1
|
Chen C, He Y, Ni Y, Tang Z, Zhang W. Identification of crosstalk genes relating to ECM-receptor interaction genes in MASH and DN using bioinformatics and machine learning. J Cell Mol Med 2024; 28:e18156. [PMID: 38429902 PMCID: PMC10907849 DOI: 10.1111/jcmm.18156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 01/01/2024] [Accepted: 01/12/2024] [Indexed: 03/03/2024] Open
Abstract
This study aimed to identify genes shared by metabolic dysfunction-associated fatty liver disease (MASH) and diabetic nephropathy (DN) and the effect of extracellular matrix (ECM) receptor interaction genes on them. Datasets with MASH and DN were downloaded from the Gene Expression Omnibus (GEO) database. Pearson's coefficients assessed the correlation between ECM-receptor interaction genes and cross talk genes. The coexpression network of co-expression pairs (CP) genes was integrated with its protein-protein interaction (PPI) network, and machine learning was employed to identify essential disease-representing genes. Finally, immuno-penetration analysis was performed on the MASH and DN gene datasets using the CIBERSORT algorithm to evaluate the plausibility of these genes in diseases. We found 19 key CP genes. Fos proto-oncogene (FOS), belonging to the IL-17 signalling pathway, showed greater centrality PPI network; Hyaluronan Mediated Motility Receptor (HMMR), belonging to ECM-receptor interaction genes, showed most critical in the co-expression network map of 19 CP genes; Forkhead Box C1 (FOXC1), like FOS, showed a high ability to predict disease in XGBoost analysis. Further immune infiltration showed a clear positive correlation between FOS/FOXC1 and mast cells that secrete IL-17 during inflammation. Combining the results of previous studies, we suggest a FOS/FOXC1/HMMR regulatory axis in MASH and DN may be associated with mast cells in the acting IL-17 signalling pathway. Extracellular HMMR may regulate the IL-17 pathway represented by FOS through the Mitogen-Activated Protein Kinase 1 (ERK) or PI3K-Akt-mTOR pathway. HMMR may serve as a signalling carrier between MASH and DN and could be targeted for therapeutic development.
Collapse
Affiliation(s)
- Chao Chen
- Instrumentation and Service Center for Science and TechnologyBeijing Normal UniversityZhuhaiChina
| | - Yuxi He
- Pediatric Research InstituteThe Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical UniversityWenzhouChina
| | - Ying Ni
- Zhuhai Branch of State Key Laboratory of Earth Surface Processes and Resource Ecology, Advanced Institute of Natural SciencesBeijing Normal UniversityZhuhaiChina
- Engineering Research Center of Natural Medicine, Ministry of Education, Advanced Institute of Natural SciencesBeijing Normal UniversityZhuhaiChina
| | - Zhanming Tang
- Zhuhai Branch of State Key Laboratory of Earth Surface Processes and Resource Ecology, Advanced Institute of Natural SciencesBeijing Normal UniversityZhuhaiChina
- Engineering Research Center of Natural Medicine, Ministry of Education, Advanced Institute of Natural SciencesBeijing Normal UniversityZhuhaiChina
| | - Wensheng Zhang
- Zhuhai Branch of State Key Laboratory of Earth Surface Processes and Resource Ecology, Advanced Institute of Natural SciencesBeijing Normal UniversityZhuhaiChina
- Engineering Research Center of Natural Medicine, Ministry of Education, Advanced Institute of Natural SciencesBeijing Normal UniversityZhuhaiChina
| |
Collapse
|
2
|
Jiang X, Li T, Hai X, Zheng X, Wang Z, Lyu F. Integrated behavior and transcriptomic analysis provide valuable insights into the response mechanisms of Dastarcus helophoroides Fairmaire to light exposure. Front Physiol 2023; 14:1250836. [PMID: 38107477 PMCID: PMC10722319 DOI: 10.3389/fphys.2023.1250836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 11/22/2023] [Indexed: 12/19/2023] Open
Abstract
Light traps have been widely used to monitor and manage pest populations, but natural enemies are also influenced. The Dastarcus helophoroides Fairmaire is an important species of natural enemy for longhorn beetles. However, the molecular mechanism of D. helophoroides in response to light exposure is still scarce. Here, integrated behavioral, comparative transcriptome and weighted gene co-expression network analyses were applied to investigate gene expression profiles in the head of D. helophoroides at different light exposure time. The results showed that the phototactic response rates of adults were 1.67%-22.5% and females and males displayed a negative phototaxis under different light exposure [6.31 × 1018 (photos/m2/s)]; the trapping rates of female and male were influenced significantly by light exposure time, diel rhythm, and light wavelength in the behavioral data. Furthermore, transcriptome data showed that a total of 1,052 significantly differentially expressed genes (DEGs) were identified under different light exposure times relative to dark adaptation. Bioinformatics analyses revealed that the "ECM-receptor interaction," "focal adhesion," "PI3K-Akt signaling," and "lysosome" pathways were significantly downregulated with increasing light exposure time. Furthermore, nine DEGs were identified as hub genes using WGCNA analysis. The results revealed molecular mechanism in negative phototactic behavior response of D. helophoroides under the light exposure with relative high intensity, and provided valuable insights into the underlying molecular response mechanism of nocturnal beetles to light stress.
