TLR4/ NF-κB signaling pathway.展开更多
Transcriptome deep sequencing(RNA‐seq)hasbecome a routine method for global geneexpression profiling.However,its application tolarge‐scale experiments remains limited by costand labor constraints.Here we describe am...Transcriptome deep sequencing(RNA‐seq)hasbecome a routine method for global geneexpression profiling.However,its application tolarge‐scale experiments remains limited by costand labor constraints.Here we describe amassively parallel 3′end RNA‐seq(MP3RNA‐seq)method that introduces unique samplebarcodes during reverse transcription to permitsample pooling immediately following this initialstep.MP3RNA‐seq allows for handling of hun-dreds of samples in a single experiment,at acost of about$6 per sample for libraryconstruction and sequencing.MP3RNA‐seq iseffective for not only high‐throughput geneexpression profiling,but also genotyping.Todemonstrate its utility,we applied MP3RNA‐seqto 477 double haploid lines of maize.We iden-tified 19,429 genes expressed in at least 50%ofthe lines and 35,836 high‐quality singlenucleotide polymorphisms for genotypinganalysis.Armed with these data,we performedexpression and agronomic trait quantitativetrait locus(QTL)mapping and identified 25,797expression QTLs for 15,335 genes and 21 QTLsfor plant height,ear height,and relative earheight.We conclude that MP3RNA‐seq is highlyreproducible,accurate,and sensitive forhigh‐throughput gene expression profiling andgenotyping,and should be generally applicableto most eukaryotic species.展开更多
Multiple myeloma(MM)is an aggressive plasma cell malignancy with high degrees of variability in outcome,some patients experience long remissions,whilst others survive less than two years from diagnosis.Therapy refract...Multiple myeloma(MM)is an aggressive plasma cell malignancy with high degrees of variability in outcome,some patients experience long remissions,whilst others survive less than two years from diagnosis.Therapy refractoriness and relapse remain challenges in MM management,and there is a need for improved prognostication and targeted therapies to improve overall survival(OS).The past decade has seen a surge in gene expression profiling(GEP)studies which have elucidated the molecular landscape of MM and led to the identification of novel gene signatures that predict OS and outperform current clinical predictors.In this review,we discuss the limitations of current prognostic tools and the emerging role of GEP in diagnostics and in the development of personalised medicine approaches to combat drug resistance.展开更多
To determine cancer pathway activities in nine types of primary tumors and NCI60 cell lines, we applied an in silico approach by examining gene signatures reflective of consequent pathway activation using gene express...To determine cancer pathway activities in nine types of primary tumors and NCI60 cell lines, we applied an in silico approach by examining gene signatures reflective of consequent pathway activation using gene expression data. Supervised learning approaches predicted that the Ras pathway is active in -70% of lung adenocarcinomas but inactive in most squamous cell carcinomas, pulmonary carcinoids, and small cell lung carcinomas. In contrast, the TGF-β, TNF-α, Src, Myc, E2F3, and β-catenin pathways are inactive in lung adenocarcinomas. We predicted an active Ras, Myc, Src, and/or E2F3 pathway in significant percentages of breast cancer, colorectal carcinoma, and gliomas. Our results also suggest that Ras may be the most prevailing oncogenic pathway. Additionally, many NCI60 cell lines exhibited a gene signature indicative of an active Ras, Myc, and/or Src, but not E2F3, β-catenin, TNF-α, or TGF-β pathway. To our knowledge, this is the first comprehensive survey of cancer pathway activities in nine major tumor types and the most widely used NCI60 cell lines. The ＂gene expression pathway signatures＂ we have defined could facilitate the understanding of molecular mechanisms in cancer development and provide guidance to the selection of appropriate cell lines for cancer research and pharmaceutical compound screening.展开更多
Stamen is a unique plant organ wherein germ cells or microsporocytes that commit to meiosis are initiated from somatic cells during its early developmental process. While genes determining stamen identity are known ac...Stamen is a unique plant organ wherein germ cells or microsporocytes that commit to meiosis are initiated from somatic cells during its early developmental process. While genes determining stamen identity are known according to the ABC model of floral development, little information is available on how these genes affect germ cell initiation. By using the Affymetrix GeneChip Rice Genome Array to assess 51 279 tran- scripts, we established a dynamic gene expression profile （GEP） of the early developmental process of rice （Oryza sativa） stamen. Systematic analysis of the GEP data revealed novel expression patterns of some developmentally important genes including meiosis-, tapetum-, and phytohormone-related genes. Following the finding that a substantial amount of nuclear genes encoding photosynthetic proteins are ex- pressed at the low levels in early rice stamen, through the ChlP-seq analysis we found that a C-class MADS box protein, OsMADS58, binds many nuclear-encoded genes participated in photosystem and light reac- tions and the expression levels of most of them are increased when expression of OsMADS58 is downre- gulated in the osmads58 mutant. Furthermore, more pro-chloroplasts are observed and increased signals of reactive oxygen species are detected in the osmads58 mutant anthers. These findings implicate a novel link between stamen identity determination and hypoxia status establishment.展开更多
