scholarly journals MicroRNA Expression in Selected Carcinomas of the Gastrointestinal Tract

2011 ◽  
Vol 2011 ◽  
pp. 1-10 ◽  
Author(s):  
Nicole C. Panarelli ◽  
Rhonda K. Yantiss
Keyword(s):  
Gastrointestinal Tract ◽  
Mirna Expression ◽  
Tumor Suppressor Genes ◽  
Noncoding Rna ◽  
Messenger Rnas ◽  
Rna Sequences ◽  
Regulate Gene Expression ◽  
Number Of Genes ◽  
Mirna Species ◽  
Posttranscriptional Level

MicroRNAs (miRNAs) comprise a recently discovered class of small, 18–25 nucleotide, noncoding RNA sequences that regulate gene expression at the posttranscriptional level by binding to and inhibiting the translation of target messenger RNAs (mRNAs). Characteristic patterns of miRNA expression have been described in several malignancies of the gastrointestinal tract, and numerous investigators have demonstrated interactions between specific miRNA species and target oncogenes or tumor-suppressor genes. It is clear that miRNAs play an important role in regulating expression of a number of genes involved in gastrointestinal carcinogenesis, and, thus, these molecules may represent either diagnostic markers of, or therapeutic targets for, some types of malignancy. This paper summarizes the literature regarding miRNA expression in carcinomas of the colon, pancreas, and liver and discusses some of the mechanisms by which these molecules participate in gastrointestinal oncogenesis.

scholarly journals MicroRNAs as biomarkers for the diagnosis and prognosis of human cancer

2010 ◽  
Vol 1 (1) ◽  
pp. 14 ◽  
Author(s):  
Daniela Asslaber ◽  
Josefina Piñón Hofbauer ◽  
Richard Greil ◽  
Alexander Egle
Keyword(s):  
Mirna Expression ◽  
Tumor Suppressors ◽  
Noncoding Rna ◽  
Human Cancer ◽  
Regulate Gene Expression ◽  
Rna Molecules ◽  
Small Noncoding Rna ◽  
Diagnosis And Prognosis ◽  
Posttranscriptional Level ◽  
Regulate Gene

miRNAs are small-noncoding RNA molecules that regulate gene expression on a posttranscriptional level. A number of oncogenes and tumor suppressors were found to be targets of miRNAs and global miRNA expression signatures were able to distinguish between cancerous and non-cancerous tissues. Therefore it was not surprising that some miRNAs could be linked to the pathogenesis of cancer. In this review we provide an overview of the use of microRNAs as diagnostic and prognostic tools in cancer and focus on the use of miRNA expression as biomarker for disease activity.

scholarly journals MicroRNAs in Human Pituitary Adenomas

2014 ◽  
Vol 2014 ◽  
pp. 1-11 ◽  
Author(s):  
Xu-Hui Li ◽  
Elaine Lu Wang ◽  
Hai-Meng Zhou ◽  
Katsuhiko Yoshimoto ◽  
Zhi Rong Qian
Keyword(s):  
Pituitary Adenomas ◽  
Cell Cycle Control ◽  
Noncoding Rnas ◽  
Human Pituitary ◽  
Intracranial Neoplasms ◽  
Regulate Gene Expression ◽  
Cellular Processes ◽  
Number Of Genes ◽  
Novel Biomarkers ◽  
Posttranscriptional Level

MicroRNAs (miRNAs) are a class of recently identified noncoding RNAs that regulate gene expression at posttranscriptional level. Due to the large number of genes regulated by miRNAs, miRNAs play important roles in many cellular processes. Emerging evidence indicates that miRNAs are dysregulated in pituitary adenomas, a class of intracranial neoplasms which account for 10–15% of diagnosed brain tumors. Deregulated miRNAs and their targets contribute to pituitary adenomas progression and are associated with cell cycle control, apoptosis, invasion, and pharmacological treatment of pituitary adenomas. To provide an overview of miRNAs dysregulation and functions of these miRNAs in pituitary adenoma progression, we summarize the deregulated miRNAs and their targets to shed more light on their potential as therapeutic targets and novel biomarkers.

