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Zhong Y, Wu Q, Cai L, Chen Y, Shen Q. CDC167 exhibits potential as a biomarker for airway inflammation in asthma. Mamm Genome 2024; 35:135-148. [PMID: 38580753 PMCID: PMC11130062 DOI: 10.1007/s00335-024-10037-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 03/01/2024] [Indexed: 04/07/2024]
Abstract
Current asthma treatments have been discovered to decrease the risk of disease progression. Herein, we aimed to characterize novel potential therapeutic targets for asthma. Differentially expressed genes (DEGs) for GSE64913 and GSE137268 datasets were characterized. Weighted correlation network analysis (WGCNA) was used to identify trait-related module genes within the GSE67472 dataset. The intersection of the module genes of interest, as well as the DEGs, comprised the key module genes that underwent additional candidate gene screening using machine learning. In addition, a bioinformatics-based approach was used to analyze the relative expression levels, diagnostic values, and reverently enriched pathways of the screened candidate genes. Furthermore, the candidate genes were silenced in asthmatic mice, and the inflammation and lung injury in the mice were validated. A total of 1710 DEGs were characterized in GSE64913 and GSE137268 for asthma patients. WGCNA identified 2367 asthma module genes, of which 285 overlapped with 1710 DEGs. Four candidate genes, CDC167, POSTN, SEC14L1, and SERPINB2, were validated using the intersection genes of three machine learning algorithms, including Least Absolute Shrinkage and Selection Operator, Random Forest, and Support Vector Machine. All the candidate genes were significantly upregulated in asthma patients and demonstrated diagnostic utility for asthma. Furthermore, silencing CDC167 reduced the levels of inflammatory cytokines significantly and alleviated lung injury in ovalbumin (OVA)-induced asthmatic mice. Our study demonstrated that CDC167 exhibits potential as diagnostic markers and therapeutic targets for asthma patients.
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Affiliation(s)
- Yukai Zhong
- Department of Pediatrics, Kongjiang Hospital of Shanghai Yangpu District, Shanghai, 200093, China
| | - Qiong Wu
- Department of Respiratory, Kongjiang Hospital of Shanghai Yangpu District, No. 480 Shuang Yang Road, Yangpu District, Shanghai, 200093, China
| | - Li Cai
- Department of Colorectal Surgery, Kongjiang Hospital of Shanghai Yangpu District, Shanghai, 200093, China
| | - Yuanjing Chen
- Department of Respiratory, Kongjiang Hospital of Shanghai Yangpu District, No. 480 Shuang Yang Road, Yangpu District, Shanghai, 200093, China.
| | - Qi Shen
- Department of Geriatric Medicine, Tongji University Affiliated Yangpu Hospital, No. 450 Teng Yue Road, Yangpu District, Shanghai, 200090, China.
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Yi TT, Yu JM, Liang YY, Wang SQ, Lin GC, Wu XD. Identification of cystic fibrosis transmembrane conductance regulator as a prognostic marker for juvenile myelomonocytic leukemia via the whole-genome bisulfite sequencing of monozygotic twins and data mining. Transl Pediatr 2022; 11:1521-1533. [PMID: 36247890 PMCID: PMC9561505 DOI: 10.21037/tp-22-381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/08/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Linked deoxyribonucleic acid (DNA) hypermethylation investigations of promoter methylation levels of candidate genes may help to increase the progressiveness and mortality rates of juvenile myelomonocytic leukemia (JMML), which is a unique myelodysplastic/myeloproliferative neoplasm caused by excessive monocyte and granulocyte proliferation in infancy/early childhood. However, the roles of hypermethylation in this malignant disease are uncertain. METHODS Bone marrow samples from a JMML patient and peripheral blood samples from a healthy monozygotic twin and an unrelated healthy donor were collected with the informed consent of the participant's parents. Whole-genome bisulfite sequencing (WGBS) was then performed. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to analyze specific differentially methylated region (DMG) related genes. The target genes were screened with Cytoscape and Search Tool for the Retrieval of Interacting Genes/Proteins (STRING), which are gene/protein interaction databases. A data mining platform was used to examine the expression level data of the healthy control and JMML patient tissues in Gene Expression Omnibus data sets, and a survival analysis was performed for all the JMML patients. RESULTS The STRING analysis revealed that the red node [i.e., the cystic fibrosis transmembrane conductance regulator (CFTR)] was the gene of interest. The gene-expression microarray data set analysis suggested that the CFTR expression levels did not differ significantly between the JMML patients and healthy controls (P=0.81). A statistically significant difference was observed in the CFTR promoter methylation level but not in the CFTR gene body methylation level. The overall survival analysis demonstrated that a high level of CFTR expression was associated with a worse survival rate in patients with JMML (P=0.039). CONCLUSIONS CFTR promoter hypermethylation may be a novel biomarker for the diagnosis, monitoring of disease progression, and prognosis of JMML.
