Noncoding RNAs and Colorectal Cancer:A General Overview

MicroRNA ◽  
2020 ◽  
Vol 09 ◽  
Author(s):  
Jonathan Souza Sarraf ◽  
Taynah Cascaes Puty ◽  
Emanuely Magno da Silva ◽  
Thais Suellen Ramos Allen ◽  
Yasmim Souza Sarraf ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Clinical Practice ◽  
Noncoding Rnas ◽  
Target Prediction ◽  
Small Interfering Rnas ◽  
Noncoding Regions ◽  
Rna Molecules ◽  
Small Noncoding Rnas ◽  
Non Coding Rnas ◽  
Nucleolar Rnas

Background: Colorectal cancer (CRC) is the second most prevalent cancer in the world when nonmelanoma skin cases are not considered. Different epigenetic mechanisms play a role in the development of cancer. Noncoding RNAs (ncRNAs) are RNA molecules transcribed from noncoding regions of the genome. These are divided into sncRNAs (small noncoding RNAs: <200 nucleotides - including miRNAs [microRNAs], siRNAs [small interfering RNAs], piRNAs [piwi-interacting RNAs], snoRNAs [small nucleolar RNAs]) and lncRNAs (long noncoding RNAs: >200 nucleotides – includingcircular RNAs [circRNAs]). NcRNAs can act as oncogenes or as tumor suppressor genes in CRC and are potential biomarkers of diagnosis, with possible clinical implications. Objective: This article aims to make a general review around all types of non-coding RNAs and influence in colorectal cancer, focus in biomarkesof CRC and their possible applications in clinical practice, as well as review their biogenesis and functions. Furthermore, we seek to summarize possible databases available for new searches and studies that require sequence annotation, comparison sequences and target prediction for ncRNAs with the hope ofgathering information that can aid in the process of understanding and translating the use of ncRNAs into clinical practice.

scholarly journals MicroRNA-124 Regulates the Proliferation of Colorectal Cancer Cells by TargetingiASPP

2013 ◽  
Vol 2013 ◽  
pp. 1-10 ◽  
Author(s):  
Kuijie Liu ◽  
Hua Zhao ◽  
Hongliang Yao ◽  
Sanlin Lei ◽  
Zhendong Lei ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Cancer Cells ◽  
Target Prediction ◽  
Inhibitory Effect ◽  
Luciferase Reporter ◽  
Luciferase Reporter Gene ◽  
Small Noncoding Rnas ◽  
Colorectal Cancer Cells ◽  
Microrna 124

MicroRNAs are a class of small, noncoding RNAs that function as critical regulators of gene expression by targeting mRNAs for translational repression or degradation. In this study, we demonstrate that expression of microRNA-124 (miR-124) is significantly downregulated in colorectal cancer tissues and cell lines, compared to the matched adjacent tissues. We identified and confirmed inhibitor of apoptosis-stimulating protein of p53 (iASPP) as a novel, direct target of miR-124 using target prediction algorithms and luciferase reporter gene assays. Overexpression of miR-124 suppressed iASPP protein expression, upregulated expression of the downstream signaling molecule nuclear factor-kappa B (NF-κB), and attenuated cell viability, proliferation, and colony formation in SW480 and HT-29 colorectal cancer cells in vitro. Forced overexpression ofiASPPpartly rescued the inhibitory effect of miR-124 on SW480 and HT29 cell proliferation. Taken together, these findings shed light on the role and mechanism of action of miR-124, indicate that the miR-124/iASPP axis can regulate the proliferation of colorectal cancer cells, and suggest that miR-124 may serve as a potential therapeutic target for colorectal cancer.

scholarly journals Studying RNA–DNA interactome by Red-C identifies noncoding RNAs associated with various chromatin types and reveals transcription dynamics

2020 ◽  
Vol 48 (12) ◽  
pp. 6699-6714 ◽  
Author(s):  
Alexey A Gavrilov ◽  
Anastasiya A Zharikova ◽  
Aleksandra A Galitsyna ◽  
Artem V Luzhin ◽  
Natalia M Rubanova ◽  
...  
Keyword(s):  
Messenger Rna ◽  
Noncoding Rnas ◽  
K562 Cells ◽  
Biological Processes ◽  
Intron Splicing ◽  
Rna Molecules ◽  
Proximity Ligation ◽  
Data Support ◽  
Non Coding Rnas ◽  
Kinetics Of

