1
|
Xi J, Xi Y, Zhang Z, Hao Y, Wu F, Bian B, Hao G, Li W, Zhang S. Hsa_circ_0060937 accelerates non-small cell lung cancer progression via modulating miR-195-5p/HMGB3 pathway. Cell Cycle 2021; 20:2040-2052. [PMID: 34470585 DOI: 10.1080/15384101.2021.1969203] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Circular RNAs (circRNAs) exert a critical effect on tumorigenesis and development. Our research aimed to clarify the function and underlying mechanism of circ_0060937 inNSCLC. The concentrations of circ_0060937, miR-195-5p and high-mobility group box 3 (HMGB3) were monitored via qRT-PCR and western blot assays. Additionally, cell proliferation, apoptosis, migration and invasion were assessed using CCK-8, colony formation, flow cytometry and transwell assays. Glycolysis was evaluated via detecting glucose uptake and lactate product. The association between miR-195-5p and circ_0060937/HMGB3 were validated using dual-luciferase reporter, RNA pull-down and RIP assays. Furthermore,in vivo experiment was performed to analyze tumorigenesis.Circ_0060937 and HMGB3 levels were elevated, whereas miR-195-5p level was dropped in NSCLC. Circ_0060937 down-regulation restrainedNSCLC cell proliferation, migration, invasion and glycolysis, and triggered apoptosis. Knockdown of circ_0060937 restrained NSCLC development via absorbing miR-195-5p. Circ_0060937 silencing inhibited NSCLC progression by mediating HMGB3. Besides, circ_0060937 depletion suppressed tumor growth in vivo.Circ_0060937 knockdown hindered NSCLC development and glycolysis via regulating miR-195-5p/HMGB3 pathway.
Collapse
Affiliation(s)
- Junfeng Xi
- Department of Oncology, The Second Affliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Department of Cardiothoracic Surgery, The First Hospital of Yulin City, Yulin, China
| | - Yunfeng Xi
- Department of Dermatology, The First Hospital of Yulin City, Yulin, China
| | - Zhibin Zhang
- Department of Cardiothoracic Surgery, The First Hospital of Yulin City, Yulin, China
| | - Yanhong Hao
- Department of Cardiothoracic Surgery, The First Hospital of Yulin City, Yulin, China
| | - Fei Wu
- Department of Oncology, The Second Affliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Burong Bian
- Deapartment of Oncology, The First Hospital of Yulin City, Yulin, China
| | - Guangjun Hao
- Deapartment of Oncology, The First Hospital of Yulin City, Yulin, China
| | - Weiwei Li
- Department of Cardiothoracic Surgery, The First Hospital of Yulin City, Yulin, China
| | - Shuqun Zhang
- Department of Oncology, The Second Affliated Hospital of Xi'an Jiaotong University, Xi'an, China
| |
Collapse
|
2
|
CXCL13 Signaling in the Tumor Microenvironment. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1302:71-90. [PMID: 34286442 DOI: 10.1007/978-3-030-62658-7_6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Chemokines have emerged as important players in tumorigenic process. An extensive body of literature generated over the last two or three decades strongly implicate abnormally activated or functionally disrupted chemokine signaling in liaising most-if not all-hallmark processes of cancer. It is well-known that chemokine signaling networks within the tumor microenvironment are highly versatile and context-dependent: exert both pro-tumoral and antitumoral activities. The C-X-C motif chemokine ligand 13 (CXCL13), and its cognate receptor CXCR5, represents an emerging example of chemokine signaling axes, which express the ability to modulate tumor growth and progression in either way. Collateral evidence indicate that CXCL13-CXCR5 axis may directly modulate tumor growth by inducing proliferation of cancer cells, as well as promoting invasive phenotypes and preventing their apoptosis. In addition, CXCL13-CXCR5 axis may also indirectly modulate tumor growth by regulating noncancerous cells, particularly the immune cells, within the tumor microenvironment. Here, we review the role of CXCL13, together with CXCR5, in the human tumor microenvironment. We first elaborate their patterns of expression, regulation, and biological functions in normal physiology. We then consider how their aberrant activity, as a result of differential overexpression or co-expression, may directly or indirectly modulate the growth of tumors through effects on both cancerous and noncancerous cells.
Collapse
|
3
|
Liu Z, Lai J, Jiang H, Ma C, Huang H. Collagen XI alpha 1 chain, a potential therapeutic target for cancer. FASEB J 2021; 35:e21603. [PMID: 33999448 DOI: 10.1096/fj.202100054rr] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/26/2021] [Accepted: 04/02/2021] [Indexed: 11/11/2022]
Abstract
Extracellular matrix (ECM) plays an important role in the progression of cancer. Collagen is the most abundant component in ECM, and it is involved in the biological formation of cancer. Although type XI collagen is a minor fibrillar collagen, collagen XI alpha 1 chain (COL11A1) has been found to be upregulated in a variety of cancers including ovarian cancer, breast cancer, thyroid cancer, pancreatic cancer, non-small-cell lung cancer, and transitional cell carcinoma of the bladder. High levels of COL11A1 usually predict poor prognosis, while COL11A1 is related to angiogenesis, invasion, and drug resistance of cancer. However, little is known about the specific mechanism by which COL11A1 regulates tumor progression. Here, we have organized and summarized the recent developments regarding elucidation of the relationship between COL11A1 and various cancers, as well as the interaction between COL11A1 and intracellular signaling pathways. In addition, we have selected therapeutic agents targeting COL11A1. All these indicate the possibility of using COL11A1 as a target for cancer treatment.
Collapse
Affiliation(s)
- Ziqiang Liu
- Department of Neurosurgery, the First Hospital of Jilin University, Changchun, China
| | - Jiacheng Lai
- Department of Neurosurgery, the First Hospital of Jilin University, Changchun, China
| | - Heng Jiang
- Department of Neurosurgery, the First Hospital of Jilin University, Changchun, China
| | - Chengyuan Ma
- Department of Neurosurgery, the First Hospital of Jilin University, Changchun, China
| | - Haiyan Huang
- Department of Neurosurgery, the First Hospital of Jilin University, Changchun, China
| |
Collapse
|
4
|
Xu Y, Zuo W, Wang X, Zhang Q, Gan X, Tan N, Jia W, Liu J, Li Z, Zhou B, Zhao D, Xie Z, Tan Y, Zheng S, Liu C, Li H, Chen Z, Yang X, Huang Z. Deciphering the effects of PYCR1 on cell function and its associated mechanism in hepatocellular carcinoma. Int J Biol Sci 2021; 17:2223-2239. [PMID: 34239351 PMCID: PMC8241733 DOI: 10.7150/ijbs.58026] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 05/16/2021] [Indexed: 12/28/2022] Open
Abstract
Overexpression of pyrroline-5-carboxylate reductase 1 (PYCR1) has been associated with the development of certain cancers; however, no studies have specifically examined the role of PYCR1 in hepatocellular carcinoma (HCC). Based on The Cancer Genome Atlas expression array and meta-analysis conducted using the Gene Expression Omnibus database, we determined that PYCR1 was upregulated in HCC compared to adjacent nontumor tissues (P < 0.05). These data were verified using quantitative real-time polymerase chain reaction, western blotting, and immunohistochemistry analysis. Additionally, patients with low PYCR1 expression showed a higher overall survival rate than patients with high PYCR1 expression. Furthermore, PYCR1 overexpression was associated with the female sex, higher levels of alpha-fetoprotein, advanced clinical stages (III and IV), and a younger age (< 45 years old). Silencing of PYCR1 inhibited cell proliferation, invasive migration, epithelial-mesenchymal transition, and metastatic properties in HCC in vitro and in vivo. Using RNA sequencing and bioinformatics tools for data-dependent network analysis, we found binary relationships among PYCR1 and its interacting proteins in defined pathway modules. These findings indicated that PYCR1 played a multifunctional role in coordinating a variety of biological pathways involved in cell communication, cell proliferation and growth, cell migration, a mitogen-activated protein kinase cascade, ion binding, etc. The structural characteristics of key pathway components and PYCR1-interacting proteins were evaluated by molecular docking, and hotspot analysis showed that better affinities between PYCR1 and its interacting molecules were associated with the presence of arginine in the binding site. Finally, a candidate regulatory microRNA, miR-2355-5p, for PYCR1 mRNA was discovered in HCC. Overall, our study suggests that PYCR1 plays a vital role in HCC pathogenesis and may potentially serve as a molecular target for HCC treatment.
