scholarly journals Genome-wide mRNA and miRNA expression profiling reveal multiple regulatory networks in colorectal cancer

2015 ◽  
Vol 6 (1) ◽  
pp. e1614-e1614 ◽  
Author(s):  
R Vishnubalaji ◽  
R Hamam ◽  
M-H Abdulla ◽  
M A V Mohammed ◽  
M Kassem ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Mirna Expression ◽  
Expression Profiling ◽  
Regulatory Networks ◽  
Genome Wide ◽  
Mirna Expression Profiling

scholarly journals Left-Sided Colorectal Cancer Distinct in Indigenous African Patients Compared to Other Ethnic Groups in South Africa.

2021 ◽  
Author(s):  
M. McCabe ◽  
C. Penny ◽  
P. Magangane ◽  
S. Mirza ◽  
Y. Perner
Keyword(s):  
Colorectal Cancer ◽  
South Africa ◽  
Ethnic Groups ◽  
Mirna Expression ◽  
Expression Profiling ◽  
Expression Patterns ◽  
Molecular Characteristics ◽  
Anatomical Site ◽  
Molecular Features ◽  
Mirna Expression Profiling

Abstract Introduction: A large proportion of indigenous African (IA) colorectal cancer (CRC) patients in South Africa are young (<50years), with no unique histopathological or molecular characteristics. Anatomical site as well as microsatellite instability (MSI) status have shown to be associated with different clinicopathological and molecular features. This study aimed to ascertain key histopathological and miRNA expression patterns in microsatellite stable (MSS) and low-frequency MSI (MSI-L) patients, to provide insight into the mechanism of the disease. Methods: A retrospective cohort (2011-2015) of MSS/MSI-L CRC patient samples diagnosed at Charlotte Maxeke Johannesburg Academic Hospital was analyzed. Samples were categorized by site [Right colon cancer (RCC) versus left (LCC)], ethnicity [IA versus other ethnic groups (OEG)] and MSI status (MSI-L vs MSS). T-test, Fischer’s exact and Chi-square tests were conducted. Additional miRNA expression profiling was performed on IA patient samples. Results: IA patients with LCC demonstrated an increased prevalence in males, sigmoid colon, signet-ring-cell morphology, MSI-L with BAT25/26 marker instability and advanced disease association. MiRNA expression profiling revealed unique clustering, with dysregulation of let-7 and miRNA-125. Conclusion: This study revealed distinct histopathological features for LCC, and suggests BAT25/26, miRNAs let-7a-5p and miRNA-125a/b-5p as negative prognostic markers in African CRC patients. Larger confirmatory studies are recommended.

scholarly journals Genome-Wide Uncovering of STAT3-Mediated miRNA Expression Profiles in Colorectal Cancer Cell Lines

2014 ◽  
Vol 2014 ◽  
pp. 1-11 ◽  
Author(s):  
Jufeng Zhang ◽  
Xia Luo ◽  
Huiming Li ◽  
Ling Deng ◽  
Ying Wang
Keyword(s):  
Colorectal Cancer ◽  
Cell Lines ◽  
Mirna Expression ◽  
Target Genes ◽  
Expression Profiles ◽  
Small Noncoding Rnas ◽  
Genome Wide ◽  
Go Enrichment ◽  
Mirna Expression Profiles ◽  
Mirna Expression Profiling

Colorectal cancer (CRC) is one of the most common malignancies resulting in high mortality worldwide. Signal transducer and activator of transcription 3 (STAT3) is an oncogenic transcription factor which is frequently activated and aberrantly expressed in CRC. MicroRNAs (miRNAs) are a class of small noncoding RNAs which play important roles in many cancers. However, little is known about the global miRNA profiles mediated by STAT3 in CRC cells. In the present study, we applied RNA interference to inhibit STAT3 expression and profiled the miRNA expression levels regulated by STAT3 in CRC cell lines with deep sequencing. We found that 26 and 21 known miRNAs were significantly overexpressed and downexpressed, respectively, in the STAT3-knockdown CRC cell line SW480 (SW480/STAT3-siRNA) compared to SW480 transfected with scrambled siRNAs (SW480/siRNA-control). The miRNA expression profiling was then validated by quantitative real-time PCR for selected known miRNAs. We further predicted the putative target genes for the dysregulated miRNAs and carried out functional annotation including GO enrichment and KEGG pathway analysis for selected miRNA targets. This study directly depicts STAT3-mediated miRNA profiles in CRC cells, which provides a possible way to discover biomarkers for CRC therapy.

Liposarcoma miRNA signatures identified from genome-wide miRNA expression profiling

2014 ◽  
Vol 10 (8) ◽  
pp. 1373-1386 ◽  
Author(s):  
Yuhong Zhou ◽  
Yong Zhang ◽  
Yuan Huang ◽  
Ruoying Tan ◽  
Tianshu Liu ◽  
...  
Keyword(s):  
Mirna Expression ◽  
Expression Profiling ◽  
Genome Wide ◽  
Mirna Expression Profiling

scholarly journals Genome-Wide miRNA Expression Profiling Identifies miR-9-3 and miR-193a as Targets for DNA Methylation in Non–Small Cell Lung Cancers

