scholarly journals Expression Profiles Reveal Involvement of VEGF, IGF1, BIRC5, and MMP1 in Vulvar Carcinogenesis

2021 ◽  
Vol 20 ◽  
pp. 153303382110049
Author(s):  
Tao Zhang ◽  
Qin Liu ◽  
Minghua Yu ◽  
Yibing Lan ◽  
Jianghong Zhou
Keyword(s):  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Clinical Stage ◽  
Clinicopathological Characteristics ◽  
Gene Expression Omnibus ◽  
Expression Levels ◽  
Key Genes ◽  
Well Differentiated ◽  
New Biomarkers

Objective: The objective of this study was to identify key genes and shed light on the underlying molecular mechanisms of vulvar squamous cell carcinoma (VSCC). Methods: Bioinformatic software was utilized for the identification and characterization of key differentially expressed genes (DEGs) from microarrays GSE63678 and GSE38228, which contain VSCC and normal vulvar tissue data. These microarrays were obtained from Gene Expression Omnibus (GEO). Immunohistochemical assays (55 VSCC and 50 normal vulvar tissues) were utilized to validate the expression of VEGF, IGF1, BIRC5, and MMP1 screened from the identified DEGs. SPSS 18.0 software was used for statistical analyses of the relationships between IGF1, BIRC5, VEGF, MMP1 expression levels and patient clinicopathological characteristics. Results: A total of 141 DEGs were identified, among which 18 genes were closely correlated with the biological characteristics of VSCC. Four of the 18 genes ( VEGF, IGF1, BIRC5, and MMP1) screened from the GEO database were markedly enriched in pathways in cancer ( P < 0.05), and could be considered key genes in VSCC based on KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis in DAVID (Database for Annotation, Visualization and Integrated Discovery).The expression levels of these 4 hub genes, determined by immunohistochemical assays, were consistent with the bioinformatics results. Higher expression of IGF1 showed significant association with well-differentiated carcinomas ( P = 0.017). BIRC5 expression levels showed a positive correlation with clinical stage ( P = 0.039); compared with those in menopause for over 10 years, patients in menopause for less than 10 years at the time of diagnosis tended to have significantly higher expression of BIRC5 ( P = 0.003). VEGF and MMP1 expression levels were not correlated with any of the tested clinicopathological characteristics. Conclusion: VEGF, IGF1, BIRC5, and MMP1 were identified as being associated with VSCC using integrated bioinformatic methods, which may provide important insights into the pathogenesis of this disease and help to identify new biomarkers.

scholarly journals Biosyntheses characterization of alkaloids and flavonoids in Sophora flavescens by combining metabolome and transcriptome

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Guangfei Wei ◽  
Yongzhong Chen ◽  
Xiaotong Guo ◽  
Jianhe Wei ◽  
Linlin Dong ◽  
...  
Keyword(s):  
High Performance ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Principal Component ◽  
Sophora Flavescens ◽  
Expression Levels ◽  
Chromatography Analysis ◽  
Metabolite Profiles ◽  
Root Tissues

AbstractSophora flavescens are widely used for their pharmacological effects. As its main pharmacological components, alkaloids and flavonoids are distributed in the root tissues wherein molecular mechanisms remain elusive. In this study, metabolite profiles are analyzed using metabolomes to obtain biomarkers detected in different root tissues. These biomarkers include alkaloids, phenylpropanoids, and flavonoids. The high-performance liquid chromatography analysis results indicate the differences in principal component contents. Oxymatrine, sophoridine, and matrine contents are the highest in the phloem, whereas trifolirhizin, maackiain, and kushenol I contents are the highest in the xylem. The transcript expression profiles also show tissue specificity in the roots. A total of 52 and 39 transcripts involved in alkaloid and flavonoid syntheses are found, respectively. Among them, the expression levels of LYSA1, LYSA2, AO2, AO6, PMT1, PMT17, PMT34, and PMT35 transcripts are highly and positively correlated with alkaloids contents. The expression levels of 4CL1, 4CL3, 4CL12, CHI5, CHI7, and CHI9 transcripts are markedly and positively correlated with flavonoids contents. Moreover, the quantitative profiles of alkaloids and flavonoids are provided, and the pivotal genes regulating their distribution in S. flavescens are determined. These results contribute to the existing data for the genetic improvement and target breeding of S. flavescens.