Collapse
Affiliation(s)
- Yanzhen Xu
- Department of pathology, Affiliated hospital of Guilin Medical University, Guilin, 541001, Guangxi, China
- Scientific Research Center, Guilin Medical University, Guilin, 541001, Guangxi, China
- Department of Pathology, Affiliated Hangzhou First People's Hospital, School of Medicine, Zhejiang University, 310000, Hangzhou, China
| | - Wenpu Zuo
- Scientific Research Center, Guilin Medical University, Guilin, 541001, Guangxi, China
- Medical Scientific Research Center, Guangxi Medical University, Nanning, 530000, Guangxi, China
| | - Xiao Wang
- Scientific Research Center, Guilin Medical University, Guilin, 541001, Guangxi, China
- Guangxi Health Commission Key Laboratory of Disease Proteomics Research, Guilin Medical University, Guilin, 541001, Guangxi, China
| | - Qinle Zhang
- Genetic and metabolic central laboratory, the maternal and children's health hospital of Guangxi, Nanning, 530000, Guangxi, China
| | - Xiang Gan
- Scientific Research Center, Guilin Medical University, Guilin, 541001, Guangxi, China
- Guangxi Health Commission Key Laboratory of Disease Proteomics Research, Guilin Medical University, Guilin, 541001, Guangxi, China
| | - Ning Tan
- Scientific Research Center, Guilin Medical University, Guilin, 541001, Guangxi, China
| | - Wenxian Jia
- Scientific Research Center, Guilin Medical University, Guilin, 541001, Guangxi, China
- Guangxi Health Commission Key Laboratory of Disease Proteomics Research, Guilin Medical University, Guilin, 541001, Guangxi, China
| | - Jiayi Liu
- Scientific Research Center, Guilin Medical University, Guilin, 541001, Guangxi, China
| | - Zhouquan Li
- Scientific Research Center, Guilin Medical University, Guilin, 541001, Guangxi, China
- Guangxi Health Commission Key Laboratory of Disease Proteomics Research, Guilin Medical University, Guilin, 541001, Guangxi, China
| | - Bo Zhou
- Scientific Research Center, Guilin Medical University, Guilin, 541001, Guangxi, China
- Guangxi Health Commission Key Laboratory of Disease Proteomics Research, Guilin Medical University, Guilin, 541001, Guangxi, China
| | - Dong Zhao
- Scientific Research Center, Guilin Medical University, Guilin, 541001, Guangxi, China
| | - Zhibin Xie
- Department of Urology, the Five Affiliated Hospital of Guangxi Medical University, Nanning, 530000, Guangxi, China
| | - Yanjun Tan
- Scientific Research Center, Guilin Medical University, Guilin, 541001, Guangxi, China
- Guangxi Health Commission Key Laboratory of Disease Proteomics Research, Guilin Medical University, Guilin, 541001, Guangxi, China
| | - Shengfeng Zheng
- Scientific Research Center, Guilin Medical University, Guilin, 541001, Guangxi, China
| | - Chengwu Liu
- Department of Pathophysiology, Guangxi Medical University, Nanning, 530000, Guangxi, China
| | - Hongtao Li
- Scientific Research Center, Guilin Medical University, Guilin, 541001, Guangxi, China
- Guangxi Health Commission Key Laboratory of Disease Proteomics Research, Guilin Medical University, Guilin, 541001, Guangxi, China
| | - Zhijian Chen
- Department of Clinical Laboratory, the First Affiliated Hospital of Guangxi Medical University, Nanning, 530000, Guangxi, China
| | - Xiaoli Yang
- Scientific Research Center, Guilin Medical University, Guilin, 541001, Guangxi, China
- Guangxi Health Commission Key Laboratory of Disease Proteomics Research, Guilin Medical University, Guilin, 541001, Guangxi, China
| | - Zhaoquan Huang
- Department of pathology, Affiliated hospital of Guilin Medical University, Guilin, 541001, Guangxi, China
- Department of Pathology, the First Affiliated Hospital of Guangxi Medical University, Nanning, 530000, Guangxi, China
| |
Collapse
|
5
|
Shi Y, Chang D, Li W, Zhao F, Ren X, Hou B. Identification of core genes and clinical outcomes in tumors originated from endoderm (gastric cancer and lung carcinoma) via bioinformatics analysis. Medicine (Baltimore) 2021; 100:e25154. [PMID: 33761685 PMCID: PMC10545272 DOI: 10.1097/md.0000000000025154] [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: 02/16/2020] [Revised: 11/30/2020] [Accepted: 02/23/2021] [Indexed: 12/24/2022] Open
Abstract
ABSTRACT During last decade, bioinformatics analysis has provided an effective way to study the relationship between various genes and biological processes. In this study, we aimed to identify potential core candidate genes and underlying mechanisms of progression of lung and gastric carcinomas which both originated from endoderm. The expression profiles, GSE54129 (gastric carcinoma) and GSE27262 (lung carcinoma), were collected from GEO database. One hundred eleven patients with gastric carcinoma and 21 health people were included in this research. Meanwhile, there were 25 lung carcinoma patients. Then, 75 differentially expressed genes were selected via GEO2R online tool and Venn software, including 31 up-regulated genes and 44 down-regulated genes. Next, we used Database for Annotation, Visualization, and Integrated Discovery and Metascpe software to analyze Kyoto Encyclopedia of Gene and Genome pathway and gene ontology. Furthermore, Cytoscape software and MCODE App were performed to construct complex of these differentially expressed genes . Twenty core genes were identified, which mainly enriched in extracellular matrix-receptor interaction, focal adhesion, and PI3K-Akt pathway (P < .01). Finally, the significant difference of gene expression between cancer tissues and normal tissues in both lung and gastric carcinomas was examined by Gene Expression Profiling Interactive Analysis database. Twelve candidate genes with positive statistical significance (P < .01), COMP CTHRC1 COL1A1 SPP1 COL11A1 COL10A1 CXCL13 CLDN3 CLDN1 matrix metalloproteinases 7 ADAM12 PLAU, were picked out to further analysis. The Kaplan-Meier plotter website was applied to examine relationship among these genes and clinical outcomes. We found 4 genes (ADAM12, SPP1, COL1A1, COL11A1) were significantly associated with poor prognosis in both lung and gastric carcinoma patients (P < .05). In conclusion, these candidate genes may be potential therapeutic targets for cancer treatment.
Collapse
Affiliation(s)
- Yewen Shi
- Department of Otorhinolaryngology Head and Neck Surgery, the Second Affiliated Hospital of Xi’an Jiaotong University
| | - Dongmin Chang
- Department of Surgical Oncology, the First Affiliated Hospital of Xi’an Jiaotong University
| | - Wenhan Li
- Department of Surgical Oncology, Shaanxi Provincial People's Hospital
- The Third Affiliated Hospital, the School of Medicine Xi’an Jiaotong University
| | - FengYu Zhao
- Department of Surgical Oncology, the First Affiliated Hospital of Xi’an Jiaotong University
| | - Xiaoyong Ren
- Department of Otorhinolaryngology Head and Neck Surgery, the Second Affiliated Hospital of Xi’an Jiaotong University
| | - Bin Hou
- The Third Affiliated Hospital, the School of Medicine Xi’an Jiaotong University
- Department of Thoracic Surgery, Shaanxi Provincial People's Hospital, Xi’an, Shaanxi, China
| |
Collapse
|
6
|
Xiong Y, Lei J, Zhao J, Lu Q, Feng Y, Qiao T, Xin S, Han Y, Jiang T. A gene-based survival score for lung adenocarcinoma by multiple transcriptional datasets analysis. BMC Cancer 2020; 20:1046. [PMID: 33129284 PMCID: PMC7603718 DOI: 10.1186/s12885-020-07473-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 09/29/2020] [Indexed: 02/06/2023] Open
Abstract
Background Lung adenocarcinoma (LUAD) remains a crucial factor endangering human health. Gene-based clinical predictions could be of great help for cancer intervention strategies. Here, we tried to build a gene-based survival score (SS) for LUAD via analyzing multiple transcriptional datasets. Methods We first acquired differentially expressed genes between tumors and normal tissues from intersections of four LUAD datasets. Next, survival-related genes were preliminarily unscrambled by univariate Cox regression and further filtrated by LASSO regression. Then, we applied PCA to establish a comprehensive SS based on survival-related genes. Subsequently, we applied four independent LUAD datasets to evaluate prognostic prediction of SS. Moreover, we explored associations between SS and clinicopathological features. Furthermore, we assessed independent predictive value of SS by multivariate Cox analysis and then built prognostic models based on clinical stage and SS. Finally, we performed pathway enrichments analysis and investigated immune checkpoints expression underlying SS in four datasets. Results We established a 13 gene-based SS, which could precisely predict OS and PFS of LUAD. Close relations were elicited between SS and canonical malignant indictors. Furthermore, SS could serve as an independent risk factor for OS and PFS. Besides, the predictive efficacies of prognostic models were also reasonable (C-indexes: OS, 0.7; PFS, 0.7). Finally, we demonstrated enhanced cell proliferation and immune escape might account for high clinical risk of SS. Conclusions We built a 13 gene-based SS for prognostic prediction of LUAD, which exhibited wide applicability and could contribute to LUAD management.
Collapse
Affiliation(s)
- Yanlu Xiong
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, 569 Xinsi Road, Baqiao District, Xi'an City, 710038, Shaanxi Province, China
| | - Jie Lei
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, 569 Xinsi Road, Baqiao District, Xi'an City, 710038, Shaanxi Province, China
| | - Jinbo Zhao
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, 569 Xinsi Road, Baqiao District, Xi'an City, 710038, Shaanxi Province, China
| | - Qiang Lu
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, 569 Xinsi Road, Baqiao District, Xi'an City, 710038, Shaanxi Province, China
| | - Yangbo Feng
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, 569 Xinsi Road, Baqiao District, Xi'an City, 710038, Shaanxi Province, China
| | - Tianyun Qiao
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, 569 Xinsi Road, Baqiao District, Xi'an City, 710038, Shaanxi Province, China
| | - Shaowei Xin
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, 569 Xinsi Road, Baqiao District, Xi'an City, 710038, Shaanxi Province, China
| | - Yong Han
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, 569 Xinsi Road, Baqiao District, Xi'an City, 710038, Shaanxi Province, China. .,Department of Thoracic Surgery, Air Force Medical Center, PLA, 30 Fucheng Road, Haidian District, Beijing, 100142, China.
| | - Tao Jiang
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, 569 Xinsi Road, Baqiao District, Xi'an City, 710038, Shaanxi Province, China.
| |
Collapse
|
7
|
Wang J, He Z, Duan R. [Expression of ASPM in Lung Adenocarcinoma and Its Relationship with Development and Prognosis]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2020; 23:29-35. [PMID: 31948535 PMCID: PMC7007395 DOI: 10.3779/j.issn.1009-3419.2020.01.05] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
BACKGROUND Previous studies have shown that ASPM is a tumorigenesis associated protein, mutations in ASPM can lead to MCPH. This study mainly explores the relationship between the ASPM expression of lung adenocarcinoma and the development and prognosis of lung cancer. The aim of this study was to investigate the relationship between the expression of abnormal spindle-like microcephaly-associated protein (ASPM) in lung adenocarcinoma and the development and prognosis in lung cancer. METHODS A total of 90 cases of lung adenocarcinoma tissue specimens and 90 cases of benign pulmonary lesions were collected, the expression of ASPM was detected by immunohistochemical technique, and the expression of ASPM in 12 pairs of tissues was detected by real-time quantity polymerase chain reaction and western blot. RESULTS (1) The expression of ASPM in the tissue specimens of benign pulmonary lesions was negative while the expression level of ASPM in lung adenocarcinoma was significantly higher than lung tissue of benign pulmonary lesions (P<0.05). (2) The expression level of ASPM has no remarkable difference in lung adenocarcinoma with lymph node development and the lung cancer without lymph node development, there was no statistically significant (P<0.05). (3) The ASPM expression level in the tumor's size ≥4 cm was significantly higher than than of the size<4 cm (P<0.05). (4) Hierarchical analysis results show that T stage is related to ASPM expression level (P<0.05). (5) The high expression level of ASPM in lung adenocarcinoma was significantly positively correlated with the poor prognosis (P<0.05). CONCLUSIONS (1) The expression level of ASPM in lung cancer is obviously increased and closely related to the progress of lung adenocarcinoma. (2) The expression level of ASPM in lung adenocarcinoma was significantly positively correlated with poor prognosis (P<0.05). (3) Detection of the expression level of ASPM in lung adenocarcinoma help to predict the prognosis of lung adenocarcinoma in advance.
