scholarly journals Unraveling reno-protective effects of SGLT2 inhibition in human proximal tubular cells

2019 ◽  
Vol 316 (3) ◽  
pp. F449-F462 ◽  
Author(s):  
Markus Pirklbauer ◽  
Ramona Schupart ◽  
Lisa Fuchs ◽  
Petra Staudinger ◽  
Ulrike Corazza ◽  
...  
Keyword(s):  
Gene Expression ◽  
Mrna Expression ◽  
Cell Lines ◽  
Molecular Mechanisms ◽  
Mrna Level ◽  
Pathway Enrichment Analysis ◽  
Protective Effects ◽  
Proximal Tubular ◽  
Pt Cell ◽  
Tgf Β1

Large clinical trials demonstrated that SGLT2 inhibitors (SGLT2i) slow the progression of kidney function decline in type 2 diabetes. Because the underlying molecular mechanisms are largely unknown, we studied the effects of SGLT2i on gene expression in two human proximal tubular (PT) cell lines under normoglycemic conditions, utilizing two SGLT2i, namely empagliflocin and canagliflocin. Genome-wide expression analysis did not reveal substantial differences between these two SGLT2i. Microarray hybridization analysis identified 94 genes that were both upregulated by TGF-β1 and downregulated by either of the two SGLT2i in HK-2 and RPTEC/TERT1 (renal proximal tubular epithelial cells/telomerase reverse transcriptase 1) cells. Extracellular matrix organization showed the highest significance in pathway enrichment analysis. Differential gene expression of three annotated genes of interest within this pathway was verified on mRNA level in both cell lines. Whereas TGF-β1 induced mRNA expression of thrombospondin 1 (THBS1; 4.3-fold), tenascin C (TNC; 8-fold), and platelet-derived growth factor subunit B (PDGF-B; 4.2-fold), SGLT2i downregulated basal mRNA expression of THBS1 (0.2-fold), TNC (0.5 fold), and PDGF-B (0.6-fold). Administration of SGLT2i in the presence of TGF-β1 resulted in a significant inhibition of TGF-β1-induced THBS1 and TNC mRNA expression and TGF-β1-induced THBS1, TNC, and PDGF-BB protein expression. We conclude that SGLT2i block basal and TGF-β1-induced expression of key mediators of renal fibrosis and kidney disease progression in two independent human PT cell lines.

scholarly journals Identification of Potential Key Genes and Pathways in Enzalutamide-Resistant Prostate Cancer Cell Lines: A Bioinformatics Analysis with Data from the Gene Expression Omnibus (GEO) Database

2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Long Zheng ◽  
Xiaojie Dou ◽  
Xiaodong Ma ◽  
Wei Qu ◽  
Xiaoshuang Tang
Keyword(s):  
Gene Expression ◽  
Prostate Cancer ◽  
Cell Lines ◽  
Molecular Mechanisms ◽  
Enrichment Analysis ◽  
Gene Expression Omnibus ◽  
Gene Set Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
Key Genes ◽  
Geo Database

Enzalutamide (ENZ) has been approved for the treatment of advanced prostate cancer (PCa), but some patients develop ENZ resistance initially or after long-term administration. Although a few key genes have been discovered by previous efforts, the complete mechanisms of ENZ resistance remain unsolved. To further identify more potential key genes and pathways in the development of ENZ resistance, we employed the GSE104935 dataset, including 5 ENZ-resistant (ENZ-R) and 5 ENZ-sensitive (ENZ-S) PCa cell lines, from the Gene Expression Omnibus (GEO) database. Integrated bioinformatics analyses were conducted, such as analysis of differentially expressed genes (DEGs), Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, protein-protein interaction (PPI) analysis, gene set enrichment analysis (GSEA), and survival analysis. From these, we identified 201 DEGs (93 upregulated and 108 downregulated) and 12 hub genes (AR, ACKR3, GPER1, CCR7, NMU, NDRG1, FKBP5, NKX3-1, GAL, LPAR3, F2RL1, and PTGFR) that are potentially associated with ENZ resistance. One upregulated pathway (hedgehog pathway) and seven downregulated pathways (pathways related to androgen response, p53, estrogen response, TNF-α, TGF-β, complement, and pancreas β cells) were identified as potential key pathways involved in the occurrence of ENZ resistance. Our findings may contribute to further understanding the molecular mechanisms of ENZ resistance and provide some clues for the prevention and treatment of ENZ resistance.