Collapse
Affiliation(s)
- Xianglan Jiang
- College of Forestry, Hebei Agricultural University, Baoding, Hebei, China
| | - Tengfei Li
- College of Forestry, Hebei Agricultural University, Baoding, Hebei, China
| | - Xiaoxia Hai
- College of Forestry, Hebei Agricultural University, Baoding, Hebei, China
| | - Xiang Zheng
- Laboratory of Enzyme Preparation, Hebei Research Institute of Microbiology Co., Ltd., Baoding, Hebei, China
| | - Zhigang Wang
- College of Forestry, Hebei Agricultural University, Baoding, Hebei, China
| | - Fei Lyu
- College of Forestry, Hebei Agricultural University, Baoding, Hebei, China
| |
Collapse
|
3
|
Zhang Y, Gu T, Xu S, Wang J, Zhu X. Anti-Liver Fibrosis Role of miRNA-96-5p via Targeting FN1 and Inhibiting ECM-Receptor Interaction Pathway. Appl Biochem Biotechnol 2023; 195:6840-6855. [PMID: 36943602 DOI: 10.1007/s12010-023-04385-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2023] [Indexed: 03/23/2023]
Abstract
The aberrant expression of mRNAs participates in the pathogenesis of hepatic fibrosis. However, the precise mechanisms regulated by microRNAs (miRNAs) remain unclear. This study aims to investigate the functions about differentially expressed mRNAs (DEMs) in liver fibrosis and their regulatory mechanisms. The DEMs datasets about hepatic stellate cells (HSCs) obtained from hepatic fibrosis mice versus HSCs obtained from normal mice were downloaded from the GEO database (GSE120281). According to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of the GSE120281 datasets, ECM-receptor interaction was the most significant enrichment pathway that was correlated with hepatic fibrosis, and the fibronectin 1 (FN1) gene was upregulated most significantly in the signaling pathway. Downregulation of the expression of the FN1 gene by transfecting with FN1-siRNA alleviated the activity of HSCs. Four different bioinformatics web-based tools were used to predict that microRNA-96-5p (miR-96-5p) would directly target FN1, and a luciferase assay further confirmed this. Moreover, miR-96-5p was declined in activated HSCs and FN1, whereas laminin γ1 (LAMC1), collagen 1α1 (COL1A1) in the ECM-receptor interaction pathway, and the fibrosis marker α-smooth muscle actin (α-SMA) could be reduced by upregulation of the miRNA. Additionally, miR-96-5p expression was low in CCl4-induced liver fibrosis mice. Increased miR-96-5p expression alleviated liver fibrosis, improved liver function, and inhibited the expression of α-SMA, FN1, COL1A1, and LAMC1. In conclusion, this study indicated that upregulation of miR-96-5p could reduce HSC activation and relieve hepatic fibrosis by restraining the FN1/ECM-receptor interaction pathway.
Collapse
Affiliation(s)
- Yong Zhang
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China
- Department of General Surgery, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, China
| | - Tengfei Gu
- Department of Anesthesiology, People's Hospital of Lianshui County, Huaian, 223400, China
| | - Sanrong Xu
- Department of General Surgery, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, China
| | - Jingzhi Wang
- Department of Radiotherapy Oncology, The Affiliated Yancheng First Hospital of Nanjing University Medical School, The First People's Hospital of Yancheng, Yancheng, 224006, China.
| | - Xinguo Zhu
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China.
