<i>In silico</i> identification of novel lncRNAs with a potential role in diagnosis of gastric cancer

Delshad, Encieh; Shamsabadi, Fatemeh T.; Bahramian, Shabbou; Mehravar, Fatemeh; Maghsoudi, Hossein; Shafiee, Mohammad

doi:10.1080/07391102.2019.1624615

Cited by 6 publications

(8 citation statements)

References 32 publications

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“…Previous studies showed that identified two lncRNAs, the PRRT3-AS1 and H1FX-AS1, were focused on cancer progression [31,32,33,34]. Both lncRNAs were upregulated in the progressive state compared to spontaneous regression, which indicates that these lncRNAs were functioning as tumor enhancers in CLL cells.…”

Section: Discussionmentioning

confidence: 94%

“…On the contrary, high expression levels of lncRNA H1FX-AS1 are associated with a poor prognosis in gastric cancer. It is predicted that this lncRNA was related to epithelial to mesenchymal transition (EMT) and metastasis pathways [34]. Additionally, in-silico prediction analysis indicated several targets of the H1FX-AS1 lncRNA, such as H1FX, COPG1, and MIR6826 that can be used as potential therapeutic targets in gastric cancer [34].…”

Section: Discussionmentioning

confidence: 99%

“…It is predicted that this lncRNA was related to epithelial to mesenchymal transition (EMT) and metastasis pathways [34]. Additionally, in-silico prediction analysis indicated several targets of the H1FX-AS1 lncRNA, such as H1FX, COPG1, and MIR6826 that can be used as potential therapeutic targets in gastric cancer [34]. Since H1FX-AS1 is upregulated in the progressive state of CLL, the precise roles of this lncRNA should be examined for CLL cells.…”

Section: Discussionmentioning

confidence: 99%

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Identification of LncRNAs as Therapeutic Targets in Chronic Lymphocytic Leukemia

Dolaner

Kaur

Brodsky

et al. 2021

CUSJ

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Chronic Lymphocytic Leukemia (CLL) is one kind of blood cancer that has a very heterogeneous biological background, which results in diverse stages of the CLL and complex treatment strategies. However, a small part of the tumor may disappear without receiving any treatment. This condition is known as “spontaneous regression” and occurs as a result of a poorly investigated mechanism. Exposing the underlying causes of this condition can lead to a novel treatment approach for CLL and other types of cancer. While most such mechanisms have been assumed to be directly linked to protein coding genes, a recent approach was aimed to carry out more comprehensive studies by focusing on non-protein coding genes as well as protein-coding genes at the RNA level. In this article, we applied in-silico analysis of total RNA expression data from 24 CLL samples to determine possible regulatory mechanisms of spontaneous regression in CLL. These were selected by comparing spontaneous regression with progressive samples of CLL at the transcriptional level. As a result, 33 lncRNAs were found to be significantly differentially expressed among these conditions based on differential gene expression analysis. Current study suggested lncRNAs, PTPN22-AS1, PCF11-AS1, SYNGAP1-AS1, PRRT3-AS1 and H1FX-AS1 as potential therapeutic targets to trigger spontaneous regression. Eventually, the results presented here reveal new insights into the spontaneous regression and the relation with the non-coding RNAs, particularly lncRNAs.

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Section: Discussionmentioning

confidence: 94%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Identification of LncRNAs as Therapeutic Targets in Chronic Lymphocytic Leukemia

Dolaner

Kaur

Brodsky

et al. 2021

CUSJ

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“…Numerous studies have shown that lncRNAs can be crucial players in the occurrence and development of human tumors by acting as oncogenes or cancer suppressor genes (7). Moreover, lncRNAs can be considered useful markers for cancer diagnosis and prognosis (8)(9)(10).…”

