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Yan C, He L, Ma Y, Cheng J, Shen L, Singla RK, Zhang Y. Establishing and Validating an Innovative Focal Adhesion-Linked Gene Signature for Enhanced Prognostic Assessment in Endometrial Cancer. Reprod Sci 2024; 31:2468-2480. [PMID: 38653857 DOI: 10.1007/s43032-024-01564-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 04/12/2024] [Indexed: 04/25/2024]
Abstract
Studies have highlighted the significant role of focal adhesion signaling in cancer. Nevertheless, its specific involvement in the pathogenesis of endometrial cancer and its clinical significance remains uncertain. We analyzed TCGA-UCEC and GSE119041 datasets with corresponding clinical data to investigate focal adhesion-related gene expression and their clinical significance. A signature, "FA-riskScore," was developed using LASSO regression in the TCGA cohort and validated in the GSE dataset. The FA-riskScore was compared with four existing models in terms of their prediction performance. We employed univariate and multivariate Cox regression analyses towards FA-riskScore to assess its independent prognostic value. A prognostic evaluation nomogram based on our model and clinical indexes was established subsequently. Biological and immune differences between high- and low-risk groups were explored through functional enrichment, PPI network analysis, mutation mining, TME evaluation, and single-cell analysis. Sensitivity tests on commonly targeted drugs were performed on both groups, and Connectivity MAP identified potentially effective molecules for high-risk patients. qRT-PCR validated the expressions of FA-riskScore genes. FA-riskScore, based on FN1, RELN, PARVG, and PTEN, indicated a poorer prognosis for high-risk patients. Compared with published models, FA-riskScore achieved better and more stable performance. High-risk groups exhibited a more challenging TME and suppressive immune status. qRT-PCR showed differential expression in FN1, RELN, and PTEN. Connectivity MAP analysis suggested that BU-239, potassium-canrenoate, and tubocurarine are effective for high-risk patients. This study introduces a novel prognostic model for endometrial cancer and offers insights into focal adhesion's role in cancer pathogenesis.
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Affiliation(s)
- Cuiyin Yan
- Department of Obstetrics and Gynecology, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, China
| | - Leilei He
- Department of Obstetrics and Gynecology, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, China
| | - Yuhui Ma
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Hong Kong, SAR, China
| | - Jing Cheng
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Hong Kong, SAR, China
| | - Li Shen
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.
- Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland.
| | - Rajeev K Singla
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, 144411, India.
| | - Yueming Zhang
- Department of Obstetrics and Gynecology, The Fourth Affiliated Hospital of Soochow University, Suzhou, China.
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Chu MY, Huang HC, Li EM, Xu LY. CypA: A Potential Target of Tumor Radiotherapy and/or Chemotherapy. Curr Med Chem 2021; 28:3787-3802. [PMID: 33121398 DOI: 10.2174/0929867327666201029161055] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/18/2020] [Accepted: 09/20/2020] [Indexed: 02/05/2023]
Abstract
Cyclophilin A (CypA) is a ubiquitous and highly conserved protein. CypA, the intracellular target protein for the immunosuppressant cyclosporine A (CsA), plays important cellular roles through peptidyl-prolyl cis-trans isomerase (PPIase). Increasing evidence shows that CypA is up-regulated in a variety of human cancers. In addition to being involved in the occurrence and development of multiple tumors, overexpression of CypA has also been shown to be strongly associated with malignant transformation. Surgery, chemotherapy and radiotherapy are the three main treatments for cancer. Chemotherapy and radiotherapy are often used as direct or adjuvant treatments for cancer. However, various side effects and resistance to both chemotherapy and radiotherapy bring great challenges to these two forms of treatment. According to recent reports, CypA can improve the chemosensitivity and/or radiosensitivity of cancers, possibly by affecting the expression of drug-resistant related proteins, cell cycle arrest and activation of the mitogen-activated protein kinase (MAPK) signaling pathways. In this review, we focus on the role of CypA in cancer, its impact on cancer chemotherapeutic and radiotherapy sensitivity, and the mechanism of action. It is suggested that CypA may be a novel potential therapeutic target for cancer chemotherapy and/or radiotherapy.
