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Jian G, Xie D, Kuang X, Zheng P, Liu H, Dong X. Identification and validation of miR-29b-3p and LIN7A as important diagnostic markers for bone non-union by WGCNA. J Cell Mol Med 2024; 28:e18522. [PMID: 38957040 PMCID: PMC11220363 DOI: 10.1111/jcmm.18522] [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: 10/30/2023] [Revised: 05/27/2024] [Accepted: 06/04/2024] [Indexed: 07/04/2024] Open
Abstract
Bone non-union is a common fracture complication that can severely impact patient outcomes, yet its mechanism is not fully understood. This study used differential analysis and weighted co-expression network analysis (WGCNA) to identify susceptibility modules and hub genes associated with fracture healing. Two datasets, GSE125289 and GSE213891, were downloaded from the GEO website, and differentially expressed miRNAs and genes were analysed and used to construct the WGCNA network. Gene ontology (GO) analysis of the differentially expressed genes showed enrichment in cytokine and inflammatory factor secretion, phagocytosis, and trans-Golgi network regulation pathways. Using bioinformatic site prediction and crossover gene search, miR-29b-3p was identified as a regulator of LIN7A expression that may negatively affect fracture healing. Potential miRNA-mRNA interactions in the bone non-union mechanism were explored, and miRNA-29-3p and LIN7A were identified as biomarkers of skeletal non-union. The expression of miRNA-29b-3p and LIN7A was verified in blood samples from patients with fracture non-union using qRT-PCR and ELISA. Overall, this study identified characteristic modules and key genes associated with fracture non-union and provided insight into its molecular mechanisms. Downregulated miRNA-29b-3p was found to downregulate LIN7A protein expression, which may affect the healing process after fracture in patients with bone non-union. These findings may serve as a prognostic biomarker and potential therapeutic target for bone non-union.
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Affiliation(s)
- Guojian Jian
- Department of OrthopedicsChenggong Hospital of Xiamen University (the 73th Group Military Hospital of People's Liberation Army)XiamenFujianChina
| | - Desheng Xie
- Department of OrthopedicsChenggong Hospital of Xiamen University (the 73th Group Military Hospital of People's Liberation Army)XiamenFujianChina
| | - Ximu Kuang
- Department of OrthopedicsChenggong Hospital of Xiamen University (the 73th Group Military Hospital of People's Liberation Army)XiamenFujianChina
| | - Peihuang Zheng
- Department of OrthopedicsChenggong Hospital of Xiamen University (the 73th Group Military Hospital of People's Liberation Army)XiamenFujianChina
| | - Haoyuan Liu
- Department of OrthopedicsChenggong Hospital of Xiamen University (the 73th Group Military Hospital of People's Liberation Army)XiamenFujianChina
| | - Xuehong Dong
- Department of OrthopedicsChenggong Hospital of Xiamen University (the 73th Group Military Hospital of People's Liberation Army)XiamenFujianChina
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Diaz MJ, Fadil A, Tran JT, Batchu S, Root KT, Tran AX, Lucke-Wold B. Primary and Metastatic Cutaneous Melanomas Discriminately Enrich Several Ligand-Receptor Interactions. LIFE (BASEL, SWITZERLAND) 2023; 13:life13010180. [PMID: 36676129 PMCID: PMC9865490 DOI: 10.3390/life13010180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/30/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023]
Abstract
INTRODUCTION Cutaneous melanoma remains a leading cancer with sobering post-metastasis mortality rates. To date, the ligand-receptor interactome of melanomas remains weakly studied despite applicability to anti-cancer drug discovery. Here we leverage established crosstalk methodologies to characterize important ligand-receptor pairs in primary and metastatic cutaneous melanoma. METHODS Bulk transcriptomic data, representing 470 cutaneous melanoma samples, was retrieved from the Broad Genome Data Analysis Center Firehose portal. Tumor and stroma compartments were computationally derived as a function of tumor purity estimates. Identification of preferential ligand-receptor interactions was achieved by relative crosstalk scoring of 1380 previously established pairs. RESULTS Metastatic cutaneous melanoma uniquely enriched PTH2-PTH1R for tumor-to-stroma signaling. The Human R-spondin ligand family was involved in 4 of the 15 top-scoring stroma-to-tumor interactions. Receptor ACVR2B was involved in 3 of the 15 top-scoring tumor-to-tumor interactions. CONCLUSIONS Numerous gene-level differences in ligand-receptor crosstalk between primary and metastatic cutaneous melanomas. Further investigation of notable pairings is warranted.