| |
Collapse
|
4
|
Chen C, Chen J, Wang Y, Fang L, Guo C, Sang T, Peng H, Zhao Q, Chen S, Lin X, Wang X. Ganoderma lucidum polysaccharide inhibits HSC activation and liver fibrosis via targeting inflammation, apoptosis, cell cycle, and ECM-receptor interaction mediated by TGF-β/Smad signaling. Phytomedicine 2023; 110:154626. [PMID: 36603342 DOI: 10.1016/j.phymed.2022.154626] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 11/09/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Ganoderma lucidum polysaccharide (GLP) has many biological properties, however, the anti-fibrosis effect of GLP is unknown at present. PURPOSE This study aimed to examine the anti-fibrogenic effect of GLP and its underlying molecular mechanisms in vivo and in vitro. STUDY DESIGN Both CCl4-induced mouse and TGF-β1-induced HSC-T6 cellular models of fibrosis were established to examine the anti-fibrogenic effect of a water-soluble GLP (25 kDa) extracted from the sporoderm-removed spores of G. lucidum.. METHOD Serum markers of liver injury, histology and fibrosis of liver tissues, and collagen formation were examined using an automatic biochemical analyzer, H&E staining, Sirius red staining, immunohistochemistry, immunofluorescence, ELISA, Western blotting, and qRT-PCR. RNA-sequencing, enrichment pathway analysis, Western blotting, qRT-PCR, and flow cytometry were employed to identify the potential molecular targets and signaling pathways that are responsible for the anti-fibrotic effect of GLP. RESULTS We showed that GLP (150 and 300 mg/kg) significantly inhibited hepatic fibrogenesis and inflammation in CCl4-treated mice as mediated by the TLR4/NF-κB/MyD88 signaling pathway. We further demonstrated that GLP significantly inhibited hepatic stellate cell (HSCs) activation in mice and in TGF-β1-induced HSC-T6 cells as manifested by reduced collagen I and a-SMA expressions. RNA-sequencing uncovered inflammation, apoptosis, cell cycle, ECM-receptor interaction, TLR4/NF-κB, and TGF-β/Smad signalings as major pathways suppressed by GLP administration. Further studies demonstrated that GLP elicits anti-fibrotic actions that are associated with a novel dual effect on apoptosis in vivo (inhibit) or in vitro (promote), suppression of cell cycle in vivo, induction of S phase arrest in vitro, and attenuation of ECM-receptor interaction-associated molecule expressions including integrins ITGA6 and ITGA8. Furthermore, GLP significantly inhibited the TGF-β/Smad signaling in mice, and reduced TGF-β1 or its agonist SRI-011381-induced Smad2 and Smad3 phosphorylations, but increased Samd7 expression in HSC-T6 cells. CONCLUSION This study provides the first evidence that GLP could be a promising dietary strategy for treating liver fibrosis, which protects against liver fibrosis and HSC activation through targeting inflammation, apoptosis, cell cycle, and ECM-receptor interactions that are mediated by TGF-β/Smad signaling.
Collapse
Affiliation(s)
- Chaojie Chen
- School of Pharmaceutical Science, Zhejiang Chinese Medical University, 260 Baichuan Road, Hangzhou 311400, PR China
| | - Jiajun Chen
- School of Pharmaceutical Science, Zhejiang Chinese Medical University, 260 Baichuan Road, Hangzhou 311400, PR China
| | - Ying Wang
- School of Pharmaceutical Science, Zhejiang Chinese Medical University, 260 Baichuan Road, Hangzhou 311400, PR China
| | - Liu Fang
- School of Pharmaceutical Science, Zhejiang Chinese Medical University, 260 Baichuan Road, Hangzhou 311400, PR China
| | - Cuiling Guo
- School of Pharmaceutical Science, Zhejiang Chinese Medical University, 260 Baichuan Road, Hangzhou 311400, PR China
| | - Tingting Sang
- School of Pharmaceutical Science, Zhejiang Chinese Medical University, 260 Baichuan Road, Hangzhou 311400, PR China
| | - He Peng
- School of Pharmaceutical Science, Zhejiang Chinese Medical University, 260 Baichuan Road, Hangzhou 311400, PR China
| | - Qian Zhao
- School of Pharmaceutical Science, Zhejiang Chinese Medical University, 260 Baichuan Road, Hangzhou 311400, PR China
| | - Shengjia Chen
- School of Pharmaceutical Science, Zhejiang Chinese Medical University, 260 Baichuan Road, Hangzhou 311400, PR China
| | - Xiaojian Lin
- School of Pharmaceutical Science, Zhejiang Chinese Medical University, 260 Baichuan Road, Hangzhou 311400, PR China
| | - Xingya Wang
- School of Pharmaceutical Science, Zhejiang Chinese Medical University, 260 Baichuan Road, Hangzhou 311400, PR China.
