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Methylation of hypoxia-inducible factor 3 subunit alpha contributes to poor prognosis in lung adenocarcinoma
J Appl Genet. 2023 Sep 14. doi: 10.1007/s13353-023-00784-6. Online ahead of print.ABSTRACTHypoxia-inducible factor 3 subunit alpha (HIF3A) has been implicated in various types of cancers, while its precise role in the lung adenocarcinoma remains unclear. Our study aimed to investigate the roles of HIF3A in lung adenocarcinoma and its regulation by DNA methylation. We utilized bioinformatic tools, including UALCAN and KMPlot, to analyze the relationship between HIF3A expression, DNA methylation, and patient survival rate in lung adenocarcinoma. We also used siRNA-mediated knockdown of HIF3A and DNA-methyltransferase 1 (DNMT...
Source: J Appl Genet - September 14, 2023 Category: Genetics & Stem Cells Authors: Qin Shi Xiuxia Zheng Ying Hu Zhan Zhou Minshan Fang Xinhui Huang Source Type: research

GSE207250 MiRNA array analysis of VMRC-LCD cells following ASCL1 knockdown function.
Contributors : Takayoshi Enokido ; Naoya Miyashita ; Akira SaitoSeries Type : Non-coding RNA profiling by arrayOrganism : Homo sapiens ; synthetic constructTo investigate the function of ASCL1 in ASCL1-positive lung adenocarcinoma, we established VMRC-LCD cell line in which the target gene has been knocked down by siRNA.We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different cells.
Source: GEO: Gene Expression Omnibus - July 1, 2023 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by array Homo sapiens synthetic construct Source Type: research

Transcriptomic and functional studies reveal miR-431-5p as a tumour suppressor in pancreatic ductal adenocarcinoma cells
Gene. 2022 Feb 16:146346. doi: 10.1016/j.gene.2022.146346. Online ahead of print.ABSTRACTThe lactate receptor HCAR1 (hydroxycarboxylic acid receptor 1) is highly expressed in pancreatic ductal adenocarcinoma (PDAC), where it regulates lactate transport between the cancer cells. Little is known about the underlying cause of high HCAR1 expression in PDAC, and in the present study, we investigated whether HCAR1 could be a target of miRNA regulation. By searching for predicted miRNA candidates in silico, we identified miR-431-5p as a possible regulator of HCAR1. We found miR-431-5p to repress HCAR1 expression through direct bi...
Source: Gene - February 19, 2022 Category: Genetics & Stem Cells Authors: Oyvind P Haugen Cuong Khuu Hanne M Weidemann Tor Paaske Utheim Linda Hildegard Bergersen Source Type: research

KRT18 Modulates Alternative Splicing of Genes Involved in Proliferation and Apoptosis Processes in Both Gastric Cancer Cells and Clinical Samples
Keratin 18 (KRT18), one of the most abundant keratins in epithelial and endothelial cells, has been reported to be aberrantly expressed in many malignancies and extensively regarded as a biomarker and important regulator in multiple cancers, including gastric cancer (GC). But the molecular regulatory mechanisms of KRT18 in GC patients and cells are largely unknown. In the present study, we analyzed the expression level of KRT18 in 450 stomach adenocarcinoma tissue samples from TCGA database and found a significantly higher expression level in tumor tissues. We then explored the potential functions of KRT18 in AGS cells (hu...
Source: Frontiers in Genetics - July 5, 2021 Category: Genetics & Stem Cells Source Type: research