scholarly journals Comparative pathway enrichment analysis in gastrointestinal cell lines Caco-2, HT-29, HEPG2, and colon fibroblasts using a custom expression panel for tight-junction and cytoskeletal regulatory genes

2019 ◽  
Author(s):  
JM Robinson
Keyword(s):  
Gene Expression ◽  
Comparative Analysis ◽  
Tight Junction ◽  
Cell Lines ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
Intestinal Epithelial ◽  
Expression Data ◽  
Pathway Enrichment ◽  
Ht 29

AbstractThis brief report details results from a comparative analysis of Nanostring expression data between cell lines HEPG2, Caco-2, HT-29, and colon fibroblasts. Raw and normalized data are available publicly in the NCBI GEO/Bioproject databases. Results identify cell-line specific variations in gene expression relevant to intestinal epithelial function.

scholarly journals Bioinformatic analysis identifies potential biomarkers and therapeutic targets of septic-shock-associated acute kidney injury

Hereditas ◽  
2021 ◽  
Vol 158 (1) ◽  
Author(s):  
Yun Tang ◽  
Xiaobo Yang ◽  
Huaqing Shu ◽  
Yuan Yu ◽  
Shangwen Pan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Septic Shock ◽  
Acute Kidney Injury ◽  
Molecular Mechanisms ◽  
Therapeutic Targets ◽  
Kidney Injury ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
Blood Samples ◽  
Potential Biomarkers

Abstract Background Sepsis and septic shock are life-threatening diseases with high mortality rate in intensive care unit (ICU). Acute kidney injury (AKI) is a common complication of sepsis, and its occurrence is a poor prognostic sign to septic patients. We analyzed co-differentially expressed genes (co-DEGs) to explore relationships between septic shock and AKI and reveal potential biomarkers and therapeutic targets of septic-shock-associated AKI (SSAKI). Methods Two gene expression datasets (GSE30718 and GSE57065) were downloaded from the Gene Expression Omnibus (GEO). The GSE57065 dataset included 28 septic shock patients and 25 healthy volunteers and blood samples were collected within 0.5, 24 and 48 h after shock. Specimens of GSE30718 were collected from 26 patients with AKI and 11 control patents. AKI-DEGs and septic-shock-DEGs were identified using the two datasets. Subsequently, Gene Ontology (GO) functional analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, and protein-protein interaction (PPI) network analysis were performed to elucidate molecular mechanisms of DEGs. We also evaluated co-DEGs and corresponding predicted miRNAs involved in septic shock and AKI. Results We identified 62 DEGs in AKI specimens and 888, 870, and 717 DEGs in septic shock blood samples within 0.5, 24 and 48 h, respectively. The hub genes of EGF and OLFM4 may be involved in AKI and QPCT, CKAP4, PRKCQ, PLAC8, PRC1, BCL9L, ATP11B, KLHL2, LDLRAP1, NDUFAF1, IFIT2, CSF1R, HGF, NRN1, GZMB, and STAT4 may be associated with septic shock. Besides, co-DEGs of VMP1, SLPI, PTX3, TIMP1, OLFM4, LCN2, and S100A9 coupled with corresponding predicted miRNAs, especially miR-29b-3p, miR-152-3p, and miR-223-3p may be regarded as promising targets for the diagnosis and treatment of SSAKI in the future. Conclusions Septic shock and AKI are related and VMP1, SLPI, PTX3, TIMP1, OLFM4, LCN2, and S100A9 genes are significantly associated with novel biomarkers involved in the occurrence and development of SSAKI.