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Affiliation(s)
- Man-Yu Chu
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China
| | - He-Cheng Huang
- Department of Radiation Oncology, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University, Shantou, China
| | - En-Ming Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China
| | - Li-Yan Xu
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China
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Xiao Q, Luo J, Liang C, Cai J, Li G, Cao B. CeModule: an integrative framework for discovering regulatory patterns from genomic data in cancer. BMC Bioinformatics 2019; 20:67. [PMID: 30732558 PMCID: PMC6367773 DOI: 10.1186/s12859-019-2654-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 01/24/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Non-coding RNAs (ncRNAs) are emerging as key regulators and play critical roles in a wide range of tumorigenesis. Recent studies have suggested that long non-coding RNAs (lncRNAs) could interact with microRNAs (miRNAs) and indirectly regulate miRNA targets through competing interactions. Therefore, uncovering the competing endogenous RNA (ceRNA) regulatory mechanism of lncRNAs, miRNAs and mRNAs in post-transcriptional level will aid in deciphering the underlying pathogenesis of human polygenic diseases and may unveil new diagnostic and therapeutic opportunities. However, the functional roles of vast majority of cancer specific ncRNAs and their combinational regulation patterns are still insufficiently understood. RESULTS Here we develop an integrative framework called CeModule to discover lncRNA, miRNA and mRNA-associated regulatory modules. We fully utilize the matched expression profiles of lncRNAs, miRNAs and mRNAs and establish a model based on joint orthogonality non-negative matrix factorization for identifying modules. Meanwhile, we impose the experimentally verified miRNA-lncRNA interactions, the validated miRNA-mRNA interactions and the weighted gene-gene network into this framework to improve the module accuracy through the network-based penalties. The sparse regularizations are also used to help this model obtain modular sparse solutions. Finally, an iterative multiplicative updating algorithm is adopted to solve the optimization problem. CONCLUSIONS We applied CeModule to two cancer datasets including ovarian cancer (OV) and uterine corpus endometrial carcinoma (UCEC) obtained from TCGA. The modular analysis indicated that the identified modules involving lncRNAs, miRNAs and mRNAs are significantly associated and functionally enriched in cancer-related biological processes and pathways, which may provide new insights into the complex regulatory mechanism of human diseases at the system level.
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Affiliation(s)
- Qiu Xiao
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410082, China
- Hunan Provincial Key Laboratory of Intelligent Computing and Language Information Processing, Hunan Normal University, Changsha, 410081, China
| | - Jiawei Luo
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410082, China.
| | - Cheng Liang
- College of Information Science and Engineering, Shandong Normal University, Jinan, 250000, China
| | - Jie Cai
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410082, China
| | - Guanghui Li
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410082, China
| | - Buwen Cao
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410082, China
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Selected reaction monitoring approach for validating peptide biomarkers. Proc Natl Acad Sci U S A 2017; 114:13519-13524. [PMID: 29203663 DOI: 10.1073/pnas.1712731114] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
We here describe a selected reaction monitoring (SRM)-based approach for the discovery and validation of peptide biomarkers for cancer. The first stage of this approach is the direct identification of candidate peptides through comparison of proteolytic peptides derived from the plasma of cancer patients or healthy individuals. Several hundred candidate peptides were identified through this method, providing challenges for choosing and validating the small number of peptides that might prove diagnostically useful. To accomplish this validation, we used 2D chromatography coupled with SRM of candidate peptides. We applied this approach, called sequential analysis of fractionated eluates by SRM (SAFE-SRM), to plasma from cancer patients and discovered two peptides encoded by the peptidyl-prolyl cis-trans isomerase A (PPIA) gene whose abundance was increased in the plasma of ovarian cancer patients. At optimal thresholds, elevated levels of at least one of these two peptides was detected in 43 (68.3%) of 63 women with ovarian cancer but in none of 50 healthy controls. In addition to providing a potential biomarker for ovarian cancer, this approach is generally applicable to the discovery of peptides characteristic of various disease states.
