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Mao Y, Hou X, Fu S, Luan J. Transcriptomic and machine learning analyses identify hub genes of metabolism and host immune response that are associated with the progression of breast capsular contracture. Genes Dis 2024; 11:101087. [PMID: 38292203 PMCID: PMC10825289 DOI: 10.1016/j.gendis.2023.101087] [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: 07/11/2023] [Revised: 08/03/2023] [Accepted: 08/16/2023] [Indexed: 02/01/2024] Open
Abstract
Capsular contracture is a prevalent and severe complication that affects the postoperative outcomes of patients who receive silicone breast implants. At present, prosthesis replacement is the major treatment for capsular contracture after both breast augmentation procedures and breast reconstruction following breast cancer surgery. However, the mechanism(s) underlying breast capsular contracture remains unclear. This study aimed to identify the biological features of breast capsular contracture and reveal the potential underlying mechanism using RNA sequencing. Sample tissues from 12 female patients (15 breast capsules) were divided into low capsular contracture (LCC) and high capsular contracture (HCC) groups based on the Baker grades. Subsequently, 41 lipid metabolism-related genes were identified through enrichment analysis, and three of these genes were identified as candidate genes by SVM-RFE and LASSO algorithms. We then compared the proportions of the 22 types of immune cells between the LCC and HCC groups using a CIBERSORT analysis and explored the correlation between the candidate hub features and immune cells. Notably, PRKAR2B was positively correlated with the differentially clustered immune cells, which were M1 macrophages and follicular helper T cells (area under the ROC = 0.786). In addition, the expression of PRKAR2B at the mRNA or protein level was lower in the HCC group than in the LCC group. Potential molecular mechanisms were identified based on the expression levels in the high and low PRKAR2B groups. Our findings indicate that PRKAR2B is a novel diagnostic biomarker for breast capsular contracture and might also influence the grade and progression of capsular contracture.
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Affiliation(s)
- Yukun Mao
- Breast Plastic and Reconstructive Surgery Center, Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100144, China
| | - Xueying Hou
- Breast Plastic and Reconstructive Surgery Center, Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100144, China
| | - Su Fu
- Breast Plastic and Reconstructive Surgery Center, Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100144, China
| | - Jie Luan
- Breast Plastic and Reconstructive Surgery Center, Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100144, China
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Niu Z, Ren G, Huang L, Mu L. Circ_0008529 Contributes to Renal Tubular Cell Dysfunction in High Glucose Stress via miR-185-5p/SMAD2 Pathway in Diabetic Nephropathy. Biochem Genet 2022; 61:963-978. [DOI: 10.1007/s10528-022-10296-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 10/18/2022] [Indexed: 11/02/2022]
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Gao Y, Gao Y, Niu Z, Liu J, Feng H, Sun J, Wang L, Pan L. CCCTC-binding factor-mediated microRNA-340-5p suppression aggravates myocardial injury in rats with severe acute pancreatitis through activation of the HMGB1/TLR4 axis. Immunopharmacol Immunotoxicol 2022; 44:306-315. [PMID: 35238277 DOI: 10.1080/08923973.2022.2043898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
BACKGROUND Severe acute pancreatitis (SAP) is a life-threatening disorder associated with multisystem organ failure. This study aimed to investigate the function of high mobility group box 1 (HMGB1) in SAP-induced myocardial injury. METHODS A rat model with SAP was induced. The pathological changes in rat pancreatic and cardiac tissues were examined by HE staining. Cardiomyocyte apoptosis in rat cardiac tissues, and the serum levels of myocardial injury markers and pro-inflammatory cytokines were examined. Rat primary cardiomyocytes were treated with H2O2 for in vitro experiments. The regulatory molecules of HMGB1 were predicted by bioinformatics analysis. Altered expression of HMGB1, microRNA (miR)-340-5p and CCCTC-binding factor (CTCF) was introduced in rats or cells to investigate their roles in myocardial injury. RESULTS CTCF and HMGB1 were highly expressed but miR-340-5p was poorly expressed in cardiac tissues of rats with SAP. HMGB1 silencing reduced toll-like receptor 4 (TLR4) expression to promote proliferation and reduce apoptosis of H2O2-treated cardiomyocytes. miR-340-5p targeted HMGB1 mRNA, while CTCF suppressed miR-340-5p transcription. CTCF upregulation or miR-340-5p downregulation blocked the effects of HMGB1 silencing on cardiomyocytes. In vivo, CTCF silencing alleviated injury in rat pancreatic and cardiac tissues and reduced the expression of creatine kinase-MB (CK-MB), lactic dehydrogenase, interleukin (IL)-1β, IL-6 and tumor necrosis factor-α (TNF-α) in rat serum. But further overexpression of HMGB1 or inhibition of miR-340-5p aggravated the symptoms in rats. CONCLUSION This study demonstrated that CTCF reduces transcription of miR-340-5p to promote HMGB1 expression, which activates TLR4 expression and promotes myocardial injury in rats with SAP.