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Affiliation(s)
- Tian-Tian Yi
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jie-Ming Yu
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yi-Yang Liang
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Si-Qi Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Guan-Chuan Lin
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xue-Dong Wu
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou, China
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Ruhle M, Espinal-Enríquez J, Hernández-Lemus E. The Breast Cancer Protein Co-Expression Landscape. Cancers (Basel) 2022; 14:cancers14122957. [PMID: 35740621 PMCID: PMC9221059 DOI: 10.3390/cancers14122957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/03/2022] [Accepted: 06/11/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Proteins are among the most fundamental building blocks and molecular players behind the functions of cells and tissues. Their abundance and interaction patterns shape, to a large extent, what happens at the cellular and organ levels. This is also true regarding tumor tissues. In this work, we explored the patterns of abundance and co-occurrence of a large number of proteins in breast cancer cells and their healthy counterparts. We discovered the main differences and tried to see whether those differences may be associated with relevant aspects of the biology of these tumors. Our final goal is to provide information to empower cancer clinicians and pharmacologists to develop better diagnostic, prognostic, and therapeutic tools. Abstract Breast cancer is a complex phenotype (or better yet, several complex phenotypes) characterized by the interplay of a large number of cellular and biomolecular entities. Biological networks have been successfully used to capture some of the heterogeneity of intricate pathophenotypes, including cancer. Gene coexpression networks, in particular, have been used to study large-scale regulatory patterns. Ultimately, biological processes are carried out by proteins and their complexes. However, to date, most of the tumor profiling research has focused on the genomic and transcriptomic information. Here, we tried to expand this profiling through the analysis of open proteomic data via mutual information co-expression networks’ analysis. We could observe that there are distinctive biological processes associated with communities of these networks and how some transcriptional co-expression phenomena are lost at the protein level. These kinds of data and network analyses are a broad resource to explore cellular behavior and cancer research.
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Affiliation(s)
- Martín Ruhle
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City 14610, Mexico; (M.R.); (J.E.-E.)
| | - Jesús Espinal-Enríquez
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City 14610, Mexico; (M.R.); (J.E.-E.)
- Center for Complexity Sciences, Universidad Nacional Autonoma de Mexico, Mexico City 04510, Mexico
| | - Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City 14610, Mexico; (M.R.); (J.E.-E.)
- Center for Complexity Sciences, Universidad Nacional Autonoma de Mexico, Mexico City 04510, Mexico
- Correspondence: ; Tel.: +52-5555-5350-1970
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Inferred inactivation of the Cftr gene in the duodena of mice exposed to hexavalent chromium (Cr(VI)) in drinking water supports its tumor-suppressor status and implies its potential role in Cr(VI)-induced carcinogenesis of the small intestines. Toxicol Appl Pharmacol 2021; 433:115773. [PMID: 34688701 DOI: 10.1016/j.taap.2021.115773] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 10/12/2021] [Accepted: 10/19/2021] [Indexed: 12/12/2022]
Abstract
Carcinogenicity of hexavalent chromium [Cr (VI)] has been supported by a number of epidemiological and animal studies; however, its carcinogenic mode of action is still incompletely understood. To identify mechanisms involved in cancer development, we analyzed gene expression data from duodena of mice exposed to Cr(VI) in drinking water. This analysis included (i) identification of upstream regulatory molecules that are likely responsible for the observed gene expression changes, (ii) identification of annotated gene expression data from public repositories that correlate with gene expression changes in duodena of Cr(VI)-exposed mice, and (iii) identification of hallmark and oncogenic signature gene sets relevant to these data. We identified the inactivated CFTR gene among the top scoring upstream regulators, and found positive correlations between the expression data from duodena of Cr(VI)-exposed mice and other datasets in public repositories associated with the inactivation of the CFTR gene. In addition, we found enrichment of signatures for oncogenic signaling, sustained cell proliferation, impaired apoptosis and tissue remodeling. Results of our computational study support the tumor-suppressor role of the CFTR gene. Furthermore, our results support human relevance of the Cr(VI)-mediated carcinogenesis observed in the small intestines of exposed mice and suggest possible groups that may be more vulnerable to the adverse outcomes associated with the inactivation of CFTR by hexavalent chromium or other agents. Lastly, our findings predict, for the first time, the role of CFTR inactivation in chemical carcinogenesis and expand the range of plausible mechanisms that may be operative in Cr(VI)-mediated carcinogenesis of intestinal and possibly other tissues.
