In silico identification of potential miRNAs -mRNA inflammatory networks implicated in the pathogenesis of COVID-19

Sheikhshabani, Somayeh Hashemi; Amini‐Farsani, Zeinab; Modarres, Parastoo; Amini-Farsani, Zahra; Feyzabad, Sharareh Khazaei; Shaygan, Nasibeh; Hussen, Bashdar Mahmud; Omrani, Mir Davood; Ghafouri‐Fard, Soudeh

doi:10.1016/j.humgen.2023.201172

Cited by 8 publications

(4 citation statements)

References 47 publications

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“…Our study also predicted hsa-miR-5193 involved in the onset of PD, which needs more research to validate this conclusion. A study of COVID-19 found that miR-6721-5p was involved in inflammatory pathways, the latter was also one of the main mechanisms of PD, and our study on NETs in PD patients also found the same result (Hashemi Sheikhshabani et al, 2023).…”

Section: Discussionsupporting

confidence: 85%

Bioinformatics gene analysis for potential biomarkers and therapeutic targets of Parkinson’s disease based on neutrophil extracellular traps

Wang,

Gu,

Chen

et al. 2024

Front. Aging Neurosci.

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IntroductionNeutrophil extracellular traps (NETs) provide key innate immune mechanisms, and studies have shown innate immunity and adaptive immunity are directly linked to Parkinson’s disease (PD) pathology. However, limited research has been conducted on NETs in the context of PD.MethodsA differential analysis was implemented to acquire differentially expressed genes (DEGs) between PD and control as well as between high- and low-score groups determined by a gene set variation analysis (GSVA). Then, the genes within the critical module, obtained through a weighted gene co-expression network analysis (WGCNA), were intersected with the DEGs to identify the overlapping genes. Then, five kinds of algorithms in the protein–protein interaction (PPI) were performed to identify potential biomarkers. Subsequently, a nomogram for forecasting PD probability was created. An enrichment analysis and an immune infiltration analysis were performed on the identified biomarkers. qRT-PCR was performed to validate the expression trends of three biomarkers.ResultsWe revealed 798 DEGs between PD and control groups as well as 168 DEGs between high- and low-score groups obtained by differential analyses. The pink module containing 926 genes was identified as the critical module. According to the intersection of these gene sets, a total of 43 overlapping genes were screened out. Furthermore, GPR78, CADM3, and CACNA1E were confirmed as biomarkers. Moreover, we found that biomarkers mainly participated in pathways, such as the ‘hydrogen peroxide catabolic process’, and ‘cell cycle’; five kinds of differential immune cells between PD and control groups were identified. Finally, the qRT-PCR analysis demonstrated the up-regulation of GPR78, CADM3, and CACNA1E in the PD group.DiscussionOur study authenticated GPR78, CADM3, and CACNA1E as the biomarkers associated with PD. These findings provide an original reference for the diagnosis and treatment of PD.

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Section: Discussionsupporting

confidence: 85%

Bioinformatics gene analysis for potential biomarkers and therapeutic targets of Parkinson’s disease based on neutrophil extracellular traps

Wang,

Gu,

Chen

et al. 2024

Front. Aging Neurosci.

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“…miR-6721-5p had decreased expression levels in the cerebrospinal fluid of osseous-associated cervical spondylomyelopathy-affected dogs compared to clinically normal dogs [40]. miR-6721-5p was found to affect the expression of key genes in NF-KB, JAK/STAT and MAPK signaling pathways implicated in COVID-19 pathogenesis [41]. KHK was found to localize to Purkinje cells in the cerebellum [42].…”

Section: Discussionmentioning

confidence: 99%

Analysis of the lncRNA-miRNA-mRNA network to explore the regulation mechanism in human traumatic brain injury