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Chen X, Wang YW, Xing AY, Xiang S, Shi DB, Liu L, Li YX, Gao P. Suppression of SPIN1-mediated PI3K-Akt pathway by miR-489 increases chemosensitivity in breast cancer. J Pathol 2016; 239:459-72. [DOI: 10.1002/path.4743] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 05/05/2016] [Accepted: 05/06/2016] [Indexed: 01/23/2023]
Affiliation(s)
- Xu Chen
- Department of Pathology, School of Medicine; Shandong University; Jinan People's Republic of China
| | - Ya-Wen Wang
- Department of Pathology, School of Medicine; Shandong University; Jinan People's Republic of China
| | - Ai-Yan Xing
- Department of Pathology, School of Medicine; Shandong University; Jinan People's Republic of China
| | - Shuai Xiang
- Department of Pathology, School of Medicine; Shandong University; Jinan People's Republic of China
| | - Duan-Bo Shi
- Department of Pathology, School of Medicine; Shandong University; Jinan People's Republic of China
| | - Lei Liu
- Department of Pathology, School of Medicine; Shandong University; Jinan People's Republic of China
| | - Yan-Xiang Li
- Department of Pathology, School of Medicine; Shandong University; Jinan People's Republic of China
| | - Peng Gao
- Department of Pathology, School of Medicine; Shandong University; Jinan People's Republic of China
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Li F, Chen H, Huang Y, Zhang Q, Xue J, Liu Z, Zheng F. miR-34c plays a role of tumor suppressor in HEC‑1-B cells by targeting E2F3 protein. Oncol Rep 2015; 33:3069-74. [PMID: 25846116 DOI: 10.3892/or.2015.3894] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 03/12/2015] [Indexed: 11/06/2022] Open
Abstract
Endometrial carcinoma (EC) is a common malignancy of the female genital tract with a poor prognosis. It has been reported that miR-34c is significantly reduced in EC, but research concerning its function in EC is rare. In the present study, the expression of miR-34c was upregulated in the EC cell line, HEC-1-B, by transfecting the cells with hsa-miR-34c-5p mimics. Then, after determining the transfection efficiency by RT-qPCR, we analyzed the effects of miR-34c on the HEC-1-B cells. We found that overexpression of miR-34c significantly inhibited cell proliferation, colony formation, migration and invasion and induced cell cycle arrest and apoptosis. Finally, western blot analysis demonstrated that the expression of E2F3 was reduced after upregulation of the expression of miR-34c in the HEC-1-B cells, and the effects of miR-34c are likely associated with the reduction in E2F3 protein. In conclusion, our study demonstrated that miR-34c plays a role of tumor suppressor in HEC-1-B cells, and E2F3 protein may be a target of miR-34c.
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Affiliation(s)
- Fuyao Li
- Department of Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Huijun Chen
- Department of Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Yibo Huang
- Department of Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Qian Zhang
- Department of Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Jisen Xue
- Department of Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Zan Liu
- Department of General Surgery, Zhuzhou Kind Hospital, Zhuzhou, Hunan 412000, P.R. China
| | - Feiyun Zheng
- Department of Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
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Feng MX, Li JP, Wang H, Shen YX, Tan LJ, Wang Q, Wang YQ. Clinical significance of cyclophilin a expression in esophageal squamous cell carcinoma. Genet Test Mol Biomarkers 2014; 19:182-6. [PMID: 25420107 DOI: 10.1089/gtmb.2014.0067] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
OBJECTIVE To explore the expression of cyclophilin A (CypA) in esophageal tissues and its clinical significance. METHOD Expression of CypA was detected in 236 esophageal cancer tissues and 236 normal tissues by using an immunohistochemical method, and the relationship between CypA expression and clinical outcomes was observed. RESULTS There were 166 patients with high expression of CypA (70.23%) and a higher expression in 69.3% of males and 73.3% in females. The CypA expression was irrelevant to age, tumor location, lymph node metastasis, and tumor differentiation degree. The Kaplan-Meier survival curve analysis showed that the expression of CypA was associated with the prognosis of patients with esophageal squamous cell carcinoma. CONCLUSION The poor prognosis of esophageal cancer patients was associated with high expression of CypA.
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Affiliation(s)
- Ming-Xiang Feng
- 1 Department of Thoracic Surgery, Zhongshan Hospital, Fudan University , Shanghai, China
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Construction of pancreatic cancer double-factor regulatory network based on chip data on the transcriptional level. Mol Biol Rep 2014; 41:2875-83. [PMID: 24469724 DOI: 10.1007/s11033-014-3143-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 01/11/2014] [Indexed: 12/24/2022]
Abstract
Transcription factor (TF) and microRNA (miRNA) have been discovered playing crucial roles in cancer development. However, the effect of TFs and miRNAs in pancreatic cancer pathogenesis remains vague. We attempted to reveal the possible mechanism of pancreatic cancer based on transcription level. Using GSE16515 datasets downloaded from gene expression omnibus database, we first identified the differentially expressed genes (DEGs) in pancreatic cancer by the limma package in R. Then the DEGs were mapped into DAVID to conduct the kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis. TFs and miRNAs that DEGs significantly enriched were identified by Fisher's test, and then the pancreatic cancer double-factor regulatory network was constructed. In our study, total 1117 DEGs were identified and they significantly enriched in 4 KEGG pathways. A double-factor regulatory network was established, including 29 DEGs, 24 TFs, 25 miRNAs. In the network, LAMC2, BRIP1 and miR155 were identified which may be involved in pancreatic cancer development. In conclusion, the double-factor regulatory network was found to play an important role in pancreatic cancer progression and our results shed new light on the molecular mechanism of pancreatic cancer.
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