Fasciclin-like arabinogalactan proteins(FLAs),a subclass of arabinogalactan proteins(AGPs),are usually involved in cell development in plants.To investigate the expression profiling as well
Gene expression profiling at early stages(0～2 DPA) of fiber development in Gossypium hirsutum identified a number of transcription factors which were down regulated in fiberless mutants relative to wild type controls...Gene expression profiling at early stages(0～2 DPA) of fiber development in Gossypium hirsutum identified a number of transcription factors which were down regulated in fiberless mutants relative to wild type controls and which could play a role in controlling early fiber development.Chief among these was GhMYB25,a Mixta-like MYB gene.Transgenic GhMYB25-silenced cotton展开更多
OBJECTIVE:To explore electro-acupuncture's(EA's)effect on gene expression in heart of rats with stress-induced pre-hypertension and try to reveal its biological mechanism based on gene chip technology.METHODS:...OBJECTIVE:To explore electro-acupuncture's(EA's)effect on gene expression in heart of rats with stress-induced pre-hypertension and try to reveal its biological mechanism based on gene chip technology.METHODS:Twenty-seven Wistar male rats were randomly divided into 3 groups.The stress-induced hypertensive rat model was prepared by electric foot-shocks combined with generated noise.Molding cycle lasted for 14 days and EA intervene was applied on rats in model + EA group during model preparation.Rat Gene 2.0 Sense Target Array technology was used for the determination of gene expression profiles and the screened key genes were verified by real-time quantitative polymerase chain reaction(RT-PCR) method.RESULTS:Compared with blank control group,390 genes were changed in model group;compared with model control group,330 genes were changed in model + EA group.Significance analysis of gene function showed that the differentially expressed genes are those involved in biological process,molecular function and cellular components.RT-PCR result of the screened key genes is consistent with that of gene chip test.CONCLUTION:EA could significantly lower blood pressure of stress-induced pre-hypertension rats and affect its gene expression profile in heart.Genes that related to the contraction of vascular smooth muscle may be involved in EA's anti-hypertensive mechanism.展开更多
基金supported through National Research Foundation(NRF)of Korea grants funded by the Korean Government(No.NRF-2022R1F1A1064405)the research fund of Catholic Kwandong University and Catholic Kwandong University International St.Mary’s Hospital for S.-W Kim.
文摘Objectives:Despite the considerable regenerative capacity exhibited by adipose-derived mesenchymal stem cells(ASCs),their genetic and molecular mechanisms remain incompletely understood.Methods:In this study,we analyzed the global gene expression profile of adipose-derived mesenchymal stem cells(ASCs)using microarray analysis and compared it with stromal vascular fraction(SVF)cells.Results:Microarray analysis revealed that ASCs express elevated levels of genes related to the extracellular matrix(ECM;extracellular matrix)and collagen,which are critical components of tissue remodeling and wound healing.Additionally,genes associated with cell growth,differentiation,motility,and plasticity were highly expressed.When compared to stromal vascular fraction(SVF)cells,ASCs demonstrated enrichment of genes involved in anti-inflammatory responses,immune modulation,tissue repair,cell adhesion,and migration processes.Gene Set Enrichment Analysis(GSEA;Gene Set Enrichment Analysis)showed activation of pathways related to angiogenesis,such as vascular endothelial growth factor(VEGF),Integrin,Wnt signaling pathways,transforming growth factor-beta(TGF-β),extracellular matrix(ECM),and matrix metalloproteinase(MMP),highlighting the significant angiogenic potential of ASCs.Gene Ontology(GO;Gene Ontology)analysis further linked ASCs to biological processes associated with the regulation of cell proliferation and muscle cell differentiation.Conclusion:These findings collectively underscore the suitability of adipose-derived mesenchymal stem cells(ASCs)as a promising candidate for regenerative medicine,particularly in applications involving tissue repair,immune modulation,and promotion of angiogenesis.
