Molecular analysis of long non-coding RNA GAS5 and microRNA-34a expression signature in common solid tumors: A pilot study (original) (raw)
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Research Square (Research Square), 2023
BACKGROUND Breast cancer as one of the most causes of cancer-related mortality in women has attracted the attention of researchers. Recently, biological biomarkers play important roles in the early diagnosis of breast cancers in clinics. They considered non-invasive biomarkers for cancer diagnosis and play an important role in the prevention of tumor development. OBJECTIVE We aimed to investigate lnc RNA MIR17HG which is the host gene for generating miR17-92 cluster. We employed bioinformatics and experimental approaches to evaluate the expression level of variants of lnc RNA MIR17HG and its derived miRNAs (miR18a-5p and miR20a-5p) and also its neighbor gene (GPC5). In addition, we evaluated the correlation of candidate genes to predict the similarity function of targeted genes in breast tumors and nally, we surveyed the e cacy of selected genes as new potential diagnostic biomarkers in discriminating against breast cancer patients and non-cancerous. METHODS We used bioinformatic tools to analyze TCGA data in order to predict results at the rst step. The expression levels of candidate genes were assessed within tumors and adjacent normal tissues by qRT-PCR. Their impacts as diagnosis breast cancer biomarkers were evaluated by ROC curve analysis. The relation of candidate genes is also evaluated by Pearson's correlation coe cients. RESULTS According to our ndings, MIR17HG and its derived miRNAs showed up-regulation and GPC5 showed down-regulation in BC. They also have a positive linear correlation in breast tumors and could discriminate between cancer and non-cancerous breast tissues. CONCLUSIONS Our data analysis showed differentially expressed of MIR17HG and its derived miRNAs and GPC5 in breast tissues compared to adj-normal tissue. Also, we demonstrate a linear correlation between candidate genes. In addition, selected genes can potentially act in discriminating tumor tissues and adjnormal tissue as breast cancer diagnosis biomarkers. factors cause the occurrence of cancer in people. However, environmental factors and heredity are the two most important causes of BC[1, 2] According to worldwide reports in 2021, more than 28 1550 new cases of BC have been identi ed in women and more than 2600 new cases in men[3]. On average, 1.3 million women are affected by BC, 14% of all cancer-related deaths are caused by BC[4], and 3% of women die from BC every year [5]. The highest rate of patients with this disease has been reported among women in the age group of 21 to 30 years[6], and also the best prognosis age is the aged between 35 to 49[7]. Recently, the important role of noncoding has been shown as a new biomarker for many cancers such as BC, and then early detection has become important in BC treatment and prevention of tumor development. So potential applications of non-coding RNAs for therapeutic application, diagnosis, and treatment have a signi cant role under extensive study speci cally in BC [8]. Noncoding transcripts are a wide range of genomes without coding potential, while associated with the regulation of differentiation and development [9].Noncoding RNAs (ncRNAs) can be smaller than 200 nucleotides to up to several kilobases. They are classi ed based on their length, biogenesis, polarity (sense or antisense), and putative functions[10]. Linear RNAs, such as small RNA and long non-coding RNAs and circular RNAs, are the most known subclasses of noncoding RNAs [11]. The ncRNAs are involved in controlling biological processes, mRNA transcription, splicing, and translation. The ncRNAs play a major role as potential therapeutic targets. Based on the studies, applications of non-coding RNAs are diagnosed as diagnostic biomarkers in personalized medicine[12]. Long noncoding RNAs (lncRNAs) are a kind of non-coding RNAs (ncRNAs) with over 200 nucleotides (nt) in length, and they have no encoding proteins. The lncRNAs have important biological functions in cellular processes such as differentiation, proliferation, and metastasis [13, 14]. In addition, lncRNAs act as vital regulators in various gene expressions, and also, they have oncogenic or tumor suppressor roles in tumorigenesis [15]. For example, previous studies revealed up-regulation of lncRNA HOTAIR in BC[16]. Moreover, the lncRNAs might have a role as a biomarker in cancer, for example, linc-RoR is found to be associated with OSCC tumor recurrence and poor prognosis [17]. Small Non-coding RNA is a family of regulatory non-coding RNAs which are 18-200 nt in length. They include Piwi-interacting RNAs (piRNAs), small interfering RNAs (siRNAs), and microRNAs (miRNAs) which known as regulators of gene expression [18, 19]. Evidence has revealed the biomarker potential of Small Noncoding RNA in biological uids, such as serum, plasma, and urine, for a wide range of diseases and early diagnosis [20]. Micro RNAs (miRNAs) are small single-stranded noncoding RNAs with a length of 18-24 nucleotides. These small non-coding RNAs are involved in cellular processes, post-transcriptional regulation of 30 to 60% of genes, biological pathways, and cell signaling [21, 22]. miRNAs play a role in the degradation and/or translation inhibition process by the speci c binding sites of the target gene mRNA 3'UTR