scholarly journals MicroRNAs in Hepatocellular Carcinoma: Regulation, Function, and Clinical Implications

2013 ◽  
Vol 2013 ◽  
pp. 1-14 ◽  
Author(s):  
Jie Sun ◽  
Haiqi Lu ◽  
Xian Wang ◽  
Hongchuan Jin
Keyword(s):  
Hepatocellular Carcinoma ◽  
Tumor Suppressor Genes ◽  
Early Stage ◽  
Untranslated Regions ◽  
Clinical Implications ◽  
Messenger Rnas ◽  
Aberrant Expression ◽  
Regulate Gene Expression ◽  
Poor Understanding ◽  
Regulation Function

Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide and the third cause of cancer-related death. Poor understanding of the mechanisms underlying the pathogenesis of HCC makes it difficult to be diagnosed and treated at early stage. MicroRNAs (miRNAs), a class of noncoding single-stranded RNAs of ~22 nucleotides in length, posttranscriptionally regulate gene expression by base pairing with the3′untranslated regions (3′UTRs) of target messenger RNAs (mRNAs). Aberrant expression of miRNAs is found in many if not all cancers, and many deregulated miRNAs have been proved to play crucial roles in the initiation and progression of cancers by regulating the expression of various oncogenes or tumor suppressor genes. In this Paper, we will summarize the regulations and functions of miRNAs aberrantly expressed in HCC and discuss the potential application of miRNAs as diagnostic and prognostic biomarkers of HCC and their potential roles in the intervention of HCC.

scholarly journals PlncRNA-HDeep: plant long noncoding RNA prediction using hybrid deep learning based on two encoding styles

2021 ◽  
Vol 22 (S3) ◽  
Author(s):  
Jun Meng ◽  
Qiang Kang ◽  
Zheng Chang ◽  
Yushi Luan
Keyword(s):  
Deep Learning ◽  
Noncoding Rna ◽  
Nearest Neighbor ◽  
Short Term Memory ◽  
Biological Activities ◽  
Support Vector ◽  
Multiple Perspectives ◽  
K Nearest Neighbor ◽  
Rna Sequences ◽  
Deep Learning Model

Abstract Background Long noncoding RNAs (lncRNAs) play an important role in regulating biological activities and their prediction is significant for exploring biological processes. Long short-term memory (LSTM) and convolutional neural network (CNN) can automatically extract and learn the abstract information from the encoded RNA sequences to avoid complex feature engineering. An ensemble model learns the information from multiple perspectives and shows better performance than a single model. It is feasible and interesting that the RNA sequence is considered as sentence and image to train LSTM and CNN respectively, and then the trained models are hybridized to predict lncRNAs. Up to present, there are various predictors for lncRNAs, but few of them are proposed for plant. A reliable and powerful predictor for plant lncRNAs is necessary. Results To boost the performance of predicting lncRNAs, this paper proposes a hybrid deep learning model based on two encoding styles (PlncRNA-HDeep), which does not require prior knowledge and only uses RNA sequences to train the models for predicting plant lncRNAs. It not only learns the diversified information from RNA sequences encoded by p-nucleotide and one-hot encodings, but also takes advantages of lncRNA-LSTM proposed in our previous study and CNN. The parameters are adjusted and three hybrid strategies are tested to maximize its performance. Experiment results show that PlncRNA-HDeep is more effective than lncRNA-LSTM and CNN and obtains 97.9% sensitivity, 95.1% precision, 96.5% accuracy and 96.5% F1 score on Zea mays dataset which are better than those of several shallow machine learning methods (support vector machine, random forest, k-nearest neighbor, decision tree, naive Bayes and logistic regression) and some existing tools (CNCI, PLEK, CPC2, LncADeep and lncRNAnet). Conclusions PlncRNA-HDeep is feasible and obtains the credible predictive results. It may also provide valuable references for other related research.

