PMID- 36267772
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20221022
IS  - 2305-5839 (Print)
IS  - 2305-5847 (Electronic)
IS  - 2305-5839 (Linking)
VI  - 10
IP  - 18
DP  - 2022 Sep
TI  - Screening of key pathogenic genes in advanced knee osteoarthritis based on 
      bioinformatics analysis.
PG  - 978
LID - 10.21037/atm-22-3863 [doi]
LID - 978
AB  - BACKGROUND: At present, the progression mechanism of knee osteoarthritis (KOA) 
      has not been fully elucidated, and there is a clinical need for late KOA-specific 
      diagnostic markers to provide reference for preventive treatment. This study 
      aimed to analyze the sequencing results of early- and late-stage KOA synovial 
      tissue based on the key genes of late-stage KOA in combination with a machine 
      learning algorithm. METHODS: The whole transcriptome sequencing results of 
      synovial tissue from KOA patients (GSE176223 and GSE32317) were downloaded from 
      the gene expression omnibus (GEO) database. Thirty-nine early KOA synovial tissue 
      samples and 31 late KOA synovial tissue samples were included in this study. The 
      diagnostic criteria and baseline data balance of early and late KOA were referred 
      to the data source literature, and the two groups of data had good baseline data 
      balance. R software (V3.5.1) and R packages were used for screening and 
      enrichment analysis of differentially expressed genes (DEGs). The key genes were 
      screened by weighted correlation network analysis (WGCNA) and least absolute 
      shrinkage and selection operator (LASSO) regression analysis. A receiver 
      operating characteristic curve (ROC) curve was used to evaluate the diagnostic 
      efficacy of key genes for advanced KOA. RESULTS: A total of 211 DEGs related to 
      knee arthritis were screened out. Compared with synovial tissue of early knee 
      arthritis, 111 genes were upregulated and 100 genes were downregulated in the 
      synovial tissue of late knee arthritis. Sixty-six key genes were screened out 
      through WGCNA and 34 key genes were screened out in the LASSO analysis. The genes 
      obtained by the two algorithms combined with three overlapping genes, namely 
      interleukin- 6 (IL-6), C-X-C chemokine ligand 12 (CXCL12), and macrophage 
      migration inhibitor factor (MIF). The areas under the ROC curves of CXCL12, IL-6, 
      and MIF were 0.96, 0.944, and 0.961, respectively (P<0.001). CONCLUSIONS: IL-6, 
      CXCL12, and MIF are the key pathogenic genes of KOA, which have good diagnostic 
      efficacy for advanced KOA.
CI  - 2022 Annals of Translational Medicine. All rights reserved.
FAU - Yang, Yongju
AU  - Yang Y
AD  - The Ministry of National Education Key Lab for Traditional Chinese Medicine 
      Visceral Manifestations Theory and Application, Liaoning University of 
      Traditional Chinese Medicine, Shenyang, China.
AD  - Department of Orthopaedic Rehabilitation, Affiliated Hospital of Liaoning 
      University of Traditional Chinese Medicine, Shenyang, China.
FAU - Zhang, Yuqian
AU  - Zhang Y
AD  - Academic Office, Affiliated Hospital of Liaoning University of Traditional 
      Chinese Medicine, Shenyang, China.
FAU - Min, Dongyu
AU  - Min D
AD  - Animal Experiment Center, Affiliated Hospital of Liaoning University of 
      Traditional Chinese Medicine, Shenyang, China.
FAU - Yu, Heshan
AU  - Yu H
AD  - Laboratory Department, Affiliated Hospital of Liaoning University of Traditional 
      Chinese Medicine, Shenyang, China.
FAU - Guan, Xuefeng
AU  - Guan X
AD  - Party and Government Office, Liaoning University of Traditional Chinese Medicine, 
      Shenyang, China.
LA  - eng
PT  - Journal Article
PL  - China
TA  - Ann Transl Med
JT  - Annals of translational medicine
JID - 101617978
PMC - PMC9577766
OTO - NOTNLM
OT  - Knee osteoarthritis (KOA)
OT  - diagnostic efficiency
OT  - differentially expressed genes (DEGs)
OT  - machine learning
COIS- Conflicts of Interest: All authors have completed the ICMJE uniform disclosure 
      form (available at 
      https://atm.amegroups.com/article/view/10.21037/atm-22-3863/coif). The authors 
      have no conflicts of interest to declare.
EDAT- 2022/10/22 06:00
MHDA- 2022/10/22 06:01
PMCR- 2022/09/01
CRDT- 2022/10/21 03:00
PHST- 2022/07/15 00:00 [received]
PHST- 2022/09/02 00:00 [accepted]
PHST- 2022/10/21 03:00 [entrez]
PHST- 2022/10/22 06:00 [pubmed]
PHST- 2022/10/22 06:01 [medline]
PHST- 2022/09/01 00:00 [pmc-release]
AID - atm-10-18-978 [pii]
AID - 10.21037/atm-22-3863 [doi]
PST - ppublish
SO  - Ann Transl Med. 2022 Sep;10(18):978. doi: 10.21037/atm-22-3863.