Role of hedgehog signaling related non-coding RNAs in developmental and pathological conditions

HajiEsmailPoor, Zanyar; Tabnak, Peyman; Ahmadzadeh, Behnam; Ebrahimi, Seyedeh Sanaz; Faal, Bahareh; Mashatan, Noushin

doi:10.1016/j.biopha.2022.113507

Cited by 7 publications

(5 citation statements)

References 179 publications

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“…The chronic infections of HBV and HCV are associated with an increase in expression of Hh pathway components and, in turn, with an increase in HCC tumor size, liver fibrosis, maintenance of cancer stem cells, initiation of epithelial-mesenchymal transition, metastasis, and drug resistance [59] . It is known that the HBV-encoded X protein accounts for HBV-induced activation of Hh signaling through promoting the protein stability and nuclear translocation of Gli1/2 by a direct protein-protein interaction, concomitant with increased transcriptional activity of Gli1/2 [66,67] .…”

Section: Enrichment Analysis 3311 Enrichment Analysis For Proteins As...mentioning

confidence: 99%

Identification of Proteins and Genes Associated with Hedgehog Signaling Pathway Involved in Neoplasm Formation Using Text-Mining Approach

Biziukova,

Ivanov,

Tarasova

2024

Big Data Min. Anal.

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Analysis of molecular mechanisms that lead to the development of various types of tumors is essential for biology and medicine, because it may help to find new therapeutic opportunities for cancer treatment and cure including personalized treatment approaches. One of the pathways known to be important for the development of neoplastic diseases and pathological processes is the Hedgehog signaling pathway that normally controls human embryonic development. Systematic accumulation of various types of biological data, including interactions between proteins, regulation of genes transcription, proteomics, and metabolomics experiments results, allows the application of computational analysis of these big data for identification of key molecular mechanisms of certain diseases and pathologies and promising therapeutic targets. The aim of this study is to develop a computational approach for revealing associations between human proteins and genes interacting with the Hedgehog pathway components, as well as for identifying their roles in the development of various types of tumors. We automatically collect sets of abstract texts from the NCBI PubMed bibliographic database. For recognition of the Hedgehog pathway proteins and genes and neoplastic diseases we use a dictionary-based named entity recognition approach, while for all other proteins and genes machine learning method is used. For association extraction, we develop a set of semantic rules. We complete the results of the text analysis with the gene set enrichment analysis. The identified key pathways that may influence the Hedgehog pathway and their roles in tumor development are then verified using the information in the literature.

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Section: Enrichment Analysis 3311 Enrichment Analysis For Proteins As...mentioning

confidence: 99%

Identification of Proteins and Genes Associated with Hedgehog Signaling Pathway Involved in Neoplasm Formation Using Text-Mining Approach

Biziukova,

Ivanov,

Tarasova

2024

Big Data Min. Anal.

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“…This sets off a chain of intracellular events that activate transcription factors known as GLI proteins. GLI proteins regulate the expression of target genes in the pathway as well as other downstream signaling pathways [ 63 ]. There is evidence that GLI1 and FOXM1 are co-expressed in GBM cells.…”

Section: Foxm1mentioning

confidence: 99%

“…Due to the ability of circular RNAs and long non-coding RNAs to act as a sponge for shared microRNAs at the post-transcriptional level, they are also referred to as competing endogenous RNAs (ceRNAs). In addition, the mechanism of action by which microRNAs exert their role is mostly through targeting the 3′ UTR of mRNAs [ 63 ]. Since FOXM1 acts as an oncogene in cancers and glioma is not an exception, those miRNAs whose target is FOXM1 are usually downregulated, leading to its overexpression and exacerbating glioma’s malignancy.…”

Section: Foxm1mentioning

confidence: 99%

Forkhead box transcription factors (FOXOs and FOXM1) in glioma: from molecular mechanisms to therapeutics

Tabnak,

Hasanzade Bashkandi,

Ebrahimnezhad

et al. 2023

Cancer Cell Int

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Glioma is the most aggressive and malignant type of primary brain tumor, comprises the majority of central nervous system deaths, and is categorized into different subgroups according to its histological characteristics, including astrocytomas, oligodendrogliomas, glioblastoma multiforme (GBM), and mixed tumors. The forkhead box (FOX) transcription factors comprise a collection of proteins that play various roles in numerous complex molecular cascades and have been discovered to be differentially expressed in distinct glioma subtypes. FOXM1 and FOXOs have been recognized as crucial transcription factors in tumor cells, including glioma cells. Accumulating data indicates that FOXM1 acts as an oncogene in various types of cancers, and a significant part of studies has investigated its function in glioma. Although recent studies considered FOXO subgroups as tumor suppressors, there are pieces of evidence that they may have an oncogenic role. This review will discuss the subtle functions of FOXOs and FOXM1 in gliomas, dissecting their regulatory network with other proteins, microRNAs and their role in glioma progression, including stem cell differentiation and therapy resistance/sensitivity, alongside highlighting recent pharmacological progress for modulating their expression.

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“…Based on their length and shape, ncRNAs can be classified into different classes, including microRNAs (miRNAs), circular RNAs (circRNAs), and long non-coding RNAs (lncRNAs). These three regulatory ncRNAs play crucial roles in various biological processes [ 5 ]. miRNAs, consisting of fewer than 200 nucleotides, function both in the nucleus and cytoplasm by regulating gene expression at the post-transcriptional level.…”

Section: Introductionmentioning

confidence: 99%

“…Their length can vary from 100 to 10,000 nucleotides. circRNAs exert their biological functions through various mechanisms, including competitively sponging miRNAs, transcriptional regulation, and forming regulatory complexes with proteins [ 5 , 8 , 9 ]. Similar to other classes of ncRNAs, many lncRNAs have been identified using gene sequencing technologies.…”

Section: Introductionmentioning

confidence: 99%

Role of long non-coding RNA ELFN1-AS1 in carcinogenesis

HajiEsmailpoor,

Fayazi,

Teymouri

et al. 2024

Discov Onc

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As one of the leading causes of death worldwide, cancer significantly burdens patients and the healthcare system. The role of long non-protein coding RNAs (lncRNAs) in carcinogenesis has been extensively studied. The lncRNA ELFN1-AS1 was discovered recently, and subsequent studies have revealed its aberrantly high expression in various cancer tissues. In vitro and in vivo experiments have consistently demonstrated the close association between increased ELFN1-AS1 expression and malignant tumor characteristics, particularly in gastrointestinal malignancies. Functional assays have further revealed the mechanistic role of ELFN1-AS1 as a competitive endogenous RNA for microRNAs, inducing tumor growth, invasive features, and drug resistance. Additionally, the investigation into the clinical implication of ELFN1-AS1 has demonstrated its potential as a diagnostic, therapeutic, and, notably, prognostic marker. This review provides a comprehensive summary of evidence regarding the involvement of ELFN1-AS1 in cancer initiation and development, highlighting its clinical significance.

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Role of hedgehog signaling related non-coding RNAs in developmental and pathological conditions

Cited by 7 publications

References 179 publications

Identification of Proteins and Genes Associated with Hedgehog Signaling Pathway Involved in Neoplasm Formation Using Text-Mining Approach

Identification of Proteins and Genes Associated with Hedgehog Signaling Pathway Involved in Neoplasm Formation Using Text-Mining Approach

Forkhead box transcription factors (FOXOs and FOXM1) in glioma: from molecular mechanisms to therapeutics

Role of long non-coding RNA ELFN1-AS1 in carcinogenesis

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