Construction of a chromosome 17 transcriptome in serous ovarian cancer identifies differentially expressed genes

2008 ◽  
Vol 18 (5) ◽  
pp. 963-975 ◽  
Author(s):  
P. M. Wojnarowicz ◽  
A. Breznan ◽  
S. L. Arcand ◽  
A. Filali-Mouhim ◽  
D. M. Provencher ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Differentially Expressed Genes ◽  
Molecular Genetic ◽  
Primary Cultures ◽  
Differentially Expressed ◽  
Chromosome 17 ◽  
Data Set ◽  
Malignant Ovarian Tumor ◽  
Ovarian Surface Epithelial ◽  
Subtype A

Cytogenetic, molecular genetic, and functional analyses have implicated chromosome 17 genes in epithelial ovarian cancer (EOC). To further characterize the contribution of chromosome 17 genes in EOC, the Affymetrix U133A GeneChip was used to perform transcriptome analyses of 15 primary cultures of normal ovarian surface epithelial (NOSE) cells and 17 malignant ovarian tumor (TOV) samples of the serous histopathologic subtype. A two-way comparative analysis of 776 known genes and expressed sequences identified 253 genes that exhibited at least a threefold difference in expression in at least one TOV sample compared to the mean of NOSE samples. Within this data set, 99 of the 253 (39.1%) genes exhibited similar patterns of expression across all tested samples, suggesting a high degree of concordance in the chromosome 17 transcriptome. This observation was supported by hierarchical clustering analysis that segregated the TOV and NOSE samples into two separate groups. There were 77 genes that were differentially expressed in at least 50% of the TOV samples. Five genes (AdoRA2B at 17p12, CCL2 at 17q12, ACLY at 17q21.2, WIPI1 at 17q24.2, and SLC16A3 at 17q25.3) were significantly (P< 5.13E−11) differentially expressed at least threefold in all serous TOV samples, and all five genes were underexpressed in these TOV samples as compared to the NOSE samples. Interestingly, several of these differentially expressed genes have been previously associated with response to hypoxia.

scholarly journals Differential gene expression analysis of ankylosing spondylitis shows deregulation of the HLA-DRB, HLA-DQB, ITM2A, and CTLA4 genes

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Rowan AlEjielat ◽  
Anas Khaleel ◽  
Amneh H. Tarkhan
Keyword(s):  
Gene Expression ◽  
Ankylosing Spondylitis ◽  
Differentially Expressed Genes ◽  
Gene Network ◽  
Disease Diagnosis ◽  
Receptor Activation ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Inflammatory Disorder ◽  
Data Set

Abstract Background Ankylosing spondylitis (AS) is a rare inflammatory disorder affecting the spinal joints. Although we know some of the genetic factors that are associated with the disease, the molecular basis of this illness has not yet been fully elucidated, and the genes involved in AS pathogenesis have not been entirely identified. The current study aimed at constructing a gene network that may serve as an AS gene signature and biomarker, both of which will help in disease diagnosis and the identification of therapeutic targets. Previously published gene expression profiles of 16 AS patients and 16 gender- and age-matched controls that were profiled on the Illumina HumanHT-12 V3.0 Expression BeadChip platform were mined. Patients were Portuguese, 21 to 64 years old, were diagnosed based on the modified New York criteria, and had Bath Ankylosing Spondylitis Disease Activity Index scores > 4 and Bath Ankylosing Spondylitis Functional Index scores > 4. All patients were receiving only NSAIDs and/or sulphasalazine. Functional enrichment and pathway analysis were performed to create an interaction network of differentially expressed genes. Results ITM2A, ICOS, VSIG10L, CD59, TRAC, and CTLA-4 were among the significantly differentially expressed genes in AS, but the most significantly downregulated genes were the HLA-DRB6, HLA-DRB5, HLA-DRB4, HLA-DRB3, HLA-DRB1, HLA-DQB1, ITM2A, and CTLA-4 genes. The genes in this study were mostly associated with the regulation of the immune system processes, parts of cell membrane, and signaling related to T cell receptor and antigen receptor, in addition to some overlaps related to the IL2 STAT signaling, as well as the androgen response. The most significantly over-represented pathways in the data set were associated with the “RUNX1 and FOXP3 which control the development of regulatory T lymphocytes (Tregs)” and the “GABA receptor activation” pathways. Conclusions Comprehensive gene analysis of differentially expressed genes in AS reveals a significant gene network that is involved in a multitude of important immune and inflammatory pathways. These pathways and networks might serve as biomarkers for AS and can potentially help in diagnosing the disease and identifying future targets for treatment.