Abstract Non-coding RNAs (ncRNAs) participate in various biological processes, including regulating transcription and sustaining genome 3D organization. Here, we present a method termed Red-C that exploits proximity ligation to identify contacts with the genome for all RNA molecules present in the nucleus. Using Red-C, we uncovered the RNA–DNA interactome of human K562 cells and identified hundreds of ncRNAs enriched in active or repressed chromatin, including previously undescribed RNAs. Analysis of the RNA–DNA interactome also allowed us to trace the kinetics of messenger RNA production. Our data support the model of co-transcriptional intron splicing, but not the hypothesis of the circularization of actively transcribed genes.

Small regulatory noncoding RNAs in Drosophila melanogaster: biogenesis and biological functions

2020 ◽  
Vol 19 (4) ◽  
pp. 309-323
Author(s):  
Saeed Soleimani ◽  
Zahra Valizadeh Arshad ◽  
Sharif Moradi ◽  
Ali Ahmadi ◽  
Seyed Javad Davarpanah ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Regulation Of Gene Expression ◽  
Noncoding Rnas ◽  
Critical Discussion ◽  
Rnai Pathway ◽  
Biological Functions ◽  
Small Interfering Rnas ◽  
Heterochromatin Formation ◽  
Small Noncoding Rnas ◽  
Small Ncrnas

Abstract RNA interference (RNAi) is an important phenomenon that has diverse genetic regulatory functions at the pre- and posttranscriptional levels. The major trigger for the RNAi pathway is double-stranded RNA (dsRNA). dsRNA is processed to generate various types of major small noncoding RNAs (ncRNAs) that include microRNAs (miRNAs), small interfering RNAs (siRNAs) and PIWI-interacting RNAs (piRNAs) in Drosophila melanogaster (D. melanogaster). Functionally, these small ncRNAs play critical roles in virtually all biological systems and developmental pathways. Identification and processing of dsRNAs and activation of RNAi machinery are the three major academic interests that surround RNAi research. Mechanistically, some of the important biological functions of RNAi are achieved through: (i) supporting genomic stability via degradation of foreign viral genomes; (ii) suppressing the movement of transposable elements and, most importantly, (iii) post-transcriptional regulation of gene expression by miRNAs that contribute to regulation of epigenetic modifications such as heterochromatin formation and genome imprinting. Here, we review various routes of small ncRNA biogenesis, as well as different RNAi-mediated pathways in D. melanogaster with a particular focus on signaling pathways. In addition, a critical discussion of the most relevant and latest findings that concern the significant contribution of small ncRNAs to the regulation of D. melanogaster physiology and pathophysiology is presented.

scholarly journals Regulatory non-coding RNAs: a new frontier in regulation of plant biology

2021 ◽  
Author(s):  
Sailaja Bhogireddy ◽  
Satendra K. Mangrauthia ◽  
Rakesh Kumar ◽  
Arun K. Pandey ◽  
Sadhana Singh ◽  
...  
Keyword(s):  
Stress Responses ◽  
Crop Improvement ◽  
Plant Biology ◽  
Circular Rnas ◽  
Homologous Sequence ◽  
Small Interfering Rnas ◽  
Rna Molecules ◽  
New Frontier ◽  
Non Coding Rnas

AbstractBeyond the most crucial roles of RNA molecules as a messenger, ribosomal, and transfer RNAs, the regulatory role of many non-coding RNAs (ncRNAs) in plant biology has been recognized. ncRNAs act as riboregulators by recognizing specific nucleic acid targets through homologous sequence interactions to regulate plant growth, development, and stress responses. Regulatory ncRNAs, ranging from small to long ncRNAs (lncRNAs), exert their control over a vast array of biological processes. Based on the mode of biogenesis and their function, ncRNAs evolved into different forms that include microRNAs (miRNAs), small interfering RNAs (siRNAs), miRNA variants (isomiRs), lncRNAs, circular RNAs (circRNAs), and derived ncRNAs. This article explains the different classes of ncRNAs and their role in plant development and stress responses. Furthermore, the applications of regulatory ncRNAs in crop improvement, targeting agriculturally important traits, have been discussed.