scholarly journals Whole transcriptome analysis of adrenal glands from prenatal glucocorticoid programmed hypertensive rodents

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Sujeenthar Tharmalingam ◽  
Sandhya Khurana ◽  
Alyssa Murray ◽  
Jeremy Lamothe ◽  
T. C. Tai
Keyword(s):  
Gene Expression ◽  
Circadian Rhythm ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Adrenal Glands ◽  
Genetic Model ◽  
Pathway Enrichment Analysis ◽  
Wistar Kyoto ◽  
Whole Transcriptome Analysis ◽  
Whole Transcriptome

Abstract Prenatal glucocorticoid exposure is associated with the development of hypertension in adults. We have previously demonstrated that antenatal dexamethosone (DEX) administration in Wistar-Kyoto dams results in offspring with increased blood pressure coupled with elevated plasma epinephrine levels. In order to elucidate the molecular mechanisms responsible for prenatal DEX-mediated programming of hypertension, a whole-transcriptome analysis was performed on DEX programmed WKY male adrenal glands using the Rat Gene 2.0 microarray. Differential gene expression (DEG) analysis of DEX-exposed offspring compared with saline-treated controls revealed 142 significant DEGs (109 upregulated and 33 downregulated genes). DEG pathway enrichment analysis demonstrated that genes involved in circadian rhythm signaling were most robustly dysregulated. RT-qPCR analysis confirmed the increased expression of circadian genes Bmal1 and Npas2, while Per2, Per3, Cry2 and Bhlhe41 were significantly downregulated. In contrast, gene expression profiling of Spontaneously Hypertensive (SHR) rats, a genetic model of hypertension, demonstrated decreased expression of Bmal1 and Npas2, while Per1, Per2, Per3, Cry1, Cry2, Bhlhe41 and Csnk1D were all upregulated compared to naïve WKY controls. Taken together, this study establishes that glucocorticoid programmed adrenals have impaired circadian signaling and that changes in adrenal circadian rhythm may be an underlying molecular mechanism responsible for the development of hypertension.

HOXB9 Is Overexpressed in Blast Cells from a Subset of Acute Myeloid Leukemia Patients and Supports Proliferation of AML Cell Lines.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 65-65
Author(s):  
Stefan Heinrichs ◽  
Claudia Schoch ◽  
Donna S. Neuberg ◽  
A. Thomas Look
Keyword(s):  
Gene Expression ◽  
Cell Lines ◽  
Molecular Mechanisms ◽  
Hox Genes ◽  
Rare Event ◽  
Cellular Growth ◽  
Hoxa Cluster ◽  
Aberrant Expression ◽  
Retroviral Transduction ◽  
Myeloid Malignancies