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Chen C, Tian J, He Z, Xiong W, He Y, Liu S. Identified Three Interferon Induced Proteins as Novel Biomarkers of Human Ischemic Cardiomyopathy. Int J Mol Sci 2021; 22:13116. [PMID: 34884921 PMCID: PMC8657967 DOI: 10.3390/ijms222313116] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/11/2021] [Accepted: 11/15/2021] [Indexed: 11/16/2022] Open
Abstract
Ischemic cardiomyopathy is the most frequent type of heart disease, and it is a major cause of myocardial infarction (MI) and heart failure (HF), both of which require expensive medical treatment. Precise biomarkers and therapy targets must be developed to enhance improve diagnosis and treatment. In this study, the transcriptional profiles of 313 patients' left ventricle biopsies were obtained from the PubMed database, and functional genes that were significantly related to ischemic cardiomyopathy were screened using the Weighted Gene Co-Expression Network Analysis and protein-protein interaction (PPI) networks enrichment analysis. The rat myocardial infarction model was developed to validate these findings. Finally, the putative signature genes were blasted through the common Cardiovascular Disease Knowledge Portal to explore if they were associated with cardiovascular disorder. Three interferon stimulated genes (IFIT2, IFIT3 and IFI44L), as well as key pathways, have been identified as potential biomarkers and therapeutic targets for ischemic cardiomyopathy, and their alternations or mutations have been proven to be strongly linked to cardiac disorders. These novel signature genes could be utilized as bio-markers or potential therapeutic objectives in precise clinical diagnosis and treatment of ischemic cardiomyopathy.
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Affiliation(s)
- Cheng Chen
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (C.C.); (J.T.); (Z.H.); (W.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiao Tian
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (C.C.); (J.T.); (Z.H.); (W.X.)
- School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Zhicheng He
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (C.C.); (J.T.); (Z.H.); (W.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenyong Xiong
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (C.C.); (J.T.); (Z.H.); (W.X.)
| | - Yingying He
- School of Chemical Science & Technology, Yunnan University, Kunming 650091, China
| | - Shubai Liu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (C.C.); (J.T.); (Z.H.); (W.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
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6
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Wu D, Hu S, Hou Y, He Y, Liu S. Identification of potential novel biomarkers to differentiate malignant thyroid nodules with cytological indeterminate. BMC Cancer 2020; 20:199. [PMID: 32164602 PMCID: PMC7066786 DOI: 10.1186/s12885-020-6676-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 02/24/2020] [Indexed: 12/23/2022] Open
Abstract
Background The fine-needle aspiration (FNA) biopsy was broadly applied to clinical diagnostics evaluation for thyroid carcinomas nodule, while companioning with higher uncertainty rate (15~30%) to identify malignancy for cytological indeterminate cases. It is requirement to discover novel molecular biomarkers to differentiate malignant thyroid nodule more precise. Methods We employed weighted gene co-expression network analysis (WGCNA) to discover genes significantly associated with malignant histopathology for cytological indeterminate nodules. In addition, identified significantly genes were validated through another independently investigations of thyroid carcinomas patient’s samples via cBioportal and Geipa. The key function pathways of significant genes involving were blast through GenClip. Results Twenty-four signature genes were identified significantly related to thyroid nodules malignancy. Furthermore, five novel genes with missense mutation, FN1 (R534P), PROS1((K200I), (Q571K)), SCEL (T320S), SLC34A2(T688M) and TENM1 (S1131F), were highlighted as potential biomarkers to rule out nodules malignancy. It was identified that the key functional pathways involving in thyroid carcinomas. Conclusion These results will be helpful to better understand the mechanism of thyroid nodules malignant transformation and characterize the potentially biomarkers for thyroid carcinomas early diagnostics.