Collapse
Affiliation(s)
- Junjie Wang
- Department of Oncology, Xinxiang Central Hospital, Xinxiang 453000, China
| | - Zhenyu He
- Department of Radiotherapy, Cancer Hospital, Sun Yat-Sen University, Guangzhou 510060, China
| | - Renhui Duan
- Department of Oncology, Xinxiang Central Hospital, Xinxiang 453000, China
| |
Collapse
|
8
|
Kazanietz MG, Durando M, Cooke M. CXCL13 and Its Receptor CXCR5 in Cancer: Inflammation, Immune Response, and Beyond. Front Endocrinol (Lausanne) 2019; 10:471. [PMID: 31354634 PMCID: PMC6639976 DOI: 10.3389/fendo.2019.00471] [Citation(s) in RCA: 160] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 06/28/2019] [Indexed: 12/25/2022] Open
Abstract
It is well-established that the chemokine C-X-C motif ligand 13 (CXCL13) and its receptor, the G-protein coupled receptor (GPCR) CXCR5, play fundamental roles in inflammatory, infectious and immune responses. Originally identified as a B-cell chemoattractant, CXCL13 exerts important functions in lymphoid neogenesis, and has been widely implicated in the pathogenesis of a number of autoimmune diseases and inflammatory conditions, as well as in lymphoproliferative disorders. Current evidence also indicates that the CXCL13:CXCR5 axis orchestrates cell-cell interactions that regulate lymphocyte infiltration within the tumor microenvironment, thereby determining responsiveness to cytotoxic and immune-targeted therapies. In this review, we provide a comprehensive perspective of the involvement of CXCL13 and its receptor in cancer progression. Studies in recent years postulated novel roles for this chemokine in controlling the cancer cell phenotype, and suggest important functions in the growth and metastatic dissemination of solid tumors. Carcinogens have been found to induce CXCL13 production, and production of this chemokine within the tumor milieu has been shown to impact the proliferation, migration, and invasive properties of cancer cells. Thus, the complex networks of cellular interactions involving tumoral CXCL13 and CXCR5 integrate to promote cancer cell autonomous and non-autonomous responses, highlighting the relevance of autocrine and paracrine interactions in dictating the cancer phenotype. Dissecting the molecular and signaling events regulated by CXCL13 and how this chemokine dynamically controls the interaction between the cancer cell and the tumor microenvironment is key to identify novel effectors and therapeutic targets for cancer treatment.
Collapse
Affiliation(s)
| | | | - Mariana Cooke
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| |
Collapse
|
9
|
Li W, Zhang X, Li Z, Jiang F, Zhao H, Wei B. Identification of genes associated with matrix metalloproteinases in invasive lung adenocarcinoma. Oncol Lett 2018; 16:123-130. [PMID: 29928392 PMCID: PMC6006458 DOI: 10.3892/ol.2018.8683] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 02/07/2017] [Indexed: 11/06/2022] Open
Abstract
The aim of the present study was to identify genes with similar function to that of matrix metalloproteinases (MMPs) in invasive lung adenocarcinoma (AC) and to screen the transcription factors that regulate MMPs. The gene expression dataset GSE2514, including 20 invasive lung AC samples and 19 adjacent normal lung samples, was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened using the limma package in R. Genes with similar function to MMPs were identified by K-means clustering. Their correlations with MMPs were validated using Pearson correlation analysis. The expression of MMPs in lung cancer and normal tissues was evaluated by western blot analysis. Protein-protein interaction (PPI) network and transcriptional regulatory network analyses were performed with Retrieval of Interacting Genes and Database for Annotation, Visualization and Integrated Discovery, respectively. As a result, 269 DEGs were identified between invasive lung AC samples and normal lung samples, including 78 upregulated and 191 downregulated genes. Four MMPs (MMP1, MMP7, MMP9 and MMP12), which were upregulated in lung AC, were clustered into one group with other genes, including NAD(P)H quinone oxidoreductase 1, claudin 3 (CLDN3), S100 calcium-binding protein P, serine protease inhibitor Kazal type 1, collagen type XI α 1 chain, periostin and desmoplakin (DSP), following cluster analysis. Pearson correlation analysis further confirmed correlations between MMP9-CLDN3, MMP9-DSP and MMP12-DSP. PPI network analysis also indicated multiple interactions between MMPs-associated genes. Furthermore, MMPs were commonly regulated by CCAAT/enhancer binding protein α transcription factor. These findings may provide further insight into the mechanisms of MMPs in invasive lung AC.
Collapse
Affiliation(s)
- Weiqing Li
- Department of Thoracic Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, P.R. China
| | - Xugang Zhang
- Department of Thoracic Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, P.R. China
| | - Zhitian Li
- Department of Thoracic Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, P.R. China
| | - Fusheng Jiang
- Department of Thoracic Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, P.R. China
| | - Hongwei Zhao
- Department of Interventional Treatment, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, P.R. China
| | - Bo Wei
- Department of Thoracic Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, P.R. China
| |
Collapse
|
10
|
Medeiros Tavares Marques JC, Cornélio DA, Nogueira Silbiger V, Ducati Luchessi A, de Souza S, Batistuzzo de Medeiros SR. Identification of new genes associated to senescent and tumorigenic phenotypes in mesenchymal stem cells. Sci Rep 2017; 7:17837. [PMID: 29259202 PMCID: PMC5736717 DOI: 10.1038/s41598-017-16224-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 11/08/2017] [Indexed: 02/06/2023] Open
Abstract
Although human mesenchymal stem cells (hMSCs) are a powerful tool for cell therapy, prolonged culture times result in replicative senescence or acquisition of tumorigenic features. To identify a molecular signature for senescence, we compared the transcriptome of senescent and young hMSCs with normal karyotype (hMSCs/n) and with a constitutional inversion of chromosome 3 (hMSC/inv). Senescent and young cells from both lineages showed differentially expressed genes (DEGs), with higher levels in senescent hMSCs/inv. Among the 30 DEGs in senescent hMSC/inv, 11 are new candidates for biomarkers of cellular senescence. The functional categories most represented in senescent hMSCs were related to cellular development, cell growth/proliferation, cell death, cell signaling/interaction, and cell movement. Mapping of DEGs onto biological networks revealed matrix metalloproteinase-1, thrombospondin 1, and epidermal growth factor acting as topological bottlenecks. In the comparison between senescent hMSCs/n and senescent hMSCs/inv, other functional annotations such as segregation of chromosomes, mitotic spindle formation, and mitosis and proliferation of tumor lines were most represented. We found that many genes categorized into functional annotations related to tumors in both comparisons, with relation to tumors being highest in senescent hMSCs/inv. The data presented here improves our understanding of the molecular mechanisms underlying the onset of cellular senescence as well as tumorigenesis.
Collapse
Affiliation(s)
- Joana Cristina Medeiros Tavares Marques
- Faculdade de Ciências da Saúde do Trairi (FACISA), Universidade Federal do Rio Grande do Norte (UFRN), Rua Traíri, S/N, Centro, Santa Cruz, Rio Grande do Norte (RN), 59200-000, Brazil
| | - Déborah Afonso Cornélio
- Laboratório de Biologia Molecular e Genômica, Centro de Biociências, UFRN, Campus Universitário, Avenida Senador Salgado Filho, 3000, Lagoa nova, Natal, RN, 59078-900, Brazil
| | - Vivian Nogueira Silbiger
- Departamento de Análises Clínicas e Toxicológicas, Centro de Ciências da Saúde, CCS/UFRN, Av General Cordeiro de Farias S/N, Petropolis, Natal, 59010-115, RN, Brazil
| | - André Ducati Luchessi
- Departamento de Análises Clínicas e Toxicológicas, Centro de Ciências da Saúde, CCS/UFRN, Av General Cordeiro de Farias S/N, Petropolis, Natal, 59010-115, RN, Brazil
| | - Sandro de Souza
- Instituto do Cérebro, Instituto de Metrópole Digital, UFRN, Av. Nascimento de Castro, 2155, UFRN, 59056-450, RN, Brazil
| | - Silvia Regina Batistuzzo de Medeiros
- Laboratório de Biologia Molecular e Genômica, Centro de Biociências, UFRN, Campus Universitário, Avenida Senador Salgado Filho, 3000, Lagoa nova, Natal, RN, 59078-900, Brazil.
