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Zhang W, Zhang M, Sun M, Hu M, Yu M, Sun J, Zhang X, Du B. Metabolomics-transcriptomics joint analysis: unveiling the dysregulated cell death network and developing a diagnostic model for high-grade neuroblastoma. Front Immunol 2024; 14:1345734. [PMID: 38239355 PMCID: PMC10794662 DOI: 10.3389/fimmu.2023.1345734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 12/14/2023] [Indexed: 01/22/2024] Open
Abstract
High-grade neuroblastoma (HG-NB) exhibits a significantly diminished survival rate in comparison to low-grade neuroblastoma (LG-NB), primarily attributed to the mechanism of HG-NB is unclear and the lacking effective therapeutic targets and diagnostic model. Therefore, the current investigation aims to study the dysregulated network between HG-NB and LG-NB based on transcriptomics and metabolomics joint analysis. Meanwhile, a risk diagnostic model to distinguish HG-NB and LG-NB was also developed. Metabolomics analysis was conducted using plasma samples obtained from 48 HG-NB patients and 36 LG-NB patients. A total of 39 metabolites exhibited alterations, with 20 showing an increase and 19 displaying a decrease in HG-NB. Additionally, transcriptomics analysis was performed on NB tissue samples collected from 31 HG-NB patients and 20 LG-NB patients. Results showed that a significant alteration was observed in a total of 1,199 mRNAs in HG-NB, among which 893 were upregulated while the remaining 306 were downregulated. In particular, the joint analysis of both omics data revealed three aberrant pathways, namely the cAMP signaling pathway, PI3K-Akt signaling pathway, and TNF signaling pathway, which were found to be associated with cell death. Notably, a diagnostic model for HG-NB risk classification was developed based on the genes MGST1, SERPINE1, and ERBB3 with an area under the receiver operating characteristic curve of 0.915. In the validation set, the sensitivity and specificity were determined to be 75.0% and 80.0%, respectively.
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Affiliation(s)
- Wancun Zhang
- Health Commission of Henan Province Key Laboratory for Precision Diagnosis and Treatment of Pediatric Tumor, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory for Prevention and Treatment of Pediatric Disease, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Children’s Genetics and Metabolic Diseases, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Mengxin Zhang
- Health Commission of Henan Province Key Laboratory for Precision Diagnosis and Treatment of Pediatric Tumor, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Meng Sun
- Henan Key Laboratory of Children’s Genetics and Metabolic Diseases, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Minghui Hu
- Health Commission of Henan Province Key Laboratory for Precision Diagnosis and Treatment of Pediatric Tumor, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Muchun Yu
- Henan International Joint Laboratory for Prevention and Treatment of Pediatric Disease, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Jushan Sun
- Health Commission of Henan Province Key Laboratory for Precision Diagnosis and Treatment of Pediatric Tumor, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Xianwei Zhang
- Health Commission of Henan Province Key Laboratory for Precision Diagnosis and Treatment of Pediatric Tumor, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Bang Du
- Health Commission of Henan Province Key Laboratory for Precision Diagnosis and Treatment of Pediatric Tumor, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory for Prevention and Treatment of Pediatric Disease, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Children’s Genetics and Metabolic Diseases, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou, China
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Liao Y, Li R, Pei J, Zhang J, Chen B, Dong H, Feng X, Zhang H, Shang Y, Sui L, Kong Y. Melatonin suppresses tumor proliferation and metastasis by targeting GATA2 in endometrial cancer. J Pineal Res 2024; 76:e12918. [PMID: 37814536 DOI: 10.1111/jpi.12918] [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: 02/27/2023] [Revised: 08/30/2023] [Accepted: 09/12/2023] [Indexed: 10/11/2023]
Abstract
Endometrial cancer (EC) is a reproductive system disease that occurs in perimenopausal and postmenopausal women. However, its etiology is unclear. Melatonin (MT) has been identified as a therapeutic agent for EC; however, its exact mechanism remains unclear. In the present study, we determined that GATA-binding protein 2 (GATA2) is expressed at low levels in EC and regulated by MT. MT upregulates the expression of GATA2 through MT receptor 1A (MTNR1A), whereas GATA2 can promote the expression of MTNR1A by binding to its promoter region. In addition, in vivo and in vitro experiments showed that MT inhibited the proliferation and metastasis of EC cells by upregulating GATA2 expression. The protein kinase B (AKT) pathway was also affected. In conclusion, these findings suggest that MT and GATA2 play significant roles in EC development.
