Identification of lncRNA NR_028138.1 as a biomarker and construction of a ceRNA network for bipolar disorder

He, Ling; Zou, Pengtao; Sun, Wanlei; Fu, Yonghui; He, Wenfeng; Li, Juxiang

doi:10.1038/s41598-021-94122-7

Cited by 6 publications

(5 citation statements)

References 26 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…As one of the most common types of ncRNAs, lncRNAs are believed to play a pivotal role in the ceRNA machinery and elicit a significant effect in both physiological and pathological mechanisms. Multiple lines of evidence have implicated them in various psychiatric disorders [75][76][77]. Their differential expression in tissue, cell types, and developmental levels indicates that lncRNA expression is tightly regulated [78][79][80].…”

Section: Discussionmentioning

confidence: 99%

Deciphering the landscape of lncRNA-driven ceRNA network in schizophrenia etiology

Mukhopadhyay,

Singh,

Dohare

et al. 2024

Egypt J Med Hum Genet

View full text Add to dashboard Cite

Background The unifying hypothesis of competing endogenous RNA (ceRNA) wherein crosstalk between coding (mRNAs) and long non-coding RNAs (lncRNAs) via microRNA (miRNA) response elements, creates a pervasive regulatory network across the transcriptome, has been implicated in complex disorders including schizophrenia. Even with a wide range of high-throughput data, the etiology of schizophrenia remains elusive, necessitating a more holistic understanding of the altered genetic landscape, shifting focus from solely candidate gene studies and protein-coding variants. Objective We developed lncRNA-associated ceRNA networks to elucidate global molecular/regulatory signatures underlying schizophrenia using diverse data in the public domain. Methods Microarray dataset associated with peripheral blood mononuclear cells (PBMCs) of schizophrenia and control patients was used to identify differentially expressed mRNAs. Weighted gene co-expression network analysis (WGCNA) was used to identify highly correlated hubs, and genes from these overlapping Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene ontology (GO) term genesets were considered key mRNA players. StarBase, Human MicroRNA Disease Database, and miRWalk were used to derive mRNA-miRNA and miRNA-lncRNA relationships. Finally, the key mRNAs, interacting lncRNAs and miRNAs were chosen to reconstruct sub-ceRNA networks based on network centrality scores. Results Bioinformatics analysis revealed the involvement of three differentially expressed mRNAs, namely ADRA1A, HAP1 and HOMER3 in the schizophrenia ceRNA networks with lncRNAs NEAT1, XIST, and KCNQ1OT1 modulating their activity by a suggestive sequestering of miR-3163, miR-214-3p and miR-2467-3p, respectively. Conclusions Furthermore, based on contextual evidence, we propose how ceRNAs could orchestrate crosstalk between neurostructural dynamics and immune/inflammatory processes and enable unifying these disparate models of schizophrenia etiology.

show abstract

Section: Discussionmentioning

confidence: 99%

Deciphering the landscape of lncRNA-driven ceRNA network in schizophrenia etiology

Mukhopadhyay,

Singh,

Dohare

et al. 2024

Egypt J Med Hum Genet

View full text Add to dashboard Cite

show abstract

“…Overall, our study provides a detailed landscape of lncRNAs in NPD and their role as competitive endogenous RNAs using a modular approach. The prior studies on the ceRNA network in NPD mapped differentially expressed mRNAs and lncRNAs to the putative interactions from the databases (He et al, 2021 ; Li et al, 2021 ; Sabaie et al, 2021a , b ). However, these studies do not consider the co-expression pattern of miRNA, lncRNA, and mRNA, and all the potential RNAs may not be differentially expressed.…”

Section: Discussionmentioning

confidence: 99%

“…On the other hand, only a few studies investigate the miRNA sponging in neurodegenerative and NPDs. These studies are restricted to inferring ceRNA primarily based on differential expressed lncRNAs and mRNA (Zhou et al, 2019 ; Zhang X. et al, 2020 , Zhang J. et al, 2021 ; Zhang Y. et al, 2021 ; He et al, 2021 ; Sabaie et al, 2021a , b ). There is a need to infer miRNA sponge modules by considering the expression of miRNA, lncRNAs, and mRNA.…”

Section: Introductionmentioning

confidence: 99%

Inferring miRNA sponge modules across major neuropsychiatric disorders

Balasubramanian

Vinod²

2022

Front. Mol. Neurosci.