| |
Collapse
|
5
|
Gu Y, Huang K, Zhang M, Teng F, Ge L, Zhou J, Xu J, Jia X. Long Noncoding RNA CTD-2589M5.4 Inhibits Ovarian Cancer Cell Proliferation, Migration, and Invasion Via Downregulation of the Extracellular Matrix-Receptor Interaction Pathway. Cancer Biother Radiopharm 2022; 37:580-588. [PMID: 34242057 DOI: 10.1089/cbr.2020.4429] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Background: The authors' previous study showed that the long noncoding RNA CTD-2589M5.4 was significantly upregulated in multidrug-resistant ovarian cancer cells. However, the role of CTD-2589M5.4 in the progression of ovarian cancer remains unclear. The purpose of this current study was to illuminate the biological function and possible mechanism of CTD-2589M5.4 in ovarian cancer development. Materials and Methods: The expression of CTD-2589M5.4 was examined via real-time quantitative PCR in primary ovarian cancer tissues (POCTs) and ovarian cancer cell lines. The biological function of CTD-2589M5.4 was analyzed via CCK-8 proliferation, wound healing, transwell, and flow cytometry assays in CTD-2589M5.4-overexpressed/silenced and control ovarian cancer cells. The mechanism of CTD-2589M5.4 function in ovarian cancer progression was analyzed utilizing high-throughput RNA-sequencing, Kyoto Encyclopedia of Genes and Genomes analysis, qRT-PCR, Western blot, and rescue experiments. Results: CTD-2589M5.4 expression was decreased in the POCTs and ovarian cancer cells compared with the normal ovarian tissues (p < 0.05) and normal ovarian epithelial cells (p < 0.05). Overexpression of CTD-2589M5.4 inhibited the proliferation, invasion, and migration of ovarian cancer cells, while knockdown of CTD-2589M5.4 had the opposite effect. Furthermore, a total of 750 and 233 genes were notably upregulated and downregulated, respectively, in the CTD-2589M5.4-overexpressed A2780 cells, while the extracellular matrix (ECM)-receptor interaction pathway was significantly downregulated. In addition, overexpression of fibronectin 1 significantly abrogated the tumor suppressive function of CTD-2589M5.4. Conclusions: This study demonstrated that CTD-2589M5.4 could inhibit ovarian cancer cell proliferation, invasion, and migration, at least partially by way of downregulating the ECM-receptor interaction pathway, therefore providing a potential therapeutic target for the prevention and/or treatment of ovarian cancer.
Collapse
Affiliation(s)
- Yuanyuan Gu
- Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China.,Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ke Huang
- Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Min Zhang
- Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Fang Teng
- Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Lili Ge
- Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Juan Zhou
- Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Juan Xu
- Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Xuemei Jia
- Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| |
Collapse
|
6
|
Guo Y, Ren C, Huang W, Yang W, Bao Y. Oncogenic ACSM1 in prostate cancer is through metabolic and extracellular matrix-receptor interaction signaling pathways. Am J Cancer Res 2022; 12:1824-1842. [PMID: 35530294 PMCID: PMC9077067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 04/01/2022] [Indexed: 06/14/2023] Open
Abstract
Acyl-coenzyme A synthetase medium chain family member 1 (ACSM1) is a medium chain Acyl-CoA Synthetase family member and plays an important role in fatty acid metabolism. The oncogenic roles of ACSM1 are largely unknown. Using comprehensive approaches, we analyzed gene expression profiles and genomic datasets and identified that the expression of ACSM1 was specifically increased in prostate cancer in comparison to the adjacent non-tumor tissues. The increased expression of ACSM1 was associated with increased risks of poor prognosis and shorter survival time. Moreover, genomic copy number alterations of ACSM1, including deletion, amplification, and amino acid changes were frequently observed in prostate cancers, although these mutations did not correlate with gene expression levels. However, ACSM1 gene amplifications were significantly corrected with increased risks of prostate cancer metastasis, and ACSM1 genetic alterations were significantly associated with worse disease-free. And progress-free survival. Gene function stratification and gene set enrichment analysis revealed that the oncogenic roles of ACSM1 in prostate cancer were mainly through metabolic pathways and extracellular matrix (ECM)-receptor interaction signaling pathways, but not associated with microenvironmental immunological signaling pathways, and that ACSM1 expression was not associated with immune cell infiltration in the cancer microenvironment or prostate cancer immune subtypes. In conclusion, the present work has demonstrated that ACSM1 can be specifically and significantly elevated in prostate cancer. ACSM1 gene expression and genomic amplification exhibit important clinical significance through metabolic and ECM-receptor interaction signaling pathways. Thus, ACSM1 may be a novel oncogene and serve as a biomarker for prostate cancer screening and prognosis prediction, and/or a therapeutic target.
Collapse
Affiliation(s)
- Yongchen Guo
- Department of Immunology, Mudanjiang Medical UniversityMudanjiang 157011, China
| | - Chunna Ren
- The Second Affiliated Hospital of Mudanjiang Medical UniversityMudanjiang 157011, China
| | - Wentao Huang
- Hongqi Hospital Affiliated to Mudanjiang Medical UniversityMudanjiang 157011, China
| | - Wancai Yang
- Department of Pathology, University of Illinois at ChicagoIL 60612, USA
| | - Yonghua Bao
- Department of Pathology, Mudanjiang Medical UniversityMudanjiang 157011, China
| |
Collapse
|
7
|
Jia B, Yu S, Yu D, Liu N, Zhang S, Wu A. Mycotoxin deoxynivalenol affects myoblast differentiation via downregulating cytoskeleton and ECM-integrin-FAK-RAC-PAK signaling pathway. Ecotoxicol Environ Saf 2021; 226:112850. [PMID: 34607188 DOI: 10.1016/j.ecoenv.2021.112850] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 06/13/2023]
Abstract
As a common mycotoxin, deoxynivalenol (DON) contaminates cereal grains and feed in field or during processing and storage. DON elicits a spectrum of adverse effects in animals including anorexia and growth retardation. Especially, the presence of DON has also been detected in muscle, suggesting that DON may has the potential to affect the development of muscle. However, the relevant research is very rare and the molecular mechanism remains unclear. Myoblasts differentiation into multinucleated myotubes is one of the crucial steps of skeletal muscle development. In the present study, we investigated the effects of DON on differentiation of myoblasts using murine C2C12 cells model. The results indicated that DON dose-dependent inhibited the formation of myotubes in C2C12 cells. After performing omics techniques, a total of 149 differentially expressed genes were identified. The expression of cytoskeleton proteins and extracellular matrix (ECM) proteins were downregulated by DON. Furthermore, DON significantly downregulated the expression of integrin αv and integrin β5, leading to inhibition of the ECM-integrin receptor interaction. The focal adhesion kinase (FAK) and phosphorylated forms, ras-related C3 botulinum toxin substrate (RAC) and p21-activated kinases 1 (PAK1) were also downregulated by DON. Taken together, our findings suggest that DON has the potent to affect the differentiation of myoblasts via downregulating of cytoskeleton and ECM-integrin-FAK-RAC-PAK signaling pathway.