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Affiliation(s)
- Yangyou Liao
- Core Laboratory of Glycobiology and Glycoengineering, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Ruiling Li
- Core Laboratory of Glycobiology and Glycoengineering, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Jingyuan Pei
- Core Laboratory of Glycobiology and Glycoengineering, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Juan Zhang
- Core Laboratory of Glycobiology and Glycoengineering, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Bo Chen
- Core Laboratory of Glycobiology and Glycoengineering, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Haojie Dong
- Core Laboratory of Glycobiology and Glycoengineering, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Xiaoyu Feng
- Core Laboratory of Glycobiology and Glycoengineering, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Hongshuo Zhang
- Core Laboratory of Glycobiology and Glycoengineering, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Yuhong Shang
- Department of Gynecology, First Affiliated Hospital, Dalian Medical University, Dalian, Liaoning, China
| | - Linlin Sui
- Core Laboratory of Glycobiology and Glycoengineering, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Ying Kong
- Core Laboratory of Glycobiology and Glycoengineering, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
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Zhang J, Dong Y, Shi Z, He H, Chen J, Zhang S, Wu W, Zhang Q, Han C, Hao L. P3H4 and PLOD1 expression associates with poor prognosis in bladder cancer. Clin Transl Oncol 2022; 24:1524-1532. [PMID: 35149972 DOI: 10.1007/s12094-022-02791-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/21/2022] [Indexed: 12/24/2022]
Abstract
PURPOSE The prolyl 3-hydroxylase family member 4 gene (P3H4) is involved in the development of human cancers. The association of P3H4 with bladder cancer (BC) prognosis is unclear. This study aimed to analyze the association of P3H4 with BC prognosis. METHODS RNA-Seq data were downloaded from The Cancer Genome Atlas project and BC microarray datasets (GSE13507, GSE31684, and GSE32548) were downloaded from the Gene Expression Omnibus database. We analyzed the differences in P3H4 expression levels between BC tumors and non-tumor tissues and between samples with different clinical information. The association of P3H4 and P3H4-related genes with BC prognosis and the possibility of using P3H4 expression as a prognostic biomarker in BC patients were also analyzed. RevMan was used to perform the meta-analysis. RESULTS P3H4 was upregulated in BC tissues compared with the adjacent non-tumor tissues (p = 4.06e-08). Univariate Cox regression analysis and meta-analysis showed that high P3H4 expression level contributed to a poor BC prognosis (Hazard ratio, HR = 1.348, 95% CI 1.140-1.594, p = 4.89e-04; meta-analysis: HR = 1.45, 95% CI 1.10-1.91; p = 9.00e-03). Among the genes related to P3H4, the PLOD1 gene was closely associated with P3H4 expression (r = 0.620, p = 2.49e-44). Also, a meta-analysis showed that PLOD1 expression was associated with a poor prognosis in BC patients (HR = 1.77, 95% CI 1.31-2.38; p = 2.00e-04). CONCLUSIONS The P3H4 and PLOD1 genes might be used as reliable prognostic biomarkers for BC.