| |
Collapse
|
11
|
Huang J, Wang L, Jiang M, Chen Q, Zhang X, Wang Y, Jiang Z, Zhang Z. Low BIK outside-inside-out interactive inflammation immune-induced transcription-dependent apoptosis through FUT3-PMM2-SQSTM1-SFN-ZNF384. Immunol Res 2016; 64:461-9. [PMID: 26423071 DOI: 10.1007/s12026-015-8701-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Eighteen different Pearson mutual-positive-correlation BIK-activatory molecular feedback upstream and downstream networks were constructed from 79 overlapping of 376 GRNInfer and 98 Pearson under BIK CC ≥ 0.25 in low normal adjacent tissues of Taiwan compared with high lung adenocarcinoma. Our identified BIK interactive total feedback molecular network showed FUT3 [fucosyltransferase 3 (galactoside 3(4)-L-fucosyltransferase Lewis blood group)], PMM2 (phosphomannomutase 2), SQSTM1 (sequestosome 1), SFN_2 [REX2 RNA exonuclease 2 homolog (S. cerevisiae)] and ZNF384 (zinc finger protein 384) in low normal adjacent tissues of lung adenocarcinoma. BIK interactive total feedback terms included mitochondrial envelope, endomembrane system, integral to membrane, Golgi apparatus, cytoplasm, nucleus, cytosol, intracellular signaling cascade, mitochondrion, extracellular space, inflammation, immune response, apoptosis, cell differentiation, cell cycle, regulation of cell cycle, cell proliferation, estrogen-responsive protein Efp controls cell cycle and breast tumors growth, induction or regulation of apoptosis based on integrative GO, KEGG, GenMAPP, BioCarta and disease databases in low normal adjacent tissues of lung adenocarcinoma. Therefore, we propose low BIK outside-inside-out interactive inflammation immune-induced transcription-dependent apoptosis through FUT3-PMM2-SQSTM1-SFN-ZNF384 in normal adjacent tissues of lung adenocarcinoma.
Collapse
Affiliation(s)
- Juxiang Huang
- Biomedical Center, School of Electronic Engineering, Beijing University of Posts and Telecommunications, Beijing, 100876, China
| | - Lin Wang
- Biomedical Center, School of Electronic Engineering, Beijing University of Posts and Telecommunications, Beijing, 100876, China.
| | - Minghu Jiang
- Lab of Computational Linguistics, School of Humanities and Social Sciences, Tsinghua University, Beijing, 100084, China
| | - Qingchun Chen
- Biomedical Center, School of Electronic Engineering, Beijing University of Posts and Telecommunications, Beijing, 100876, China
| | - Xiaoyu Zhang
- Biomedical Center, School of Electronic Engineering, Beijing University of Posts and Telecommunications, Beijing, 100876, China
| | - Yangming Wang
- Biomedical Center, School of Electronic Engineering, Beijing University of Posts and Telecommunications, Beijing, 100876, China
| | - Zhenfu Jiang
- Biomedical Center, School of Electronic Engineering, Beijing University of Posts and Telecommunications, Beijing, 100876, China
| | - Zhongjie Zhang
- College of Information, North China University of Technology, Beijing, 100043, China
| |
Collapse
|
12
|
Wang L, Huang J, Jiang M, Diao H, Zhou H, Li X, Chen Q, Jiang Z, Feng H. Adenosylmethionine decarboxylase 1 (AMD1)-mediated mRNA processing and cell adhesion activated & inhibited transition mechanisms by different comparisons between chimpanzee and human left hemisphere. Cell Biochem Biophys 2015; 70:279-88. [PMID: 24652003 DOI: 10.1007/s12013-014-9902-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
To understand adenosylmethionine decarboxylase 1 (AMD1)-mediated mRNA processing and cell adhesion activated & inhibited transition mechanisms between chimpanzee and human left hemisphere, AMD1-activated different complete (all no positive correlation, Pearson correlation coefficient < 0.25) and uncomplete (partly no positive correlation except AMD1, Pearson < 0.25) networks were identified in higher human compared with lower chimpanzee left hemisphere from the corresponding AMD1-stimulated (Pearson ≥ 0.25) or inhibited (Pearson ≤ -0.25) overlapping molecules of Pearson and GRNInfer, respectively. This result was verified by the corresponding scatter matrix. As visualized by GO, KEGG, GenMAPP, BioCarta, and disease database integration, we proposed mainly that AMD1-stimulated different complete network was involved in AMD1 activation with cytoplasm ubiquitin specific peptidase (tRNA-guanine transglycosylase) to nucleus paired box-induced mRNA processing, whereas the corresponding inhibited network participated in AMD1 repression with cytoplasm protocadherin gamma and adaptor-related protein complex 3-induced cell adhesion in lower chimpanzee left hemisphere. However, AMD1-stimulated network contained AMD1 activation with plakophilin and phosphodiesterase to SH3 binding glutamic acid-rich protein to dynein and zinc finger-induced cell adhesion, whereas the corresponding inhibited different complete network included AMD1 repression with mitochondrial denine nucleotide translocator, brain protein, and ADH dehydrogenase to ribonucleoprotein-induced mRNA processing in higher human left hemisphere. Our AMD1 different networks were verified by AMD1-activated or -inhibited complete and uncomplete networks within and between chimpanzee left hemisphere or (and) human left hemisphere.
Collapse
Affiliation(s)
- Lin Wang
- Bioinformatics Center, School of Electronic Engineering, Beijing University of Posts and Telecommunications, Beijing, 100876, China,
| | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Wang L, Huang J, Jiang M, Chen Q, Jiang Z, Feng H. CAMK1 phosphoinositide signal-mediated protein sorting and transport network in human hepatocellular carcinoma (HCC) by biocomputation. Cell Biochem Biophys 2015; 70:1011-6. [PMID: 24825433 DOI: 10.1007/s12013-014-0011-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We data-analyzed and constructed the high-expression CAMK1 phosphoinositide signal-mediated protein sorting and transport network in human hepatocellular carcinoma (HCC) compared with low-expression (fold change ≥ 2) no-tumor hepatitis/cirrhotic tissues (HBV or HCV infection) in GEO data set, using integration of gene regulatory network inference method with gene ontology (GO). Our result showed that CAMK1 transport subnetwork upstream KCNQ3, LCN2, NKX2_5, NUP62, SORT1, STX1A activated CAMK1, and downstream CAMK1-activated AFP, ENAH, KPNA2, SLC4A3; CAMK1 signal subnetwork upstream BRCA1, DKK1, GPSM2, LEF1, NR5A1, NUP62, SORT1, SSTR5, TBL3 activated CAMK1, and downstream CAMK1-activated MAP2K6, SFRP4, SSTR5, TSHB, UBE2C in HCC. We proposed that CAMK1 activated network enhanced endosome to lysosome transport, endosome transport via multivesicular body sorting pathway, Golgi to endosome transport, intracellular protein transmembrane transport, intracellular protein transport, ion transport, mRNA transport, plasma membrane to endosome transport, potassium ion transport, protein transport, vesicle-mediated transport, anion transport, intracellular transport, androgen receptor signaling pathway, cell surface receptor-linked signal transduction, hormone-mediated signaling, induction of apoptosis by extracellular signals, signal transduction by p53 class mediator resulting in transcription of p21 class mediator, signal transduction resulting in induction of apoptosis, phosphoinositide-mediated signaling, Wnt receptor signaling pathway, as a result of inducing phosphoinositide signal-mediated protein sorting, and transport in HCC. Our hypothesis was verified by CAMK1 functional regulation subnetwork containing positive regulation of calcium ion transport via voltage gated calcium channel, cell proliferation, DNA repair, exocytosis, I-kappaB kinase/NF-kappaB cascade, immunoglobulin-mediated immune response, mast cell activation, natural killer cell-mediated cytotoxicity directed against tumor cell target, protein ubiquitination, sodium ion transport, survival gene product activity, T cell-mediated cytotoxicity, transcription, transcription from RNA polymerase II promoter, transcription initiation from RNA polymerase II promoter, transcription via serum response element binding, exit from mitosis, ubiquitin ligase activity during mitotic cell cycle, regulation of angiogenesis, apoptosis, cell growth, cell proliferation, cyclin-dependent protein kinase activity, gene expression, insulin secretion, steroid biosynthesis, transcription from RNA polymerase II promoter, transcription from RNA polymerase III promoter, cell cycle, cell migration, DNA recombination, and protein metabolism; also by CAMK1 negative functional regulation subnetwork including negative regulation of apoptosis, cell proliferation, centriole replication, fatty acid biosynthesis, lipoprotein lipase activity, MAPK activity, progression through cell cycle, transcription, transcription from RNA polymerase II promoter, cell growth, phosphorylation, and ubiquitin ligase activity during mitotic cell cycle in HCC.