Scientific Reports
Long non-coding RNAs (lncRNAs) and microRNAs are involved in numerous physio-pathological conditions included cancer. To better understand the molecular mechanism of the oral antitumor multikinase inhibitor sorafenib, we profiled the expression of a panel of lncRNAs and miRNAs by qPCR array in a sorafenib-treated hepatocellular carcinoma (HCC) cell line. Among the most affected ncRNAs, we found that sorafenib mediated the dysregulation of the lncRNAs GAS5, HOTTIP and HOXA-AS2 and the miR-126-3p, in a panel of human cancer cell lines (HCC, renal and breast carcinomas). By luciferase gene reporter assay, we discovered that GAS5 may act as a sponge for miR-126-3p in HCC cells. The expression level of GAS5 and miR-126-3p was verified in human liquid and/or solid biopsies from HCC patients. miR-126-3p expression in HCC tissues was decreased respect to their correspondent peritumoral tissues. The levels of plasmatic circulating miR-126-3p and GAS5 were significantly higher and lower in HCC patients compared to healthy subjects, respectively. This study highlighted the capability of sorafenib to modulate the expression of a wide range of ncRNAs and specifically, GAS5 and miR-126-3p were involved in the response to sorafenib of different cancer cell types. Non-coding RNAs (ncRNAs) can be divided into 2 classes according to their size: short ncRNAs with less than 200 nt and long ncRNAs (lncRNAs) with more than 200 nt. lncRNAs are a heterogeneous group of RNAs ranging from 200 to 100,000 nt in length with very limited or absent protein-coding capacity. They have been implicated in controlling gene expression, imprinting, and inactivation of X-chromosome, but the effects or mechanisms of action of most lncRNAs remain unknown 1,2. LncRNAs have been emerging as essential players in the pathogenesis of cancer and their dysregulation has been closely associated with tumor development, progression and metastasis 3,4. Among the short ncRNAs, microRNAs (miRNAs) are one of the best studied and characterized classes. Mature miRs are about 22 nt long and they mainly control post-transcriptional gene expression by promoting degradation or repressing translation of target mRNAs 5. In human cancer, the dysregulation of miRNAs expression has been extensively reported 6,7. Human hepatocellular carcinoma (HCC) is the most common malignancy of the liver worldwide and ranks as the third cause of cancer-related deaths. HCC develops in cirrhotic liver in 80-90% of patients. HBV, HCV infections and alcohol abuse are the main risk factors of cirrhosis and consequently HCC 8,9. Sorafenib is an oral multikinase inhibitor used to treat advanced and unresecable HCCs 10. It is a small molecule that inhibits several serine/threonine and tyrosine kinases (CRAF, BRAF, VEGFR-2 and-3, PDGFR-ß, FGFR-1, c-kit, and Fms-like tyrosine kinase 3 (Flt-3)) in multiple oncogenic signaling pathways 11,12. Although it is an effective anti-tumor treatment, some patients are non-responder, that is resistant to or developing resistance during therapy with sorafenib. For these reasons, efforts have been put into identifying strategies to make sorafenib a more active
Oncology and Translational Medicine, 2022
Objective Long non-coding RNAs (lncRNAs) regulate tumor development and progression by promoting tumor proliferation, invasion, and metastasis. The aim of the study was to investigate the effects of lncRNA growth arrest-special 5 (GAS5) on proliferation and apoptosis of hepatocellular carcinoma (HCC) cells through miR-26a-5p action. Methods Expression levels of GAS5 were detected in cancerous and paracancerous tissue of 80 HCC patients by RT-qPCR. The starBase tool predicted that GAS5 had binding sites for the miRNA miR-26a-5p, which was also highly expressed in HCC tissue. The relationship between GAS5 and miR-26a-5p was confirmed using a luciferase reporter assay. The role of these lncRNAs was further explored by transfecting plasmids into SMMC-7721 cells and classifying the cells as follows: NC group, GAS5 group, anti-miR-26a-5p group, and GAS5 + miR-26a-5p group. Cell proliferation, cell cycle, and apoptosis were detected in each group. The relationship between miR-26a-5p and phosphatase and tensin homolog deleted on chromosome 10 (PTEN) was analyzed by TargetScan database prediction and luciferase reporter assay. Western blotting was used to quantify PTEN, phosphatidylinositol 3-kinase (PI3K), phosphorylated protein kinase B (p-Akt), cyclin D1, and human P27 protein (P27). Results GAS5 was downregulated, while miR-26a-5p was upregulated in HCC tissue compared to in paracancerous tissue. High GAS5 levels and low miR-26a-5p levels inhibited cell proliferation, increased the number of G0/G1 phase cells, promoted cell apoptosis, promoted PTEN and P27 expression, and inhibited PI3K, P-Akt, and cyclin D1 expression at the protein level. Upregulation of miR-26a-5p attenuated the effects of GAS5 upregulation on the proliferation, cell cycle, and apoptosis of HCC cells and on the expression of PTNE/PI3K/Akt signaling pathway-related proteins. Conclusion Low GAS5 levels regulate the proliferation and apoptosis of HCC cells via the PTNE/PI3K/ Akt signaling pathway and are linked to upregulation of miR-26a-5p.