scholarly journals Elucidation of molecular mechanisms of flower form development in tree peony ( Paeonia suffriticosa ) through comparative transcriptome analysis of floral parts

2019 ◽  
Author(s):  
Jiuxing Lu ◽  
Yun Zheng ◽  
Haoning Wang ◽  
Zheng Wang ◽  
Yonghua Li ◽  
...  
Keyword(s):  
Woody Plants ◽  
Molecular Mechanisms ◽  
High Expression ◽  
Limited Information ◽  
Mads Box ◽  
Mads Box Genes ◽  
Tree Peony ◽  
Expression Levels ◽  
Key Genes ◽  
Flower Form

Abstract Background: Tree peony (Paeonia suffruticasa) is an economically, medicinally ornamentally important woody flowering woody plants in East Asia and is a common also ornamental shrub in Europe and North America. It is well known and prized for their beautiful flowers in many different forms. Samen petalody has been shown to be the most effective way to modify flower forms. However, there is limited information on the molecular mechanisms of stamen petalody and flower form formation in tree peony.Results: In this study, RNA sequencing was used to assemble and annotate the unigenes in the tree peony to identify the critical genes related to flower parts formation and verify the key genes in different flower forms of tree peony cultivar. A total of 76,007 high quality unigenes were assembled and 30,505 were successfully annotated. A total of 1,833 TFs were identified in our study, among them 16 MADS-box genes were found and characterized. Six key genes were selected to verity their functions in stamen petalody. AG and SEP showed high expression level in carpals and sepals separately both in stamen petalody group and non-stamen petalody groups. PI and AP3 showed high expression levels in inter-petals in stamen petalody groups than in staments in non-stamen petalody.Conclusion: Sixteen MADS-box genes were identified for the first time in tree peony through RNA-seq method. We identified six key genes based on their differential expression levels in different flower parts. These six key genes represented all categories in the ABCDE model to verify the functions in stamen petalody. PI and AP3 were verified to likely play important roles in regulating stamen petalody in tree peony. Our study has helped establish the flower development model in tree peony, identified key molecular mechanisms in the development of different flower forms, and provided valuable information in improving genetic diversity of tree peony and many other woody plants.

scholarly journals SMC4, CCNB1 and CKS1B as potential targets and new critical biomarkers for the prognosis of human bladder cancer

2021 ◽  
Author(s):  
Hongpeng Fang ◽  
Zhansen Huang ◽  
Xianzi Zeng ◽  
Jiaming Wan ◽  
Jieying Wu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bladder Cancer ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Gene Expression Omnibus ◽  
Transcriptional Level ◽  
Hub Genes ◽  
Kaplan Meier ◽  
High Form

Abstract Background As a common malignant cancer of the urinary system, the precise molecular mechanisms of bladder cancer remain to be illuminated. The purpose of this study was to identify core genes with prognostic value as potential oncogenes for the diagnosis, prognosis or novel therapeutic targets of bladder cancer. Methods The gene expression profiles GSE3167 and GSE7476 were available from the Gene Expression Omnibus (GEO) database. Next, PPI network was built to filter the hub gene through the STRING database and Cytoscape software and GEPIA and Kaplan-Meier plotter were implemented. Frequency and type of hub genes and sub groups analysis were performed in cBioportal and ULCAN database. Finally,We used RT-qPCR to confirm our results. Results Totally, 251 DEGs were excavated from two datasets in our study. We only founded high expression of SMC4, TYMS, CCNB1, CKS1B, NUSAP1 and KPNA2 was associated with worse outcomes in bladder cancer patients and no matter from the type of mutation or at the transcriptional level of hub genes, the tumor showed a high form of expression. However, only the expression of SMC4,CCNB1and CKS1B remained changed between the cancer and the normal samples in our results of RT-qPCR. Conclusion In conclusion,These findings indicate that the SMC4,CCNB1 and CKS1B may serve as critical biomarkers in the development and poor prognosis.

