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Methylation Factor MRPL15 Identified As a Potential Biological Target in Alzheimer’S Disease

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Methylation Factor MRPL15 Identified As a Potential Biological Target in Alzheimer’S Disease www.aging-us.com AGING 2021, Vol. 13, No. 10 Research Paper Methylation factor MRPL15 identified as a potential biological target in Alzheimer’s disease Li Gao1, Jianmei Li1, Ming Yan1,&, Maimaiti Aili1.& 1Prescription Laboratory of Xinjiang Traditional Uyghur Medicine, Xinjiang Institute of Traditional Uighur Medicine, Urmuqi 830011, China Correspondence to: Ming Yan, Maimaiti Aili; email: [email protected], https://orcid.org/0000-0002-1598-3455; [email protected], https://orcid.org/0000-0003-1335-1136 Keywords: Alzheimer’s disease, risk genes, MRPL15, immune inflammation, methylation Received: June 19, 2020 Accepted: October 3, 2020 Published: May 19, 2021 Copyright: © 2021 Gao et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ABSTRACT Alzheimer’s disease (AD) is the most common form of dementia. However, the molecular basis of the development and progression of AD is still unclear. To elucidate the molecular processes related to AD, we obtained the expression profiles and analyzed the differentially expressed genes (DEGs). The genes potentially involved in the AD process were identified by PPI network and STEM analysis. The molecular mechanisms related to the recognition of AD were determined by GSEA and enrichment analysis. The differences from immune cells in AD were calculated. The methylation factors were identified by methylation difference analysis. Among them, MRPL15 was identified as suitable for diagnosing AD. Its expression trend had been verified in GSE5281. Importantly, MRPL15 was also a methylation factor. In addition, macrophages and neutrophils were up-regulated in AD patients. This was consistent with previous immune inflammation responses identified as being involved in the development of AD. The results of the present study revealed the genetic changes and molecular mechanisms involved in the process of the development and deterioration of AD patients. The potential AD risk genes and potential biological targets were identified. It provided evidence that immune inflammation and immune cells play an important role in AD. INTRODUCTION Biomarkers are expected to promote the development of more effective drugs for treating AD and establish a Alzheimer’s disease (AD) is a complex and diverse more personalized medical treatment method. AD is neurodegenerative disease, which is clinically defined by a combination of amyloid and τ proteins, characterized by a decline in cognitive abilities and accompanied by degeneration of neurons and their behavioral disorders [1, 2]. AD is the most common synapses, glial activation and neuroinflammation [6]. cause of dementia. The risk of AD increases with age, Synaptic dysfunction and loss are the events in early- and the incidence rate is also increasing in the USA due onset AD [7]. The series of pathophysiological events of to its aging population [3]. There are about 50 million late-onset AD are not yet fully understood [8]. Microglia people suffering from dementia in the world and and astrocytes are the two main types of glial cells in the Alzheimer’s disease accounts for 60-70% of cases [4]. pathogenesis of AD. Inflammation is considered to be a It has been predicted that the incidence rate of AD will factor in the pathogenesis of AD [9]. Microglia are triple to over 15 million people by 2050, with an annual immune effector cells of the central nervous system in cost of over $ 700 billion [5]. Currently, there is a great vivo, and they play an important role in the dynamic need for effective preventative and curative treatments balance of the brain and in immune response [10]. to either prevent, slow the progression or preferably Astrocytes are the most abundant type of glial cells in the cure AD. central nervous system. They play an important role in www.aging-us.com 13560 AGING homeostasis, synapsis, signal transmission and synaptic genes were differentially expressed between people plasticity, and in providing nutritional and metabolic with MCI and the control group, and 382 genes were support to neurons [11]. Brain insulin resistance caused differentially expressed between patients with AD and by insulin-related disorders, is an additional pathological MCI (Figure 2A). mechanism of AD [12]. AD is a multifactor disease involving genome, epigenome, and environmental factors To identify the key genes in the process from mild [13]. Next generation molecular and high flux cognitive impairment to Alzheimer’s disease, we technologies are expected to elucidate the mechanism obtained a PPI network composed of 1901 DEGs. These and network