LncRNAs roles in Chemoresistance of Cancer cells

2021 ◽  
Vol 21 ◽  
Author(s):  
Sina Taghvimi ◽  
Sepideh Abbaszadeh ◽  
Fatemeh Bahrami Banan ◽  
Elahe Soltani Fard ◽  
Zeinab Jamali ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Noncoding Rnas ◽  
Signal Pathway ◽  
Tumor Formation ◽  
Minimum Length ◽  
Limiting Factor ◽  
Rna Molecules ◽  
Important Health ◽  
Non Coding Rnas ◽  
Important Health Issue

: Cancer is an important health issue worldwide. Cancer therapy is multifaceted, and drug resistance is still the major limiting factor in treatment of patients with this disease. Although the mechanisms of anticancer drug resistance have been broadly investigated, a massive biological signal pathway of Non-coding RNAs (ncRNAs) involved in this process has not been completely understood. Long noncoding RNAs (lncRNAs) are a kind of transcripts with a minimum length of 200 nucleotides in size which have a limited potential for coding proteins. The roles of these RNA molecules have been evaluated in relation to several pathological processes including tumor formation and progression. Increasing evidence haverecently reported that non-coding RNAs (ncRNAs), particularly long non-coding RNAs have significant roles in many cellular and genomic processes, and because of their potential in regulation specific genes, they are also involved in drug resistance. In this review, we review the literature on the features oflncRNA, their regulation roles in the gene expression related to chemoresistance and the potential of these RNAs as targeted therapies for personalized treatment in cancers.

scholarly journals Circulating Exosomal miRNAs as Biomarkers for the Diagnosis and Prognosis of Colorectal Cancer

2020 ◽  
Vol 22 (1) ◽  
pp. 346
Author(s):  
Katiusse Alves dos Santos ◽  
Isabelle Cristina Clemente dos Santos ◽  
Carollyne Santos Silva ◽  
Hériks Gomes Ribeiro ◽  
Igor de Farias Domingos ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Genetic Factors ◽  
Malignant Tumors ◽  
Noncoding Rnas ◽  
Distant Metastases ◽  
Stable Form ◽  
Overall Survival Rate ◽  
Small Noncoding Rnas ◽  
Diagnosis And Prognosis ◽  
Exosomal Mirnas

Colorectal cancer (CRC) is one of the most common malignant tumors in the gastrointestinal tract. It is a multifactorial disease that involves environmental factors, genetic factors, and lifestyle factors. Due to the absence of specific and sensitive biomarkers, CRC patients are usually diagnosed at an advanced stage and consequently suffer from a low 5-year overall survival rate. Despite improvements in surgical resection and adjuvant chemotherapy, the prognosis of patients with CRC remains unfavorable due to local and distant metastases. Several studies have shown that small noncoding RNAs, such as microRNAs packed in exosomes, are potential biomarkers in various types of cancers, including CRC, and that they can be detected in a stable form in both serum and plasma. In this review, we report the potential of circulating exosomal miRNAs to act as biomarkers for the diagnosis and prognosis of CRC.

scholarly journals Exosomal microRNAs and other non-coding RNAs as colorectal cancer biomarkers: a review

Mutagenesis ◽  
2019 ◽  
Vol 35 (3) ◽  
pp. 243-260 ◽  
Author(s):  
Antonio Francavilla ◽  
Szimonetta Turoczi ◽  
Sonia Tarallo ◽  
Pavel Vodicka ◽  
Barbara Pardini ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Expression Profiles ◽  
Predictive Markers ◽  
Circular Rnas ◽  
Rna Molecules ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
Prognostic And Predictive Markers