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Affiliation(s)
- Michael J. Diaz
- College of Medicine, University of Florida, Gainesville, FL 32610, USA
- Correspondence:
| | - Angela Fadil
- College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Jasmine T. Tran
- School of Medicine, University of Indiana, Indianapolis, IN 46202, USA
| | - Sai Batchu
- Cooper Medical School, Rowan University, Camden, NJ 08103, USA
| | - Kevin T. Root
- College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Andrew X. Tran
- Department of Dermatology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Brandon Lucke-Wold
- Department of Neurosurgery, University of Florida, Gainesville, FL 32611, USA
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Liu C, Liu Y, Yu Y, Zhao Y, Zhang D, Yu A. Identification of Up-Regulated ANXA3 Resulting in Fracture Non-Union in Patients With T2DM. Front Endocrinol (Lausanne) 2022; 13:890941. [PMID: 35813617 PMCID: PMC9263855 DOI: 10.3389/fendo.2022.890941] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/23/2022] [Indexed: 11/22/2022] Open
Abstract
Diabetes mellitus is a metabolic disorder that increases fracture risk and interferes with bone formation and impairs fracture healing. Genomic studies on diabetes and fracture healing are lacking. We used a weighted co-expression network analysis (WGCNA) method to identify susceptibility modules and hub genes associated with T2DM and fracture healing. First, we downloaded the GSE95849, GSE93213, GSE93215, and GSE142786 data from the Gene Expression Omnibus (GEO) website, analyzed differential expression genes and constructed a WGCNA network. Second, we screened out 30 hub genes, which were found to be enriched in neutrophil activation, translational initiation, RAGE receptor binding, propanoate metabolism, and other pathways through Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set enrichment analysis (GSEA) analyses. Third, we searched for genes related to bone metabolism and fracture healing in the published genome-wide single nucleotide polymorphism (SNP) data, built a protein-protein interaction (PPI) network with hub genes, and found that they were associated with metabolic process, blood vessel development, and extracellular matrix organization. ANXA3 was identified as the biomarker based on gene expression and correlation analysis. And the AUC value of it was 0.947. Fourth, we explored that ANXA3 was associated with neutrophils in fracture healing process by single-cell RNA sequencing analysis. Finally, we collected clinical patient samples and verified the expression of ANXA3 by qRT-PCR in patents with T2DM and fracture non-union. In conclusion, this is the first genomics study on the effect of T2DM on fracture healing. Our study identified some characteristic modules and hub genes in the etiology of T2DM-associated fracture non-union, which may help to further investigate the molecular mechanisms. Up-regulated ANXA3 potentially contributed to fracture non-union in T2DM by mediating neutrophils. It can be a prognostic biomarker and potential therapeutic target.
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Affiliation(s)
| | | | | | | | | | - Aixi Yu
- *Correspondence: Dong Zhang, ; Aixi Yu,
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Yang H, Lu Y, Yang H, Zhu Y, Tang Y, Li L, Liu C, Yuan J. Integrated weighted gene co-expression network analysis uncovers STAT1(signal transducer and activator of transcription 1) and IFI44L (interferon-induced protein 44-like) as key genes in pulmonary arterial hypertension. Bioengineered 2021; 12:6021-6034. [PMID: 34516357 PMCID: PMC8806536 DOI: 10.1080/21655979.2021.1972200] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 12/12/2022] Open
Abstract
Despite the multiple diagnostic and therapeutic strategies implemented in clinical practice, the mortality rate of patients with pulmonary arterial hypertension (PAH) remains high. Understanding the mechanisms and key genes involved could provide insight into the drivers of the pathogenesis of PAH. In this research, we aimed to examine the mechanisms underlying PAH and identify key genes with potential usefulness as clinical biomarkers of PAH and thereby establish therapeutic targets for PAH. The datasets GSE117261, GSE113439, and GSE53408 were downloaded from the Gene Expression Omnibus (GEOs) database. We used weighted gene coexpression network analysis (WGCNA) to identify networks and the most relevant modules in PAH. Functional enrichment analysis was performed for the selected clinically relevant modules. The least absolute shrinkage and selection operator (LASSO) was applied to identify key genes in lung samples from patients with PAH. The genes were validated in a monocrotaline-induced PAH rat model. Three clinically relevant modules were identified through average linkage hierarchical clustering. The genes in the clinically relevant modules were related to endothelial cell differentiation, inflammation, and autoimmunity. Seven genes were screened as key genes significantly associated with PAH. Interferon-induced protein 44-like (IFI44L) and signal transducer and activator of transcription 1 (STAT1) were expressed at higher levels in the lung tissues of the PAH rat model than in those of the controls. Our findings reveal the novel pathological mechanisms underlying PAH and indicate that STAT1 and IFI44L may represent potential therapeutic targets in PAH.