A microRNA expression signature of human solid tumors defines cancer gene targets
Proceedings of The National Academy of Sciences, 2006
Small noncoding microRNAs (miRNAs) can contribute to cancer development and progression and are differentially expressed in normal tissues and cancers. From a large-scale miRnome analysis on 540 samples including lung, breast, stomach, prostate, colon, and pancreatic tumors, we identified a solid cancer miRNA signature composed by a large portion of overexpressed miRNAs. Among these miRNAs are some with well characterized cancer association, such as miR-17-5p, miR-20a, miR-21, miR-92, miR-106a, and miR-155. The predicted targets for the differentially expressed miRNAs are significantly enriched for protein-coding tumor suppressors and oncogenes (P < 0.0001). A number of the predicted targets, including the tumor suppressors RB1 (Retinoblastoma 1) and TGFBR2 (transforming growth factor, beta receptor II) genes were confirmed experimentally. Our results indicate that miRNAs are extensively involved in cancer pathogenesis of solid tumors and support their function as either dominant or recessive cancer genes.
Long noncoding RNA associated-competing endogenous RNAs in gastric cancer
Scientific reports, 2014
Some long noncoding RNAs (lncRNAs) play important roles in the regulation of gene expression by acting as competing endogenous RNAs (ceRNAs). However, the roles of lncRNA associated-ceRNAs in oncogenesis are not fully understood. Here, based on lncRNA microarray data of gastric cancer, bioinformatic algorithm miRcode and microRNA (miRNA) targets database TarBase, we first constructed an lncRNA-miRNA-mRNA network. Then, we confirmed it by data of six types of other cancer including head and neck squamous cell carcinoma, prostate cancer, papillary thyroid carcinoma, pituitary gonadotrope tumors, ovarian cancer, and chronic lymphocytic leukemia. The results showed a clear cancer-associated ceRNA network. Eight lncRNAs (AC009499.1, GACAT1, GACAT3, H19, LINC00152, AP000288.2, FER1L4, and RP4-620F22.3) and nine miRNAs (miR-18a-5p, miR-18b-5p, miR-19a-3p, miR-20b-5p, miR-106a-5p, miR-106b-5p, miR-31-5p, miR-139-5p, and miR-195-5p) were involved. For instance, through its miRNA response ele...
The Biological Role and Translational Implications of the Long Non-Coding RNA GAS5 in Breast Cancer
Cancers
The lncRNA GAS5 plays a significant role in tumorigenicity and progression of breast cancer (BC). In this review, we first summarize the role of GAS5 in cell biology, focusing on its expression data in human normal tissues. We present data on GAS5 expression in human BC tissues, highlighting its downregulation in all major BC classes. The main findings regarding the molecular mechanisms underlying GAS5 dysregulation are discussed, including DNA hypermethylation of the CpG island located in the promoter region of the gene. We focused on the action of GAS5 as a miRNA sponge, which is able to sequester microRNAs and modulate the expression levels of their mRNA targets, particularly those involved in cell invasion, apoptosis, and drug response. In the second part, we highlight the translational implications of GAS5 in BC. We discuss the current knowledge on the role of GAS5 as candidate prognostic factor, a responsive molecular therapeutic target, and a circulating biomarker in liquid b...
Non-Coding RNA, 2019
Long non-coding RNA (lncRNA) genes encode non-messenger RNAs that lack open reading frames (ORFs) longer than 300 nucleotides, lack evolutionary conservation in their shorter ORFs, and do not belong to any classical non-coding RNA category. LncRNA genes equal, or exceed in number, protein-coding genes in mammalian genomes. Most mammalian genomes harbor ~20,000 protein-coding genes that give rise to conventional messenger RNA (mRNA) transcripts. These coding genes exhibit sweeping evolutionary conservation in their ORFs. LncRNAs function via different mechanisms, including but not limited to: (1) serving as “enhancer” RNAs regulating nearby coding genes in cis; (2) functioning as scaffolds to create ribonucleoprotein (RNP) complexes; (3) serving as sponges for microRNAs; (4) acting as ribo-mimics of consensus transcription factor binding sites in genomic DNA; (5) hybridizing to other nucleic acids (mRNAs and genomic DNA); and, rarely, (6) as templates encoding small open reading fram...
