Immune-associated biomarkers for early diagnosis of Parkinson’s disease based on hematological lncRNA–mRNA co-expression

Lei, Kecheng; Zhang, Liwen; He, Yijing; Sun, Hui; Tong, Weifang; Jin, Lingjing

doi:10.1042/bsr20202921

Cited by 14 publications

(8 citation statements)

References 64 publications

(71 reference statements)

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“…McGlynn et al (Unsinger et al, 2010) showed that the increased IL7R expression in T cells likely serves to enhance IL7's effect and improves survival in sepsis, suggesting that IL7R is a crucial T-cell developmental pathway. Prior studies had showed that lncRNA LINC00861 was related to cancers (Zhang et al, 2017;Lv et al, 2018;Zheng et al, 2020;Liu et al, 2021), chronic obstructive pulmonary disease (Qian et al, 2018), atrial fibrillation (Ruan et al, 2020), and Parkinson's disease (Lei et al, 2020;Liu et al, 2021). Our works strongly suggested that the deregulation of lncRNA LINC00861 correlated with IL7R might promote sepsis development through mediating functions of T cells.…”

Section: Discussionsupporting

confidence: 51%

Dysregulated lncRNAs are Involved in the Progress of Sepsis by Constructing Regulatory Networks in Whole Blood Cells

et al. 2021

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Sepsis is a highly heterogeneous syndrome that is caused by an unbalanced host response to an infection. Long noncoding RNAs (lncRNAs) have been reported to exert regulatory roles in a variety of biological processes, and became potential biomarkers and therapeutic targets for diverse diseases. However, current understanding on the roles of lncRNAs in sepsis is extremely limited. Herein, to decipher the underlying functions of lncRNAs, we reexplored the 83 transcriptome datasets from specimens with sepsis, no_sepsis by final diagnosis, and control. The results of differentially expressed genes (DEGs), differentially expressed lncRNA (DElncRNA) analysis, and co-expression analysis of lncRNA–mRNA pairs were obtained. We found that the expression pattern of lncRNAs was significantly activated in sepsis specimens, which was clearly distinguished in sepsis from no_sepsis and control specimens. By performing co-expression analysis, we found DElncRNAs were closely related to T-cell activation and immune response–related terms in sepsis by regulating mRNA expression in the trans manner. The lncRNA–mRNA network and the qRT-PCR test revealed that lncRNAs LINC00861, RP11-284N8.3, and CTB-61M7.2 were significantly correlated with the pathogenesis of sepsis. In addition, weighted gene co-expression analysis (WGCNA) and cis-regulation analysis also revealed sepsis-specific lncRNAs were highly associated with important biological processes correlated with sepsis. In summary, the systematic dysregulation of lncRNAs is tightly involved in the remodeling of gene expression regulatory network in sepsis, and the lncRNA–mRNA expression network may be used to refine biomarker predictions for developing novel therapeutic approaches in sepsis.

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Section: Discussionsupporting

confidence: 51%

Dysregulated lncRNAs are Involved in the Progress of Sepsis by Constructing Regulatory Networks in Whole Blood Cells

et al. 2021

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“…Interestingly, we observed that the variant rs79761481, recovered employing DaTscan data, was located within the CD6 gene. This gene belongs to the CD genes family, which have been associated with PD onset at immune system level [84]. The remaining variants recovered during the Individual view phase were mapped in intergenic regions.…”

Section: Resultsmentioning

confidence: 99%

Multi view based imaging genetics analysis on Parkinson disease

Cerri

Tognon

Avesani

et al. 2021

Preprint

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Longitudinal studies integrating imaging and genetic data have recently become widespread among bioinformatics researchers. Combining such heterogeneous data allows a better understanding of complex diseases origins and causes. Through a multi-view based workflow proposal, we show the common steps and tools used in imaging genetics analysis, interpolating genotyping, neuroimaging and transcriptomic data. We describe the advantages of existing methods to analyze heterogeneous datasets, using Parkinson's Disease (PD) as a case study. Parkinson's disease is associated with both genetic and neuroimaging factors, however such imaging genetics associations are at an early investigation stage. Therefore it is desirable to have a free and open source workflow that integrates different analysis flows in order to recover potential genetic biomarkers in PD, as in other complex diseases.

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“…IFN-alpha inducible (IRI) family members are closely related to the inflammatory immune response in COVID-19 and PD (Shaath et al 2020). IFI6 is an immune-associated early predictor for PD (Lei et al 2020;Yu et al 2020). IFI35 is involved in type I interferon signaling pathway and have a vital role in inflammation response in SARS-CoV-2-infected cells (Hachim (Yu et al 2020).…”

Section: Discussionmentioning

confidence: 99%

Discovering Common Pathogenic Mechanisms of COVID-19 and Parkinson Disease: An Integrated Bioinformatics Analysis

et al. 2022

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Coronavirus disease 2019 (COVID-19) has emerged since December 2019 and was later characterized as a pandemic by WHO, imposing a major public health threat globally. Our study aimed to identify common signatures from different biological levels to enlighten the current unclear association between COVID-19 and Parkinson's disease (PD) as a number of possible links, and hypotheses were reported in the literature. We have analyzed transcriptome data from peripheral blood mononuclear cells (PBMCs) of both COVID-19 and PD patients, resulting in a total of 81 common differentially expressed genes (DEGs). The functional enrichment analysis of common DEGs are mostly involved in the complement system, type II interferon gamma (IFNG) signaling pathway, oxidative damage, microglia pathogen phagocytosis pathway, and GABAergic synapse. The protein-protein interaction network (PPIN) construction was carried out followed by hub detection, revealing 10 hub genes (MX1, IFI27, C1QC, C1QA, IFI6, NFIX, C1S, XAF1, IFI35, and ELANE). Some of the hub genes were associated with molecular mechanisms such as Lewy bodies-induced inflammation, microglia activation, and cytokine storm. We investigated regulatory elements of hub genes at transcription factor and miRNA levels. The major transcription factors regulating hub genes are SOX2, XAF1, RUNX1, MITF, and SPI1. We propose that these events may have important roles in the onset or progression of PD. To sum up, our analysis describes possible mechanisms linking COVID-19 and PD, elucidating some unknown clues in between. Keywords COVID-19• Parkinson disease • Transcriptome analysis • Regulatory networks • Signaling pathways • Bioinformatics Abbreviations BP Biological process CC Cellular component CNS Central nervous system COVID-19 Coronavirus disease 2019 CS Cytokine storm ETS E26 transformation-specific * Javad Zahiri

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Immune-associated biomarkers for early diagnosis of Parkinson’s disease based on hematological lncRNA–mRNA co-expression

Cited by 14 publications

References 64 publications

Dysregulated lncRNAs are Involved in the Progress of Sepsis by Constructing Regulatory Networks in Whole Blood Cells

Dysregulated lncRNAs are Involved in the Progress of Sepsis by Constructing Regulatory Networks in Whole Blood Cells

Multi view based imaging genetics analysis on Parkinson disease

Discovering Common Pathogenic Mechanisms of COVID-19 and Parkinson Disease: An Integrated Bioinformatics Analysis

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