Detection of ovarian cancer-specific gene by differentially expressed gene polymerase chain reaction prescreening and direct DNA sequencing

2007 ◽  
Vol 25 (18_suppl) ◽  
pp. 21106-21106 ◽  
Author(s):  
J. Kim ◽  
J. H. Pak ◽  
W. H. Choi ◽  
J. Y. Kim ◽  
W. D. Joo ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Ribosomal Protein ◽  
Differentially Expressed Genes ◽  
Triosephosphate Isomerase ◽  
Differentially Expressed Gene ◽  
Differentially Expressed ◽  
Specific Gene ◽  
Cancer Tissue ◽  
Normal Ovary ◽  
Ribosomal Protein L11

21106 Background: To detect the genes differentially expressed in the ovarian cancer, we analysed the genes in the ovarian cancer and normal ovary by differentially expressed gene(DEG) PCR using the RNA extracted from the both tissues. We examined the relationship between the specific genes of ovarian cancer and pathogenesis of ovarian cancer. Methods: Differentially expressed genes were screened by ACP-based PCR. Differentially expressed bands were extracted from agarose gel, and then directly sequenced. Finally we determined the clinical importances of differentially expressed genes. Results: Some genes were overexpressed in the ovarian cancer tissue than normal ovary, such as plexin B1(PLXNB1), aminoacylase 1(ACY1), solute carrier family 25 protein(SLC25A5), triosephosphate isomerase 1(TPI 1), poliovirus receptor-related 3 protein(PVRL 3), clusterin, LY6/PLAUR domain containing 1 protein(LYPDC 1). And other five genes were more expressed in the normal ovary than ovarian cancer, such as ribosomal protein L11 and L23, tenascin XB (TNXB), complement component 1 and actin alpha 2. Conclusions: Clusterin was highly expressed in the tissue from ovarian cancer, which was identified with anti- or proapoptotic activity regulated by calcium homeostasis in prostate, breast and colorectal cancers. And it suggests the possibility that regulation of clusterin activity provides the prospect of breaking down cancer cells‘ resistance to apoptosis in the ovarian cancer. Ribosomal protein L11 and L23 was highly expressed in normal ovary, which plays an important role in regulating the stability and function of the p53 tumor suppressor protein. It suggests that suppression of ribosomal protein L11 may act an important role in proliferation of ovarian cancer and over-expression of ribosomal protein L11 may act an important role in cell cycle arrest in the treatment of the ovarian cancer. No significant financial relationships to disclose.

scholarly journals The inducible response of the nematode Caenorhabditis elegans to members of its natural microbiome across development and adult life

2019 ◽  
Author(s):  
W Yang ◽  
C Petersen ◽  
B Pees ◽  
J Zimmermann ◽  
S Waschina ◽  
...  
Keyword(s):  
Energy Metabolism ◽  
Metabolic Network ◽  
Differentially Expressed Genes ◽  
Adult Life ◽  
Differentially Expressed ◽  
Promoter Regions ◽  
Data Set ◽  
C Elegans ◽  
Folate Biosynthesis ◽  
Transcriptome Response

AbstractThe biology of all organisms is influenced by the associated community of microorganisms. In spite of its importance, it is usually not well understood how exactly this microbiome affects host functions and what are the underlying molecular processes. To rectify this knowledge gap, we took advantage of the nematode C. elegans as a tractable, experimental model system and assessed the inducible transcriptome response after colonization with members of its native microbiome. For this study, we focused on two isolates of the genus Ochrobactrum. These bacteria are known to be abundant in the nematode’s microbiome and are capable of colonizing and persisting in the nematode gut, even under stressful conditions. The transcriptome response was assessed across development and three time points of adult life, using general and C. elegans-specific enrichment analyses to identify affected functions. Our assessment revealed an influence of the microbiome members on the nematode’s dietary response, development, fertility, immunity, and energy metabolism. This response is mainly regulated by a GATA transcription factor, most likely ELT-2, as indicated by the enrichment of (i) the GATA motif in the promoter regions of inducible genes and (ii) of ELT-2 targets among the differentially expressed genes. We compared our transcriptome results with a corresponding previously characterized proteome data set, highlighting a significant overlap in the differentially expressed genes and the affected functions. Our analysis further identified a core set of 86 genes that consistently responded to the microbiome members across development and adult life, including several C-type lectin-like genes and genes known to be involved in energy metabolism or fertility. We additionally assessed the consequences of induced gene expression with the help of metabolic network model analysis, using a previously established metabolic network for C. elegans. This analysis complemented the enrichment analyses by revealing an influence of the Ochrobactrum isolates on C. elegans energy metabolism and furthermore metabolism of specific amino acids, fatty acids, and also folate biosynthesis. Our findings highlight the multifaceted impact of naturally colonizing microbiome isolates on C. elegans life history and thereby provide a framework for further analysis of microbiome-mediated host functions.