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Affiliation(s)
- Junjie Zhang
- Medical College of Soochow University, Suzhou, 215123, Jiangsu, China.,Department of Urology, Xuzhou Central Hospital, 199 Jiefang South Road, Xuzhou, 221009, Jiangsu, China
| | - Yang Dong
- Medical College of Soochow University, Suzhou, 215123, Jiangsu, China.,Department of Urology, Xuzhou Central Hospital, 199 Jiefang South Road, Xuzhou, 221009, Jiangsu, China
| | - Zhenduo Shi
- Department of Urology, Xuzhou Central Hospital, 199 Jiefang South Road, Xuzhou, 221009, Jiangsu, China
| | - Houguang He
- Department of Urology, Xuzhou Central Hospital, 199 Jiefang South Road, Xuzhou, 221009, Jiangsu, China
| | - Jiangang Chen
- Medical College of Soochow University, Suzhou, 215123, Jiangsu, China
| | - Shaoqi Zhang
- Medical College of Soochow University, Suzhou, 215123, Jiangsu, China
| | - Wei Wu
- Medical College of Soochow University, Suzhou, 215123, Jiangsu, China
| | - Qianjin Zhang
- Medical College of Soochow University, Suzhou, 215123, Jiangsu, China
| | - Conghui Han
- Medical College of Soochow University, Suzhou, 215123, Jiangsu, China.,Department of Urology, Xuzhou Central Hospital, 199 Jiefang South Road, Xuzhou, 221009, Jiangsu, China
| | - Lin Hao
- Medical College of Soochow University, Suzhou, 215123, Jiangsu, China. .,Department of Urology, Xuzhou Central Hospital, 199 Jiefang South Road, Xuzhou, 221009, Jiangsu, China.
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Jahangiri L, Pucci P, Ishola T, Pereira J, Cavanagh ML, Turner SD. Deep analysis of neuroblastoma core regulatory circuitries using online databases and integrated bioinformatics shows their pan-cancer roles as prognostic predictors. Discov Oncol 2021; 12:56. [PMID: 35201514 PMCID: PMC8777518 DOI: 10.1007/s12672-021-00452-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/16/2021] [Indexed: 12/29/2022] Open
Abstract
AIM Neuroblastoma is a heterogeneous childhood cancer derived from the neural crest. The dual cell identities of neuroblastoma include Mesenchymal (MES) and Adrenergic (ADRN). These identities are conferred by a small set of tightly-regulated transcription factors (TFs) binding super enhancers, collectively forming core regulatory circuitries (CRCs). The purpose of this study was to gain a deep understanding of the role of MES and ADRN TFs in neuroblastoma and other cancers as potential indicators of disease prognosis, progression, and relapse. METHODS To that end, we first investigated the expression and mutational profile of MES and ADRN TFs in neuroblastoma. Moreover, we established their correlation with neuroblastoma risk groups and overall survival while establishing their extended networks with long non-coding RNAs (lncRNAs). Furthermore, we analysed the pan-cancer expression and mutational profile of these TFs and their correlation with patient survival and finally their network connectivity, using a panel of bioinformatic tools including GEPIA2, human pathology atlas, TIMER2, Omicsnet, and Cytoscape. RESULTS We show the association of multiple MES and ADRN TFs with neuroblastoma risk groups and overall survival and find significantly higher expression of various MES and ADRN TFs compared to normal tissues and their association with overall survival and disease-free survival in multiple cancers. Moreover, we report the strong correlation of the expression of these TFs with the infiltration of stromal and immune cells in the tumour microenvironment and with stemness and metastasis-related genes. Furthermore, we reveal extended pan-cancer networks comprising these TFs that influence the tumour microenvironment and metastasis and may be useful indicators of cancer prognosis and patient survival. CONCLUSION Our meta-analysis shows the significance of MES and ADRN TFs as indicators of patient prognosis and the putative utility of these TFs as potential novel biomarkers.