Collapse
Affiliation(s)
- Lin Wang
- Biomedical Center, School of Electronic Engineering, Beijing University of Posts and Telecommunications, Beijing, 100876, China,
| | | | | | | | | | | |
Collapse
|
14
|
Zhou H, Wang L, Huang J, Jiang M, Zhang X, Zhang L, Wang Y, Jiang Z, Zhang Z. High EGFR_1 Inside-Out Activated Inflammation-Induced Motility through SLC2A1-CCNB2-HMMR-KIF11-NUSAP1-PRC1-UBE2C. J Cancer 2015; 6:519-24. [PMID: 26000042 PMCID: PMC4439936 DOI: 10.7150/jca.11404] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 02/20/2015] [Indexed: 12/29/2022] Open
Abstract
48 different Pearson mutual-positive-correlation epidermal growth factor receptor (EGFR_1)-activatory molecular feedback, up- and down-stream network was constructed from 171 overlapping of 366 GRNInfer and 223 Pearson under EGFR_1 CC ≥0.25 in high lung adenocarcinoma compared with low human normal adjacent tissues. Our identified EGFR_1 inside-out upstream activated molecular network showed SLC2A1 (solute carrier family 2 (facilitated glucose transporter) member 1), CCNB2 (cyclin B2), HMMR (hyaluronan-mediated motility receptor (RHAMM)), KIF11 (kinesin family member 11), NUSAP1 (nucleolar and spindle associated protein 1), PRC1 (protein regulator of cytokinesis 1), UBE2C (ubiquitin-conjugating enzyme E2C) in high lung adenocarcinoma. EGFR_1 inside-out upstream activated terms network includes intracellular, membrane fraction, cytoplasm, plasma membrane, integral to membrane, basolateral plasma membrane, transmembrane transport, nucleus, cytosol, cell surface; T cell homeostasis, inflammation; microtubule cytoskeleton, embryonic development (sensu Mammalia), cell cycle, mitosis, thymus development, cell division, regulation of cell cycle, Contributed--cellular process--Hs cell cycle KEGG, cytokinesis, M phase, M phase of mitotic cell cycle, estrogen-responsive protein Efp controls cell cycle and breast tumors growth, cell motility, locomotion, locomotory behavior, neoplasm metastasis, spindle pole, spindle microtubule, microtubule motor activity, microtubule-based movement, mitotic spindle organization and biogenesis, mitotic centrosome separation, spindle pole body organization and biogenesis, microtubule-based process, microtubule, cytokinesis after mitosis, mitotic chromosome condensation, establishment of mitotic spindle localization, positive regulation of mitosis, mitotic spindle elongation, spindle organization and biogenesis, positive regulation of exit from mitosis, regulation of cell proliferation, positive regulation of cell proliferation based on integrative GO, KEGG, GenMAPP, BioCarta and disease databases in high lung adenocarcinoma. Therefore, we propose high EGFR_1 inside-out activated inflammation-induced motility through SLC2A1-CCNB2-HMMR-KIF11-NUSAP1-PRC1-UBE2C in lung adenocarcinoma.
Collapse
Affiliation(s)
- Huilei Zhou
- 1. Biomedical Center, School of Electronic Engineering, Beijing University of Posts and Telecommunications, Beijing, 100876, China
| | - Lin Wang
- 1. Biomedical Center, School of Electronic Engineering, Beijing University of Posts and Telecommunications, Beijing, 100876, China
| | - Juxiang Huang
- 1. Biomedical Center, School of Electronic Engineering, Beijing University of Posts and Telecommunications, Beijing, 100876, China
| | - Minghu Jiang
- 2. Lab of Computational Linguistics, School of Humanities and Social Sciences, Tsinghua University, Beijing, 100084, China
| | - Xiaoyu Zhang
- 1. Biomedical Center, School of Electronic Engineering, Beijing University of Posts and Telecommunications, Beijing, 100876, China
| | - Liyuan Zhang
- 1. Biomedical Center, School of Electronic Engineering, Beijing University of Posts and Telecommunications, Beijing, 100876, China
| | - Yangming Wang
- 1. Biomedical Center, School of Electronic Engineering, Beijing University of Posts and Telecommunications, Beijing, 100876, China
| | - Zhenfu Jiang
- 1. Biomedical Center, School of Electronic Engineering, Beijing University of Posts and Telecommunications, Beijing, 100876, China
| | - Zhongjie Zhang
- 3. College of information, North China University of Technology, Beijing, 100043, China
| |
Collapse
|
15
|
Vázquez-Villa F, García-Ocaña M, Galván JA, García-Martínez J, García-Pravia C, Menéndez-Rodríguez P, González-del Rey C, Barneo-Serra L, de Los Toyos JR. COL11A1/(pro)collagen 11A1 expression is a remarkable biomarker of human invasive carcinoma-associated stromal cells and carcinoma progression. Tumour Biol 2015; 36:2213-22. [PMID: 25761876 DOI: 10.1007/s13277-015-3295-4] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 02/27/2015] [Indexed: 12/14/2022] Open
Abstract
The COL11A1 human gene codes for the α1 chain of procollagen 11A1 and mature collagen 11A1, an extracellular minor fibrillar collagen. Under regular conditions, this gene and its derived products are mainly expressed by chondrocytes and mesenchymal stem cells as well as osteoblasts. Normal epithelial cells and quiescent fibroblasts from diverse locations do not express them. Mesenchyme-derived tumors and related conditions, such as scleroderma and keloids, are positive for COL11A1/(pro)collagen 11A1 expression, as well as high-grade human gliomas/glioblastomas. This expression is almost absent in benign pathological processes such as breast hyperplasia, sclerosing adenosis, idiopathic pulmonary fibrosis, cirrhosis, pancreatitis, diverticulitis, and inflammatory bowel disease. By contrast, COL11A1/(pro)collagen 11A1 is highly expressed by activated stromal cells of the desmoplastic reaction of different human invasive carcinomas, and this expression is correlated with carcinoma aggressiveness and progression, and lymph node metastasis. COL11A1 upregulation has been shown to be associated to TGF-β1, Wnt, and Hh signaling pathways, which are especially active in cancer-associated stromal cells. At the front of invasive carcinomas, neoplastic epithelial cells, putatively undergoing epithelial-to-mesenchymal transition, and carcinoma-derived cells with highly metastatic capabilities, can express COL11A1. Thus, in established metastases, the expression of COL11A1/(pro)collagen 11A1 could rely on both the metastatic epithelial cells and/or the accompanying activated stromal cells. COL11A1/(pro)collagen 11A1 expression is a remarkable biomarker of human carcinoma-associated stromal cells and carcinoma progression.
Collapse
Affiliation(s)
- Fernando Vázquez-Villa
- Surgery Department, School of Medicine and Health Sciences, University of Oviedo, 33006, Oviedo, Spain
| | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Low glucose transporter SLC2A5-inhibited human normal adjacent lung adenocarcinoma cytoplasmic pro-B cell development mechanism network. Mol Cell Biochem 2014; 399:71-6. [PMID: 25326153 DOI: 10.1007/s11010-014-2233-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 09/27/2014] [Indexed: 01/09/2023]
Abstract
Solute carrier family 2 (facilitated glucose/fructose transporter) member 5 (SLC2A5)-inhibited seven different molecular Pearson mutual-positive-correlation networks constructed by 24 overlapping molecules from 368 GRNInfer and 34 Pearson under SLC2A5 CC ≤-0.25 in low human normal adjacent tissues were compared with high lung adenocarcinoma. Based on GO, KEGG, GenMAPP, BioCarta, and disease databases, our result showed that low SLC2A5-inhibited network included Golgi apparatus of AP1M2_1; cell cycle of CUL7, SAC3D1; protein amino acid dephosphorylation of STYXL1; pro-B cell-cell differentiation of SOX4_3; and FAD biosynthesis of FLAD1. Thus, we propose low glucose transporter SLC2A5-inhibited human normal adjacent lung adenocarcinoma cytoplasmic pro-B cell development mechanism network through repression of protein amino acid dephosphorylation to FAD biosynthesis.
Collapse
|
17
|
Diao H, Wang L, Huang J, Jiang M, Zhou H, Li X, Chen Q, Jiang Z, Feng H. BRCA1-mediated inflammation and growth activated & inhibited transition mechanisms between no-tumor hepatitis/cirrhotic tissues and HCC. J Cell Biochem 2014; 115:641-50. [PMID: 24151232 DOI: 10.1002/jcb.24699] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Accepted: 10/16/2013] [Indexed: 12/23/2022]
Abstract
To understand breast cancer 1 early onset (BRCA1)-mediated inflammation and growth activated and inhibited transition mechanisms between no-tumor hepatitis/cirrhotic tissues (HBV or HCV infection) and human hepatocellular carcinoma (HCC), BRCA1-activated different complete (all no positive correlation, Pearson correlation coefficient <0.25) and uncomplete (partly no positive correlation except BRCA1, Pearson <0.25) networks were identified in higher HCC compared with lower no-tumor hepatitis/cirrhotic tissues (HBV or HCV infection) from the corresponding BRCA1-stimulated (Pearson ≥0.25) or inhibited (Pearson ≤-0.25) overlapping molecules of Pearson and GRNInfer, respectively. This result was verified by the corresponding scatter matrix. As visualized by GO, KEGG, GenMAPP, BioCarta, and disease database integration, we proposed mainly that BRCA1-stimulated different complete network was involved in BRCA1 activation with integral to membrane killer cell lectin-like receptor C to nucleus interferon regulatory factor 5-induced inflammation, whereas the corresponding inhibited network participated in BRCA1 repression with matrix roundabout axon guidance receptor homolog 1 to plasma membrane versican-induced growth in lower no-tumor hepatitis/cirrhotic tissues (HBV or HCV infection). However, BRCA1-stimulated network contained BRCA1 activation with endothelium-specific to lysosomal transmembrane and carbamoyl synthetase to tastin, histone cluster and cyclin-induced growth, whereas the corresponding inhibited different complete network included BRCA1 repression with ovalbumin, thyroid stimulating hormone beta and Hu antigen C to cytochrome P450 to transducin-induced inflammation in higher HCC. Our BRCA1 different networks were verified by BRCA1-activated or -inhibited complete and uncomplete networks within and between no-tumor hepatitis/cirrhotic tissues (HBV or HCV infection) or (and) HCC.
Collapse
Affiliation(s)
- Haizhen Diao
- Bioinformatics Center, School of Electronic Engineering, Beijing University of Posts and Telecommunications, Beijing, 100876, China; State key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Huang J, Wang L, Jiang M, Chen Q, Jiang Z, Feng H. AGR2-mediated lung adenocarcinoma metastasis novel mechanism network through repression with interferon coupling cytoskeleton to steroid metabolism-dependent humoral immune response. Cell Immunol 2014; 290:102-6. [PMID: 24960290 DOI: 10.1016/j.cellimm.2014.05.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 05/04/2014] [Accepted: 05/27/2014] [Indexed: 12/22/2022]
Abstract
7 anterior gradient homolog 2 (AGR2)-inhibited different molecular mutual positive correlation network was constructed in lung adenocarcinoma compared with human normal adjacent tissues by 17 overlapping molecules of 358 GRNInfer and 19 Pearson (AGR2 CC⩽-0.25). Based on GO, KEGG, GenMAPP, BioCarta and disease databases, we determined AGR2-mediated lung adenocarcinoma metastasis through repression with cytoskeleton of MAST1; steroid metabolism of SOAT2; humoral immune response of POU2AF1; interferon alpha-inducible of IFI6; immunoglobulin of IGKC_3, CTA_246H3.1. Thus we proposed AGR2-mediated lung adenocarcinoma metastasis novel mechanism network through repression with interferon coupling cytoskeleton to steroid metabolism-dependent humoral immune response.
