Identification of differentially expressed long non-coding RNAs associated with dilated cardiomyopathy using integrated bioinformatics approaches

Luo, Xiaohui; Luo, Pengdan; Zhang, Yushun

doi:10.5582/ddt.2020.01010

Cited by 6 publications

(5 citation statements)

References 37 publications

(34 reference statements)

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“…Si (2023) has screened the associated genes and biological pathways of inflammatory dilated cardiomyopathy (DCMi) [ 50 ]. Luo et al (2020) identified novel long non-coding RNA (lncRNA) biomarkers associated with DCM and revealed the potential molecular mechanisms of DCM development using bioinformatics approaches (dataset GSE5406 from GEO) [ 51 ]. Zhang et al (2022) screened diagnostic biomarkers and identified the landscape of immune infiltration in DCM (dataset GSE141910 from Geo).…”

Section: Discussionmentioning

confidence: 99%

CCND1 Overexpression in Idiopathic Dilated Cardiomyopathy: A Promising Biomarker?

Dehghani,

Stanek,

Bagherabadi

et al. 2023

Genes

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Cardiomyopathy, a disorder of electrical or heart muscle function, represents a type of cardiac muscle failure and culminates in severe heart conditions. The prevalence of dilated cardiomyopathy (DCM) is higher than that of other types (hypertrophic cardiomyopathy and restrictive cardiomyopathy) and causes many deaths. Idiopathic dilated cardiomyopathy (IDCM) is a type of DCM with an unknown underlying cause. This study aims to analyze the gene network of IDCM patients to identify disease biomarkers. Data were first extracted from the Gene Expression Omnibus (GEO) dataset and normalized based on the RMA algorithm (Bioconductor package), and differentially expressed genes were identified. The gene network was mapped on the STRING website, and the data were transferred to Cytoscape software to determine the top 100 genes. In the following, several genes, including VEGFA, IGF1, APP, STAT1, CCND1, MYH10, and MYH11, were selected for clinical studies. Peripheral blood samples were taken from 14 identified IDCM patients and 14 controls. The RT-PCR results revealed no significant differences in the expression of the genes APP, MYH10, and MYH11 between the two groups. By contrast, the STAT1, IGF1, CCND1, and VEGFA genes were overexpressed in patients more than in controls. The highest expression was found for VEGFA, followed by CCND1 (p < 0.001). Overexpression of these genes may contribute to disease progression in patients with IDCM. However, more patients and genes need to be analyzed in order to achieve more robust results.

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Section: Discussionmentioning

confidence: 99%

CCND1 Overexpression in Idiopathic Dilated Cardiomyopathy: A Promising Biomarker?

Dehghani,

Stanek,

Bagherabadi

et al. 2023

Genes

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“…Emerging evidence has revealed that lncRNA Xist acted as powerful and dynamic modifier of cardiac physiological and pathological processes. Cardiac hypertrophy, recognized as a risk predictor of sudden cardiac death, is an adaptive reaction in response to altered stress or injury to maintain cardiac function ( Li Y. et al, 2018 ; Wehbe et al, 2019 ; Luo X. et al, 2020 ). lncRNA Xist ( Sohrabifar, 2020 ) participates in the pathogenesis of complex diseases and also serves as a diagnostic marker.…”

Section: The Role Of Lncrna Xist In Non-cancer Diseasesmentioning

confidence: 99%

Biological Function of Long Non-coding RNA (LncRNA) Xist

Wang

Min

Guo

et al. 2021

Front. Cell Dev. Biol.