Collapse
Affiliation(s)
- Bingxuan Jia
- SIBS-UGENT-SJTU Joint Laboratory of Mycotoxin Research, CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Song Yu
- SIBS-UGENT-SJTU Joint Laboratory of Mycotoxin Research, CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Dianzhen Yu
- SIBS-UGENT-SJTU Joint Laboratory of Mycotoxin Research, CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Na Liu
- SIBS-UGENT-SJTU Joint Laboratory of Mycotoxin Research, CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shuo Zhang
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing 100021, China
| | - Aibo Wu
- SIBS-UGENT-SJTU Joint Laboratory of Mycotoxin Research, CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| |
Collapse
|
8
|
Qian X, Liu X, Zhu Z, Wang S, Song X, Chen G, Wu J, Cao Y, Luan X, Tang H, Cao L. Variants in LAMC3 Causes Occipital Cortical Malformation. Front Genet 2021; 12:616761. [PMID: 34354730 PMCID: PMC8329496 DOI: 10.3389/fgene.2021.616761] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 06/21/2021] [Indexed: 12/12/2022] Open
Abstract
Occipital cortical malformation (OCCM) is a disease caused by malformations of cortical development characterized by polymicrogyria and pachygyria of the occipital lobes and childhood-onset seizures. The recessive or complex heterozygous variants of the LAMC3 gene are identified as the cause of OCCM. In the present study, we identified novel complex heterozygous variants (c.470G > A and c.4030 + 1G > A) of the LAMC3 gene in a Chinese female with childhood-onset seizures. Cranial magnetic resonance imaging was normal. Functional experiments confirmed that both variant sites caused premature truncation of the laminin γ3 chain. Bioinformatics analysis predicted 10 genes interacted with LAMC3 with an interaction score of 0.4 (P value = 1.0e–16). The proteins encoded by these genes were mainly located in the basement membrane and extracellular matrix component. Furthermore, the biological processes and molecular functions from gene ontology analysis indicated that laminin γ3 chain and related proteins played an important role in structural support and cellular processes through protein-containing complex binding and signaling receptor binding. KEGG pathway enrichment predicted that the LAMC3 gene variant was most likely to participate in the occurrence and development of OCCM through extracellular matrix receptor interaction and PI3K-Akt signaling pathway.
Collapse
Affiliation(s)
- Xiaohang Qian
- Department of Neurology and Institute of Neurology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaoying Liu
- Department of Neurology and Institute of Neurology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zeyu Zhu
- Department of Neurology and Institute of Neurology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shige Wang
- Department of Neurology and Institute of Neurology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaoxuan Song
- Department of Neurology and Institute of Neurology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guang Chen
- Department of Neurology and Institute of Neurology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jingying Wu
- Department of Neurology and Institute of Neurology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuwen Cao
- Department of Neurology and Institute of Neurology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xinghua Luan
- Department of Neurology and Institute of Neurology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Neurology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Huidong Tang
- Department of Neurology and Institute of Neurology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li Cao
- Department of Neurology and Institute of Neurology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Neurology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| |
Collapse
|
9
|
Wang C, Li N, Liu Q, Su L, Wang S, Chen Y, Liu M, Lin H. The role of circRNA derived from RUNX2 in the serum of osteoarthritis and its clinical value. J Clin Lab Anal 2021; 35:e23858. [PMID: 34165827 PMCID: PMC8274987 DOI: 10.1002/jcla.23858] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/11/2021] [Accepted: 05/17/2021] [Indexed: 12/11/2022] Open
Abstract
Background Circular RNA (circRNA) has been shown to affect the pathological process of osteoarthritis (OA) and is expected to become a potential marker for disease diagnosis. This study aimed to investigate the association between circRNA derived from the gene of runt‐related transcription factor 2 (RUNX2) and OA risk. Methods The expression profile of RUNX2‐derived circRNAs in serum of OA patients was detected. Then, the cytological localization of screened differential circRNAs was studied. Luciferase (LUC) reporter assay was used to identify the microRNA (miRNA) sponge capacity of the circRNAs. Bioinformatics analysis was used to construct the functional pathway of this circRNA‐miRNAs network. And then, the diagnostic value of RUNX2‐derived circRNAs in OA was evaluated. Results RUNX2‐derived hsa_circ_0005526 (circ_RUNX2) is significantly highly expressed in OA serum and mainly located in the cytoplasm within the cartilage cell by sponging multiple miRNAs (miR‐498, miR‐924, miR‐361‐3p, and miR‐665). Bioinformatics analysis showed ECM‐receptor interaction pathway ranked the most significant pathway of circ_RUNX2‐miRNAs regulatory network in KEGG database. The ROC curve showed that there may be good diagnostic value of serum circ_RUNX2 in OA. Conclusion RUNX2‐derived circ_RUNX2 may be involved in OA development via ECM‐receptor interaction pathways and may be used as potential clinical indicator of OA.