Shao,

Zhang,

Fang

et al. 2024

NeuroReport

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Traumatic brain injury (TBI) refers to brain dysfunction with or without traumatic structural injury induced by an external force. Nevertheless, the molecular mechanism of TBI remains undefined. Differentially expressed (DE) lncRNAs, DEmRNAs and DEmiRNAs were selected between human TBI tissues and the adjacent histologically normal tissue by high-throughput sequencing. Gene ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis of overlapping DEmRNAs between predicted mRNAs of DEmiRNAs and DEmRNAs. The competitive endogenous RNA (ceRNA) network of lncRNA-miRNA-mRNA was established in light of the ceRNA theory. In the ceRNA network, the key lncRNAs were screened out. Then key lncRNAs related ceRNA subnetwork was constructed. After that, qRT-PCR was applied to validate the expression levels of hub genes. 114 DElncRNAs, 1807 DEmRNAs and 6 DEmiRNAs were DE in TBI. The TBI-related ceRNA network was built with 73 lncRNA nodes, 81 mRNA nodes and 6 miRNAs. According to topological analysis, two hub lncRNAs (ENST00000562897 and ENST00000640877) were selected to construct the ceRNA subnetwork. Subsequently, key lncRNA-miRNA-mRNA regulatory axes constructed by two lncRNAs including ENST00000562897 and ENST00000640877, two miRNAs including miR-6721-5p and miR-129-1-3p, two mRNAs including ketohexokinase (KHK) and cyclic nucleotide-gated channel beta1 (CNGB1), were identified. Furthermore, qRT-PCR results displayed that the expression of ENST00000562897, KHK and CNGB1 were significantly decreased in TBI, while the miR-6721-5p expression levels were markedly increased in TBI. The results of our study reveal a new insight into understanding the ceRNA regulation mechanism in TBI and select key lncRNA-miRNA-mRNA axes for prevention and treatment of TBI.

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“…This gene is particularly studied in cancer, where, depending on its type, MAPK9 may act as both a tumor suppressor and inducer [ 58 ]. Studies have also shown low levels of MAPK9 in COVID-19 patients [ 59 , 60 ], suggesting its role in the induction and development of the inflammatory process regardless of the type of disease. Our study revealed an increased level of miR-1275 in HaCaT culture after the addition of CsA compared to culture with LPS alone.…”

Section: Discussionmentioning

confidence: 99%

Gene expression profile of mitogen-activated kinases and microRNAs controlling their expression in HaCaT cell culture treated with lipopolysaccharide A and cyclosporine A

Wójcik,

Zmarzły,

Derkacz

et al. 2024

Cell Cycle

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Studies indicate that mitogen-activated protein kinases (MAPKs) are activated and overexpressed in psoriatic lesions. The aim of the study was to assess changes in the expression pattern of genes encoding MAPKs and microRNA (miRNA) molecules potentially regulating their expression in human adult low-calcium high-temperature (HaCaT) keratinocytes exposed to bacterial lipopolysaccharide A (LPS) and cyclosporine A (CsA). HaCaT cells were treated with 1 µg/mL LPS for 8 h, followed by treatment with 100 ng/mL cyclosporine A for 2, 8, or 24 h. Untreated cells served as controls. The molecular analysis consists of microarray, quantitative real-time polymerase chain reaction, and enzyme-linked immunosorbent assay analyses. The statistical analysis of the obtained results was performed using Transcriptome Analysis Console and STATISTICA 13.5 PL with the statistical significance threshold of p < 0.05. Changes in the expression profile of six mRNAs: dual-specificity phosphatase 1 ( DUSP1) , dual-specificity phosphatase 4 ( DUSP4) , mitogen-activated protein kinase kinase 2 ( MAP2K2) , mitogen-activated protein kinase kinase 7 ( MAP2K7) , mitogen-activated protein kinase kinase kinase 2 ( MAP3K2) and mitogen-activated protein kinase 9 ( MAPK9) in cell culture exposed to LPS or LPS and the drug compared to the control. We observed that under the LPS and cyclosporine treatment, the expression o/ miR-34a, miR-1275, miR-3188, and miR-382 changed significantly ( p < 0.05). We demonstrated a potential relationship between DUSP1 and miR-34a; DUSP4 and miR-34a, miR-382, and miR-3188; MAPK9 and miR-1275, MAP2K7 and mir-200-5p; MAP3K2 and mir-200-5p, which may be the subject of further research in the context of psoriasis.

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In silico identification of potential miRNAs -mRNA inflammatory networks implicated in the pathogenesis of COVID-19

Cited by 8 publications

References 47 publications

Bioinformatics gene analysis for potential biomarkers and therapeutic targets of Parkinson’s disease based on neutrophil extracellular traps

Bioinformatics gene analysis for potential biomarkers and therapeutic targets of Parkinson’s disease based on neutrophil extracellular traps

Analysis of the lncRNA-miRNA-mRNA network to explore the regulation mechanism in human traumatic brain injury

Gene expression profile of mitogen-activated kinases and microRNAs controlling their expression in HaCaT cell culture treated with lipopolysaccharide A and cyclosporine A

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