scholarly journals Bioinformatic Analysis: Screening and Identification of Differentially Expressed Genes Modified by m6A in Ovarian Cancer

2020 ◽  
Author(s):  
Huidong Liu ◽  
Wen-wen Zhang ◽  
Ge Lou
Keyword(s):  
Ovarian Cancer ◽  
Differentially Expressed Genes ◽  
Clinical Sample ◽  
Therapeutic Targets ◽  
Enrichment Analysis ◽  
Underlying Mechanism ◽  
Bioinformatic Analysis ◽  
Gene Expression Omnibus ◽  
Differentially Expressed ◽  
Kegg Pathways

Abstract Background: N6-methyladenosine(m6A) is one of the most common RNA modifications that occurs at the nitrogen-6 position of adenine. Emerging evidence has revealed that regulatory functions of m6A play an essential role in the development of cancer. However the study of m6A in ovarian cancer(OC) is still in our infancy. In this work ,we aimed to identify and analysis the differentially expressed genes(DEGs） modified by m6A which can provide new therapeutic targets and key biomarkers in OC.Methods: We downloaded Microarray datasets GSE146553 and GSE124766 from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were identified by GEO2R analysis tools. Subsequently, The DAVID database was used to construct Enrichment analysis of GO and KEGG pathways. Next, the DEGs modified by m6A were identified by m6AVar database. Finally, the functional analysis and clinical sample validation of these genes were verified by ONCOMINE, GEPIA, cBioPortal online platform and Kaplan-Meier Plotter.Results:152 DEGs were selected ,and the DEGs were mainly enriched in extracellular exosome, spindle microtubule, response to hypoxia and cell cycle .And we identified 15 DEGs which were modified by m6A:MAPK10、MXRA5、CHD7、MECOM、SCN7A、GREB、PRUNE2、MX2、TOP2A、JAM2、DST、LAPTM5、CDKN2A、GATM and ANGPTL1. After statistical analysis, two DEGs (SCN7A and GAMT) were selected for detailed study. We revealed that SCN7A and GAMT were expressed at a low level in OC. Afterwards, Survival analysis showed that SCN7A and GAMT expression were correlated with OC overall survival. And the expression of SCN7A and GAMT mRNA decreasing in different TNM stages. Finally, we presumed that the modification of m6A spongs GAMT via EIF4A3 or FUS to participate in the occcurrence and the development of OC.Conclusion: Altogether, the current study identified and analysised the DEGs modified by m6A in OC. It will help us to investigate the underlying mechanism and progression of OC. In addition, it can provide new diagnostic markers and potential therapeutic targets in OC.

scholarly journals Expression of immune response genes in human corneal epithelial cells interacting with Aspergillus flavus conidia

BMC Genomics ◽  
2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Divya Arunachalam ◽  
Shruthi Mahalakshmi Ramanathan ◽  
Athul Menon ◽  
Lekshmi Madhav ◽  
Gopalakrishna Ramaswamy ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Cell Line ◽  
Differentially Expressed Genes ◽  
Primary Cultures ◽  
Differentially Expressed ◽  
Corneal Epithelial Cell ◽  
Epithelial Cell Line ◽  
Corneal Epithelial Cells ◽  
Corneal Epithelial ◽  
Human Corneal Epithelial Cells