文摘The emergence of a huge volume of "omics" data enables a computational approach to the investigation of the biology of cancer. The cancer informatics approach is a useful supplement to the traditional experimental approach. I reviewed several reports that used a bioinformatics approach to analyze the associations among aging, stem cells, and cancer by microarray gene expression profiling. The high expression of aging- or human embryonic stem cell-related molecules in cancer suggests that certain important mechanisms are commonly underlying aging, stem cells, and cancer. These mechanisms are involved in cell cycle regulation, metabolic process, DNA damage response, apoptosis, p53 signaling pathway, immune/inflammatory response, and other processes, suggesting that cancer is a developmental and evolutional disease that is strongly related to aging. Moreover, these mechanisms demonstrate that the initiation, proliferation, and metastasis of cancer are associated with the deregulation of stem cells. These findings provide insights into the biology of cancer. Certainly, the findings that are obtained by the informatics approach should be justified by experimental validation. This review also noted that next-generation sequencing data provide enriched sources for cancer informatics study.
基金the Thailand Research Fund, Grant No. TRG4880004 and the Grants of Khon Kaen University 2004 and 2006 Grants-in-Aid for Scientific Research from the Ministry of Education, Science, Sports and Culture of Japan the Grant for Student of Liver Fluke and Cholangiocarcinoma Research Center, Faculty of Medicine, Khon Kaen University, 2003-2005
文摘AIM： To investigate the mechanism of fibroblast cell proliferation stimulated by the Opisthorchis viverrini excretory/secretory （ES） product. METHODS： NIH-3T3, mouse fibroblast cells were treated with O. viverrini ES product by non-contact co-cultured with the adult parasites. Total RNA from NIH-3T3 treated and untreated with O. viverrini was extracted, reverse transcribed and hybridized with the mouse 15K complementary DNA （cDNA） array. The result was analyzed by ArrayVision version 5 and GeneSpring version 5 softwares. After normalization, the ratios of gene expression of parasite treated to untreated NIH-3T3 cells of 2-and more-fold upregulated was defined as the differentially expressed genes. The expression levels of the signal transduction genes were validated by semiquantitative SYBR-based real-time RT-PCR. RESULTS： Among a total of 15 000 genes/ESTs, 239 genes with established cell proliferation-related function were 2 fold-and more-up-regulated by O. viverrini ES product compared to those in cells without exposure to the parasitic product. These genes were classified into groups including energy and metabolism, signal transduction, protein synthesis and translation, matrix and structural protein, transcription control, cell cycle and DNA replication. Moreover, the expressions of serinethreonine kinase receptor, receptor tyrosine kinase and collagen production-related genes were up-regulated by O.viverrini ES product, The expression level of signal transduction genes, pkC, pdgfra, jak 1, eps 8, tgfβ 1/4,strap and h ras measured by real-time RT-PCR confirmed their expression levels to those obtained from cDNA array. However, only the up-regulated expression of pkC,eps 8 and tgfβ3 1/4 which are the downstream signaling molecules of either epidermal growth factor （EGF） or transforming growth factor-β （TGF-β） showed statistical significance （P 〈 0.05）.CONCLUSION： O. viverrini ES product stimulates the significant changes of gene expression in several functional categories and these mainly include transcripts related to cell proliferation. The TGF-β and EGF signal transduction pathways are indicated as the possible pathways of O. viverrini-driven cell proliferation.
文摘Objective: Ajoene, a major compound extracted from crashed garlic, has been shown to have antitumor, antimycotic, antimicrobial, antimutagenic functions in vivo or in vitro and treated as a potential antitumor drug. However, the molecular mechanisms underlying the tumor cytotoxicity of ajoene and even garlic substances are poorly defined. In the present study, we aimed to generate gene expression profiles of HL-60 cell treated by ajoene. Methods: A cDNA microarray presenting 2400 of genes amplified from human leukocyte cDNA library was constructed and the gene expression profiles of HL-60 cell induced by ajoene were generated. Results: After data analysis, 28 differentially expressed genes were identified and sequenced. These genes include 21 known genes and 7 ESTs. Most of the known genes are related to cell apoptosis, such as secretory granule (PRG1), beta-2 microglobulin (B2M), 16S ribosomal RNA gene and ribosomal protein S12. Several genes are related to cell differentiation, including the genes similar to H3 histone and ribosomal protein L31. Northern blot analysis was used to verify and quantify the expression of selected genes. Conclusion: Ajoene can induce HL-60 cell apoptosis significantly and may play a role in differentiation. cDNA microarray technology can be a valuable tool to gain insight into molecular events of pharmacological mechanism of herbal medicine.