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Affiliation(s)
- Yazhou Gao
- Department of Emergency Medicine, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, P.R. China
| | - Yanxia Gao
- Department of Emergency Medicine, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, P.R. China
| | - Zequn Niu
- Department of Emergency Medicine, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, P.R. China
| | - Jie Liu
- Department of Emergency Medicine, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, P.R. China
| | - Hui Feng
- Department of Emergency Medicine, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, P.R. China
| | - Jiangli Sun
- Department of Emergency Medicine, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, P.R. China
| | - Liming Wang
- Department of Emergency Medicine, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, P.R. China
| | - Longfei Pan
- Department of Emergency Medicine, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, P.R. China
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Zhang J, Jiang P, Tu Y, Li N, Huang Y, Jiang S, Kong W, Yuan R. Identification and validation of long non-coding RNA associated ceRNAs in intrauterine adhesion. Bioengineered 2021; 13:1039-1048. [PMID: 34968168 PMCID: PMC8805920 DOI: 10.1080/21655979.2021.2017578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Intrauterine adhesion (IUA) is an endometrial fibrotic disease with unclear pathogenesis. Increasing evidence suggested the important role of competitive endogenous RNA (ceRNA) in diseases. This study aimed to identify and verify the key long non-coding RNA (lncRNA) associated-ceRNAs in IUA. The lncRNA/mRNA expression file was obtained by transcriptome sequencing of IUA and normal samples. The microRNAs expression date was downloaded from the Gene Expression Omnibus database. Differential expressions of mRNAs, lncRNAs and miRNAs were analyzed using the DESeq2 (2010) R package. Protein interaction network was constructed to explore hub genes. TargetScan and miRanda databases were used to predicate the interaction. Enrichment analysis in Gene Ontology and Kyoto Encyclopedia of Genes and Genomes were performed to identify the biological functions of ceRNAs. Regression analysis of ceRNAs’ expression level was performed. There were 915 mRNAs and 418 lncRNAs differentially expressed. AURKA, CDC20, IL6, ASPM, CDCA8, BIRC5, UBE2C, H2AFX, RRM2 and CENPE were identified as hub genes. The ceRNAs network, including 28 lncRNAs, 28 miRNAs, and 299 mRNAs, was constructed. Regression analysis showed a good positive correlation between ceRNAs expression levels (r > 0.700, p < 0.001). The enriched functions include ion transmembrane transport, focal adhesion, cAMP signaling pathway and cGMP-PKG signaling pathway. The novel lncRNA-miRNA-mRNA network in IUA was excavated. Crucial lncRNAs such as ADIRF-AS1, LINC00632, DIO3OS, MBNL1-AS1, MIR1-1HG-AS1, AC100803.2 was involved in the development of IUA. cGMP-PKG signaling pathway and ion transport might be new directions for IUA pathogenesis research.