Collapse
Affiliation(s)
- Juxiang Huang
- Biomedical Center, School of Electronic Engineering, Beijing University of Posts and Telecommunications, Beijing 100876, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Lin Wang
- Biomedical Center, School of Electronic Engineering, Beijing University of Posts and Telecommunications, Beijing 100876, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
| | - Minghu Jiang
- Lab of Computational Linguistics, School of Humanities and Social Sciences, Tsinghua University, Beijing 100084, China
| | - Qingchun Chen
- Biomedical Center, School of Electronic Engineering, Beijing University of Posts and Telecommunications, Beijing 100876, China
| | - Zhenfu Jiang
- School of Mechanical Electronic & Information Engineering, China University of Mining and Technology, Beijing 100083, China
| | - Haitao Feng
- Dean Department, Heilongjiang University of Chinese Medicine, Harbin 150040, China
| |
Collapse
|
19
|
Wang L, Huang J, Jiang M, Lin H, Qi L, Diao H. Inhibited PTHLH downstream leukocyte adhesion-mediated protein amino acid N-linked glycosylation coupling Notch and JAK-STAT cascade to iron-sulfur cluster assembly-induced aging network in no-tumor hepatitis/cirrhotic tissues (HBV or HCV infection) by systems-theoretical analysis. Integr Biol (Camb) 2013; 4:1256-62. [PMID: 22955522 DOI: 10.1039/c2ib20148h] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We analyzed the different biological processes and occurrence numbers between low expression inhibited PTHLH downstream-mediated aging gene ontology (GO) network of no-tumor hepatitis/cirrhotic tissues (HBV or HCV infection) and the corresponding high expression (fold change ≥2) inhibited GO network of human hepatocellular carcinoma (HCC). Inhibited PTHLH downstream-mediated aging network consisted of aging, branched chain family amino acid biosynthesis, cellular metabolism, cholesterol biosynthesis, coupled to cyclic nucleotide second messenger, cytolysis, 'de novo' GDP-l-fucose biosynthesis, detection of mechanical stimulus, glucose homeostasis, G-protein signaling, leukocyte adhesion, iron-sulfur cluster assembly, JAK-STAT cascade, Notch signaling pathway, nucleotide-sugar metabolism, peptidyl-tyrosine sulfation, protein amino acid N-linked glycosylation, protein amino acid phosphorylation, response to drug, rRNA processing, translational initiation, ubiquitin-dependent protein catabolism, homophilic cell adhesion in no-tumor hepatitis/cirrhotic tissues. We proposed inhibited PTHLH downstream leukocyte adhesion-mediated protein amino acid N-linked glycosylation coupling Notch and JAK-STAT cascade to iron-sulfur cluster assembly-induced aging network. Our hypothesis was verified by the same inhibited PTHLH downstream-mediated aging GO network in no-tumor hepatitis/cirrhotic tissues with the corresponding activated GO network of HCC, or the different with the corresponding activated GO network of no-tumor hepatitis/cirrhotic tissues. Inhibited PTHLH downstream leukocyte adhesion-mediated protein amino acid N-linked glycosylation coupling Notch and JAK-STAT cascade to iron-sulfur cluster assembly-induced aging network included TSTA3, ALK, CIAO1, NOTCH3 in no-tumor hepatitis/cirrhotic tissues from the GEO data set using gene regulatory network inference method and our programming.
Collapse
Affiliation(s)
- Lin Wang
- Biomedical Center, School of Electronic Engineering, Beijing University of Posts and Telecommunications, Beijing, 100876, China.
| | | | | | | | | | | |
Collapse
|
20
|
Qi L, Wang L, Huang J, Jiang M, Diao H, Zhou H, Li X, Jiang Z. Activated amelogenin Y-linked (AMELY) regulation and angiogenesis in human hepatocellular carcinoma by biocomputation. Oncol Lett 2013; 5:1075-1079. [PMID: 23426651 PMCID: PMC3576279 DOI: 10.3892/ol.2013.1122] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2012] [Accepted: 01/07/2013] [Indexed: 12/18/2022] Open
Abstract
In the present study, a comparison of the biological processes and gene ontology (GO) in human hepatocellular carcinoma (HCC) with high expression (fold change ≥2) of amelogenin Y-linked (AMELY)-activated upstream regulation networks with non-tumor hepatitis/cirrhotic tissues (HBV or HCV infection) with low expression of activated networks was performed. The principle biological processes involved in non-tumor hepatitis/cirrhotic tissues include positive regulation of mismatch repair, regulation of transcription from RNA polymerase II promoters, negative regulation of cell-cell adhesion, protein ubiquitinatin and protein catabolism. The main biological processes involved in the development of HCC include positive regulation of calcium ion transport into the cytosol, cell proliferation, DNA replication, fibroblast proliferation, immune response, microtubule polymerization and protein secretion. Specific transcription from RNA polymerase II promoters, regulation of angiogenesis, cell growth, protein metabolism, Wnt receptor signaling pathways, negative regulation of endothelial cell differentiation, microtubule depolymerization, peptidase activity and progression through the cell cycle are also involved. Positive regulation of transcription is involved in both processes. An activated AMELY-coupled upstream positive regulation of immune response-mediated protein secretion to Wnt signaling and calcium into cytosol-induced regulation of cell growth and angiogenesis in HCC is proposed. The AMELY upstream regulation molecular network model was constructed with BUB1B, CST6, ESM1, HOXA5, LEF1, MAPT, MYBL2, NOTCH3, PLA2G1B, PROK1, ROBO1, SCML2 and UBE2C in HCC from a Gene Expression Omnibus (GEO) dataset by gene regulation network inference methods and our programming methods.
Collapse
Affiliation(s)
- Lianxiu Qi
- Biomedical Center, School of Electronic Engineering, Beijing University of Posts and Telecommunications, Beijing 100876
| | | | | | | | | | | | | | | |
Collapse
|
21
|
Wang L, Huang J, Jiang M, Lin H, Qi L, Diao H. Activated PTHLH coupling feedback phosphoinositide to G-protein receptor signal-induced cell adhesion network in human hepatocellular carcinoma by systems-theoretic analysis. ScientificWorldJournal 2012; 2012:428979. [PMID: 22997493 PMCID: PMC3444843 DOI: 10.1100/2012/428979] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 07/29/2012] [Indexed: 12/27/2022] Open
Abstract
Studies were done on analysis of biological processes in the same high expression (fold change ≥2) activated PTHLH feedback-mediated cell adhesion gene ontology (GO) network of human hepatocellular carcinoma (HCC) compared with the corresponding low expression activated GO network of no-tumor hepatitis/cirrhotic tissues (HBV or HCV infection). Activated PTHLH feedback-mediated cell adhesion network consisted of anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolism, cell adhesion, cell differentiation, cell-cell signaling, G-protein-coupled receptor protein signaling pathway, intracellular transport, metabolism, phosphoinositide-mediated signaling, positive regulation of transcription, regulation of cyclin-dependent protein kinase activity, regulation of transcription, signal transduction, transcription, and transport in HCC. We proposed activated PTHLH coupling feedback phosphoinositide to G-protein receptor signal-induced cell adhesion network. Our hypothesis was verified by the different activated PTHLH feedback-mediated cell adhesion GO network of HCC compared with the corresponding inhibited GO network of no-tumor hepatitis/cirrhotic tissues, or the same compared with the corresponding inhibited GO network of HCC. Activated PTHLH coupling feedback phosphoinositide to G-protein receptor signal-induced cell adhesion network included BUB1B, GNG10, PTHR2, GNAZ, RFC4, UBE2C, NRXN3, BAP1, PVRL2, TROAP, and VCAN in HCC from GEO dataset using gene regulatory network inference method and our programming.
Collapse
Affiliation(s)
- Lin Wang
- Biomedical Center, School of Electronic Engineering, Beijing University of Posts and Telecommunications, Beijing 100876, China.
| | | | | | | | | | | |
Collapse
|
22
|
Tissue-specific transplantation antigen P35B (TSTA3) immune response-mediated metabolism coupling cell cycle to postreplication repair network in no-tumor hepatitis/cirrhotic tissues (HBV or HCV infection) by biocomputation. Immunol Res 2012; 52:258-68. [PMID: 22528125 DOI: 10.1007/s12026-012-8337-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We constructed the low-expression tissue-specific transplantation antigen P35B (TSTA3) immune response-mediated metabolism coupling cell cycle to postreplication repair network in no-tumor hepatitis/cirrhotic tissues (HBV or HCV infection) compared with high-expression (fold change ≥ 2) human hepatocellular carcinoma in GEO data set, by using integration of gene regulatory network inference method with gene ontology analysis of TSTA3-activated up- and downstream networks. Our results showed TSTA3 upstream-activated CCNB2, CKS1B, ELAVL3, GAS7, NQO1, NTN1, OCRL, PLA2G1B, REG3A, SSTR5, etc. and TSTA3 downstream-activated BAP1, BRCA1, CCL20, MCM2, MS4A2, NTN1, REG1A, TP53I11, VCAN, SLC16A3, etc. in no-tumor hepatitis/cirrhotic tissues. TSTA3-activated network enhanced the regulation of apoptosis, cyclin-dependent protein kinase activity, cell migration, insulin secretion, transcription, cell division, cell proliferation, DNA replication, postreplication repair, cell differentiation, T-cell homeostasis, neutrophil-mediated immunity, neutrophil chemotaxis, interleukin-8 production, inflammatory response, immune response, B-cell activation, humoral immune response, actin filament organization, xenobiotic metabolism, lipid metabolism, phospholipid metabolism, leukotriene biosynthesis, organismal lipid catabolism, phosphatidylcholine metabolism, arachidonic acid secretion, activation of phospholipase A2, deoxyribonucleotide biosynthesis, heterophilic cell adhesion, activation of MAPK activity, signal transduction by p53 class mediator resulting in transcription of p21 class mediator, G-protein-coupled receptor protein signaling pathway, response to toxin, acute-phase response, DNA damage response, intercellular junction assembly, cell communication, and cell recognition, as a result of inducing immune response-mediated metabolism coupling cell cycle to postreplication repair in no-tumor hepatitis/cirrhotic tissues.