Identification of odorant-binding protein genes inGaleruca daurica(Coleoptera: Chrysomelidae) and analysis of their expression profiles

2017 ◽  
Vol 107 (4) ◽  
pp. 550-561 ◽  
Author(s):  
L. Li ◽  
Y.-T. Zhou ◽  
Y. Tan ◽  
X.-R. Zhou ◽  
B.-P. Pang
Keyword(s):  
Amino Acid ◽  
Molecular Mechanisms ◽  
Insect Pests ◽  
Expression Profiles ◽  
Open Reading Frames ◽  
Amino Acid Residues ◽  
Expression Levels ◽  
Molecular Weights ◽  
Related Proteins ◽  
Odorant Binding

AbstractOdorant-binding proteins (OBPs) play a fundamental role in insect olfaction. In recent years,Galeruca daurica(Joannis) (Coleoptera: Chrysomelidae) has become one of the most important insect pests in the Inner Mongolian grasslands of China. This pest only feeds on the species ofAlliumplants, implying the central role of olfaction in its search for specific host plants. However, the olfaction-related proteins have not been investigated in this beetle. In this study, we identified 29 putative OBP genes, namely GdauOBP1–29, from the transcriptome database ofG. dauricaassembled in our laboratory by using RNA-Seq. All 29 genes had the full-length open reading frames except GdauOBP29, encoding proteins in length from 119 to 202 amino acids with their predicted molecular weights from 12 to 22 kDa with isoelectric points from 3.88 to 8.84. Predicted signal peptides consisting of 15–22 amino acid residues were found in all except GdauOBP6, GdauOBP13 and GdauOBP29. The amino acid sequence identity between the 29 OBPs ranged 8.33–71.83%. GdauOBP1–12 belongs to the Classic OBPs, while the others belong with the Minus-C OBPs. Phylogenetic analysis indicated that GdauOBPs are the closest to CbowOBPs fromColaphellus bowringi. RT-PCR and qRT-PCR analyses showed that all GdauOBPs were expressed in adult antennae, 11 of which with significant differences in their expression levels between males and females. Most GdauOBPs were also expressed in adult heads (without antennae), thoraxes, abdomens, legs and wings. Moreover, the expression levels of the GdauOBPs varied during the different development stages ofG. dauricawith most GdauOBPs expressed highly in the adult antennae but scarcely in eggs and pupae. These results provide insights for further research on the molecular mechanisms of chemical communications inG. daurica.

scholarly journals EXPRESSION ANALYSIS OF THE COFFE (Coffea arabica L.) FRIGIDA4-like GENE (CaFRL4)

2018 ◽  
Vol 5 (Especial) ◽  
pp. 204-213
Author(s):  
Matheus Martins Daude ◽  
André Almeida Lima ◽  
Antonio Chalfun Junior ◽  
Horllys Gomes Barreto
Keyword(s):  
Molecular Mechanisms ◽  
Functional Characterization ◽  
Foreign Market ◽  
Expression Levels ◽  
Future Studies ◽  
Coffea Arabica L ◽  
Production Losses ◽  
Flowering Process