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Affiliation(s)
- Han Yang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Lu
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hongmin Yang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yaoxi Zhu
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yaohan Tang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lixia Li
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Changhu Liu
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jing Yuan
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Li Y, Gao Y, Niu X, Tang M, Li J, Song B, Guan X. LncRNA BASP1-AS1 interacts with YBX1 to regulate Notch transcription and drives the malignancy of melanoma. Cancer Sci 2021; 112:4526-4542. [PMID: 34533860 PMCID: PMC8586662 DOI: 10.1111/cas.15140] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 09/08/2021] [Accepted: 09/12/2021] [Indexed: 12/14/2022] Open
Abstract
Melanoma is a fatal skin malignant tumor with a poor prognosis. We found that long noncoding RNA BASP1-AS1 is essential for the development and prognosis of melanoma. The methylation, RNA sequencing, copy number variation, mutation data, and sample follow-up information of melanoma from The Cancer Genome Atlas (TCGA) were analyzed using weighted gene co-expression network analysis and 366 samples common to the three omics were selected for multigroup clustering analysis. A four-gene prognostic model (BASP1-AS1, LOC100506098, ARHGAP27P1, and LINC01532) was constructed in the TCGA cohort and validated using the GSE65904 series. The expression of BASP1-AS1 was upregulated in melanoma tissues and various melanoma cell lines. Functionally, the ectopic expression of BASP1-AS1 promoted cell proliferation, migration, and invasion in both A375 and SK-MEL-2 cells. Mechanically, BASP1-AS1 interacted with YBX1 and recruited it to the promoter of NOTCH3, initiating its transcription process. The activation of the Notch signaling then resulted in the transcription of multiple oncogenes, including c-MYC, PCNA, and CDK4, which contributed to melanoma progression. Thus, BASP1-AS1 could act as a potential biomarker for cutaneous malignant melanoma.
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Affiliation(s)
- YaLing Li
- Department of DermatologyThe First Hospital of China Medical University and National Joint Engineering Research Center for Theranostics of Immunological Skin DiseasesThe First Hospital of China Medical University and Key Laboratory of ImmunodermatologyMinistry of Health and Ministry of EducationShenyangChina
| | - YaLi Gao
- Department of DermatologyThe First Afflicated Hospital of Sun Yat‐sen UniversityGuangzhouChina
| | - XueLi Niu
- Department of DermatologyThe First Hospital of China Medical University and National Joint Engineering Research Center for Theranostics of Immunological Skin DiseasesThe First Hospital of China Medical University and Key Laboratory of ImmunodermatologyMinistry of Health and Ministry of EducationShenyangChina
| | - MingSui Tang
- Department of DermatologyThe First Hospital of China Medical University and National Joint Engineering Research Center for Theranostics of Immunological Skin DiseasesThe First Hospital of China Medical University and Key Laboratory of ImmunodermatologyMinistry of Health and Ministry of EducationShenyangChina
| | - JingYi Li
- Department of DermatologyThe First Hospital of China Medical University and National Joint Engineering Research Center for Theranostics of Immunological Skin DiseasesThe First Hospital of China Medical University and Key Laboratory of ImmunodermatologyMinistry of Health and Ministry of EducationShenyangChina
| | - Bing Song
- Department of DermatologyThe First Hospital of China Medical University and National Joint Engineering Research Center for Theranostics of Immunological Skin DiseasesThe First Hospital of China Medical University and Key Laboratory of ImmunodermatologyMinistry of Health and Ministry of EducationShenyangChina
- School of DentistryCardiff UniversityCardiffUK
| | - XiuHao Guan
- Department of DermatologyThe First Hospital of China Medical University and National Joint Engineering Research Center for Theranostics of Immunological Skin DiseasesThe First Hospital of China Medical University and Key Laboratory of ImmunodermatologyMinistry of Health and Ministry of EducationShenyangChina
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Hu H, Ling B, Shi Y, Wu H, Zhu B, Meng Y, Zhang GM. Plasma Exosome-Derived SENP1 May Be a Potential Prognostic Predictor for Melanoma. Front Oncol 2021; 11:685009. [PMID: 34422639 PMCID: PMC8374070 DOI: 10.3389/fonc.2021.685009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 07/16/2021] [Indexed: 01/06/2023] Open
Abstract