Collapse
|
23
|
Huang J, Wang L, Jiang M, Lin H, Qi L, Diao H. PTHLHcoupling upstream negative regulation of fatty acid biosynthesis and Wnt receptor signal to downstream peptidase activity-induced apoptosis network in human hepatocellular carcinoma by systems-theoretical analysis. J Recept Signal Transduct Res 2012; 32:250-6. [DOI: 10.3109/10799893.2012.700717] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
24
|
Lin H, Wang L, Jiang M, Huang J, Qi L. P-glycoprotein(ABCB1)inhibited network of mitochondrion transport along microtubule and BMP signal-induced cell shape in chimpanzee left cerebrum by systems-theoretical analysis. Cell Biochem Funct 2012; 30:582-7. [DOI: 10.1002/cbf.2837] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2011] [Revised: 03/01/2012] [Accepted: 04/02/2012] [Indexed: 12/20/2022]
Affiliation(s)
- Hong Lin
- Biomedical Center, School of Electronic Engineering; Beijing University of Posts and Telecommunications; Beijing; China
| | - Lin Wang
- Biomedical Center, School of Electronic Engineering; Beijing University of Posts and Telecommunications; Beijing; China
| | - Minghu Jiang
- Lab of Computational Linguistics, School of Humanities and Social Sciences; Tsinghua University; Beijing; China
| | - Juxiang Huang
- Biomedical Center, School of Electronic Engineering; Beijing University of Posts and Telecommunications; Beijing; China
| | - Lianxiu Qi
- Biomedical Center, School of Electronic Engineering; Beijing University of Posts and Telecommunications; Beijing; China
| |
Collapse
|
25
|
Drozdov I, Bornschein J, Wex T, Valeyev NV, Tsoka S, Malfertheiner P. Functional and topological properties in hepatocellular carcinoma transcriptome. PLoS One 2012; 7:e35510. [PMID: 22539975 PMCID: PMC3335123 DOI: 10.1371/journal.pone.0035510] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2011] [Accepted: 03/16/2012] [Indexed: 12/14/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a leading cause of global cancer mortality. However, little is known about the precise molecular mechanisms involved in tumor formation and pathogenesis. The primary goal of this study was to elucidate genome-wide molecular networks involved in development of HCC with multiple etiologies by exploring high quality microarray data. We undertook a comparative network analysis across 264 human microarray profiles monitoring transcript changes in healthy liver, liver cirrhosis, and HCC with viral and alcoholic etiologies. Gene co-expression profiling was used to derive a consensus gene relevance network of HCC progression that consisted of 798 genes and 2,012 links. The HCC interactome was further confirmed to be phenotype-specific and non-random. Additionally, we confirmed that co-expressed genes are more likely to share biological function, but not sub-cellular localization. Analysis of individual HCC genes revealed that they are topologically central in a human protein-protein interaction network. We used quantitative RT-PCR in a cohort of normal liver tissue (n = 8), hepatitis C virus (HCV)-induced chronic liver disease (n = 9), and HCC (n = 7) to validate co-expressions of several well-connected genes, namely ASPM, CDKN3, NEK2, RACGAP1, and TOP2A. We show that HCC is a heterogeneous disorder, underpinned by complex cross talk between immune response, cell cycle, and mRNA translation pathways. Our work provides a systems-wide resource for deeper understanding of molecular mechanisms in HCC progression and may be used further to define novel targets for efficient treatment or diagnosis of this disease.
Collapse
Affiliation(s)
- Ignat Drozdov
- British Heart Foundation Centre of Excellence, King's College London, London, United Kingdom
- Centre for Bioinformatics, Department of Informatics, School of Natural and Mathematical Sciences, King's College London, London, United Kingdom
- * E-mail: (PM); (ID)
| | - Jan Bornschein
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke-University of Magdeburg, Magdeburg, Germany
| | - Thomas Wex
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke-University of Magdeburg, Magdeburg, Germany
| | - Najl V. Valeyev
- Centre for Systems, Dynamics and Control, College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, United Kingdom
| | - Sophia Tsoka
- Centre for Bioinformatics, Department of Informatics, School of Natural and Mathematical Sciences, King's College London, London, United Kingdom
| | - Peter Malfertheiner
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke-University of Magdeburg, Magdeburg, Germany
- * E-mail: (PM); (ID)
| |
Collapse
|
26
|
Sun L, Wang L, Jiang M, Huang J, Lin H. Glycogen debranching enzyme 6 (AGL), enolase 1 (ENOSF1), ectonucleotide pyrophosphatase 2 (ENPP2_1), glutathione S-transferase 3 (GSTM3_3) and mannosidase (MAN2B2) metabolism computational network analysis between chimpanzee and human left cerebrum. Cell Biochem Biophys 2012; 61:493-505. [PMID: 21735130 DOI: 10.1007/s12013-011-9232-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We identified significantly higher expression of the genes glycogen debranching enzyme 6 (AGL), enolase 1 (ENOSF1), ectonucleotide pyrophosphatase 2 (ENPP2_1), glutathione S-transferase 3 (GSTM3_3) and mannosidase (MAN2B2) from human left cerebrums versus chimpanzees. Yet the distinct low- and high-expression AGL, ENOSF1, ENPP2_1, GSTM3_3 and MAN2B2 metabolism networks between chimpanzee and human left cerebrum remain to be elucidated. Here, we constructed low- and high-expression activated and inhibited upstream and downstream AGL, ENOSF1, ENPP2_1, GSTM3_3 and MAN2B2 metabolism network between chimpanzee and human left cerebrum in GEO data set by gene regulatory network inference method based on linear programming and decomposition procedure, under covering AGL, ENOSF1, ENPP2_1, GSTM3_3 and MAN2B2 pathway and matching metabolism enrichment analysis by CapitalBio MAS 3.0 integration of public databases, including Gene Ontology, KEGG, BioCarta, GenMapp, Intact, UniGene, OMIM, etc. Our results show that the AGL, ENOSF1, ENPP2_1, GSTM3_3 and MAN2B2 metabolism network has more activated and less inhibited molecules in chimpanzee, but less activated and more inhibited in the human left cerebrum. We inferred stronger carbohydrate, glutathione and proteoglycan metabolism, ATPase activity, but weaker base excision repair, arachidonic acid and drug metabolism as a result of inducing cell growth in low-expression AGL, ENOSF1, ENPP2_1, GSTM3_3 and MAN2B2 metabolism network of chimpanzee left cerebrum; whereas stronger lipid metabolism, amino acid catabolism, DNA repair but weaker inflammatory response, cell proliferation, glutathione and carbohydrate metabolism as a result of inducing cell differentiation in high-expression AGL, ENOSF1, ENPP2_1, GSTM3_3 and MAN2B2 metabolism network of human left cerebrum. Our inferences are consistent with recent reports and computational activation and inhibition gene number patterns, respectively.
Collapse
Affiliation(s)
- Lingjun Sun
- Biomedical Center, School of Electronic Engineering, Beijing University of Posts and Telecommunications, Beijing 100876, China
| | | | | | | | | |
Collapse
|
27
|
Sun L, Pan J, Peng L, Fang L, Zhao X, Sun L, Yang Z, Ran Y. Combination of haptoglobin and osteopontin could predict colorectal cancer hepatic metastasis. Ann Surg Oncol 2012; 19:2411-9. [PMID: 22219064 DOI: 10.1245/s10434-011-2177-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Indexed: 12/11/2022]
Abstract
PURPOSE This study aimed to identify novel molecular markers for the early detection of colorectal cancer liver metastasis. METHODS Genes related to hepatic metastasis were screened from the Oncomine database. The candidate markers were tested by immunohistochemistry, and their predictive accuracy was assessed by the cross-validation method and an independent test set. RESULTS We got three datasets containing 2,973 genes that were highly expressed in primary colon cancer tissues compared with non-metastatic colon cancer tissues and identified 7 candidate molecules for immunohistochemical validation. A total of 213 colorectal cancer samples were randomly divided into a training set (113 cases) and a blind testing set (100 cases). In the training set, immunohistochemical analysis showed that HP, OPN, and PTGIS expression were significantly higher in the hepatic metastasis group than in the non-metastasis group. Logistic regression analysis showed that HP and OPN levels in primary tumors and lymph node metastasis status were the only significant (P<0.05) parameters for detecting liver metastasis. The predictive accuracy of markers was assessed by the cross-validation method and an independent test set. In leave-one-out cross-validation, the two markers combined with clinicopathologic features resulted in 91.2% sensitivity and 96.4% specificity for hepatic metastasis detection. In an independent test set, the combination achieved 94.5% sensitivity and 88.9% specificity for predicting the hepatic metastasis of colorectal cancer. CONCLUSIONS Our results suggest that combined HP and OPN expression levels are significantly related to liver metastasis and prognosis, and, if this is validated, they could be used as accurate predictors of liver metastasis in colorectal cancer.
