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Du J, Zhou T, Zhang W, Peng W. Developing the new diagnostic model by integrating bioinformatics and machine learning for osteoarthritis. J Orthop Surg Res 2024; 19:832. [PMID: 39695788 DOI: 10.1186/s13018-024-05340-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2024] [Accepted: 12/03/2024] [Indexed: 12/20/2024] Open
Abstract
BACKGROUND Osteoarthritis (OA) is a common cause of disability among the elderly, profoundly affecting quality of life. This study aims to leverage bioinformatics and machine learning to develop an artificial neural network (ANN) model for diagnosing OA, providing new avenues for early diagnosis and treatment. METHODS From the Gene Expression Omnibus (GEO) database, we first obtained OA synovial tissue microarray datasets. Differentially expressed genes (DEGs) associated with OA were identified through utilization of the Limma package and weighted gene co-expression network analysis (WGCNA). Subsequently, protein-protein interaction (PPI) network analysis and machine learning were employed to identify the most relevant potential feature genes of OA, and ANN diagnostic model and receiver operating characteristic (ROC) curve were constructed to evaluate the diagnostic performance of the model. In addition, the expression levels of the feature genes were verified using real-time quantitative polymerase chain reaction (qRT-PCR). Finally, immune cell infiltration analysis was performed using CIBERSORT algorithm to explore the correlation between feature genes and immune cells. RESULTS The Limma package and WGCNA identified a total of 72 DEGs related to OA, of which 12 were up-regulated and 60 were down-regulated. Then, the PPI network analysis identified 21 hub genes, and three machine learning algorithms finally screened four feature genes (BTG2, CALML4, DUSP5, and GADD45B). The ANN diagnostic model was constructed based on these four feature genes. The AUC of the training set was 0.942, and the AUC of the validation set was 0.850. In addition, the qRT-PCR validation results demonstrated a significant downregulation of BTG2, DUSP5, and GADD45 mRNA expression levels in OA samples compared to normal samples, while CALML4 mRNA expression level exhibited an upregulation. Immune cell infiltration analysis revealed B cells memory, T cells gamma delta, B cells naive, Plasma cells, T cells CD4 memory resting, and NK cells The abnormal infiltration of activated cells may be related to the progression of OA. CONCLUSIONS BTG2, CALML4, DUSP5, and GADD45B were identified as potential feature genes for OA, and an ANN diagnostic model with good diagnostic performance was developed, providing a new perspective for the early diagnosis and personalized treatment of OA.
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Affiliation(s)
- Jian Du
- Department of Orthopedics, The Fourth Medical Centre, Chinese PLA General Hospital, No.51 Fucheng Road, Haidian District, Beijing, 100048, People's Republic of China
- Graduate School of Hebei North University, Zhangjiakou, 075000, China
| | - Tian Zhou
- Graduate School of Hebei North University, Zhangjiakou, 075000, China
| | - Wei Zhang
- Graduate School of Hebei North University, Zhangjiakou, 075000, China
| | - Wei Peng
- Department of Orthopedics, The Fourth Medical Centre, Chinese PLA General Hospital, No.51 Fucheng Road, Haidian District, Beijing, 100048, People's Republic of China.
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Suhardi VJ, Oktarina A, Hammad M, Niu Y, Li Q, Thomson A, Lopez J, McCormick J, Ayturk UM, Greenblatt MB, Ivashkiv LB, Bostrom MPG, Yang X. Prevention and treatment of peri-implant fibrosis by functionally inhibiting skeletal cells expressing the leptin receptor. Nat Biomed Eng 2024; 8:1285-1307. [PMID: 39085645 DOI: 10.1038/s41551-024-01238-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 06/25/2024] [Indexed: 08/02/2024]
Abstract
The cellular and molecular mediators of peri-implant fibrosis-a most common reason for implant failure and for surgical revision after the replacement of a prosthetic joint-remain unclear. Here we show that peri-implant fibrotic tissue in mice and humans is largely composed of a specific population of skeletal cells expressing the leptin receptor (LEPR) and that these cells are necessary and sufficient to generate and maintain peri-implant fibrotic tissue. In a mouse model of tibial implantation and osseointegration that mimics partial knee arthroplasty, genetic ablation of LEPR+ cells prevented peri-implant fibrosis and the implantation of LEPR+ cells from peri-implant fibrotic tissue was sufficient to induce fibrosis in secondary hosts. Conditional deletion of the adhesion G-protein-coupled receptor F5 (ADGRF5) in LEPR+ cells attenuated peri-implant fibrosis while augmenting peri-implant bone formation, and ADGRF5 inhibition by the intra-articular or systemic administration of neutralizing anti-ADGRF5 in the mice prevented and reversed peri-implant fibrosis. Pharmaceutical agents that inhibit the ADGRF5 pathway in LEPR+ cells may be used to prevent and treat peri-implant fibrosis.