Collapse
Affiliation(s)
- Chengyun Wang
- Department of Pediatric Orthopedics, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Nanzhu Li
- Department of Pediatric Orthopedics, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Qi Liu
- Department of Pediatric Orthopedics, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Lianbin Su
- Department of Pediatric Orthopedics, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Sisheng Wang
- Department of Pediatric Orthopedics, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Yongfa Chen
- Department of Pediatric Orthopedics, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Maosheng Liu
- Department of Pediatric Orthopedics, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Huirong Lin
- Institute of Chemical Engineering, Huaqiao University, Xiamen, China
| |
Collapse
|
10
|
Jiang MM, Zhao F, Lou TT. Assessment of Significant Pathway Signaling and Prognostic Value of GNG11 in Ovarian Serous Cystadenocarcinoma. Int J Gen Med 2021; 14:2329-2341. [PMID: 34113163 PMCID: PMC8185253 DOI: 10.2147/ijgm.s314911] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/14/2021] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND GNG11 (G protein subunit gamma 11) is a member of guanine nucleotide-binding protein (G protein) gamma family. Few studies elucidated the role of GNG11 in human disease, especially in tumors. The present study initially analyzed the function of GNG11 in ovarian serous cystadenocarcinoma. METHODS The differential expression of GNG11 mRNA in ovarian cancer and normal tissues was evaluated through Oncomine, CCLE, Gepia, UCSC Xena and UALCAN databases. The protein expression of GNG11 was assessed via HPA database. Prognosis analysis was performed by Kaplan-Meier Plotter. Restrict survival analysis to subtypes including tumor grade, cancer stage and TP53 mutation status was then carried out. GSEA enrichment analysis was performed to explore the significant pathways associated with GNG11 in ovarian cancer. Finally, the upstream miRNAs of GNG11 were predicted by DIANA, Target Scan, miRDB and miRWalk databases, and the potential key KEGG pathways were subsequently determined by DIANA. RESULTS The mRNA expression of GNG11 was down-regulated in ovarian cancer patients (P<0.05). The cancer stage of patients correlated with the expression of GNG11 (P<0.05). Survival analysis indicated that GNG11 high expression statistically shortened the overall survival time of patients (HR=1.26, P=0.0043) compared with low expression group, especially for the patients with earlier stage (HR=2.48, P=0.035) and lower grade (HR=1.72, P=0.0016). Subsequently, the consistent upstream miRNA of GNG11, hsa-miR-22-5p, was predicted from 4 databases. The differential expression profile of hsa-miR-22-5p in blood was observed in ovarian cancer patients. According to the GSEA analysis on GNG11 and KEGG analysis on hsa-miR-22-5p, the consistent pathway of ECM-receptor interaction was observed (all P<0.01). ECM-receptor interaction pathway and differential expression of hsa-miR-22-5p in blood suggested the migration risk of ovarian cancer. CONCLUSION High expression of GNG11 indicated the poor prognosis of ovarian cancer patients. GNG11 might play a crucial role in the biological process of ovarian serous cystadenocarcinoma by ECM-receptor interaction pathway, thus affecting the prognosis of patients.