Abstract The circulating human transcriptome, which includes both coding and non-coding RNA (ncRNA) molecules, represents a rich source of potential biomarkers for colorectal cancer (CRC) that has only recently been explored. In particular, the release of RNA-containing extracellular vesicles (EVs), in a multitude of different in vitro cell systems and in a variety of body fluids, has attracted wide interest. The role of RNA species in EVs is still not fully understood, but their capacity to act as a form of distant communication between cells and their higher abundance in association with cancer demonstrated their relevance. In this review, we report the evidence from both in vitro and human studies on microRNAs (miRNAs) and other ncRNA profiles analysed in EVs in relation to CRC as diagnostic, prognostic and predictive markers. The studies so far highlighted that, in exosomes, the most studied category of EVs, several miRNAs are able to accurately discriminate CRC cases from controls as well as to describe the progression of the disease and its prognosis. Most of the time, the in vitro findings support the miRNA profiles detected in human exosomes. The expression profiles measured in exosomes and other EVs differ and, interestingly, there is a variability of expression also among different subsets of exosomes according to their proteic profile. On the other hand, evidence is still limited for what concerns exosome miRNAs as early diagnostic and predictive markers of treatment. Several other ncRNAs that are carried by exosomes, mostly long ncRNAs and circular RNAs, seem also to be dysregulated in CRC. Besides various technical challenges, such as the standardisation of EVs isolation methods and the optimisation of methodologies to characterise the whole spectrum of RNA molecules in exosomes, further studies are needed in order to elucidate their relevance as CRC markers.

scholarly journals The Emerging Landscape of Long Non-Coding RNAs in Colorectal Cancer Metastasis

2021 ◽  
Vol 11 ◽  
Author(s):  
Zhiming Liao ◽  
Hui Nie ◽  
Yutong Wang ◽  
Jingjing Luo ◽  
Jianhua Zhou ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Molecular Markers ◽  
Cancer Metastasis ◽  
Gastrointestinal Cancers ◽  
Malignant Phenotype ◽  
Rna Molecules ◽  
Non Coding Rna ◽  
Colorectal Cancer Metastasis ◽  
Non Coding Rnas ◽  
Patient Prognosis

Colorectal cancer (CRC) is one of the most common gastrointestinal cancers, with extremely high rates of morbidity and mortality. The main cause of death in CRC is distant metastasis; it affects patient prognosis and survival and is one of the key challenges in the treatment of CRC. Long non-coding RNAs (lncRNAs) are a group of non-coding RNA molecules with more than 200 nucleotides. Abnormal lncRNA expression is closely related to the occurrence and progression of several diseases, including cancer. Recent studies have shown that numerous lncRNAs play pivotal roles in the CRC metastasis, and reversing the expression of these lncRNAs through artificial means can reduce the malignant phenotype of metastatic CRC to some extent. This review summarizes the major mechanisms of lncRNAs in CRC metastasis and proposes lncRNAs as potential therapeutic targets for CRC and molecular markers for early diagnosis.

scholarly journals DANSR: A Tool for the Detection of Annotated and Novel Small RNAs

2022 ◽  
Vol 8 (1) ◽  
pp. 9
Author(s):  
Jin Zhang ◽  
Abdallah M. Eteleeb ◽  
Emily B. Rozycki ◽  
Matthew J. Inkman ◽  
Amy Ly ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Small Rna ◽  
Small Rnas ◽  
Noncoding Rna ◽  
Noncoding Rnas ◽  
Biologically Relevant ◽  
Small Noncoding Rna ◽  
Small Noncoding Rnas ◽  
Rna Analysis ◽  
Length Range

Existing small noncoding RNA analysis tools are optimized for processing short sequencing reads (17–35 nucleotides) to monitor microRNA expression. However, these strategies under-represent many biologically relevant classes of small noncoding RNAs in the 36–200 nucleotides length range (tRNAs, snoRNAs, etc.). To address this, we developed DANSR, a tool for the detection of annotated and novel small RNAs using sequencing reads with variable lengths (ranging from 17–200 nt). While DANSR is broadly applicable to any small RNA dataset, we applied it to a cohort of matched normal, primary, and distant metastatic colorectal cancer specimens to demonstrate its ability to quantify annotated small RNAs, discover novel genes, and calculate differential expression. DANSR is available as an open source tool.

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