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Affiliation(s)
- Vincentius Jeremy Suhardi
- Department of Orthopedic Surgery, Hospital for Special Surgery, New York, NY, USA
- Research Institute, Hospital for Special Surgery, New York, NY, USA
| | | | - Mohammed Hammad
- Research Institute, Hospital for Special Surgery, New York, NY, USA
| | - Yingzhen Niu
- Research Institute, Hospital for Special Surgery, New York, NY, USA
- Department of Joint Surgery, The Third Hospital of Hebei Medical University, Shijiazhuang, P. R. China
| | - Qingdian Li
- Research Institute, Hospital for Special Surgery, New York, NY, USA
- Department of Orthopedics, Guangdong Provincial People's Hospital, Southern Medical University, Guangzhou, P. R. China
| | - Andrew Thomson
- Research Institute, Hospital for Special Surgery, New York, NY, USA
| | - Juan Lopez
- Research Institute, Hospital for Special Surgery, New York, NY, USA
| | - Jason McCormick
- Flow Cytometry Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Ugur M Ayturk
- Research Institute, Hospital for Special Surgery, New York, NY, USA
- Department of Orthopedic Surgery, Weill Cornell Medicine, New York, NY, USA
| | - Matthew B Greenblatt
- Research Institute, Hospital for Special Surgery, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | - Mathias P G Bostrom
- Department of Orthopedic Surgery, Hospital for Special Surgery, New York, NY, USA
- Research Institute, Hospital for Special Surgery, New York, NY, USA
- Department of Orthopedic Surgery, Weill Cornell Medicine, New York, NY, USA
| | - Xu Yang
- Research Institute, Hospital for Special Surgery, New York, NY, USA.
- Department of Orthopedic Surgery, Weill Cornell Medicine, New York, NY, USA.
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Zheng Y, Cai X, Ren F, Yao Y. The role of non-coding RNAs in fibroblast-like synoviocytes in rheumatoid arthritis. Int J Rheum Dis 2024; 27:e15376. [PMID: 39439368 DOI: 10.1111/1756-185x.15376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 09/26/2024] [Accepted: 10/06/2024] [Indexed: 10/25/2024]
Abstract
Rheumatoid arthritis (RA) is an inflammatory autoimmune disease characterized by synovial hyperplasia, and fibroblast-like synoviocytes (FLSs) constitute the majority of cells in the synovial tissue, playing a crucial role in the onset of RA. Dysregulation of FLSs function is a critical strategy in treating joint damage associated with RA. Non-coding RNAs, a class of RNA molecules that do not encode proteins, participate in the development of various diseases. This article aims to review the progress in the study of long non-coding RNAs, microRNAs, and circular RNAs in FLSs. Non-coding RNAs are involved in the pathogenesis of RA, directly or indirectly regulating FLSs' proliferation, migration, invasion, apoptosis, and inflammatory responses. Furthermore, non-coding RNAs also influence DNA methylation and osteogenic differentiation in FLSs. Therefore, non-coding RNAs hold promise as biomarkers for diagnosing RA. Targeting non-coding RNAs in FLSs locally represents a potential strategy for future therapies in RA.
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Affiliation(s)
- Yongquan Zheng
- Department of Pharmacy, Women's Hospital School of Medicine Zhejiang University, Hangzhou, China
| | - Xiaoyu Cai
- Department of Pharmacy, Hangzhou First People's Hospital, Hangzhou, China
| | - Fujia Ren
- Department of Pharmacy, Hangzhou Women's Hospital, Hangzhou, China
| | - Yao Yao
- Department of Pharmacy, Women's Hospital School of Medicine Zhejiang University, Hangzhou, China
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Mao S, Dong S, Hou B, Li Y, Sun B, Guo Y, Deng M, Liu D, Liu G. Transcriptome analysis reveals pituitary lncRNA, circRNA and mRNA affecting fertility in high- and low-yielding goats. Front Genet 2023; 14:1303031. [PMID: 38152654 PMCID: PMC10751935 DOI: 10.3389/fgene.2023.1303031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/01/2023] [Indexed: 12/29/2023] Open
Abstract
The pituitary gland serves as the central endocrine regulator of growth, reproduction, and metabolism and plays a crucial role in the reproductive process of female animals. Transcriptome analysis was conducted using pituitary gland samples from Leizhou goats with varying levels of fecundity to investigate the effects of long noncoding RNA (lncRNA), circular RNA (circRNA), and mRNA regulation on pituitary hormone secretion and its association with goat fecundity. The analysis aimed to identify lncRNAs, circRNAs, and mRNAs that influence the fertility of Leizhou goats. GO and KEGG enrichment analyses were performed on differentially expressed lncRNAs, circRNAs, and mRNAs and revealed considerable enrichment in pathways, such as regulation of hormone secretion, germ cell development, and gonadotropin-releasing hormone secretion. The pituitary lncRNAs (ENSCHIT00000010293, ENSCHIT00000010304, ENSCHIT00000010306, ENSCHIT00000010290, ENSCHIT00000010298, ENSCHIT00000006769, ENSCHIT00000006767, ENSCHIT00000006921, and ENSCHIT00000001330) and circRNAs (chicirc_029285, chicirc_026618, chicirc_129655, chicirc_018248, chicirc_122554, chicirc_087101, and chicirc_078945) identified as differentially expressed regulated hormone secretion in the pituitary through their respective host genes. Additionally, differential mRNAs (GABBR2, SYCP1, HNF4A, CBLN1, and CDKN1A) influenced goat fecundity by affecting hormone secretion in the pituitary gland. These findings contribute to the understanding of the molecular mechanisms underlying pituitary regulation of fecundity in Leizhou goats.
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Affiliation(s)
| | | | | | | | | | | | | | - Dewu Liu
- College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Guangbin Liu
- College of Animal Science, South China Agricultural University, Guangzhou, China
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