127

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Long non-coding RNAs (lncRNAs) regulate gene expression in a variety of ways at epigenetic, chromatin remodeling, transcriptional, and translational levels. Accumulating evidence suggests that lncRNA X-inactive specific transcript (lncRNA Xist) serves as an important regulator of cell growth and development. Despites its original roles in X-chromosome dosage compensation, lncRNA Xist also participates in the development of tumor and other human diseases by functioning as a competing endogenous RNA (ceRNA). In this review, we comprehensively summarized recent progress in understanding the cellular functions of lncRNA Xist in mammalian cells and discussed current knowledge regarding the ceRNA network of lncRNA Xist in various diseases. Long non-coding RNAs (lncRNAs) are transcripts that are more than 200 nt in length and without an apparent protein-coding capacity (Furlan and Rougeulle, 2016; Maduro et al., 2016). These RNAs are believed to be transcribed by the approximately 98–99% non-coding regions of the human genome (Derrien et al., 2012; Fu, 2014; Montalbano et al., 2017; Slack and Chinnaiyan, 2019), as well as a large variety of genomic regions, such as exonic, tronic, and intergenic regions. Hence, lncRNAs are also divided into eight categories: Intergenic lncRNAs, Intronic lncRNAs, Enhancer lncRNAs, Promoter lncRNAs, Natural antisense/sense lncRNAs, Small nucleolar RNA-ended lncRNAs (sno-lncRNAs), Bidirectional lncRNAs, and non-poly(A) lncRNAs (Ma et al., 2013; Devaux et al., 2015; St Laurent et al., 2015; Chen, 2016; Quinn and Chang, 2016; Richard and Eichhorn, 2018; Connerty et al., 2020). A range of evidence has suggested that lncRNAs function as key regulators in crucial cellular functions, including proliferation, differentiation, apoptosis, migration, and invasion, by regulating the expression level of target genes via epigenomic, transcriptional, or post-transcriptional approaches (Cao et al., 2018). Moreover, lncRNAs detected in body fluids were also believed to serve as potential biomarkers for the diagnosis, prognosis, and monitoring of disease progression, and act as novel and potential drug targets for therapeutic exploitation in human disease (Jiang W. et al., 2018; Zhou et al., 2019a). Long non-coding RNA X-inactive specific transcript (lncRNA Xist) are a set of 15,000–20,000 nt sequences localized in the X chromosome inactivation center (XIC) of chromosome Xq13.2 (Brown et al., 1992; Debrand et al., 1998; Kay, 1998; Lee et al., 2013; da Rocha and Heard, 2017; Yang Z. et al., 2018; Brockdorff, 2019). Previous studies have indicated that lncRNA Xist regulate X chromosome inactivation (XCI), resulting in the inheritable silencing of one of the X-chromosomes during female cell development. Also, it serves a vital regulatory function in the whole spectrum of human disease (notably cancer) and can be used as a novel diagnostic and prognostic biomarker and as a potential therapeutic target for human disease in the clinic (Liu et al., 2018b; Deng et al., 2019; Dinescu et al., 2019; Mutzel and Schulz, 2020; Patrat et al., 2020; Wang et al., 2020a). In particular, lncRNA Xist have been demonstrated to be involved in the development of multiple types of tumors including brain tumor, Leukemia, lung cancer, breast cancer, and liver cancer, with the prominent examples outlined in Table 1. It was also believed that lncRNA Xist (Chaligne and Heard, 2014; Yang Z. et al., 2018) contributed to other diseases, such as pulmonary fibrosis, inflammation, neuropathic pain, cardiomyocyte hypertrophy, and osteoarthritis chondrocytes, and more specific details can be found in Table 2. This review summarizes the current knowledge on the regulatory mechanisms of lncRNA Xist on both chromosome dosage compensation and pathogenesis (especially cancer) processes, with a focus on the regulatory network of lncRNA Xist in human disease.

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“…Camargo A et al [12] established the DCM classi cation model by analyzing the public data sets, and nally identi ed the potential biomarkers and drug targets of DCM. In addition, Luo X et al [13] used bioinformatics approaches to reveal the underlying molecular mechanisms and therapeutic targets of DCM (chip dataset GSE1156). However, the results of these data analysis have not been veri ed and further systematic research needs to be performed.…”

Section: Introductionmentioning

confidence: 99%

Insight into the underlying molecular mechanism of dilated cardiomyopathy through integrative analysis of data mining, iTRAQ-PRM proteomics and bioinformatics

Xiong

Zheng

Zhao

et al. 2023

Preprint

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Dilated cardiomyopathy (DCM) is a common cardiomyopathy worldwide, which is characterized by ventricular dilatation and systolic dysfunction. DCM is one of the most common diseases contributing to sudden death and heart failure. However, our understanding of its molecular mechanisms is limited because of its etiology and underlying mechanisms. Poor access to human myocardium is a significant limitation in the study of DCM. Firstly, DCM disease target genes were downloaded from public databases, and 935 genes were identified as key target genes. Next, a total of 787 differentially expressed proteins (DEPs), including 353 up-regulated and 434 down-regulated proteins, were identified in our animal experiment. The functional annotation of these DEPs revealed complicated molecular mechanisms including oxidation-reduction process, tricarboxylic acid cycle, protein folding, and triggered a series of molecular pathways involving TCA cycle, Oxidative phosphorylation, Cardiac muscle contraction. Finally, the DEPs were analyzed for association with the target genes screened in the public dataset. The overlapping proteins were validated by parallel reaction monitoring (PRM). We obtained 154 key proteins and further determined the importance of these three pathways. Together, this study provided deep insights into the detailed molecular mechanisms of DCM and facilitated the identification of potential proteins associated with it.

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Identification of differentially expressed long non-coding RNAs associated with dilated cardiomyopathy using integrated bioinformatics approaches

Cited by 6 publications

References 37 publications

CCND1 Overexpression in Idiopathic Dilated Cardiomyopathy: A Promising Biomarker?

CCND1 Overexpression in Idiopathic Dilated Cardiomyopathy: A Promising Biomarker?

Biological Function of Long Non-coding RNA (LncRNA) Xist

Insight into the underlying molecular mechanism of dilated cardiomyopathy through integrative analysis of data mining, iTRAQ-PRM proteomics and bioinformatics

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