Abstract Emerging evidence from studies in mice and humans suggests that HOX genes integrate the myelodysplastic and leukemogenic activities of different oncogenes. Translocations involving the MLL gene, a major upstream regulator of the HOXA cluster, have been identified in AML and define a specific cytogenetic subgroup of this disease. Recently, amplification of MLL was found in AML and MDS cases, revealing a second mechanism of deregulation of MLL and its downstream targets. However, additional leukemogenic upstream pathways have to be postulated, since upregulation of specific HOX genes, particularly HOXA9, is more frequent than MLL deregulation. Given the fact that HOXA9 is targeted by several yet to be identified mechanisms, we asked whether other members of the HOX9 paralog group are also highly expressed in myeloid malignancies. Our analysis of 449 AML patients by gene expression microarray revealed that besides HOXA9 (61% of all cases), HOXB9 is upregulated in 15% of the cases, whereas the overexpression of HOXC9 and HOXD9 expression is a very rare event (>1% of all cases). High levels of HOXB9 expression did not correlate with low levels of HOXA9 expression ruling out the possibility that HOXB9 compensates for a lack of HOXA9 activity in the leukemogenesis of a HOXA9 negative AML cases. Interestingly, within the cytogenetically defined subgroups (inv(16), t(15;17), t(8;21)) that have no HOXA9 expression at all, HOXB9 was also low or absent. To test if HOXB9 has the potential to contribute to the leukemogenic phenotype we analyzed a panel of human AML cell lines. The finding that 6 out of 24 cell lines express high levels of HOXB9 further indicates the significance of HOXB9 in myeloid malignancies. We chose K-562 and HEL as model cell lines since they express high levels of HOXB9, but lack HOXA9 expression. To reveal HOXB9 dependent pathways we designed two highly efficient siRNAs to target HOXB9 and knocked down its expression by retroviral transduction. In comparison to cells expressing a control siRNA, the resulting cell lines showed <5% of the control HOXB9 protein levels and a reduction in the cellular growth rate. Consequently, HOXB9 expression is required for the rapid growth of these AML cells. To gain insight into the molecular mechanisms underlying this phenotype we are performing global gene expression analysis. Preliminary results of our nearest neighbor analysis in K-562 cells revealed the upregulation of genes associated with erythroid differentiation upon HOXB9 knockdown. Our results indicate that HOXB9 expression inhibits the differentiation of leukemic myeloid progenitor cells, consistent with a role for the aberrant expression of this major HOX protein in leukemogenesis, by maintaining cells of the leukemic clone in an undifferentiated and rapidly proliferative state.

scholarly journals Dexamethasone enhances SOX9 expression in chondrocytes

2001 ◽  
Vol 169 (3) ◽  
pp. 573-579 ◽  
Author(s):  
I Sekiya ◽  
P Koopman ◽  
K Tsuji ◽  
S Mertin ◽  
V Harley ◽  
...  
Keyword(s):  
Gene Expression ◽  
Mrna Expression ◽  
Molecular Mechanisms ◽  
Consensus Sequence ◽  
Chondrocyte Differentiation ◽  
Sox9 Expression ◽  
Newborn Mice ◽  
Col2a1 Gene ◽  
Dose Dependent ◽  
Sox9 Protein

SOX9 is a transcription factor that activates type II procollagen (Col2a1) gene expression during chondrocyte differentiation. Glucocorticoids are also known to promote chondrocyte differentiation via unknown molecular mechanisms. We therefore investigated the effects of a synthetic glucocorticoid, dexamethasone (DEX), on Sox9 gene expression in chondrocytes prepared from rib cartilage of newborn mice. Sox9 mRNA was expressed at high levels in these chondrocytes. Treatment with DEX enhanced Sox9 mRNA expression within 24 h and this effect was observed at least up to 48 h. The effect of DEX was dose dependent, starting at 0.1 nM and maximal at 10 nM. The half life of Sox9 mRNA was approximately 45 min in the presence or absence of DEX. Western blot analysis revealed that DEX also enhanced the levels of SOX9 protein expression. Treatment with DEX enhanced Col2a1 mRNA expression in these chondrocytes and furthermore, DEX enhanced the activity of Col2-CAT (chloramphenicol acetyltransferase) construct containing a 1.6 kb intron fragment where chondrocyte-specific Sry/Sox- consensus sequence is located. The enhancing effect of DEX was specific to SOX9, as DEX did not alter the levels of Sox6 mRNA expression. These data suggest that DEX promotes chondrocyte differentiation through enhancement of SOX9.

scholarly journals Revealing the bovine embryo transcript profiles during early in vivo embryonic development