ABSTRACT Coffee is one of the most economically important commodities. In Brazil, this crop is responsible for generating more than eight million jobs. In the foreign market, Brazil is the largest producer and exporter of coffee. Due to its economic importance, several studies aiming the improvement of coffee are conducted, but there are still problems related to its productivity and quality of the beverage, such as sequential flowering, which causes production losses and a low quality drink. Thus, understanding the molecular mechanisms involved in the flowering process is essential to elucidate how flowering occurs in the coffee crop. The FRI gene is one of the main genes involved in flowering, as it positively regulates the FLC gene at expression levels that inhibit flowering. Thus, the objective of this work was to identify and analyze the expression of the FRIGIDA4-like gene (FRL4) through Bioinformatics and real-time PCR (RT-qPCR). The CaFRL4 gene was identified and showed high expression levels in leaf during flowering, which corroborates with the literature. The results obtained provide the basis for future studies involving genetic transformation in model plants and coffee, permitting the functional characterization of this gene.

scholarly journals Identification of Potential Key Genes and Molecular Mechanisms of Medulloblastoma Based on Integrated Bioinformatics Approach

2022 ◽  
Vol 2022 ◽  
pp. 1-17
Author(s):  
Md. Rakibul Islam ◽  
Lway Faisal Abdulrazak ◽  
Mohammad Khursheed Alam ◽  
Bikash Kumar Paul ◽  
Kawsar Ahmed ◽  
...  
Keyword(s):  
Gene Expression ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Clinical Information ◽  
Gene Expression Omnibus ◽  
Hub Genes ◽  
New Treatments

Background. Medulloblastoma (MB) is the most occurring brain cancer that mostly happens in childhood age. This cancer starts in the cerebellum part of the brain. This study is designed to screen novel and significant biomarkers, which may perform as potential prognostic biomarkers and therapeutic targets in MB. Methods. A total of 103 MB-related samples from three gene expression profiles of GSE22139, GSE37418, and GSE86574 were downloaded from the Gene Expression Omnibus (GEO). Applying the limma package, all three datasets were analyzed, and 1065 mutual DEGs were identified including 408 overexpressed and 657 underexpressed with the minimum cut-off criteria of ∣ log   fold   change ∣ > 1 and P < 0.05 . The Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and WikiPathways enrichment analyses were executed to discover the internal functions of the mutual DEGs. The outcomes of enrichment analysis showed that the common DEGs were significantly connected with MB progression and development. The Search Tool for Retrieval of Interacting Genes (STRING) database was used to construct the interaction network, and the network was displayed using the Cytoscape tool and applying connectivity and stress value methods of cytoHubba plugin 35 hub genes were identified from the whole network. Results. Four key clusters were identified using the PEWCC 1.0 method. Additionally, the survival analysis of hub genes was brought out based on clinical information of 612 MB patients. This bioinformatics analysis may help to define the pathogenesis and originate new treatments for MB.

scholarly journals From the human genome to the epigenome of cancer: the use of high technology in molecular oncology

2018 ◽  
Vol 72 ◽  
pp. 991-996
Author(s):  
Marzena Anna Lewandowska ◽  
Łukasz Żołna ◽  
Krzysztof Roszkowski ◽  
Janusz Kowalewski
Keyword(s):  
Human Genome ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Association Studies ◽  
Genetic Disorders ◽  
Cancer Diagnostics ◽  
Cancer Genome ◽  
The Cancer Genome Atlas ◽  
Genome Wide Association Studies

Fifteen years after the publication of the full sequence of the human genome which revolutionized medicine and biotechnology, profound elucidation of the molecular mechanisms of genetic disorders remains a challenge. National and international institutions conduct a number of research projects in genomics. Some of them are focused on the characterization of functional elements of the genome (e.g., the Genome Browser database by the ENCODE consortium), some gather information on polymorphisms (HapMap, The 1000 Genomes Project) and mutations (The Human Gene Mutation Database), while other are specifically dedicated to the genomic characterization of cancer (The Cancer Genome Atlas, The Pediatric Cancer Genome Project). Even though the projects are conducted independently, juxtapositions of the constantly updated project data may be performed, leading to interesting results. The genome-wide association studies (GWAS) allowed the identification of millions of SNPs and short insertions/deletions, as well as thousands of structural variants of polymorphic gene products. Further data-mining studies allowed the distinction between synonymous and nonsynonymous SNPs, which became the basis for the epidemiological studies of various types of genetic disorders. The results of the sequencing of entire genomes and transcriptomes may be useful in the identification of novel prognostic and predictive markers. High-throughput technologies are emerging methods in molecular diagnostics, furthermore the correlation of DNA methylation patterns and gene expression profiles may also provide useful results in cancer diagnostics.