Objective To evaluate plasma exosome-derived SUMO-specific protease (SENP)1 levels and assess their prognostic value in melanoma. Patients and Methods We extracted exosomes from the plasma of 126 melanoma patients, and identified them with transmission electron microscopy, nanoparticle tracking analysis and western blotting. The plasma exosome-derived SENP1 levels of melanoma patients and healthy controls were detected with ELISA. Results Plasma exosome-derived SENP1 levels in melanoma patients were significantly upregulated than in healthy controls (P < 0.001). Plasma exosome-derived SENP1 levels in melanoma patients with tumor size >10 cm, located in the mucosa or viscera, with Clark level IV/V, with lymph node metastasis, and TNM stages IIb-IV were significantly higher than in patients in with tumor size <10 cm, located in the skin, with Clark level I-III, without lymph node metastasis, and TNM stages IIb-IV (all P < 0.05). Disease-free survival (DFS) and overall survival (OS) were worse in melanoma patients who had higher plasma exosome-derived SENP1 levels than lower plasma exosome-derived SENP1 levels (both P < 0.001). Area under the receiver operating characteristic curve (AUROC) of plasma exosome-derived SENP1 for predicting 3-year DFS of melanoma patients was 0.82 [95% confidence interval (CI): 0.74-0.88], with a sensitivity of 81.2% (95% CI: 69.9-89.6%) and specificity of 75.4% (95% CI: 62.2-85.9%). The AUROC of plasma exosome-derived SENP1 for predicting 3-year OS of melanoma patients was 0.76 (95% CI: 0.67-0.83), with a sensitivity of 95.7% (95% CI: 85.5-99.5%) and specificity of 62.0% (95% CI: 50.4-72.7%). Conclusions Melanoma patients with higher plasma exosome-derived SENP1 levels had worse DFS and OS. The plasma exosome-derived SENP1 levels may be a potential prognostic predictor for 3-year DFS and 3-year OS of melanoma.
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Affiliation(s)
- Hejuan Hu
- Suzhou Key Laboratory for Medical Biotechnology, Suzhou Vocational Health College, Suzhou, China
| | - Bai Ling
- Department of Pharmacy, The Yancheng Clinical College of Xuzhou Medical University, Yancheng, China.,Department of Pharmacy, The First People's Hospital of Yancheng City, Yancheng, China
| | - Yuhan Shi
- Department of Pathology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Haohao Wu
- Department of Oncology, The Yancheng Clinical College of Xuzhou Medical University, Yancheng, China.,Department of Oncology, The First People's Hospital of Yancheng City, Yancheng, China
| | - Bingying Zhu
- Suzhou Key Laboratory for Medical Biotechnology, Suzhou Vocational Health College, Suzhou, China
| | - Yiling Meng
- Suzhou Key Laboratory for Medical Biotechnology, Suzhou Vocational Health College, Suzhou, China
| | - Guo-Ming Zhang
- Department of Laboratory Medicine, The Affiliated Shuyang Hospital of Xuzhou Medical University, Shuyang, China.,Department of Laboratory Medicine, Shuyang People's Hospital, Jiangsu, China
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Wang S, Xu X. An Immune-Related Gene Pairs Signature for Predicting Survival in Glioblastoma. Front Oncol 2021; 11:564960. [PMID: 33859933 PMCID: PMC8042321 DOI: 10.3389/fonc.2021.564960] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 02/12/2021] [Indexed: 01/06/2023] Open
Abstract
Background: Glioblastoma (GBM) is the frequently occurring and most aggressive form of brain tumors. In the study, we constructed an immune-related gene pairs (IRGPs) signature to predict overall survival (OS) in patients with GBM. Methods: We established IRGPs with immune-related gene (IRG) matrix from The Cancer Genome Atlas (TCGA) database (Training cohort). After screened by the univariate regression analysis and least absolute shrinkage and selection operator (LASSO) regression analysis, IRGPs were subjected to the multivariable Cox regression to develop an IRGP signature. Then, the predicting accuracy of the signature was assessed with the area under the receiver operating characteristic curve (AUC) and validated the result using the Chinese Glioma Genome Atlas (CGGA) database (Validation cohorts 1 and 2). Results: A 10-IRGP signature was established for predicting the OS of patients with GBM. The AUC for predicting 1-, 3-, and 5-year OS in Training cohort was 0.801, 0.901, and 0.964, respectively, in line with the AUC of Validation cohorts 1 and 2 [Validation cohort 1 (1 year: 0.763; 3 years: 0.786; and 5 years: 0.884); Validation cohort 2 (1 year: 0.745; 3 years: 0.989; and 5 years: 0.987)]. Moreover, survival analysis in three cohorts suggested that patients with low-risk GBM had better clinical outcomes than patients with high-risk GBM. The univariate and multivariable Cox regression demonstrated that the IRGPs signature was an independent prognostic factor. Conclusions: We developed a novel IRGPs signature for predicting OS in patients with GBM.
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Affiliation(s)
- Sheng Wang
- Zhejiang Jinhua Guangfu Hospital, Jinhua, China
| | - Xia Xu
- Department of General Medicine, Xiangya Hospital, Central South University, Changsha, China.,Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
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