Reproduction ◽  
2009 ◽  
Vol 138 (1) ◽  
pp. 95-105 ◽  
Author(s):  
Maud Vallée ◽  
Isabelle Dufort ◽  
Stéphanie Desrosiers ◽  
Aurélie Labbe ◽  
Catherine Gravel ◽  
...  
Keyword(s):  
Gene Expression ◽  
Embryonic Development ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Current Knowledge ◽  
Mrna Level ◽  
Early Embryonic Development ◽  
Bovine Embryo ◽  
Rna Content

Gene expression profiling is proving to be a powerful approach for the identification of molecular mechanisms underlying complex cellular functions such as the dynamic early embryonic development. The objective of this study was to perform a transcript abundance profiling analysis of bovine early embryonic development in vivo using a bovine developmental array. The molecular description of the first week of life at the mRNA level is particularly challenging when considering the important fluctuations in RNA content that occur between developmental stages. Accounting for the different intrinsic RNA content between developmental stages was achieved by restricting the reaction time during the global amplification steps and by using spiked controls and reference samples. Analysis based on intensity values revealed that most of the transcripts on the array were present at some point during in vivo bovine early embryonic development, while the varying number of genes detected in each developmental stage confirmed the dynamic profile of gene expression occurring during embryonic development. Pair-wise comparison of gene expression showed a marked difference between oocytes and blastocysts profiles, and principal component analysis revealed that the majority of the transcripts could be regrouped into three main clusters representing distinct RNA abundance profiles. Overall, these data provide a detailed temporal profile of the abundance of mRNAs revealing the richness of signaling processes in early mammalian development. Results presented here provide better knowledge of bovine in vivo embryonic development and contribute to the progression of our current knowledge regarding the first week of life in mammals.

scholarly journals Modulation of Borrelia burgdorferi Stringent Response and Gene Expression during Extracellular Growth with Tick Cells

2002 ◽  
Vol 70 (6) ◽  
pp. 3061-3067 ◽  
Author(s):  
Julia Bugrysheva ◽  
Elena Y. Dobrikova ◽  
Henry P. Godfrey ◽  
Marina L. Sartakova ◽  
Felipe C. Cabello
Keyword(s):  
Gene Expression ◽  
Borrelia Burgdorferi ◽  
Cell Lines ◽  
Mrna Level ◽  
Stringent Response ◽  
Global Regulator ◽  
Tick Cell ◽  
Fourfold Increase ◽  
Reciprocal Interactions

ABSTRACT Borrelia burgdorferi N40 multiplied extracellularly when it was cocultured with tick cells in L15BS medium, a medium which by itself did not support B. burgdorferi N40 growth. Growth of B. burgdorferi N40 in the presence of tick cells was associated with decreased production of (p)ppGpp, the stringent response global regulator, a fourfold decrease in relA/spoT mRNA, an eightfold net decrease in bmpD mRNA, and a fourfold increase in rpsL-bmpD mRNA compared to growth of B. burgdorferi in BSK-H medium. As a result, the polycistronic rpsL-bmpD mRNA level increased from 3 to 100% of the total bmpD message. These observations demonstrate that there are reciprocal interactions between B. burgdorferi and tick cells in vitro and indicate that the starvation-associated stringent response mediated by (p)ppGpp present in B. burgdorferi growing in BSK-H medium is ameliorated in B. burgdorferi growing in coculture with tick cell lines. These results suggest that this system can provide a useful model for identifying genes controlling interactions of B. burgdorferi with tick cells in vitro when it is coupled with genetic methods to isolate and complement B. burgdorferi mutants.

scholarly journals Expression of genes modulated by epigallocatechin-3-gallate in breast cancer cells

2018 ◽  
Vol 64 (3) ◽  
pp. 31-37
Author(s):  
Anna Bogacz ◽  
Marlena Wolek ◽  
Bogna Juskowiak ◽  
Monika Karasiewicz ◽  
Adam Kamiński ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Adjuvant Therapy ◽  
Mrna Expression ◽  
Cancer Cells ◽  
Breast Cancer Cells ◽  
Molecular Mechanisms ◽  
Mrna Level ◽  
Expression Level ◽  
Mrna Levels ◽  
Mrna Expression Level