scholarly journals Interaction between Host MicroRNAs and the Gut Microbiota in Colorectal Cancer

mSystems ◽  
2018 ◽  
Vol 3 (3) ◽  
Author(s):  
Ce Yuan ◽  
Michael B. Burns ◽  
Subbaya Subramanian ◽  
Ran Blekhman
Keyword(s):  
Gene Expression ◽  
Colorectal Cancer ◽  
Gut Microbiota ◽  
Mirna Expression ◽  
Gut Microbiome ◽  
Noncoding Rna ◽  
Microbial Community Composition ◽  
Host Cells ◽  
Microbiome Composition ◽  
Small Noncoding Rna

ABSTRACT Although variation in gut microbiome composition has been linked with colorectal cancer (CRC), the factors that mediate the interactions between CRC tumors and the microbiome are poorly understood. MicroRNAs (miRNAs) are known to regulate CRC progression and are associated with patient survival outcomes. In addition, recent studies suggested that host miRNAs can also regulate bacterial growth and influence the composition of the gut microbiome. Here, we investigated the association between miRNA expression and microbiome composition in human CRC tumor and normal tissues. We identified 76 miRNAs as differentially expressed (DE) in tissue from CRC tumors and normal tissue, including the known oncogenic miRNAs miR-182, miR-503, and mir-17~92 cluster. These DE miRNAs were correlated with the relative abundances of several bacterial taxa, including Firmicutes , Bacteroidetes , and Proteobacteria . Bacteria correlated with DE miRNAs were enriched with distinct predicted metabolic categories. Additionally, we found that miRNAs that correlated with CRC-associated bacteria are predicted to regulate targets that are relevant for host-microbiome interactions and highlight a possible role for miRNA-driven glycan production in the recruitment of pathogenic microbial taxa. Our work characterized a global relationship between microbial community composition and miRNA expression in human CRC tissues. IMPORTANCE Recent studies have found an association between colorectal cancer (CRC) and the gut microbiota. One potential mechanism by which the microbiota can influence host physiology is through affecting gene expression in host cells. MicroRNAs (miRNAs) are small noncoding RNA molecules that can regulate gene expression and have important roles in cancer development. Here, we investigated the link between the gut microbiota and the expression of miRNA in CRC. We found that dozens of miRNAs are differentially regulated in CRC tumors and adjacent normal colon and that these miRNAs are correlated with the abundance of microbes in the tumor microenvironment. Moreover, we found that microbes that have been previously associated with CRC are correlated with miRNAs that regulate genes related to interactions with microbes. Notably, these miRNAs likely regulate glycan production, which is important for the recruitment of pathogenic microbial taxa to the tumor. This work provides a first systems-level map of the association between microbes and host miRNAs in the context of CRC and provides targets for further experimental validation and potential interventions.

The role of microRNA-21 in the onset and progression of cancer

2021 ◽  
Author(s):  
Ashutosh Singh ◽  
Ashutosh Kumar Singh ◽  
Rajanish Giri ◽  
Dhruv Kumar ◽  
Rohit Sharma ◽  
...  
Keyword(s):  
Cancer Detection ◽  
Tumor Suppressor Genes ◽  
Noncoding Rna ◽  
Early Cancer ◽  
Cancer Resistance ◽  
Aberrant Expression ◽  
Small Noncoding Rna ◽  
Expression Of Genes ◽  
Oncogenic Property

MicroRNAs (miRNAs), a class of small noncoding RNA, posttranscriptionally regulate the expression of genes. Aberrant expression of miRNA is reported in various types of cancer. Since the first report of oncomiR-21 involvement in the glioma, its upregulation was reported in multiple cancers and was allied with high oncogenic property. In addition to the downregulation of tumor suppressor genes, the miR-21 is also associated with cancer resistance to various chemotherapy. The recent research is appraising miR-21 as a promising cancer target and biomarker for early cancer detection. In this review, we briefly explain the biogenesis and regulation of miR-21 in cancer cells. Additionally, the review features the assorted genes/pathways regulated by the miR-21 in various cancer and cancer stem cells.

scholarly journals The circulating miRNAs as diagnostic and prognostic markers

2019 ◽  
Vol 57 (7) ◽  
pp. 932-953 ◽  
Author(s):  
Alessandro Terrinoni ◽  
Cosimo Calabrese ◽  
Daniela Basso ◽  
Ada Aita ◽  
Sabrina Caporali ◽  
...  
Keyword(s):  
Biological Fluids ◽  
Mature Mirnas ◽  
Transcriptional Level ◽  
Circulating Mirnas ◽  
Rna Sequences ◽  
Regulate Gene Expression ◽  
Rna Translation ◽  
Cellular Processes ◽  
New Class ◽  
Clinical Biomarkers