Collapse
Affiliation(s)
- Ming-Min Jiang
- Department of Obstetrics and Gynaecology, Zhuji Central Hospital, Shaoxing, 311800, Zhejiang, People’s Republic of China
- Correspondence: Ming-Min Jiang Department of Obstetrics and Gynaecology, Zhuji Central Hospital, Shaoxing, 311800, Zhejiang, People’s Republic of ChinaTel +86-13575599091 Email
| | - Fan Zhao
- Department of Obstetrics and Gynaecology, Zhuji Central Hospital, Shaoxing, 311800, Zhejiang, People’s Republic of China
| | - Tao-Tao Lou
- Department of Obstetrics and Gynaecology, Zhuji Central Hospital, Shaoxing, 311800, Zhejiang, People’s Republic of China
| |
Collapse
|
11
|
Lazzarini R, Caffarini M, Delli Carpini G, Ciavattini A, Di Primio R, Orciani M. From 2646 to 15: differentially regulated microRNAs between progenitors from normal myometrium and leiomyoma. Am J Obstet Gynecol 2020; 222:596.e1-9. [PMID: 31874141 DOI: 10.1016/j.ajog.2019.12.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 11/15/2019] [Accepted: 12/16/2019] [Indexed: 12/18/2022]
Abstract
BACKGROUND Uterine leiomyomas (fibroids) are smooth muscle neoplasms of the myometrial layer of the uterus and are the most common benign tumors in women. Although their etiology is still unclear, progenitor cells seem to be implicated. OBJECTIVE To identify the dysregulated pathways involved in leiomyoma onset by microRNA profiling of progenitor cells isolated from normal myometrium and leiomyoma tissue. MATERIALS AND METHODS Pairs of normal myometrium and uterine fibroid specimens were collected from 12 myomectomy patients. Myometrial progenitor cells and leiomyoma progenitor cells were isolated and characterized for stemness. After total RNA extraction and profiling of their 2646 microRNAs, DIANA-miRPath analysis was applied to find any dysregulated pathways. RESULTS Only 30 microRNAs showed a significant differential regulation between myometrial progenitor cells and leiomyoma progenitor cells. Removal of those that had values close to the cut-off or that were not consistent among triplicates left 15 microRNAs, of which 7 were downregulated and 8 were upregulated in leiomyoma progenitor cells compared to myometrial progenitor cells. According to DIANA-miRPath analysis, the 7 downregulated microRNAs (hsa-miR-146b-5p; hsa-miR-335-3p; hsa-miR-335-5p; hsa-miR-135b-5p; hsa-miR-10a-3p; hsa-miR-10a-5p; hsa-miR-200a-3p) are all related to 3 pathways, "ECM-receptor interaction" (33 targeted genes), "Adherens junction" (33 targeted genes), and "Hippo signaling" (69 targeted genes), whereas the 8 upregulated miRNAs (hsa-miR-146a-5p; hsa-miR-576-3p; hsa-miR-122-5p; hsa-miR-1246; hsa-miR-595; hsa-miR-658; hsa-miR-4284; hsa-miR-924) are related to 4 pathways, "PI3K-Akt signaling pathway" (71 targeted genes), "Pathways in Cancer" (80 targeted genes), "Cell Cycle" (37 targeted genes), and "Regulation of actin cytoskeleton" (41 targeted genes). CONCLUSION The findings that only 15 of 2646 microRNAs are differentially regulated in normal myometrium and leiomyoma and that they are involved in 7 dysregulated pathways provides interesting insights into the development of uterine fibroids, and lends support to the hypothesis that leiomyoma onset is the result of alterations affecting progenitor cells.
Collapse
|
12
|
Cheng J, Zhuo H, Wang L, Zheng W, Chen X, Hou J, Zhao J, Cai J. Identification of the Combinatorial Effect of miRNA Family Regulatory Network in Different Growth Patterns of GC. Mol Ther Oncolytics 2020; 17:531-546. [PMID: 32637572 PMCID: PMC7321821 DOI: 10.1016/j.omto.2020.03.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 03/24/2020] [Indexed: 12/24/2022]
Abstract
According to the growth pattern, gastric cancer (GC) could be classified into expanding-type GC and infiltrative-type GC (Ming’s classification). The growth pattern of GC is often related to the malignant degree, invasion, metastasis, and other pathological characteristics of tumors. MicroRNAs (miRNAs) play important roles in modulating gene expression during the GC development. In this study, miR-29s were significantly correlated with the gastric carcinogenesis and Ming’s classification. Biological function of miR-29s is most closely related to the pathway of extracellular matrix (ECM)-receptor interaction. ECM structural assembly, cell movement, and cell adhesion are the main functional categories of target genes in this pathway. Among these targets, the COL4A1 gene ranked at the top in the association analysis of combined miR-29s biological function and GC subtype, and miR-29s inhibited its translation by binding to the 3′ UTR region. Infiltrative-type GC cells secrete a higher level of COL4A1 protein than do expanding-type GC cells. The expression of COL4A1 in GC is correlated with clinicopathological features. Downregulation of COL4A1 expression significantly inhibited the migration and invasion of GC cells. High COL4A1 expression was correlated with poor prognosis in survival analysis. The miR-29s regulatory network may affect the development of growth patterns and pathological progress of GC by regulating the function of COL4A1.