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Affiliation(s)
- Leila Jahangiri
- Department of Life Sciences, Birmingham City University, Birmingham, UK
- School of Science & Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS UK
- Division of Cellular and Molecular Pathology, Addenbrooke’s Hospital, University of Cambridge, Cambridge, UK
| | - Perla Pucci
- Division of Cellular and Molecular Pathology, Addenbrooke’s Hospital, University of Cambridge, Cambridge, UK
| | - Tala Ishola
- Department of Life Sciences, Birmingham City University, Birmingham, UK
| | - Joao Pereira
- Department of Neurology, Massachusetts General Hospital, Boston, MA USA
| | - Megan L. Cavanagh
- Department of Life Sciences, Birmingham City University, Birmingham, UK
| | - Suzanne D. Turner
- Division of Cellular and Molecular Pathology, Addenbrooke’s Hospital, University of Cambridge, Cambridge, UK
- CEITEC, Masaryk University, Brno, Czech Republic
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Identify potential miRNA-mRNA regulatory networks contributing to high-risk neuroblastoma. Invest New Drugs 2021; 39:901-913. [PMID: 33666785 DOI: 10.1007/s10637-021-01064-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 01/06/2021] [Indexed: 10/22/2022]
Abstract
Neuroblastoma (NB) is a common tumor in children, usually in the retroperitoneum. After various treatments, low- and intermediate-risk patients have achieved good results, but the prognosis of high-risk patients is still very poor. Therefore, it is necessary to find new effective targets for the treatment of high-risk patients. In this study, comprehensive bioinformatics analysis was used to identify the differentially expressed genes (DEG and DEM) between high-risk patients and non-high-risk patients, and it was identified that ADRB2 may affect the survival status of high-risk patients due to miR -30a-5p regulation. The GSE49710, GSE73517, and GSE121513 datasets were downloaded from the Gene Expression Synthesis (GEO) database, and DEG and DEM were selected. Then, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were applied to the selected DEGs. The STRING database and Cytoscape software were used to construct protein-protein interaction (PPI) networks and perform modular analysis of the DEGs. The TARGET data set containing information on overall survival days were used for the prognostic analysis of central genes. We identified a total of 255 DEGs from GSE49710 and GSE73517, and 193 DEMs from GSE121513. We identified the 5 most important central genes from the PPI network, performed a prognostic analysis in the target data set, and verified their expression using RT-qPCR to select the most important ADRB2 gene to predict miRNA. Integrating the differential miRNA predicted by miRDB and miRSystem and GSE121513 between the targeted miRNA and the prognosis, miR-30a-5p was finally identified as the targeted miRNA of ADRB2.
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Chen B, Sun D, Qin X, Gao XH. Screening and identification of potential biomarkers and therapeutic drugs in melanoma via integrated bioinformatics analysis. Invest New Drugs 2021; 39:928-948. [PMID: 33501609 DOI: 10.1007/s10637-021-01072-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 01/19/2021] [Indexed: 12/15/2022]
Abstract
Melanoma is a highly aggressive malignant skin tumor with a high rate of metastasis and mortality. In this study, a comprehensive bioinformatics analysis was used to clarify the hub genes and potential drugs. Download the GSE3189, GSE22301, and GSE35388 microarray datasets from the Gene Expression Omnibus (GEO), which contains a total of 33 normal samples and 67 melanoma samples. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) approach analyze DEGs based on the DAVID. Use STRING to construct protein-protein interaction network, and use MCODE and cytoHubba plug-ins in Cytoscape to perform module analysis and identified hub genes. Use Gene Expression Profile Interactive Analysis (GEPIA) to assess the prognosis of genes in tumors. Finally, use the Drug-Gene Interaction Database (DGIdb) to screen targeted drugs related to hub genes. A total of 140 overlapping DEGs were identified from the three microarray datasets, including 59 up-regulated DEGs and 81 down-regulated DEGs. GO enrichment analysis showed that these DEGs are mainly involved in the biological process such as positive regulation of gene expression, positive regulation of cell proliferation, positive regulation of MAP kinase activity, cell migration, and negative regulation of the apoptotic process. The cellular components are concentrated in the membrane, dendritic spine, the perinuclear region of cytoplasm, extracellular exosome, and membrane raft. Molecular functions include protein homodimerization activity, calmodulin-binding, transcription factor binding, protein binding, and cytoskeletal protein binding. KEGG pathway analysis shows that these DEGs are mainly related to protein digestion and absorption, PPAR signaling pathway, signaling pathways regulating stem cells' pluripotency, and Retinol metabolism. The 23 most closely related DEGs were identified from the PPI network and combined with the GEPIA prognostic analysis, CDH3, ESRP1, FGF2, GBP2, KCNN4, KIT, SEMA4D, and ZEB1 were selected as hub genes, which are considered to be associated with poor prognosis of melanoma closely related. Besides, ten related drugs that may have therapeutic effects on melanoma were also screened. These newly discovered genes and drugs provide new ideas for further research on melanoma.