Abstract A large portion of the human genome transcribes RNA sequences that do not code for any proteins. The first of these sequences was identified in 1993, and the best known noncoding RNAs are microRNA (miRNAs). It is now fully established that miRNAs regulate approximately 30% of the known genes that codify proteins. miRNAs are involved in several biological processes, like cell proliferation, differentiation, apoptosis and metastatization. These RNA products regulate gene expression at the post-transcriptional level, modulating or inhibiting protein expression by interacting with specific sequences of mRNAs. Mature miRNAs can be detected in blood plasma, serum and also in a wide variety of biological fluids. They can be found associated with proteins, lipids as well as enclosed in exosome vesicles. We know that circulating miRNAs (C-miRNAs) can regulate several key cellular processes in tissues different from the production site. C-miRNAs behave as endogenous mediators of RNA translation, and an extraordinary knowledge on their function has been obtained in the last years. They can be secreted in different tissue cells and associated with specific pathological conditions. Significant evidence indicates that the initiation and progression of several pathologies are “highlighted” by the presence of specific C-miRNAs, underlining their potential diagnostic relevance as clinical biomarkers. Here we review the current literature on the possible use of this new class of molecules as clinical biomarkers of diseases.

79 microRNA EXPRESSION IN BOVINE CUMULUS CELLS

2015 ◽  
Vol 27 (1) ◽  
pp. 133
Author(s):  
K. Uhde ◽  
L. T. A. van Tol ◽  
T. A. E. Stout ◽  
B. A. J. Roelen
Keyword(s):  
Mirna Expression ◽  
Reference Genes ◽  
Noncoding Rna ◽  
Ovarian Follicle ◽  
Cumulus Cell ◽  
Cumulus Cells ◽  
Developmental Competence ◽  
Small Samples ◽  
Variable Expression

A mammalian oocyte within an ovarian follicle is surrounded by cumulus cells, together this structure is known as the cumulus-oocyte complex (COC). Cumulus cells are important for the development of the oocyte, they support the maturation process of the oocyte within the ovary and aid in sperm recognition. Because it is known that a Dicer knockout leads to infertility, microRNAs (miRNA) are focused to have an important role in oocyte development. MiRNAs are small noncoding RNA sequences that act as transcriptional regulators. Little is known about the expression of miRNA in cumulus cells or how cumulus-derived miRNA may regulate or be used to indicate the developmental competence of the maturing oocyte. Our aim was to investigate miRNA expression in oocytes and to identify and establish how specific miRNA influence the acquisition of developmental competence by bovine oocytes. Normalization of qPCR data requires stable reference genes. To this end, we tested the expression of various miRNA with respect to their ability to be used as reference miRNA for bovine cumulus cells; these included miR-103, miR-93, miR-26, let-7a, miR-191, and the small noncoding nuclear RNA U6. Cumulus-oocyte complexes were recovered from the ovaries of slaughtered cows and matured in vitro. Small samples of cumulus cells were collected from these COC before and after maturation. From the cumulus cell groups recovered at different stages, small RNA were extracted and cDNA was synthesised, followed by qRT-PCR. To identify the optimal combination of reference genes, the geNorm algorithm was used. MiR-26a and let-7a were identified as the most stably expressed miRNAs, whereas U6 showed the most variable expression levels. Future investigations are planned to identify miRNA in cumulus cells that can be used as markers for oocyte developmental competence. Using a single oocyte-embryo culture system will enable us to retrospectively relate cumulus miRNA expression to the developmental capacity of the oocyte.This work was supported by EU FP7 EpiHealthNet (N°317146).

scholarly journals Comprehensive Analysis of a Long Noncoding RNA-Associated Competing Endogenous RNA Network in Wilms Tumor