Scientific Reports
Cancer is a complex disease with a fatal outcome. Early detection of cancer, by monitoring appropriate molecular markers is very important for its therapeutic management. In this regard, the short non-coding RNA molecules, microRNAs (miRNAs) have shown great promise due to their availability in circulating fluids facilitating non-invasive detection of cancer. In this study, an in silico comparative analysis was performed to identify specific signature miRNAs dysregulated across multiple carcinomas and simultaneously identify unique miRNAs for each cancer type as well. The miRNA-seq data of cancer patient was obtained from GDC portal and their differential expressions along with the pathways regulated by both common and unique miRNAs were analyzed. Our studies show twelve miRNAs commonly dysregulated across seven different cancer types. Interestingly, four of those miRNAs (hsa-mir-210, hsa-mir-19a, hsa-mir-7 and hsa-mir-3662) are already reported as circulatory miRNAs (circRNAs); whi...
Cancer Research, 2007
MicroRNAs are small noncoding RNAs that function by regulating target gene expression posttranscriptionally. They play a critical role in developmental and physiologic processes and are implicated in the pathogenesis of several human diseases including cancer. We examined the expression profiles of 241 human microRNAs in normal tissues and the NCI-60 panel of human tumor-derived cell lines. To quantify micro-RNA expression, we employed a highly sensitive technique that uses stem-loop primers for reverse transcription followed by real-time PCR. Most microRNAs were expressed at lower levels in tumor-derived cell lines compared with the corresponding normal tissue. Agglomerative hierarchical clustering analysis of microRNA expression revealed four groups among the NCI-60 cell lines consisting of hematologic, colon, central nervous system, and melanoma tumor-derived cell lines clustered in a manner that reflected their tissue of origin. We identified specific subsets of microRNAs that provide candidate molecular signatures characteristic of the tumor-derived cell lines belonging to these four clusters. We also identified specific microRNA expression patterns that correlated with the proliferation indices of the NCI-60 cell lines, and we developed evidence for the identification of specific microRNAs as candidate oncogenes and tumor suppressor genes in different tumor types. Our results provide evidence that microRNA expression patterns may mark specific biological characteristics of tumors and/or mediate biological activities important for the pathobiology of malignant tumors. These findings call attention to the potential of microRNAs to provide etiologic insights as well as to serve as both diagnostic markers and therapeutic targets for many different tumor types. [Cancer Res 2007;67(6):2456-68]
Mammalian Genome, 2008
MicroRNAs (miRNAs) are small noncoding RNAs (ncRNAs, RNAs that do not code for proteins) that regulate the expression of target genes at the posttranscriptional or posttranslational level. Many miRNAs have conserved sequences between distantly related organisms, suggesting that these molecules participate in essential developmental and physiologic processes. miRNAs can act as tumor suppressor genes or oncogenes in human cancers. Mutations, deletions, or amplifications have been found in human cancers and shown to alter expression levels of mature and/or precursor miRNA transcripts. Moreover, a large fraction of genomic ultraconserved regions (UCRs) encode a particular set of ncRNAs whose expression is altered in human cancers. Both miRNAs and UCRs are frequently located at fragile sites and genomic regions affected in various cancers, named cancer-associated genomic regions (CAGRs). Bioinformatics studies are emerging as important tools to identify associations and/or correlations between miRNAs/ncRNAs and CAGRs. ncRNA profiling has allowed the identification of specific signatures associated with diagnosis, prognosis, and response to treatment of human tumors. Several abnormalities could contribute to the alteration of miRNA expression profiles in each kind of tumor and in each kind of tissue. This review is focused on the miRNAs and ncRNAs as genes affecting cancer risk, and we provided an updated catalog of miRNAs and UCRs located at fragile sites or at cancer susceptibility loci. These types of studies are the first step toward discoveries leading to novel approaches for cancer therapies. Noncoding RNAs and bioinformatics Recent biotechnology advances, along with a growing number of new biological-computational approaches, have allowed an expansion of the number of genomes being sequenced and annotated, as well as facilitated the development of databases to collect and analyze large amounts of genetic information. The consequent necessities of retrieving, sharing, and, in particular, understanding this vast amount of data led to the creation of genome databases, providing an open source of genetic information for scientists worldwide. Thus, there is now a strong urgency to integrate various sources of biomedical and clinical information. One of the many fields that will strongly benefit from such integration is the study of noncoding RNAs (ncR-NAs) (Barbarotto et al. 2008; Calin and Croce 2006a; Esquela-Kerscher and Slack 2006). The most studied ncRNAs are the microRNAs (miRNAs),19-24-nucleotide (nt) transcripts that regulate the expression of target