基金This work was supported by the NationalNatural Science Foundation of China(No.30070772)
文摘Objective: To establish gene expression profiles associated with malignant progression of ganglioglioma. Methods: The primary and two recurrent glioma specimens were collected intraoperatively from the same patient who experienced tumor transformation into anaplastic astrocytoma and glioblastoma multiform for the first and second recurrence respectively. Gene expression was assayed through cDNA array and bioinformatics analysis. Results: A total of 197 differentially expressed genes with differential ratio value more than 3 compared with normal brain tissue were obtained. Among 109 functionally denned genes, those associated with development ranked the first by frequency, followed by genes associated with metabolism, differentiation, signal transduction and so on. As a result of cluster analysis among 368 genes, eleven genes were up regulated with malignant progression, while six genes were down regulated. Conclusion: Gene expression profiles associated with malignant progression of glioma were successfully established, which provides a powerful tool for research on molecular mechanisms of malignant progression of gliomas.
文摘<i><span style="font-family:Verdana;"><i>Diabetes mellitus</i></span><i></i></i><span style="font-family:Verdana;"> is a chronic disease that impacts the homeostasis of blood sugar levels caused by loss or defect of insulin-producing β-cells in the Islets of Langerhans.</span> <i><span color:black;"=""><span style="font-family:Verdana;"><i>Type 1 diabetes</i></span><i></i></span></i><span style="font-family:Verdana;"> (</span><i><i></i><i><span style="font-family:Verdana;">T1D</span></i><i></i></i><span style="font-family:Verdana;">)</span><i><span color:black;"=""> </span></i><span style="font-family:Verdana;">is caused by auto-immune mediated destruction of β-cells,</span> <span color:black;"=""><span style="font-family:Verdana;">whereas in </span><i><i></i><i><span style="font-family:Verdana;">T2D</span></i><i></i></i></span><span style="font-family:Verdana;">, insulin is produced but used inefficiently.</span><span color:black;"=""> <i><i></i><i><span style="font-family:Verdana;">T2D</span></i><i></i></i></span><span style="font-family:Verdana;"> accounts for 90% of people with diabetes worldwide (</span><i><i></i><i><span style="font-family:Verdana;">WHO</span></i><i></i></i><i> </i><span style="font-family:Verdana;">1999)</span><span style="font-family:Verdana;"> and is</span> <span style="font-family:Verdana;">the fastest increasing disease worldwide (</span><span style="font-family:Verdana;"><a href="https://diabetesatlas.org/en/" target="_blank">https://diabetesatlas.org/en/</a></span><span style="font-family:Verdana;">)</span><span color:black;"=""><span style="font-family:Verdana;">. For an improved understanding of the pathomechanism of diabetes, profound knowledge of pancreas organogenesis and the associated gene regulatory networks is required. Therefore, we dissected and profiled the pancreatic endodermal and non-endodermal compartment between the embryonic stages (E) 12.5 and E 15.5 when progenitor cells commit to their different pancreatic lineages. Our associated study mined the global mRNA expression profile to increase the understanding of the secondary transition, endodermal-non-endodermal tissue interaction, and diabetic-related gene regulation. Furthermore, we validated 635 regulated pancreatic genes using the publicly available </span><i><i></i><i><span style="font-family:Verdana;">GenePaint.org</span></i><span color:black;"=""><span style="font-family:Verdana;">, respective </span><i><span style="font-family:Verdana;">gp3.mpg.de</span></i></span><i></i></i></span><span style="font-family:Verdana;"> to evaluate genes associated with genetic variants in Single-nucleotide polymorphism (SNP) related to </span><i><i></i><i><span style="font-family:Verdana;">T2D</span></i><i></i></i><span style="font-family:Verdana;">.</span>
文摘Background:With growing interest in space exploration,understanding microgravity’s impact on human health is essential.This study aims to investigate gene expression changes and migration and invasion potential infive thyroid-related cell lines cultured under simulated microgravity.Methods:Five thyroid-related cell lines—normal thyrocytes(Nthy-ori 3-1),papillary thyroid cancer(PTC)cells(SNU-790,TPC-1),poorly differentiated thyroid cancer cell(BCPAP),and anaplastic thyroid cancer cell(SNU-80)—were cultured under simulated microgravity(10-3 g)using a clinostat.Differentially expressed genes(DEGs)were analyzed using cDNA microarray,followed by functional annotation and assessment of aggressiveness via Transwell migration and invasion assays.Results:DEG analysis under simulated microgravity revealed distinct gene expression