Identificación de biomarcadores para la especificidad de género de la enfermedad de Alzheimer basada en los perfiles del transcriptoma glial

Resumen

Este estudio analizó transcriptomas de un solo núcleo de treinta y tres individuos con enfermedad de Alzheimer (EA), revelando DEG específicos del sexo en las células gliales. El análisis de enriquecimiento funcional destacó las vías sinápticas, neuronales y relacionadas con las hormonas. Se identificaron genes clave, a saber, NLGN4Y y sus reguladores, y se propusieron posibles candidatos terapéuticos para la EA específica del género.

Resumen

Recientemente se han revelado muchos biomarcadores específicos del sexo en la enfermedad de Alzheimer (EA); sin embargo, rara vez se informaron células gliales cerebrales. Este estudio analizó 220.095 transcriptomas de un solo núcleo de la corteza frontal de treinta y tres individuos con EA en la base de datos GEO. Se identificaron genes expresados diferencialmente (DEG) específicos del sexo en las células gliales, incluidos 243 en astrocitos, 1.154 en microglía y 572 en oligodendrocitos. Los análisis de anotación funcional de Gene Ontology (GO) y los análisis de enriquecimiento de vías de la Enciclopedia de Genes y Genomas de Kioto (KEGG) revelaron concentraciones funcionales en vías sinápticas, neuronales y relacionadas con hormonas. La red de interacción proteína-proteína (PPI) identificó a MT3, CALM2, DLG2, KCND2, PAKACB, CAMK2D y NLGN4Y en astrocitos, TREM2, FOS, APOE, APP y NLGN4Y en microglía, y GRIN2A, ITPR2, GNAS y NLGN4Y en oligodendrocitos como genes clave. NLGN4Y fue el único gen compartido por las tres glías y se identificó como el biomarcador de la especificidad de género de la EA. La red correguladora de factor de transcripción génica (TF)-miRNA identificó reguladores clave para NLGN4Y y sus TCM objetivo. Se identificaron Ecklonia kurome Okam (Kunbu) y Herba Ephedrae (Mahuang), y se mostraron los efectos de los ingredientes activos sobre la EA. Finalmente, el análisis de enriquecimiento de Kunbu y Mahuang sugirió que podrían actuar como candidatos terapéuticos para la especificidad de género de la EA.

Introducción

La enfermedad de Alzheimer (EA) es una enfermedad mundial con alta incidencia, y representa el 60%-80% de la demencia¹. A pesar de su alta incidencia, la patogenia mecanicista de la EA no está claramente delimitada, y^{hasta ahora no} ha habido terapias efectivas 2. Las principales patologías en la EA fueron identificadas como la atrofia neuronal y la acumulación de residuos patológicos, principalmente la proteína Tau asociada a microtúbulos y β-amiloide (Aβ)^3,4. La patogenia de la EA se asocia con autofagia anormal, estrés oxidativo, disfunción mitocondrial, inflam....

Protocolo

Los pasos 2 a 9 del análisis se implementaron utilizando el software R (ver Figura complementaria 1 y Archivo complementario 1), mientras que los pasos restantes se ejecutaron en las plataformas en línea. Los detalles de las bases de datos utilizadas en este protocolo (junto con los enlaces web) se proporcionan en la Tabla de Materiales.

1. Adquisición de datos

1. Acceda a la base de datos Ómnibus de Expresión Génica (GEO) disponible públicamente en el Centro Nacional de Información Biotecnológica.
2. Busque los datos GEO denominados E....

Discusión

Se ha identificado especificidad de género en epidemiología, patología y manifestación clínica de la EA¹⁹. Aquí, confirmamos el posible mecanismo patológico del "eje hormona-sinapsis-neurona" a partir de genes gliales específicos de género y vías relacionadas en pacientes con EA. NLGN4Y fue el único gen compartido en las tres glías y fue elegido como biomarcador para la especificidad de género de la EA. TF y miRNAs que regulan NLGN4Y estaban fuertemente relacionados con las diferencia.......