View full text Add to dashboard Cite

The role of non-coding RNAs in neuropsychiatric disorders (NPDs) is an emerging field of study. The long non-coding RNAs (lncRNAs) are shown to sponge the microRNAs (miRNAs) from interacting with their target mRNAs. Investigating the sponge activity of lncRNAs in NPDs will provide further insights into biological mechanisms and help identify disease biomarkers. In this study, a large-scale inference of the lncRNA-related miRNA sponge network of pan-neuropsychiatric disorders, including autism spectrum disorder (ASD), schizophrenia (SCZ), and bipolar disorder (BD), was carried out using brain transcriptomic (RNA-Seq) data. The candidate miRNA sponge modules were identified based on the co-expression pattern of non-coding RNAs, sharing of miRNA binding sites, and sensitivity canonical correlation. miRNA sponge modules are associated with chemical synaptic transmission, nervous system development, metabolism, immune system response, ribosomes, and pathways in cancer. The identified modules showed similar and distinct gene expression patterns depending on the neuropsychiatric condition. The preservation of miRNA sponge modules was shown in the independent brain and blood-transcriptomic datasets of NPDs. We also identified miRNA sponging lncRNAs that may be potential diagnostic biomarkers for NPDs. Our study provides a comprehensive resource on miRNA sponging in NPDs.

show abstract

“…Studies investigating the association between RNA markers and BD in biofluids or peripheral cells are presented in Table 1 . The majority of the studies we retrieved investigated only one type of RNA (mRNAs or a type of noncoding RNA), while only few studies conducted integrated analyses of mRNAs and either miRNAs [ 16 ], circRNAs [ 17 ] or lncRNAs [ 18 , 19 ]. All of the studies that conducted integrative analyses used a genome-wide approach, except the study from Eghtedarian and colleagues, who measured levels of different mRNAs and lncRNAs related to a specific pathway (the vitamin D receptor pathway) [ 18 ].…”

Section: Rna Biomarkers and Bipolar Disordermentioning

confidence: 99%

RNA Biomarkers in Bipolar Disorder and Response to Mood Stabilizers

Pisanu

Squassina

2023

IJMS

View full text Add to dashboard Cite

Bipolar disorder (BD) is a severe chronic disorder that represents one of the main causes of disability among young people. To date, no reliable biomarkers are available to inform the diagnosis of BD or clinical response to pharmacological treatment. Studies focused on coding and noncoding transcripts may provide information complementary to genome-wide association studies, allowing to correlate the dynamic evolution of different types of RNAs based on specific cell types and developmental stage with disease development or clinical course. In this narrative review, we summarize findings from human studies that evaluated the potential utility of messenger RNAs and noncoding transcripts, such as microRNAs, circular RNAs and long noncoding RNAs, as peripheral markers of BD and/or response to lithium and other mood stabilizers. The majority of available studies investigated specific targets or pathways, with large heterogeneity in the included type of cells or biofluids. However, a growing number of studies are using hypothesis-free designs, with some studies also integrating data on coding and noncoding RNAs measured in the same participants. Finally, studies conducted in neurons derived from induced-pluripotent stem cells or in brain organoids provide promising preliminary findings supporting the power and utility of these cellular models to investigate the molecular determinants of BD and clinical response.

show abstract

Identification of lncRNA NR_028138.1 as a biomarker and construction of a ceRNA network for bipolar disorder

Cited by 6 publications

References 26 publications

Deciphering the landscape of lncRNA-driven ceRNA network in schizophrenia etiology

Deciphering the landscape of lncRNA-driven ceRNA network in schizophrenia etiology

Inferring miRNA sponge modules across major neuropsychiatric disorders

RNA Biomarkers in Bipolar Disorder and Response to Mood Stabilizers

Contact Info

Product

Resources

About