2012 ◽  
Vol 18 (6) ◽  
pp. 1619-1629 ◽  
Author(s):  
Gerwin Heller ◽  
Marlene Weinzierl ◽  
Christian Noll ◽  
Valerie Babinsky ◽  
Barbara Ziegler ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Mirna Expression ◽  
Expression Profiling ◽  
Small Cell ◽  
Small Cell Lung ◽  
Lung Cancers ◽  
Genome Wide ◽  
Mirna Expression Profiling

scholarly journals Identification of Transcriptional Markers and microRNA–mRNA Regulatory Networks in Colon Cancer by Integrative Analysis of mRNA and microRNA Expression Profiles in Colon Tumor Stroma

Cells ◽  
2019 ◽  
Vol 8 (9) ◽  
pp. 1054 ◽  
Author(s):  
Md. Nazim Uddin ◽  
Mengyuan Li ◽  
Xiaosheng Wang
Keyword(s):  
Colon Cancer ◽  
Mirna Expression ◽  
Expression Profiling ◽  
Regulatory Networks ◽  
Tumor Stroma ◽  
Receptor Interaction ◽  
Colon Tumor ◽  
Ppi Network ◽  
Hub Genes ◽  
Mirna Expression Profiling

The aberrant expression of microRNAs (miRNAs) and genes in tumor microenvironment (TME) has been associated with the pathogenesis of colon cancer. An integrative exploration of transcriptional markers (gene signatures) and miRNA–mRNA regulatory networks in colon tumor stroma (CTS) remains lacking. Using two datasets of mRNA and miRNA expression profiling in CTS, we identified differentially expressed miRNAs (DEmiRs) and differentially expressed genes (DEGs) between CTS and normal stroma. Furthermore, we identified the transcriptional markers which were both gene targets of DEmiRs and hub genes in the protein–protein interaction (PPI) network of DEGs. Moreover, we investigated the associations between the transcriptional markers and tumor immunity in colon cancer. We identified 17 upregulated and seven downregulated DEmiRs in CTS relative to normal stroma based on a miRNA expression profiling dataset. Pathway analysis revealed that the downregulated DEmiRs were significantly involved in 25 KEGG pathways (such as TGF-β, Wnt, cell adhesion molecules, and cytokine–cytokine receptor interaction), and the upregulated DEmiRs were involved in 10 pathways (such as extracellular matrix (ECM)-receptor interaction and proteoglycans in cancer). Moreover, we identified 460 DEGs in CTS versus normal stroma by a meta-analysis of two gene expression profiling datasets. Among them, eight upregulated DEGs were both hub genes in the PPI network of DEGs and target genes of the downregulated DEmiRs. We found that three of the eight DEGs were negative prognostic factors consistently in two colon cancer cohorts, including COL5A2, EDNRA, and OLR1. The identification of transcriptional markers and miRNA–mRNA regulatory networks in CTS may provide insights into the mechanism of tumor immune microenvironment regulation in colon cancer.

scholarly journals Genome-wide miRNA expression profiling in potato (Solanum tuberosum L.) reveals TOR-dependent post-transcriptional gene regulatory networks in diverse metabolic pathway

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10704
Author(s):  
Kexuan Deng ◽  
Huan Yin ◽  
Fangjie Xiong ◽  
Li Feng ◽  
Pan Dong ◽  
...  
Keyword(s):  
Gene Regulatory Networks ◽  
Mirna Expression ◽  
Expression Profiling ◽  
Regulatory Networks ◽  
Large Scale ◽  
Solanum Tuberosum L ◽  
Transcriptional Level ◽  
Promote Cell Proliferation ◽  
Gene Regulatory ◽  
Mirna Expression Profiling

Target of rapamycin (TOR) operates as a hub of the signal transduction that integrates nutrient and energy signaling to promote cell proliferation and growth through mediating the transcriptional and post- transcriptional regulator networks in all eukaryotic species. MicroRNAs (miRNAs) are widespread classes of small, single-stranded, non-coding endogenous RNAs and are widely found in eukaryotes, which play a vital role in regulating gene expression by degrading targeted mRNAs or translational repression at post-transcriptional level. Recent studies found that there were necessarily close connections between miRNA and TOR pathways in mammals. However, there is little information about the interplay between the miRNA and TOR in plants. Thus, the aim of this study was to identify potential TOR-miRNA-mRNA regulatory networks in TOR signaling through global mRNA and microRNA expression profiling in potato. Based on the previous high-throughput transcriptome sequencing and filtering, a total of 2,899 genes were significantly differentially expressed in potato under TOR inhibitors treatment. Pathway analysis revealed that these genes were significantly enriched in multiple metabolic processes. Similarly, in the present study, suppression of TOR resulted in 41 miRNAs up-regulated and 45 down-regulated, revealing that TOR plays a crucial role in the regulation of miRNA regulatory network. Furthermore, integrated mRNA and miRNA expression profiling uncovered that these miRNAs participated in large-scale metabolic process in the TOR signal pathway in potato, such as regulation of autophagy and ubiquitination, and biosynthesis of secondary metabolites. Overall, the results shed new insight into TOR related post-transcriptional gene regulatory networks in potato and suggesting TOR-miRNA-targeting genes relevant networks as a potential genetic resource for potato improvement.

scholarly journals Identification of novel MiRNAs and MiRNA expression profiling during grain development in indica rice

BMC Genomics ◽  
2012 ◽  
Vol 13 (1) ◽  
pp. 264 ◽  
Author(s):  
Ying Lan ◽  
Ning Su ◽  
Yi Shen ◽  
Rongzhi Zhang ◽  
Fuqing Wu ◽  
...  
Keyword(s):  
Mirna Expression ◽  
Expression Profiling ◽  
Indica Rice ◽  
Grain Development ◽  
Mirna Expression Profiling
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