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Affiliation(s)
- Jingni Zhang
- Department of Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Peng Jiang
- Department of Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yuan Tu
- Department of Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ning Li
- Department of Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yuzhen Huang
- Department of Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Shan Jiang
- Department of Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Wei Kong
- Department of Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Rui Yuan
- Department of Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Mafi A, Yadegar N, Salami M, Salami R, Vakili O, Aghadavod E. Circular RNAs; powerful microRNA sponges to overcome diabetic nephropathy. Pathol Res Pract 2021; 227:153618. [PMID: 34649056 DOI: 10.1016/j.prp.2021.153618] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 09/09/2021] [Accepted: 09/11/2021] [Indexed: 12/13/2022]
Abstract
Diabetic nephropathy (DN), also known as diabetic kidney disease (DKD), is a drastic renal complication of type 1 and type 2 diabetes mellitus (DM). Poorly controlled DM over the years, may disrupt kidneys' blood vessels, leading to the hypertension (HTN) and DN onset. During DN, kidneys' waste filtering ability becomes disturbed. Being on a healthy lifestyle and controlling both DM and HTN are now the best proceedings to prevent or at least delay DN occurrence. Unfortunately, about one-fourth of diabetic individuals eventually experience the corresponding renal failure, and thus it is critical to discover effective diagnostic biomarkers and therapeutic strategies to combat DN. In the past few years, circular RNAs (circRNAs), as covalently closed endogenous non-coding RNAs (ncRNAs), are believed to affect DN pathogenesis in a positive manner. CircRNAs are able to impact different cellular processes and signaling pathways by targeting biological molecules or various molecular mechanisms. Still, as a key regulatory axis, circRNAs can select miRNAs as their molecular targets, in which they are considered as miRNA sponges. In this way, circRNA-induced suppression of particular miRNAs may prevent from DN progression or promotes the DN elimination. Since the expression of circRNAs has also been reported to be increased in DN-associated cells and tissues, they can be employed as either diagnostic biomarkers or therapeutic targets.
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Affiliation(s)
- Alireza Mafi
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Negar Yadegar
- Department of Medical Laboratory Sciences, School of Paramedical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Marziyeh Salami
- Department of Biochemistry, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran.
| | - Raziyeh Salami
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, Iran.
| | - Omid Vakili
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Esmat Aghadavod
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, Iran; Department of Clinical Biochemistry, School of Medicine, Kashan University of Medical Sciences, Kashan, Iran.
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Wang Y, Zhao M, Zhang Y. Identification of fibronectin 1 (FN1) and complement component 3 (C3) as immune infiltration-related biomarkers for diabetic nephropathy using integrated bioinformatic analysis. Bioengineered 2021; 12:5386-5401. [PMID: 34424825 PMCID: PMC8806822 DOI: 10.1080/21655979.2021.1960766] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Immune cell infiltration (ICI) plays a pivotal role in the development of diabetic nephropathy (DN). Evidence suggests that immune-related genes play an important role in the initiation of inflammation and the recruitment of immune cells. However, the underlying mechanisms and immune-related biomarkers in DN have not been elucidated. Therefore, this study aimed to explore immune-related biomarkers in DN and the underlying mechanisms using bioinformatic approaches. In this study, four DN glomerular datasets were downloaded, merged, and divided into training and test cohorts. First, we identified 55 differentially expressed immune-related genes; their biological functions were mainly enriched in leukocyte chemotaxis and neutrophil migration. The CIBERSORT algorithm was then used to evaluate the infiltrated immune cells; macrophages M1/M2, T cells CD8, and resting mast cells were strongly associated with DN. The ICI-related gene modules as well as 25 candidate hub genes were identified to construct a protein-protein interactive network and conduct molecular complex detection using the GOSemSim algorithm. Consequently, FN1, C3, and VEGFC were identified as immune-related biomarkers in DN, and a related transcription factor-miRNA-target network was constructed. Receiver operating characteristic curve analysis was estimated in the test cohort; FN1 and C3 had large area under the curve values (0.837 and 0.824, respectively). Clinical validation showed that FN1 and C3 were negatively related to the glomerular filtration rate in patients with DN. Six potential therapeutic small molecule compounds, such as calyculin, phenamil, and clofazimine, were discovered in the connectivity map. In conclusion, FN1 and C3 are immune-related biomarkers of DN.
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Affiliation(s)
- Yuejun Wang
- Department of Nephrology, Zhejiang Aged Care Hospital, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Mingming Zhao
- Department of Nephrology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yu Zhang
- Department of Nephrology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
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