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Classification of distinct osteoarthritis subtypes with different knee joint tissues by gene expression profiles

AIMS: Knee osteoarthritis (OA) involves a variety of tissues in the joint. Gene expression profiles in different tissues are of great importance in order to understand OA. METHODS: First, we obtained gene expression profiles of cartilage, synovium, subchondral bone, and meniscus from the Gene Expres...

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Autores principales: Xue, Yuan, Zhou, Liang, Wang, Jiaqian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The British Editorial Society of Bone & Joint Surgery 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10689063/
https://www.ncbi.nlm.nih.gov/pubmed/38035595
http://dx.doi.org/10.1302/2046-3758.1212.BJR-2023-0021.R2
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author Xue, Yuan
Zhou, Liang
Wang, Jiaqian
author_facet Xue, Yuan
Zhou, Liang
Wang, Jiaqian
author_sort Xue, Yuan
collection PubMed
description AIMS: Knee osteoarthritis (OA) involves a variety of tissues in the joint. Gene expression profiles in different tissues are of great importance in order to understand OA. METHODS: First, we obtained gene expression profiles of cartilage, synovium, subchondral bone, and meniscus from the Gene Expression Omnibus (GEO). Several datasets were standardized by merging and removing batch effects. Then, we used unsupervised clustering to divide OA into three subtypes. The gene ontology and pathway enrichment of three subtypes were analyzed. CIBERSORT was used to evaluate the infiltration of immune cells in different subtypes. Finally, OA-related genes were obtained from the Molecular Signatures Database for validation, and diagnostic markers were screened according to clinical characteristics. Quantitative reverse transcription polymerase chain reaction (qRT‐PCR) was used to verify the effectiveness of markers. RESULTS: C1 subtype is mainly concentrated in the development of skeletal muscle organs, C2 lies in metabolic process and immune response, and C3 in pyroptosis and cell death process. Therefore, we divided OA into three subtypes: bone remodelling subtype (C1), immune metabolism subtype (C2), and cartilage degradation subtype (C3). The number of macrophage M0 and activated mast cells of C2 subtype was significantly higher than those of the other two subtypes. COL2A1 has significant differences in different subtypes. The expression of COL2A1 is related to age, and trafficking protein particle complex subunit 2 is related to the sex of OA patients. CONCLUSION: This study linked different tissues with gene expression profiles, revealing different molecular subtypes of patients with knee OA. The relationship between clinical characteristics and OA-related genes was also studied, which provides a new concept for the diagnosis and treatment of OA. Cite this article: Bone Joint Res 2023;12(12):702–711.
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spelling pubmed-106890632023-12-01 Classification of distinct osteoarthritis subtypes with different knee joint tissues by gene expression profiles Xue, Yuan Zhou, Liang Wang, Jiaqian Bone Joint Res Arthritis AIMS: Knee osteoarthritis (OA) involves a variety of tissues in the joint. Gene expression profiles in different tissues are of great importance in order to understand OA. METHODS: First, we obtained gene expression profiles of cartilage, synovium, subchondral bone, and meniscus from the Gene Expression Omnibus (GEO). Several datasets were standardized by merging and removing batch effects. Then, we used unsupervised clustering to divide OA into three subtypes. The gene ontology and pathway enrichment of three subtypes were analyzed. CIBERSORT was used to evaluate the infiltration of immune cells in different subtypes. Finally, OA-related genes were obtained from the Molecular Signatures Database for validation, and diagnostic markers were screened according to clinical characteristics. Quantitative reverse transcription polymerase chain reaction (qRT‐PCR) was used to verify the effectiveness of markers. RESULTS: C1 subtype is mainly concentrated in the development of skeletal muscle organs, C2 lies in metabolic process and immune response, and C3 in pyroptosis and cell death process. Therefore, we divided OA into three subtypes: bone remodelling subtype (C1), immune metabolism subtype (C2), and cartilage degradation subtype (C3). The number of macrophage M0 and activated mast cells of C2 subtype was significantly higher than those of the other two subtypes. COL2A1 has significant differences in different subtypes. The expression of COL2A1 is related to age, and trafficking protein particle complex subunit 2 is related to the sex of OA patients. CONCLUSION: This study linked different tissues with gene expression profiles, revealing different molecular subtypes of patients with knee OA. The relationship between clinical characteristics and OA-related genes was also studied, which provides a new concept for the diagnosis and treatment of OA. Cite this article: Bone Joint Res 2023;12(12):702–711. The British Editorial Society of Bone & Joint Surgery 2023-12-01 /pmc/articles/PMC10689063/ /pubmed/38035595 http://dx.doi.org/10.1302/2046-3758.1212.BJR-2023-0021.R2 Text en © 2023 Wang et al. https://creativecommons.org/licenses/by-nc-nd/4.0/https://online.boneandjoint.org.uk/TDMThis is an open-access article distributed under the terms of the Creative Commons Attribution Non-Commercial No Derivatives (CC BY-NC-ND 4.0) licence, which permits the copying and redistribution of the work only, and provided the original author and source are credited. See https://creativecommons.org/licenses/by-nc-nd/4.0/
spellingShingle Arthritis
Xue, Yuan
Zhou, Liang
Wang, Jiaqian
Classification of distinct osteoarthritis subtypes with different knee joint tissues by gene expression profiles
title Classification of distinct osteoarthritis subtypes with different knee joint tissues by gene expression profiles
title_full Classification of distinct osteoarthritis subtypes with different knee joint tissues by gene expression profiles
title_fullStr Classification of distinct osteoarthritis subtypes with different knee joint tissues by gene expression profiles
title_full_unstemmed Classification of distinct osteoarthritis subtypes with different knee joint tissues by gene expression profiles
title_short Classification of distinct osteoarthritis subtypes with different knee joint tissues by gene expression profiles
title_sort classification of distinct osteoarthritis subtypes with different knee joint tissues by gene expression profiles
topic Arthritis
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10689063/
https://www.ncbi.nlm.nih.gov/pubmed/38035595
http://dx.doi.org/10.1302/2046-3758.1212.BJR-2023-0021.R2
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