Section: Introductionmentioning

confidence: 99%

FOXP4-AS1 May be a Potential Prognostic Biomarker in Human Cancers: A Meta−Analysis and Bioinformatics Analysis

et al. 2022

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BackgroundCancer is one of the leading causes of death worldwide. Early diagnosis can significantly lower cancer-related mortality. Studies have shown that the lncRNA Forkhead box P4 antisense RNA 1 (FOXP4-AS1) is aberrantly expressed in various solid tumors. A meta-analysis was performed to evaluate the correlation of FOXP4-AS1 with the prognosis of cancer patients and determine the clinical value of FOXP4-AS1 as a potential diagnostic marker.MethodsCorrelational studies from the Web of Science, Embase, OVID, Cochrane and PubMed databases were screened (up to April 1, 2021). Meta-analysis was performed using Stata SE12.0 software.ResultsEleven original studies with 1,332 patients who were diagnosed with a solid cancer (nasopharyngeal carcinoma, hepatocellular carcinoma, colorectal cancer, gastric cancer, osteosarcoma, mantle cell lymphoma, prostate cancer, and pancreatic ductal adenocarcinoma) were included in the meta-analysis. High expression of FOXP4-AS1 was correlated with poor overall survival (OS) (HR = 1.77, 95% CI 1.29–2.44, P < 0.001) and shorter disease−free survival (DFS) (HR = 1.66, 95% CI 1.01–2.72, P = 0.044). Subgroup analysis based on sample size, follow-up time and Newcastle-Ottawa Scale (NOS) score revealed significant differences between FOXP4-AS1 levels and OS (P < 0.05). However, the expression level of FOXP4-AS1 was not significantly correlated with the OS of gastric cancer patients (P = 0.381). High expression of FOXP4-AS1 was predictive of a larger tumor size (OR = 3.82, 95% CI 2.3–6.3, P < 0.001).ConclusionsOverexpression of FOXP4-AS1 correlates with poor prognosis of cancer patients, and is a potential prognostic biomarker and therapeutic target.Systematic Review RegistrationPROSPERO, identifier CRD42021245267.

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“…lncRNAs, sequences of RNA longer than 200 nucleotides that are not translated into proteins [26], can sponge miRNAs to moderate their regulatory effect on mRNAs; the association between lncRNAs and miRNAs is essential for gene regulation [27]. Various lncRNAs are involved in modulating mammalian spermatogenesis [28].…”

Section: Introductionmentioning

confidence: 99%

In Silico Identification of miRNA–lncRNA Interactions in Male Reproductive Disorder Associated with COVID-19 Infection

Sabetian

Castiglioni

Jahromi

et al. 2021

Cells

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Coronavirus disease 2019 (COVID-19), a global pandemic, is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Angiotensin-converting enzyme 2 (ACE2) is the receptor for SARS-CoV-2 and transmembrane serine protease 2 (TMPRSS2) facilitates ACE2-mediated virus entry. Moreover, the expression of ACE2 in the testes of infertile men is higher than normal, which indicates that infertile men may be susceptible to be infected and SARS-CoV-2 may cause reproductive disorder through the pathway induced by ACE2 and TMPRSS2. Little is known about the pathway regulation of ACE2 and TMPRSS2 expression in male reproductive disorder. Since the regulation of gene expression is mediated by microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) at the post-transcriptional level, the aim of this study was to analyze the dysregulated miRNA–lncRNA interactions of ACE2 and TMPRSS2 in male reproductive disorder. Using bioinformatics analysis, we speculate that the predicted miRNAs including miR-125a-5p, miR-125b-5p, miR-574-5p, and miR-936 as regulators of ACE2 and miR-204-5p as a modulator of TMPRSS2 are associated with male infertility. The lncRNAs with a tissue-specific expression for testis including GRM7-AS3, ARHGAP26-AS1, BSN-AS1, KRBOX1-AS1, CACNA1C-IT3, AC012361.1, FGF14-IT1, AC012494.1, and GS1-24F4.2 were predicted. The identified miRNAs and lncRNAs are proposed as potential biomarkers to study the possible association between COVID-19 and male infertility. This study encourages further studies of miRNA–lncRNA interactions to explain the molecular mechanisms of male infertility in COVID-19 patients.

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In silico identification of novel lncRNAs with a potential role in diagnosis of gastric cancer

Cited by 6 publications

References 32 publications

Identification of LncRNAs as Therapeutic Targets in Chronic Lymphocytic Leukemia

Identification of LncRNAs as Therapeutic Targets in Chronic Lymphocytic Leukemia

FOXP4-AS1 May be a Potential Prognostic Biomarker in Human Cancers: A Meta−Analysis and Bioinformatics Analysis

In Silico Identification of miRNA–lncRNA Interactions in Male Reproductive Disorder Associated with COVID-19 Infection

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