2020 ◽  
Vol 27 (2) ◽  
pp. 107327482093699
Author(s):  
Feng Zhang ◽  
Liping Zeng ◽  
Qinming Cai ◽  
Zihao Xu ◽  
Ruida Liu ◽  
...  
Keyword(s):  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Wilms Tumor ◽  
Interaction Network ◽  
Tumor Stage ◽  
Messenger Rnas ◽  
Competing Endogenous Rna ◽  
Ontology Term ◽  
Normal Tissues ◽  
Pathway Analyses

Long noncoding RNA (lncRNA) plays crucial roles in various biological processes of different cancers, especially acting as a competing endogenous RNA (ceRNA). However, the role of lncRNA-mediated ceRNA in Wilms tumor (WT), which is the most common malignant kidney cancer in children, remains unknown. In present study, RNA sequence profiles and clinical data of 125 patients with WT consisting of 119 tumor and 6 normal tissues from Therapeutically Applicable Research To Generate Effective Treatments database were analyzed. A total of 1833 lncRNAs, 156 microRNAs (miRNAs), and 3443 messenger RNAs (mRNAs) were identified as differentially expressed (DE) using “DESeq2” package. The lncRNA-miRNA-mRNA ceRNA regulatory network involving 748 DElncRNAs, 33 DEmiRNAs, and 189 DEmRNAs was constructed based on miRcode, Targetscan, miRTarBase, and miRDB database. Gene Ontology term and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed that DEmRNAs were mainly enriched in cell proliferation-related processes and tumor-related pathways, respectively, and 13 hub genes were identified by a protein–protein interaction network. Survival analysis detected 48 lncRNAs, 7 miRNAs, and 16 mRNAs to have significant impact on the overall survival of patients with WT. Additionally, we found that 6 DElncRNAs with potential prognostic value were correlated with tumor stage ( DENND5B-AS1) and histologic classification ( TMPO-AS1, RP3-523K23.2, RP11-598F7.3, LAMP5-AS1, and AC013275.2) of patients with WT. Our research provides a great insight into understanding the molecular mechanism underlying occurrence and progression of WT, as well as the potential to develop targeted therapies and prognostic biomarkers.

scholarly journals MicroRNA Theranostics in Prostate Cancer Precision Medicine

2016 ◽  
Vol 62 (10) ◽  
pp. 1318-1333 ◽  
Author(s):  
Farhana Matin ◽  
Varinder Jeet ◽  
Judith A Clements ◽  
George M Yousef ◽  
Jyotsna Batra
Keyword(s):  
Prostate Cancer ◽  
Precision Medicine ◽  
Noncoding Rna ◽  
Therapeutic Potential ◽  
Body Fluids ◽  
Messenger Rnas ◽  
Circulating Mirnas ◽  
Tumor Tissues ◽  
Early Phase Clinical Trials ◽  
Stable Forms

Abstract BACKGROUND Prostate cancer is the second most frequently diagnosed cancer in men worldwide. Theranostics, a combination of diagnostics and therapeutics, is an emerging concept in the field of precision medicine, and microRNAs (miRNAs) are predictive pioneers in this area. CONTENT miRNAs are small endogenous noncoding RNA molecules that regulate gene expression posttranscriptionally by targeting messenger RNAs. More than 60% of all protein coding genes are controlled by miRNAs, which makes them powerful regulators of the different cellular processes involved in the pathogenesis of various types of cancer, including prostate cancer. Growing evidence indicates the differential expression of miRNAs in tumor tissues. In addition, miRNAs in body fluids, known as circulating miRNAs, are present in remarkably stable forms and their alteration in prostate cancer has been well documented. Circulating miRNAs are known to originate from tumor tissues, thereby enabling intercellular communication via carriers to promote tumorigenesis and malignancy. In addition, fueled by recent advances, the use of miRNA-based anticancer therapies has been proposed with the onset of early phase clinical trials to assess the therapeutic efficacy of miRNAs. SUMMARY In this review, we summarize the theranostic utility of miRNAs and outline their diagnostic and prognostic potential in prostate cancer. In addition, we discuss the current detection methodologies and emerging innovative strategies for the detection of miRNAs in body fluids and tumor tissues in the clinical setting. We also provide insight into the current and future therapeutic potential of miRNAs in prostate cancer.

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