profiles by gravity condition,with 2980 DEGs in SNU-790,1033 in BCPAP,562 in TPC-1,477 in Nthy-ori 3-1,and 246 in SNU-80,as confirmed by hierarchical clustering.In PTC cell lines(SNU-790,TPC-1),G2–M phase–related genes were upregulated.In non-PTC cell lines(BCPAP,SNU-80),genes associated with innate immune response,Toll-like receptor signaling,were upregulated,whereas Hypoxia-Inducible Factor 1-alpha(HIF-1α)signaling-related genes were downregulated.Additionally,under simulated microgravity,significant migration was observed in SNU-790(3×104 cells)and BCPAP(2×104 and 3×104),while significant invasion occurred in SNU-790,Nthy-ori 3-1,and BCPAP at a seeding density of 2×104.Other conditions showed no significant differences.Conclusion:This study comprehensively evaluates the effects of simulated microgravity using a diverse panel of thyroid-related cell lines.Thesefindings provide valuable insight into how microgravity could influence cancer biology,emphasizing the importance of further research on cancer behavior in space environments and its implications for human health during long-term space missions.
基金supported by the Beijing Municipal Science and Technology Commission(grant number:Z191100001619001)Key project at central government level:The ability to establish sustainable use of valuable Chinese medicine resources(grant number:2060302).
文摘Infection with different viruses threatens the health of animals in the livestock and poultry industry.Immunopotentia-tors can increase natural immunity and vaccination efficacy;however,most are expensive chemical and biological compounds with questionable safety.Traditional Chinese medicines(TCMs)such as Yupingfeng(YPF),a well-known immunomodulatory remedy,provide healthy alternatives to such agents.The aim of this study was to examine the therapeutic properties of Qi-Gen powder(QG)and compare them with those of YPF.The immune organ index,cytokine levels,and other indicators were utilized to evaluate the effects of QG in an immunosuppression mouse model.QG was further assessed for its ability to enhance vaccine effectiveness in chickens immunized for Newcastle disease virus(NDV).Potential therapeutic mechanisms and targets of QG were examined in the breast cancer cell line MCF-7 using microarray technology combined with the TCM systems pharmacology database of known targets.Compared with model controls,QG improved immunological function,outperforming YPF in mice.QG also enhanced the immunological response to NDV vaccine in immune organs and increased feed intake of chickens.Further research is needed to validate the link between the PI3K/Akt/GSK-3 pathway and the immune-boosting effects of QG.
基金Supported by Contrat Universite Paul Sabatier,Toulouse,France,ASUPS 2000(N.Vaysse)AOL DRC Hopitaux de Toulouse 2001,(L.Buscail)Region Midi-Pyrenees(L.Buscail)H.Laurell was supported by a grant from European Community Plan 99 ECC QLG3-CT-1999-0908(C.Susini)The Agilent 2100 Bioanalyzer and the phosphoimager(Molecular Dynamics,Sunnyvale,CA,USA)were at the Transcriptome Platform,Toulouse Genopole,and at the molecular biology platform at the Institute Louis Bugnard,IFR31,Toulouse,France,respectively
文摘AIM： To compare gene expression profiles of pancreatic adenocarcinoma tissue specimens, human pancreatic and colon adenocarcinoma and leukemia cell lines and normal pancreas samples in order to distinguish differentially expressed genes and to validate the differential expression of a subset of genes by quantitative real-time RT-PCR （RT-QPCR） in endoscopic ultrasound-guided fine needle aspiration （EUS-guided FNA） specimens.METHODS： Commercially dedicated cancer cDNA macroarrays （Atlas Human Cancer 1.2） containing 1176 genes were used. Different statistical approaches （hierarchical clustering, principal component analysis （PCA） and SAM） were used to analyze the expression data. RT-QPCR and immunohistochemical studies were used for validation of results.RESULTS： RT-QPCR validated the increased expression of LCN2 （lipocalin 2） and for the first time PLAT （tissue-type plasminogen activator or tPA） in malignant pancreas as compared with normal pancreas. Immunohistochemical analysis confirmed the increased expression of LCN2 protein localized in epithelial cells of ducts invaded by carcinoma. The analysis of PLAT and LCN2 transcripts in 12 samples obtained through EUS-guided FNA from patients with pancreatic adenocarcinoma showed significantly increased expression levels in comparison with those found in normal tissues, indicating that a sufficient amount of high quality RNA can be obtained with this technique.CONCLUSION： Expression profiling is a useful method to identify biomarkers and potential target genes. Molecular analysis of EUS-guided FNA samples in pancreatic cancer appears as a valuable strategy for the diagnosis of pancreatic adenocarcinomas.