scholarly journals Microstructural Observation and Transcriptome Analysis of Pistil Abortion in ‘Li Guang’ Apricot

2020 ◽  
Author(s):  
Tong Zhao ◽  
Li Cheng ◽  
Cuilian Chen ◽  
De Zhang ◽  
Zhongxing Zhang ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Paraffin Section ◽  
Pollen Grains ◽  
Gansu Province ◽  
Signal Molecules ◽  
Rna Seq ◽  
Factors Affecting ◽  
Expression Levels ◽  
Pistil Abortion

Abstract Background: ‘Li Guang’ apricot, a famous local variety, originated in Dunhuang city, Gansu Province,China. It has a long flowering period and a large amount of flowers, but serious pistil abortion has become one of the key factors affecting the fruit set, yield and quality. The distribution and regulation of hormones play an important role in signal molecules of flower abortion. The critical mechanisms of hormone metabolism and the expression levels of genes involved in these processes are, however, poorly understood. Results: To clarify the critical molecular mechanisms of hormone-induced abortion in apricot, normal and abortive flower buds were taken as materials, the pistil abortion of apricot flower was studied by paraffin section, and the RNA seq was used to identify the genes related to flowering regulation. The pistil style was lower than filament. Microstructure showed that the pollen grains of abortive flowers were decreased sharply, the ovaries shrunk and the ovule primordia developed stagnately. Through RNA-Seq, 6647 differentially expressed genes, including 2543 up-regulated and 4104 down-regulated genes, were identified. According to the KEGG Pathway, the pyruvate metabolism, plant hormone signal transduction, spliceosome, RNA transport, protein processing in endoplasmic reticulum and other metabolic pathways were significantly enriched. It revealed that AUX1, AUX / IAA, TIR1, ARF, GH3 and SAUR , vital genes displayed identical differential expression profiles to auxin transduction pathway, and ABF , SnRK2 , PP2C to abscisic acid, JAZ, MYC2 to jasmonic acid. The qRT-PCR assay with independent samples showed that the expression levels of these selected genes were basically consistent with RNA-Seq results. Conclusions : In the whole differentiate stage of flower, pistil abortion represent versatile style . In this process, the changes of hormones play an important role in pistil abortion, especially IAA,GA,and CTK. Related genes involved in hormones synthesis expression regulate the content of hormones and to adapt to the occurrence of pistil abortion under adversity. At the same time, the ethylene response signal factor ERF1/2 (DN70415) was up-regulated in normal flowers, which further indicated that ethylene might be the key regulatory factor affecting the abortion of ‘Liguang’ apricot flowers.

scholarly journals Genome-Wide Identification and Characterization of bHLH Transcription Factors Related to Anthocyanin Biosynthesis in Red Walnut (Juglans regia L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Wei Zhao ◽  
Yonghui Liu ◽  
Lin Li ◽  
Haijun Meng ◽  
Ying Yang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Gene Family ◽  
Developmental Stage ◽  
Molecular Mechanisms ◽  
Anthocyanin Biosynthesis ◽  
Expression Profiles ◽  
Juglans Regia ◽  
Expression Patterns ◽  
Regulatory Elements