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Affiliation(s)
- Bo Chen
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
- Medical Research Center, Liaoning Key Laboratory of Research and Application of Animal Models for Environmental and Metabolic Diseases, Shengjing Hospital of China Medical University, Shenyang, China
| | - Donghong Sun
- Department of Dermatology, The First Hospital of China Medical University, No. 155 Nanjing North Street, Shenyang, 110001, Liaoning Province, China
| | - Xiuni Qin
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
- Medical Research Center, Liaoning Key Laboratory of Research and Application of Animal Models for Environmental and Metabolic Diseases, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xing-Hua Gao
- Department of Dermatology, The First Hospital of China Medical University, No. 155 Nanjing North Street, Shenyang, 110001, Liaoning Province, China.
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Gao S, Liu L, Li Z, Pang Y, Shi J, Zhu F. Seven Novel Genes Related to Cell Proliferation and Migration of VHL-Mutated Pheochromocytoma. Front Endocrinol (Lausanne) 2021; 12:598656. [PMID: 33828526 PMCID: PMC8021008 DOI: 10.3389/fendo.2021.598656] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 02/09/2021] [Indexed: 12/19/2022] Open
Abstract
Pheochromocytoma, as a neuroendocrine tumor with the highest genetic correlation in all types of tumors, has attracted extensive attention. Von Hipper Lindau (VHL) has the highest mutation frequency among the genes associated with pheochromocytoma. However, the effect of VHL on the proteome of pheochromocytoma remains to be explored. In this study, the VHL knockdown (VHL-KD) PC12 cell model was established by RNA interference (shRNA). We compared the proteomics of VHL-KD and VHL-WT PC12 cell lines. The results showed that the expression of 434 proteins (VHL shRNA/WT > 1.3) changed significantly in VHL-KD-PC12 cells. Among the 434 kinds of proteins, 83 were involved in cell proliferation, cell cycle and cell migration, and so on. More importantly, among these proteins, we found seven novel key genes, including Connective Tissue Growth Factor (CTGF), Syndecan Binding Protein (SDCBP), Cysteine Rich Protein 61 (CYR61/CCN1), Collagen Type III Alpha 1 Chain (COL3A1), Collagen Type I Alpha 1 Chain (COL1A1), Collagen Type V Alpha 2 Chain (COL5A2), and Serpin Family E Member 1 (SERPINE1), were overexpressed and simultaneously regulated cell proliferation and migration in VHL-KD PC12 cells. Furthermore, the abnormal accumulation of HIF2α caused by VHL-KD significantly increased the expression of these seven genes during hypoxia. Moreover, cell-counting, scratch, and transwell assays demonstrated that VHL-KD could promote cell proliferation and migration, and changed cell morphology. These findings indicated that inhibition of VHL expression could promote the development of pheochromocytoma by activating the expression of cell proliferation and migration associated genes.
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Affiliation(s)
- Shuai Gao
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Central South University, Changsha, China
| | - Longfei Liu
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China
| | - Zhuolin Li
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Central South University, Changsha, China
| | - Yingxian Pang
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China
| | - Jiaqi Shi
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Central South University, Changsha, China
| | - Feizhou Zhu
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, China
- *Correspondence: Feizhou Zhu,
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