Collapse
Affiliation(s)
- Lichao Sun
- State Key Laboratory of Molecular Oncology, Cancer Institute Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.
| | | | | | | | | | | | | | | |
Collapse
|
28
|
Signal Transducer and Activator of Transcription 2 (STAT2) Metabolism Coupling Postmitotic Outgrowth to Visual and Sound Perception Network in Human Left Cerebrum by Biocomputation. J Mol Neurosci 2012; 47:649-58. [DOI: 10.1007/s12031-011-9702-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Accepted: 12/23/2011] [Indexed: 01/09/2023]
|
29
|
Wang L, Huang J, Jiang M, Sun L. Survivin (BIRC5) cell cycle computational network in human no-tumor hepatitis/cirrhosis and hepatocellular carcinoma transformation. J Cell Biochem 2011; 112:1286-94. [PMID: 21312234 DOI: 10.1002/jcb.23030] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Survivin (BIRC5) relationship with tumor is presented in several papers. However, how the molecular network and interpretation concerning BIRC5 cell cycle between no-tumor hepatitis/cirrhosis and hepatocellular carcinoma (HCC) remains to be elucidated. Here, we constructed and analyzed significant higher expression gene BIRC5 activated and inhibited cell cycle network from HCC versus no-tumor hepatitis/cirrhosis patients (viral infection HCV or HBV) in GEO Dataset by combination of gene regulatory network inference method based on linear programming and decomposition procedure with the CapitalBio MAS 3.0 software based on the integration of public databases including Gene Ontology, KEGG, BioCarta, GenMapp, Intact, UniGene, OMIM, etc. Compared the same and different activated and inhibited BIRC5 network with GO analysis between no-tumor hepatitis/cirrhosis and HCC, our result showed BIRC5 cell cycle network weaker transcription factor activity in both no-tumor hepatitis/cirrhosis and HCC (1); stronger nucleus protein binding but weaker cytoplasm protein binding in no-tumor hepatitis/cirrhosis (2); stronger cytoplasm protein phosphatase binding but weaker ubiquitin-protein ligase activity in HCC (3). Therefore, we inferred BIRC5 cell cycle module less transcription from RNA polymerase II promoter in both no-tumor hepatitis/cirrhosis and HCC (4). We deduced BIRC5 cell cycle module different from more mitosis but less complex-dependent proteasomal ubiquitin-dependent protein catabolism as a result increasing cell division and cell numbers in no-tumor hepatitis/cirrhosis to more protein amino acid autophosphorylation but less negative regulation of ubiquitin ligase activity during mitotic cell cycle as a result increasing growth and cell volume in HCC (5).
Collapse
Affiliation(s)
- Lin Wang
- Biomedical Center, School of Electronic Engineering, Beijing University of Posts and Telecommunications, Beijing, 100876, China.
| | | | | | | |
Collapse
|
30
|
Wang L, Sun L, Huang J, Jiang M. Cyclin-dependent kinase inhibitor 3 (CDKN3) novel cell cycle computational network between human non-malignancy associated hepatitis/cirrhosis and hepatocellular carcinoma (HCC) transformation. Cell Prolif 2011; 44:291-9. [PMID: 21535270 DOI: 10.1111/j.1365-2184.2011.00752.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The relationship of cyclin-dependent kinase inhibitor 3 (CDKN3) with tumours has previously been presented in a number of publications. However, the molecular network and interpretation of CDKN3 through the cell cycle between non-malignancy associated hepatitis/cirrhosis and hepatocellular carcinoma (HCC) have remained to be elucidated. Here, we have constructed and analysed significant high expression gene CDKN3 activated and inhibited cell cycle networks from 25 HCC versus 25 non-malignancy associated hepatitis/cirrhosis patients (viral infection HCV or HBV) in GEO Dataset GSE10140-10141, by combination of a gene regulatory network inference method based on linear programming, and decomposition procedure using CapitalBio MAS 3.0 software, based on integration of public databases including Gene Ontology, KEGG, BioCarta, GenMapp, Intact, UniGene, OMIM, and others. Comparing the same and differently activated and inhibited CDKN3 networks with GO analysis, between non-malignancy associated hepatitis/cirrhosis and HCC, our results suggest a CDKN3 cell cycle network (i) with stronger DNA replication and with weaker ubiquitin-dependent protein catabolism as common characteristics in both non-malignancy associated hepatitis/cirrhosis and HCC; (ii) with more cell division and weaker mitotic G2 checkpoint in non-malignancy associated hepatitis/cirrhosis; (iii) with stronger cell cycle and weaker cytokinesis, as a result forming multinucleate cells in HCC. Thus, it is useful to identify CDKN3 cell cycle networks for comprehension of molecular mechanism between non-malignancy associated hepatitis/cirrhosis and HCC transformation.
Collapse
Affiliation(s)
- L Wang
- Biomedical Center, School of Electronic Engineering, Beijing University of Posts and Telecommunications, Beijing, China.
| | | | | | | |
Collapse
|
31
|
Huang JX, Wang L, Jiang MH. TNFRSF11B computational development network construction and analysis between frontal cortex of HIV encephalitis (HIVE) and HIVE-control patients. JOURNAL OF INFLAMMATION-LONDON 2010; 7:50. [PMID: 20920282 PMCID: PMC2959006 DOI: 10.1186/1476-9255-7-50] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Accepted: 09/30/2010] [Indexed: 12/19/2022]
Abstract
BACKGROUND TNFRSF11B computational development network construction and analysis of frontal cortex of HIV encephalitis (HIVE) is very useful to identify novel markers and potential targets for prognosis and therapy. METHODS By integration of gene regulatory network infer (GRNInfer) and the database for annotation, visualization and integrated discovery (DAVID) we identified and constructed significant molecule TNFRSF11B development network from 12 frontal cortex of HIVE-control patients and 16 HIVE in the same GEO Dataset GDS1726. RESULTS Our result verified TNFRSF11B developmental process only in the downstream of frontal cortex of HIVE-control patients (BST2, DGKG, GAS1, PDCD4, TGFBR3, VEZF1 inhibition), whereas in the upstream of frontal cortex of HIVE (DGKG, PDCD4 activation) and downstream (CFDP1, DGKG, GAS1, PAX6 activation; BST2, PDCD4, TGFBR3, VEZF1 inhibition). Importantly, we datamined that TNFRSF11B development cluster of HIVE is involved in T-cell mediated immunity, cell projection organization and cell motion (only in HIVE terms) without apoptosis, plasma membrane and kinase activity (only in HIVE-control patients terms), the condition is vital to inflammation, brain morphology and cognition impairment of HIVE. Our result demonstrated that common terms in both HIVE-control patients and HIVE include developmental process, signal transduction, negative regulation of cell proliferation, RNA-binding, zinc-finger, cell development, positive regulation of biological process and cell differentiation. CONCLUSIONS We deduced the stronger TNFRSF11B development network in HIVE consistent with our number computation. It would be necessary of the stronger TNFRSF11B development function to inflammation, brain morphology and cognition of HIVE.
Collapse
Affiliation(s)
- Ju X Huang
- Biomedical Center, School of Electronics Engineering, Beijing University of Posts and Telecommunications, Beijing, 100876, China
| | - L Wang
- Biomedical Center, School of Electronics Engineering, Beijing University of Posts and Telecommunications, Beijing, 100876, China
| | - Ming H Jiang
- Lab of Computational Linguistics, School of Humanities and Social Sciences, Tsinghua Univ., Beijing, 100084, China
| |
Collapse
|
32
|
Wang L, Huang J, Jiang M, Zheng X. AFP computational secreted network construction and analysis between human hepatocellular carcinoma (HCC) and no-tumor hepatitis/cirrhotic liver tissues. Tumour Biol 2010; 31:417-25. [PMID: 20532728 DOI: 10.1007/s13277-010-0050-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Accepted: 04/30/2010] [Indexed: 12/26/2022] Open
Abstract
Alpha-fetoprotein (AFP) computational secreted network construction and analysis of human hepatocellular carcinoma (HCC) is very useful to identify novel markers and potential targets for prognosis and therapy. By integration of gene regulatory network infer and the database for annotation, visualization, and integrated discovery, we identified and constructed significant molecule AFP secreted network from 25 no-tumor hepatitis/cirrhotic liver tissues and 25 HCC patients in the same GEO Dataset GSE10140-10141. Our result verified AFP secreted module in the upstream of no-tumor hepatitis/cirrhotic liver tissues (AMELY, LCN2, and REG3A activation; DKK1, SFRP4, and SPINK1 inhibition) and its downstream (PRSS1, REG3A, and TSHB activation; AMELY and DKK1 inhibition), and also in the upstream of HCC (LCN2, REG3A, and SFRP4 activation; AMELY and DKK1 inhibition) and its downstream (AMELY activation; DKK1, LCN2, PRSS1, SEMA3B, and SPINK1 inhibition). Importantly, we data-mined that AFP secreted cluster of HCC is involved in disease mutation (only in HCC terms) without cell surface receptor linked signal transduction, neuroactive ligand-receptor interaction, cell-cell signaling, and pancreas (only in no-tumor hepatitis/cirrhotic liver tissues terms), the condition which is vital to invasion of HCC. Our result demonstrated that common terms in both no-tumor hepatitis/cirrhotic liver tissues and HCC include secreted extracellular region, extracellular region part, extracellular space, signal peptide, signal, disulfide bond, glycosylation site N-linked (GlcNAc...), and glycoprotein, and these terms are less relative to invasion; therefore, we deduced the weaker AFP secreted network in HCC consistent with our number computation. We predicted AFP high expression localization within cells of HCC and without secretion to extracellular matrix. It would be necessary of AFP secreted function to decrease invasion of HCC.
Collapse
Affiliation(s)
- Lin Wang
- Biomedical Center, School of Electronics Engineering, Beijing University of Posts and Telecommunications, Beijing, 100876, China.
| | | | | | | |
Collapse
|