Collapse
Affiliation(s)
- Jia Cheng
- Department of Gastrointestinal Surgery, Zhongshan Hospital, Xiamen University, Xiamen, Fujian 361004, China.,Institute of Gastrointestinal Oncology, School of Medicine, Xiamen University, Xiamen, Fujian 361004, China.,Xiamen Municipal Key Laboratory of Gastrointestinal Oncology, Xiamen, Fujian 361004, China
| | - Huiqin Zhuo
- Department of Gastrointestinal Surgery, Zhongshan Hospital, Xiamen University, Xiamen, Fujian 361004, China.,Institute of Gastrointestinal Oncology, School of Medicine, Xiamen University, Xiamen, Fujian 361004, China.,Xiamen Municipal Key Laboratory of Gastrointestinal Oncology, Xiamen, Fujian 361004, China
| | - Lin Wang
- Department of Gastrointestinal Surgery, Zhongshan Hospital, Xiamen University, Xiamen, Fujian 361004, China.,Institute of Gastrointestinal Oncology, School of Medicine, Xiamen University, Xiamen, Fujian 361004, China.,Xiamen Municipal Key Laboratory of Gastrointestinal Oncology, Xiamen, Fujian 361004, China
| | - Wei Zheng
- Department of Gastrointestinal Surgery, Zhongshan Hospital, Xiamen University, Xiamen, Fujian 361004, China.,Institute of Gastrointestinal Oncology, School of Medicine, Xiamen University, Xiamen, Fujian 361004, China.,Xiamen Municipal Key Laboratory of Gastrointestinal Oncology, Xiamen, Fujian 361004, China
| | - Xin Chen
- Union Hospital, Fujian Medical University, Fuzhou, Fujian 350001, China
| | - Jingjing Hou
- Department of Gastrointestinal Surgery, Zhongshan Hospital, Xiamen University, Xiamen, Fujian 361004, China.,Institute of Gastrointestinal Oncology, School of Medicine, Xiamen University, Xiamen, Fujian 361004, China.,Xiamen Municipal Key Laboratory of Gastrointestinal Oncology, Xiamen, Fujian 361004, China
| | - Jiabao Zhao
- Department of Gastrointestinal Surgery, Zhongshan Hospital, Xiamen University, Xiamen, Fujian 361004, China.,Institute of Gastrointestinal Oncology, School of Medicine, Xiamen University, Xiamen, Fujian 361004, China.,Xiamen Municipal Key Laboratory of Gastrointestinal Oncology, Xiamen, Fujian 361004, China
| | - Jianchun Cai
- Department of Gastrointestinal Surgery, Zhongshan Hospital, Xiamen University, Xiamen, Fujian 361004, China.,Institute of Gastrointestinal Oncology, School of Medicine, Xiamen University, Xiamen, Fujian 361004, China.,Xiamen Municipal Key Laboratory of Gastrointestinal Oncology, Xiamen, Fujian 361004, China.,Union Hospital, Fujian Medical University, Fuzhou, Fujian 350001, China
| |
Collapse
|
13
|
Wang J, Zhang Q, Li S, Chen Z, Tan J, Yao J, Duan D. Low molecular weight fucoidan alleviates diabetic nephropathy by binding fibronectin and inhibiting ECM-receptor interaction in human renal mesangial cells. Int J Biol Macromol 2020; 150:304-314. [PMID: 32057847 DOI: 10.1016/j.ijbiomac.2020.02.087] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 01/26/2020] [Accepted: 02/10/2020] [Indexed: 12/13/2022]
Abstract
Diabetic nephropathy (DN) is the most common cause of end-stage renal disease (ESRD). Currently, approximately 20-40% of individuals with diabetes are diagnosed with DN. Mesangial cells (MCs) are critical for maintaining and regulating glomerular filtration, and the abnormal proliferation of MCs causes the accumulation of mesangial extracellular matrix (ECM), further promoting glomerular dysfunction and renal diseases. Low molecular weight fucoidan (LMWF) extracted from Saccharina japonica could alleviate DN, but the mechanism was not analysed. Based on the ability of LMWF to ameliorate the human renal mesangial cell (HRMC) injury caused by advanced glycation end products (AGEs), we identified fibronectin (FN) as the most obviously impacted protein in the ECM-receptor interaction by proteomic analysis. The co-localization of LMWF and FN indicated direct interaction between them, and surface plasmon resonance (SPR) analysis confirmed the specific binding with a KD of 453.7 μmol L-1. Positively charged protamine sulfate (PS) promoted the combination of LMWF and HRMCs and further enhanced the effect of LMWF on HRMC injury. Our results indicated that LMWF alleviates the HRMC injury caused by AGEs via binding FN and inhibiting the ECM-receptor interaction pathway. These results provide a foundation for the in-depth analysis of the mechanism of polysaccharide functions.
Collapse
Affiliation(s)
- Jing Wang
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Quanbin Zhang
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Shuang Li
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhihang Chen
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiaojiao Tan
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianting Yao
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Delin Duan
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; State Key Laboratory of Bioactive Seaweed Substances, Qingdao, 266400, China.
| |
Collapse
|