文摘Background Early stage （FIGO stage Ⅰ-Ⅱ） endometrioid endometrial adenocarcinoma （EEA） is very common in clinical practice.However,patients with the early stage EEA show various clinical behaviors due to biological heterogeneity.Hence,we aimed to discover distinct classes of tumors based on gene expression profiling,and analyze whether the molecular classification correlated with the histopathological stages or other clinical parameters.Methods Hierarchical clustering was performed for class discovery in 28 eady stage EEA samples using a special cDNA microarray chip containing 492 genes designed for endometrial cancer.Correlations between clinicopathologic parameters and our classification were analyzed.And the significance analysis of microarrays （SAM） array was used to identify the signature genes according to the tumor grade and myometrial invasion.Results Three tumor subtypes （subtypes Ⅰ,Ⅱ and Ⅲ） were identified by hierarchical clustering,each subtype had different clinicopathological factors,such as tumor grade,myometrial invasion status,and FIGO stage.Moreover,SAM analysis showed 34 up-regulated genes in high grade tumors,and 38 up-regulated genes and 1 down-regulated in deep myometrial invasive tumors.The overlap genes between these two high-risk factors were markedly up-regulated in subtype Ⅰ,but down-regulated in subtype Ⅲ.Conclusion We have identified novel molecular subtypes in early stage EEA.Differential gene signatures characterize each tumor subtype,which could be used for recognizing the tumor risk and providing a basis for further treatment stratification.
基金the project of Traditional Chinese Medicine Bureau of Guangdong Province:Research on the Mechanism of Shen Shu Guan Xin Fang in Reducing Hypoxia Induced Myocardial Cell Injury by Regulating miR-24 (No. 20221108)Science and Technology Projects in Guangzhou:Exploring the Intervention of Shenzhu Guanxin Formula on Myocardial Ischemia Based on MiR-24 Mediated Bim/Caspase Apoptosis Signal Pathway Mechanism Research (No. 202201010521)+1 种基金the Science and Technology Innovation Projects of Shenzhen:to Study the Mechanism of Hesperidin in Improving Heart Failure Based on Myocardial Inflammation Mediated by MtDNAs GAS-STING Signaling Pathway (No. JCYJ20220530144212026)Futian Healthcare Research Project:To Study the Anti-atherosclerosis Effects and Mechanism of Shenzhu Guanxin Decoction on Inhibiting Platelet-mediated Inflammation Based on the Theory of "Phlegm-stasis Interjunction"(No. FTWS2022012)。
文摘OBJECTIVE: To evaluate the clinical efficacy and safety of Shenzhu Guanxin recipe granules(参术冠心颗粒, SGR) in treating patients with intermediate coronary lesions(ICL), and to investigate the potential mechanism though a transcriptome sequencing approach. METHODS: ICL patients with Qi deficiency and phlegm stasis were adopted and randomly assigned to a case group or a control by random number generator in a 1∶1 randomization ratio to evaluate the clinical efficacy. RESULTS: There was no significant difference between the two groups in coronary computed tomography angiography related indexes in the two groups before and after intervention. Through the gene chip expression analysis, it is finally concluded that there are 355 differential mRNAs(190 up-regulated genes and 165 down regulated genes) when compared the SGR group and placebo group. Through protein-protein interaction network analysis of differentially expressed genes, 10 hub genes were finally obtained: CACNA2D2, CACNA2D3, DNAJC6, FGF12, SGSM2, CACNA1G, LRP6, KIF25, OXTR, UPB1. CONCLUSIONS: SGR combined with Western Medicine can be safely used to treat ICL patients with Qi deficiency and phlegm stasis. The possible mechanism of action and relevant gene loci and pathway were proposed.