Materiales

Name	Company	Catalog Number	Comments
Database
Coremine Medical database	Jointly developed by Norway, the Chinese Academy of Sciences, the Chinese Academy of Medical Sciences, the National Medical Library of the United States and other institutions		When you explore concepts in CoreMine Medical you access a database that is structured to relate important concepts, ranked by statistical relevance, to your topic. For example, if you type in "Alzheimer disease," in addition to retrieving documents and resources that discuss the disease, you will be able to view networks and lists that show how your query concept is related to other bio-medical concepts. This provides an overview of concepts that relate to your search as well as being an interface for navigating information on these concepts. Weblink: https://coremine.com/medical/
Gene Expression Omnibus (GEO)	National Center for Biotechnology Information in the United States (NCBI)		GEO is a public functional genomics data repository supporting MIAME-compliant data submissions. Array- and sequence-based data are accepted. Tools are provided to help users query and download experiments and curated gene expression profiles. Weblink: https://www.ncbi.nlm.nih.gov/geo/
Integrative Pharmacology-based Research Platform of Traditional Chinese Medicine (TCMIP, version: 2.0)	None		Introduction to the Integrated Pharmacology Based Network Computational Research Platform for Traditional Chinese Medicine [TCMIP v2.0], http://www.tcmip.cn/ ) It is an intelligent data mining platform based on the online database of the Encyclopedia of Traditional Chinese Medicine (ETCM), which integrates medical big data management and pharmacological computing services. It aims to reveal the scientific connotation of traditional Chinese medicine theory and the scientific value of original thinking in traditional Chinese medicine, summarize and pass on the experience of famous doctors, control the quality of traditional Chinese medicine, explain the principles of traditional Chinese medicine action, research and development of new Chinese medicine, especially the discovery and optimization of modern drug combinations, Provide a strong data foundation and analytical tools. Based on TCMIP v1.0, a comprehensive upgrade is implemented, including five major databases and seven functional modules. Through system integration and module integration, a comprehensive analysis of the multi-level correlation of the "disease syndrome prescription" interaction network can be quickly achieved. As an intelligent data mining platform, TCMIP v2.0 will provide a strong data foundation and analysis platform for revealing the scientific connotation of traditional Chinese medicine theory and the scientific value of original thinking in traditional Chinese medicine, summarizing and inheriting the experience of famous doctors, quality control of traditional Chinese medicine, elucidating the principles of traditional Chinese medicine action, research and development of new traditional Chinese medicine drugs, especially modern drug combination discovery and optimization. Weblink: http://www.tcmip.cn/TCMIP
NetworkAnalyst	None		Networkanalyze is an online visualization analysis platform for gene expression analysis and meta-analysis. It can perform comparative, quantitative, differential and enrichment analysis of gene expression, protein-protein interaction analysis, integration analysis of multiple datasets, and can also draw high-value images such as PCA, protein-protein interaction network diagram, heatmap, volcano diagram, Wayne diagram, etc. Weblink: https://www.networkanalyst.ca/NetworkAnalyst/
PubMed database	National Center for Biotechnology Information in the United States (NCBI)		The Pubmed database is a biomedical literature database maintained by the National Library of Medicine (NLM) in the United States, aimed at providing the latest medical research results to scientists, doctors, researchers, and students worldwide. This database collects biomedical literature from around the world, including journal articles, papers, books, etc. As of now, the Pubmed database has collected over 30 million articles and is continuously updated every week. Weblink: https://pubmed.ncbi.nlm.nih.gov/
R software	Ross Ihaka and Robert Gentleman		R is a language and environment for statistical computing and graphics. It is a GNU project which is similar to the S language and environment which was developed at Bell Laboratories (formerly AT&T, now Lucent Technologies) by John Chambers and colleagues. R can be considered as a different implementation of S. There are some important differences, but much code written for S runs unaltered under R. Weblink: https://www.r-project.org/
STRING database (STRING, version 11.0)	Swiss Institute of Bioinformatics		STRING is a database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations Weblink: https://string-db.org/
Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP)	Zhejiang Jiuwei Health Co., Ltd		TCMSP is not only a data repository, but also an analysis platform for users to comprehensively study Traditional Chinese Medicines (TCM): including identification of active components, screening of drug targets and generation of compounds-targets-diseases networks, as well as the detailed drug pharmacokinetic information involving drug-likeness (DL), oral bioavailability (OB), blood-brain barrier (BBB),intestinal epithelial permeability (Caco-2), ALogP,fractional negative surface area (FASA-) and number of  H-bond donor/acceptor  (Hdon/Hacc). So far, TCMSP has attracted broad attentions and several groups have published more than 10 papers by using our TCMSP database within about one year. Weblink: https://tcmsp-e.com