Summary Introduction: Breast cancer is the most common malignant cancer among women. Both drug resistance and metastasis are major problems in the treatment of breast cancer. Therefore, adjuvant therapy may improve patients’ survival and affect their quality of life. It is suggested that epigallocatechin gallate (EGCG) which is well known for its chemopreventive activity and acts on numerous molecular targets may inhibit the growth and metastasis of some cancers. Hence, discovering the metastatic molecular mechanisms for breast cancer may be useful for therapy. Objective: The aim of the study was to determine the effect of EGGC on the mRNA expression level of genes such as ZEB1, ABCB1, MDM2, TWIST1 and PTEN in MCF-7 breast cancer cells. Methods: MCF7/DOX were cultured in the presence of 0.2 μM DOX and EGCG (20-50 μM). The mRNA expression level was determined by real-time quantitative PCR using RealTime ready Custom Panel 96 kit. Results: Our results showed an important increase (about 2-fold for 20 μM EGCG + 0.2 μM DOX and 2.5-fold for 50 μM EGCG + 0.2 μM DOX, p<0.05) in ZEB1 expression levels. In case of ABCB1 gene lack of influence on the mRNA level was observed (p>0.05). We also observed significant decrease of ZEB1 expression in MCF7 cells with 20 μM and 50 μM EGCG (p<0.05). In addition, EGCG (20 μM) caused an increase of MDM2 and PTEN mRNA levels in almost 100% (p<0.05) and 40% (p>0.05), respectively. Lack of the influence of EGCG was noted for the TWIST1 gene expression. In case of MCF7/DOX we showed an increase of mRNA level of PTEN gene about 50% (p<0.05). Conclusions: These results suggest that EGCG may be potentially used in adjuvant therapy in the breast cancer treatment.

scholarly journals Identification of Novel Cancer Stem Cell Markers in Glioblastoma by Comparing Tumor Cells with Stem-cell-like Cell Lines

2021 ◽  
Vol 11 (2) ◽  
pp. 1567-1583
Author(s):  
Divya G.
Keyword(s):  
Gene Expression ◽  
Stem Cell ◽  
Tumor Cells ◽  
Cell Lines ◽  
Molecular Mechanisms ◽  
Cell Attachment ◽  
Microarray Dataset ◽  
Gene Expression Omnibus ◽  
Stem Cell Markers ◽  
Cancer Stem Cell Markers

Aim. The aim of this study is to identify differential gene expression for glioblastoma tumor cells, normoxic and hypoxic glioblastoma stem-like cell lines. Finding the upregulated and downregulated gene and pathway interactions. Analysis to find the differential expression genes and pathway interactions. Materials and methods. The gene expression profiling data from the microarray dataset GSE45117 from the Gene Expression Omnibus (GEO) database, as well as differentially expressed genes (DEGs) between the 2 categories, are used in this analysis. 4 Samples of Glioblastoma tumors were considered as group 1 and 4 samples of normoxic and Hypoxic glioblastoma stem-like cell lines were considered as group 2 in the GEO2R web tool that has been used to screen them. Results. The gene-gene interactions among the DEGs and the GGI network with 37 nodes and 13 edges. The stem-cell-like cell lines showed lower expression of endothelin-related genes such as EDN3 and EDNRA along with dysregulation of enzymes such as PDK1, PGK1 which points to dysregulation of cellular respiratory pathways. This effect in consensus with under expression of cell attachment genes such as COL2A1, COL5A2, COL15A1 denotes a strong shift toward metastasis. Conclusion. Thus, a computational pipeline for identifying the significant genes and pathways involved in the glioblastoma tumors and glioblastoma stem-like cell lines. This study provides a path towards discovering potential leads for the treatment of glioblastoma and aids in comprehending the underlying novel molecular mechanisms.

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