文摘Cysteine-rich polycomb-like(CPP)is a small gene family in plants,which plays key role in plant development and stress response.Although CPP transcription factors have been characterized in several other plant species,a genome-wide characterization of the CPP gene family has been absent in Camellia sinensis.In this study,we totally identified 7,8,and 8 non-redundant CsCPP genes in three published genomes,including Camellia sinensis var.assamica cv.Yunkang-10(CSA-YK10),Camellia sinensis var.sinensis cv.Biyun(CSS-BY)and Camellia sinensis var.sinensis cv.Shuchazao(CSS-SCZ).CPP proteins from tea tree and other plant species were classified into three groups,which were further divided into four subgroups based on phylogenetic relationships.Most CPP genes in the same subgroup had similar gene structures and conserved motifs.The cis-acting elements analysis indicated that CPP genes might be involved in plant growth,development and stress responses.Analysis of gene expression using qRT-PCR experiments validated that CPP genes exhibited different expression patterns across the examined tissues.All the genes were expressed differentially in a range of tissues,indicating that CPPs were involved in a range of developmental and physiological processes.This study has obtained new insights into the evolution and function of the CPP gene family in the growth and development of tea plants,and also provide candidate genes for further functional characterization in tea tree.
基金Chinese Academy of Traditional Chinese Medicine Autonomous Topic Selection Project(No.ZZ2018017)Research Development Fund Project of the Medical Experimental Center of the Chinese Academy of Traditional Chinese Medicine(No.FZ2023003)。
文摘Objective: The effect of Chuanzhi Fang (ZGC) on the whole genome expression profile of RAW264.7 cells activated by lipopolysaccharide (LPS) was analyzed, and to explore the possible mechanism of action and core target of this formula on macrophage inflammatory injury at the overall level. Methods: A model of LPS-induced inflammation in RAW264.7 cells was constructed, and the effect of ZGC intervention on the genome-wide expression of inflammatory macrophages 3was examined by gene microarray technology, GO/KEGG enrichment analysis was performed for significantly differentially expressed genes among each group. Results: The results of genome-wide expression profiling microarray analysis showed that the ZGC intervention group upregulated the expression of 5 genes including C4bp and inhibited the expression of 22 genes including Mgat3, Psma6, and Siglecg relative to the LPS model group. KEGG signaling pathway analysis results showed that ZGC mainly acted through cytokine receptor interaction and the C-type lectin receptor signaling pathway. Conclusion: ZGC can interfere with the abnormal expression of 27 genes in inflammatory macrophages, and the related genes may exert corresponding anti-inflammatory effects by affecting cytokine receptor interactions, C-type lectin receptor signaling pathway, and TLR4/ NF-κB signaling pathway.
基金supported by grants from National NaturalScience Foundation of China(31421005)National Key Re-search and Development Program(2016YFD0100404,2016YFD0101804)+1 种基金National Postdoctoral Program for Innovative Talents(BX201600149)China PostdoctoralScience Foundation(2017M611049)。
文摘Transcriptome deep sequencing(RNA‐seq)hasbecome a routine method for global geneexpression profiling.However,its application tolarge‐scale experiments remains limited by costand labor constraints.Here we describe amassively parallel 3′end RNA‐seq(MP3RNA‐seq)method that introduces unique samplebarcodes during reverse transcription to permitsample pooling immediately following this initialstep.MP3RNA‐seq allows for handling of hun-dreds of samples in a single experiment,at acost of about$6 per sample for libraryconstruction and sequencing.MP3RNA‐seq iseffective for not only high‐throughput geneexpression profiling,but also genotyping.Todemonstrate its utility,we applied MP3RNA‐seqto 477 double haploid lines of maize.We iden-tified 19,429 genes expressed in at least 50%ofthe lines and 35,836 high‐quality singlenucleotide polymorphisms for genotypinganalysis.Armed with these data,we performedexpression and agronomic trait quantitativetrait locus(QTL)mapping and identified 25,797expression QTLs for 15,335 genes and 21 QTLsfor plant height,ear height,and relative earheight.We conclude that MP3RNA‐seq is highlyreproducible,accurate,and sensitive forhigh‐throughput gene expression profiling andgenotyping,and should be generally applicableto most eukaryotic species.
基金Black H and Glavey S are conducting research financially supported by Skyline Dx.
文摘Multiple myeloma(MM)is an aggressive plasma cell malignancy with high degrees of variability in outcome,some patients experience long remissions,whilst others survive less than two years from diagnosis.Therapy refractoriness and relapse remain challenges in MM management,and there is a need for improved prognostication and targeted therapies to improve overall survival(OS).The past decade has seen a surge in gene expression profiling(GEP)studies which have elucidated the molecular landscape of MM and led to the identification of novel gene signatures that predict OS and outperform current clinical predictors.In this review,we discuss the limitations of current prognostic tools and the emerging role of GEP in diagnostics and in the development of personalised medicine approaches to combat drug resistance.