behind the complexity of AD. Epigenetic network genes were clustered into 12 interacting processes play a vital role in the central nervous system, modules (Figure 2B). The trend in the expression of the especially DNA methylation modification [14]. The modular gene in the two groups of data was similar, but methylation of genes changes significantly with an the difference in the GSE63061 data was more obvious increase in the age of people [15]. (Figure 2C). The enrichment analysis showed that the module genes were involved in 2107 biological The accuracy of clinically diagnosing AD is generally processes (BP), 366 cell components (CC) and 385 low because of the absence of suitable biomarkers. molecular functions (MF). The involvement was mainly A comprehensive, holistic and systematic analysis in the biological functions related to the nerves, in method is needed to describe and diagnose a complex aging, immunity and inflammation (Figure 2D–2F). The multifactor disease. In the present study, we screened results of the KEGG showed that the module genes for and identified the genes of patients relevant to were mainly enriched in the cell cycle, immune the different developmental stages of AD. The results inflammation related signal pathway (Figure 2G). of the present study improved the diagnosis and Importantly, in both datasets the results of the subGSEA treatment targets of AD. In addition, it deepened indicated that Osteoclast differentiation and the Toll- our understanding of the developmental mechanism like receptor signaling pathway showed a continuous of AD. up-regulation from healthy people to patients with AD (Figure 2H). However, Spliceosomes and Proteasomes RESULTS continued to decrease (Figure 2I). It is suggested that these signaling pathways can promote or inhibit the Differentially expressed genes in the development of development of Alzheimer’s disease. Alzheimer’s disease Molecular changes in the progression of Alzheimer’s The research flowchart of the study is shown in Figure 1. disease To identify the changes in gene expression during the development of AD, we compared the differences in the There are different pathological stages in patients with GSE63060 and GSE63061 datasets. Among them, 3221 AD. As AD worsens, the genes that continuously Figure 1. Flow chart. www.aging-us.com 13561 AGING Figure 2. Molecular mechanism in the development of Alzheimer’s disease. (A) Differentially expressed genes between Alzheimer’s disease (AD) and mild cognitive impairment, and between mild cognitive impairment and the control. (B) The union of the two groups of the www.aging-us.com 13562 AGING differentially expressed genes constitutes the PPI network. Each color represents a different module. (C) The expression heatmap of module genes in GSE63060 and GSE63061. The biological functions (D), cellular components (E) and molecular functions (F) of the modular genes. (G) The KEGG pathway of module genes. From control to mild cognitive impairment and then to AD, the signal pathway was continuously up- regulated (H) or down-regulated (I). express maladjustment may be involved in this process. PLEC had the highest positive correlation with B cells. First, from the GSE84422 database, we obtained the ZBTB16 had the highest positive correlation with Th1 DEGs between the patients with moderate and mild AD cells (Figure 4D). The results of the GSEA showed that (Figure 3A), and between the patients with severe and the expression of the five potential AD risk genes were moderate AD (Figure 3B). Then, by STEM analysis of mainly concentrated in the up-regulated salmonella these DEGs, we identified the genes that were infection, signaling pathways regulating pluripotency of continuously up-regulated or down-regulated from mild stem cells (Figure 4E, 4F). to severe AD (Figure 3C). Surprisingly, five genes (MED10, MRPL15, NUDT21, PLEC and ZBTB16) Regulation of methylation of Alzheimer’s disease coincided with the PPI network genes (Figure 3D). We also determined the trend in the expression of these five DNA methylation plays an important role in AD by genes in different modules of the STEM. The further affected DNA function by activating or expression of the MED10, MRPL15 and NUDT21 inhibiting gene transcription activity [16]. By analyzing genes were up-regulated, while the PLEC and ZBTB16 the methylation level of genes of AD patients, we genes were down-regulated. We thought that these genes identified a series of methylation sites (Figure 5A). In may be AD risk genes. Their specific expression trends addition, the methylation level of chromosomes at in three different stages of AD were consistent with the different positions was also different (Figure 5B). The up- and down-regulation of the STEM modules (Figure expression of MRPL15 was verified
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