Abstract Background Aspergillus flavus, one of the causative agents of human fungal keratitis, can be phagocytosed by human corneal epithelial (HCE) cells and the conidia containing phagosomes mature into phagolysosomes. But the immunological responses of human corneal epithelial cells interacting with A. flavus are not clear. In this study, we report the expression of immune response related genes of HCE cells exposed to A. flavus spores using targeted transcriptomics. Methods Human corneal epithelial cell line and primary cultures were grown in a six-well plate and used for coculture experiments. Internalization of the conidia was confirmed by immunofluorescence microscopy of the colocalized endosomal markers CD71 and LAMP1. Total RNA was isolated, and the quantity and quality of the isolated RNA were assessed using Qubit and Bioanalyzer. NanoString nCounter platform was used for the analysis of mRNA abundance using the Human Immunology panel. R-package and nSolver software were used for data analysis. KEGG and FunRich 3.1.3 tools were used to analyze the differentially expressed genes. Results Different morphotypes of conidia were observed after 6 h of coculture with human corneal epithelial cells and found to be internalized by epithelial cells. NanoString profiling showed more than 20 differentially expressed genes in immortalized human corneal epithelial cell line and more than ten differentially expressed genes in primary corneal epithelial cells. Distinct set of genes were altered in their expression in cell line and primary corneal epithelial cells. KEGG pathway analysis revealed that genes associated with TNF signaling, NF-KB signaling, and Th17 signaling were up-regulated, and genes associated with chemokine signaling and B cell receptor signaling were down regulated. FunRich pathway analysis showed that pathways such as CDC42 signaling, PI3K signaling, and Arf6 trafficking events were activated by the clinical isolates CI1123 and CI1698 in both type of cells. Conclusions Combining the transcript analysis data from cell lines and primary cultures, we showed the up regulation of immune defense genes in A. flavus infected cells. At the same time, chemokine signaling and B cell signaling pathways are downregulated. The variability in the expression levels in the immortalized cell line and the primary cultures is likely due to the variable epigenetic reprogramming in the immortalized cells and primary cultures in the absence of any changes in the genome. It highlights the importance of using both cell types in host-pathogen interaction studies.

scholarly journals Identification of two molecular subtypes of dysregulated immune lncRNAs in ovarian cancer

2020 ◽  
pp. 153537022097202
Author(s):  
Xiaojun Liu ◽  
Jinghai Gao ◽  
Jing Wang ◽  
Jing Chu ◽  
Jiahao You ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Differentially Expressed Genes ◽  
Immune Cell ◽  
Molecular Subtypes ◽  
Good Prognosis ◽  
The Cancer Genome Atlas ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Receptor Interaction ◽  
Cancer Multiple

Long non-coding RNA (lncRNA) has increasingly been identified as a key regulator in pathologies such as cancer. Multiple platforms were used for comprehensive analysis of ovarian cancer to identify molecular subgroups. However, lncRNA and its role in mapping the ovarian cancer subpopulation are still largely unknown. RNA-sequencing and clinical characteristics of ovarian cancer were acquired from The Cancer Genome Atlas database (TCGA). A total of 52 lncRNAs were identified as aberrant immune lncRNAs specific to ovarian cancer. We redefined two different molecular subtypes, C1(188) and C2(184 samples), in “iClusterPlus” R package, among which C2 grouped ovarian cancer samples have higher survival probability and longer median survival time ( P <0.05) with activated IFN-gamma response, Wound Healing and Cytotoxic lymphocytes signal; 456 differentially expressed genes were acquired in C1 and C2 subtypes using limma (3.40.6) package, among which 419 were up-regulated and 37 were down-regulated, in TCGA dataset. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analysis revealed that these genes were actively involved in ECM-receptor interaction, PI3K-Akt signaling pathway interaction KEGG pathway. Compared with the existing immune subtype, the Cluster2 sample showed a substantial increase in the proportion of the existing C2 immune subtype, accounting for 81.37%, which was associated with good prognosis. Our C1 subtype contains only 56.49% of the existing immune C1 and C4, which also explains the poor prognosis of C1. Furthermore, 52 immune-related lncRNAs were used to divide the TCGA-endometrial cancer and cervical cancer samples into two categories, and C2 had a good prognosis. The differentially expressed genes were highly correlated with immune-cell-related pathways. Based on lncRNA, two molecular subtypes of ovarian cancer were identified and had significant prognostic differences and immunological characteristics.

Molecular Cloning of Differentially Expressed Genes in Human Epithelial Ovarian Cancer

1994 ◽  
Vol 52 (2) ◽  
pp. 247-252 ◽  
Author(s):  
Samuel C. Mok ◽  
Kwong-Kwok Wong ◽  
Raymond K.W. Chan ◽  
Ching C. Lau ◽  
Sai-Wah Tsao ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Epithelial Ovarian Cancer ◽  
Molecular Cloning ◽  
Differentially Expressed Genes ◽  
Differentially Expressed
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