Basic helix-loop-helix (bHLH) proteins are transcription factors (TFs) that have been shown to regulate anthocyanin biosynthesis in many plant species. However, the bHLH gene family in walnut (Juglans regia L.) has not yet been reported. In this study, 102 bHLH genes were identified in the walnut genome and were classified into 15 subfamilies according to sequence similarity and phylogenetic relationships. The gene structure, conserved domains, and chromosome location of the genes were analyzed by bioinformatic methods. Gene duplication analyses revealed that 42 JrbHLHs were involved in the expansion of the walnut bHLH gene family. We also characterized cis-regulatory elements of these genes and performed Gene Ontology enrichment analysis of gene functions, and examined protein-protein interactions. Four candidate genes (JrEGL1a, JrEGL1b, JrbHLHA1, and JrbHLHA2) were found to have high homology to genes encoding bHLH TFs involved in anthocyanin biosynthesis in other plants. RNA sequencing revealed tissue- and developmental stage-specific expression profiles and distinct expression patterns of JrbHLHs according to phenotype (red vs. green leaves) and developmental stage in red walnut hybrid progeny, which were confirmed by quantitative real-time PCR analysis. All four of the candidate JrbHLH proteins localized to the nucleus, consistent with a TF function. These results provide a basis for the functional characterization of bHLH genes and investigations on the molecular mechanisms of anthocyanin biosynthesis in red walnut.

scholarly journals Constructing mRNA, miRNA, circRNA and lncRNA Regulatory Network by Analysis of Microarray data in Breast Cancer

2021 ◽  
Author(s):  
Bita Hassani ◽  
Hasan Mollanoori ◽  
Farkhondeh Pouresmaeili ◽  
Yazdan Asgari ◽  
Soudeh Ghafouri-Fard
Keyword(s):  
Breast Cancer ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Noncoding Rnas ◽  
Interaction Network ◽  
Gene Expression Omnibus ◽  
Good Prognosis ◽  
Therapeutic Options ◽  
Circular Rnas ◽  
Breast Tumorigenesis

Abstract Background. Luminal tumors are the utmost frequent subtype of breast cancer (BC). Despite luminal BC has relatively good prognosis, in a subset of patients, disease relapse occursto endocrine therapy ;hence, there is a critical need to identify new strategies to promote the early detection and more effective therapies. Noncoding RNAs including microRNAs, long noncoding RNAs, and circular RNAs can interact with and modulate each other via diverse molecular mechanisms and make a complicated regulatory network.ncRNAs participate in diverse biological processes and disorders such as breast tumors. Therefore, understanding their regulatory mechanisms allow to develop new field of research and therapeutic options for BC patients.Methods. In this study, BC-specific RNA expression profiles including mRNAs, miRNAs, lncRNAs, and circRNAs were retrievedfrom Gene Expression Omnibus microarray datasets, and differentially expressed(DE) items were obtained. Disease ontology, functional and pathway enrichment analyses were executed. The protein-protein interaction network was constructed, and hub mRNAs were extracted.The prognostic value of hub mRNAs in patients of BC were performed. Subsequently, a ceRNA network was established.Results. In total, 691 DE genes, 122 DE lncRNAs, 60 DE miRNAs, and 38 DE circRNAs in breast tumor samples were compared with normal samples. Subsequently, 12 hub-genesincluding FOXO3, RHOA, EZH2, KIT, HSP90B1, NCOA3, RAC1, IGF1, CAV1, CXCR4, CCNB1, and ITGB1 were screened from the network. Kaplan-Meier Plotter results revealed that FOXO3 and RHOA were a suitable prognostic marker for patients with breast cancer. Finally, we determined possible ncRNAs (circ0007535, circ0002727, circ0005240, circ0014130, circ0044927, circ0007001, circ0089153,NORAD, MALAT1, TUG1, ZFAS1, OPI5-AS1, miR183,miR182, miR101, miR200c, miR200b, miR149, miR342, and miR1207) which could crosstalk with each other to regulateFOXO3 and RHOA through different regulatory patterns. Conclusion. These data might improve our perception of the breast tumorigenesis and could develop new field of research and therapeutic options for BC patients.

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