GSE173433 Single-cell RNA-seq following APE1/Ref-1 knockdown in Pancreatic Ductal Adenocarcinoma
Series Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensAPE1 was knocked down using siRNA in low passage patient-derived PDAC cells and the resulting cells, along with control cells were analysed using scRNA-seq to identify differentially expressed genes and pathways as a result of APE1 knock-down.
Source: GEO: Gene Expression Omnibus - April 28, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE164921 Global transcriptomic changes in alveolar epithelial type II (ATII) cells upon GRK6 depletion based on RNA-seq
Contributors : Y Zhou ; L Yao ; S Yao ; Y WangSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensG protein coupled receptor kinase 6 (GRK6) is a member of the GRKs family, which is expressed in various tissues and involved in the development of several diseases, including lung adenocarcinoma. Our previous study suggested that GRK6 expression was significantly down-regulated in lung adenocarcinoma patients, and its level was an independent prognostic factor for overall survival. Here, by performing RNA-sequencing (RNA-seq) in alveolar epithelial type II (ATII) cells transfected with eithe...
Source: GEO: Gene Expression Omnibus - April 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE167590 SOX9 modulates cancer biomarker and cilia genes in pancreatic cancer
We report 93 differentially expressed (DE) genes, with convergence on alterations to Notch-signaling pathways and ciliogenesis. These results point to SOX9 and Notch activity being in a positive feedback loop; and, SOX9 regulating cilia production in PDAC. We additionally performed ChIP-seq in PANC-1 cells to identify direct targets of SOX9 binding and integrated these results with our DE gene list. Nine of the top ten downregulated genes have evidence of direct SOX9 binding at their promoter regions.  One of these targets was the cancer stem cell marker EpCAM. Using whole-mount in situ hybridization to detect epcam ...
Source: GEO: Gene Expression Omnibus - February 27, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

Deregulation of a Cis-Acting lncRNA in Non-small Cell Lung Cancer May Control HMGA1 Expression
ConclusionOur results suggest that HMGA1-lnc is a novel cis-acting lncRNA that negatively regulates HMGA1 gene expression in lung cells. Further characterization of this regulatory mechanism may advance our understanding of the maintenance of lung cancer phenotypes and uncover a novel therapeutic intervention point for tumors driven by HMGA1.
Source: Frontiers in Genetics - January 11, 2021 Category: Genetics & Stem Cells Source Type: research

GSE132813 Master transcription factors form interconnected circuitry and orchestrate transcriptional networks in esophageal adenocarcinoma
Contributors : Jian Pan ; Tiago C Silva ; Nicole Gull ; Qian Yang ; Jasmine Plummer ; Stephanie Chen ; Kenji Daigo ; Takao Hamakubo ; Ling-Wen Ding ; Samuel J Klempner ; Benjamin P Berman ; H P Koeffler ; De-Chen LinSeries Type : Genome binding/occupancy profiling by high throughput sequencing ; Expression profiling by high throughput sequencing ; OtherOrganism : Homo sapiensWe profiled fresh-frozen esophageal tumor and normal samples and cell lines with chromatin immunoprecipitation sequencing (ChIP-Seq). Mathematically modeling was performed to establish (super)-enhancers landscapes and inter-connected transcriptional ci...
Source: GEO: Gene Expression Omnibus - June 14, 2020 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Expression profiling by high throughput sequencing Other Homo sapiens Source Type: research

Genes, Vol. 10, Pages 921: Wnt-11 Expression Promotes Invasiveness and Correlates with Survival in Human Pancreatic Ductal Adeno Carcinoma
ysal-Onganer Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest forms of cancer, proving difficult to manage clinically. Wnt-11, a developmentally regulated gene producing a secreted protein, has been associated with various carcinomas but has not previously been studied in PDAC. The present study aimed to elucidate these aspects first in vitro and then in a clinical setting in vivo. Molecular analyses of Wnt-11 expression as well as other biomarkers involved qRT-PCR, RNA-seq and siRNA. Proliferation was measured by MTT; invasiveness was quantified by Boyden chamber (Matrigel) assay. Wnt-11 mRNA was presen...
Source: Genes - November 10, 2019 Category: Genetics & Stem Cells Authors: Dart Arisan Owen Hao Jiang Uysal-Onganer Tags: Article Source Type: research

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