文摘To determine cancer pathway activities in nine types of primary tumors and NCI60 cell lines, we applied an in silico approach by examining gene signatures reflective of consequent pathway activation using gene expression data. Supervised learning approaches predicted that the Ras pathway is active in -70% of lung adenocarcinomas but inactive in most squamous cell carcinomas, pulmonary carcinoids, and small cell lung carcinomas. In contrast, the TGF-β, TNF-α, Src, Myc, E2F3, and β-catenin pathways are inactive in lung adenocarcinomas. We predicted an active Ras, Myc, Src, and/or E2F3 pathway in significant percentages of breast cancer, colorectal carcinoma, and gliomas. Our results also suggest that Ras may be the most prevailing oncogenic pathway. Additionally, many NCI60 cell lines exhibited a gene signature indicative of an active Ras, Myc, and/or Src, but not E2F3, β-catenin, TNF-α, or TGF-β pathway. To our knowledge, this is the first comprehensive survey of cancer pathway activities in nine major tumor types and the most widely used NCI60 cell lines. The ＂gene expression pathway signatures＂ we have defined could facilitate the understanding of molecular mechanisms in cancer development and provide guidance to the selection of appropriate cell lines for cancer research and pharmaceutical compound screening.
文摘Stamen is a unique plant organ wherein germ cells or microsporocytes that commit to meiosis are initiated from somatic cells during its early developmental process. While genes determining stamen identity are known according to the ABC model of floral development, little information is available on how these genes affect germ cell initiation. By using the Affymetrix GeneChip Rice Genome Array to assess 51 279 tran- scripts, we established a dynamic gene expression profile （GEP） of the early developmental process of rice （Oryza sativa） stamen. Systematic analysis of the GEP data revealed novel expression patterns of some developmentally important genes including meiosis-, tapetum-, and phytohormone-related genes. Following the finding that a substantial amount of nuclear genes encoding photosynthetic proteins are ex- pressed at the low levels in early rice stamen, through the ChlP-seq analysis we found that a C-class MADS box protein, OsMADS58, binds many nuclear-encoded genes participated in photosystem and light reac- tions and the expression levels of most of them are increased when expression of OsMADS58 is downre- gulated in the osmads58 mutant. Furthermore, more pro-chloroplasts are observed and increased signals of reactive oxygen species are detected in the osmads58 mutant anthers. These findings implicate a novel link between stamen identity determination and hypoxia status establishment.
文摘Fasciclin-like arabinogalactan proteins(FLAs),a subclass of arabinogalactan proteins(AGPs),are usually involved in cell development in plants.To investigate the expression profiling as well
文摘Gene expression profiling at early stages(0～2 DPA) of fiber development in Gossypium hirsutum identified a number of transcription factors which were down regulated in fiberless mutants relative to wild type controls and which could play a role in controlling early fiber development.Chief among these was GhMYB25,a Mixta-like MYB gene.Transgenic GhMYB25-silenced cotton
基金the National Natural Science Foundation of China(Based on the Systems Biology of Acupuncture on Irritable Early Hypertension Control Mechanism and Intervention Study Targets Research,No.81072861)
文摘OBJECTIVE:To explore electro-acupuncture's(EA's)effect on gene expression in heart of rats with stress-induced pre-hypertension and try to reveal its biological mechanism based on gene chip technology.METHODS:Twenty-seven Wistar male rats were randomly divided into 3 groups.The stress-induced hypertensive rat model was prepared by electric foot-shocks combined with generated noise.Molding cycle lasted for 14 days and EA intervene was applied on rats in model + EA group during model preparation.Rat Gene 2.0 Sense Target Array technology was used for the determination of gene expression profiles and the screened key genes were verified by real-time quantitative polymerase chain reaction(RT-PCR) method.RESULTS:Compared with blank control group,390 genes were changed in model group;compared with model control group,330 genes were changed in model + EA group.Significance analysis of gene function showed that the differentially expressed genes are those involved in biological process,molecular function and cellular components.RT-PCR result of the screened key genes is consistent with that of gene chip test.CONCLUTION:EA could significantly lower blood pressure of stress-induced pre-hypertension rats and affect its gene expression profile in heart.Genes that related to the contraction of vascular smooth muscle may be involved in EA's anti-hypertensive mechanism.