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Affiliation(s)
- Dandan Wu
- Institute of Life Sciences, Jiangsu University, 301 Xuefu Road, JinKou District, Zhenjiang, 212013, PR China
| | - Shudong Hu
- Department of Radiology, Affiliated Renmin Hospital of Jiangsu University, Zhenjiang, Jiangsu, PR China
| | - Yongzhong Hou
- Institute of Life Sciences, Jiangsu University, 301 Xuefu Road, JinKou District, Zhenjiang, 212013, PR China
| | - Yingying He
- Institute of Life Sciences, Jiangsu University, 301 Xuefu Road, JinKou District, Zhenjiang, 212013, PR China.
| | - Shubai Liu
- Institute of Life Sciences, Jiangsu University, 301 Xuefu Road, JinKou District, Zhenjiang, 212013, PR China.
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Sax SN, Gentry PR, Van Landingham C, Clewell HJ, Mundt KA. Extended Analysis and Evidence Integration of Chloroprene as a Human Carcinogen. RISK ANALYSIS : AN OFFICIAL PUBLICATION OF THE SOCIETY FOR RISK ANALYSIS 2020; 40:294-318. [PMID: 31524302 PMCID: PMC7028114 DOI: 10.1111/risa.13397] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 05/09/2019] [Accepted: 08/09/2019] [Indexed: 05/11/2023]
Abstract
β-Chloroprene is used in the production of polychloroprene, a synthetic rubber. In 2010, Environmental Protection Agency (EPA) published the Integrated Risk Information System "Toxicological Review of Chloroprene," concluding that chloroprene was "likely to be carcinogenic to humans." This was based on findings from a 1998 National Toxicology Program (NTP) study showing multiple tumors within and across animal species; results from occupational epidemiological studies; a proposed mutagenic mode of action; and structural similarities with 1,3-butadiene and vinyl chloride. Using mouse data from the NTP study and assuming a mutagenic mode of action, EPA calculated an inhalation unit risk (IUR) for chloroprene of 5 × 10-4 per µg/m3 . This is among the highest IURs for chemicals classified by IARC or EPA as known or probable human carcinogens and orders of magnitude higher than the IURs for carcinogens such as vinyl chloride, benzene, and 1,3-butadiene. Due to differences in pharmacokinetics, mice appear to be uniquely responsive to chloroprene exposure compared to other animals, including humans, which is consistent with the lack of evidence of carcinogenicity in robust occupational epidemiological studies. We evaluated and integrated all lines of evidence for chloroprene carcinogenicity to assess whether the 2010 EPA IUR could be scientifically substantiated. Due to clear interspecies differences in carcinogenic response to chloroprene, we applied a physiologically based pharmacokinetic model for chloroprene to calculate a species-specific internal dose (amount metabolized/gram of lung tissue) and derived an IUR that is over 100-fold lower than the 2010 EPA IUR. Therefore, we recommend that EPA's IUR be updated.
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Co-expression of key gene modules and pathways of human breast cancer cell lines. Biosci Rep 2019; 39:BSR20181925. [PMID: 31285391 PMCID: PMC6639467 DOI: 10.1042/bsr20181925] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 06/30/2019] [Accepted: 07/06/2019] [Indexed: 02/06/2023] Open
Abstract
Breast cancer (BC) is the most common leading cause of cancer-related death in women worldwide. Gene expression profiling analysis for human BCs has been studied previously. However, co-expression analysis for BC cell lines is still devoid to date. The aim of the study was to identify key pathways and hub genes that may serve as a biomarker for BC and uncover potential molecular mechanism using weighted correlation network analysis. We analyzed microarray data of BC cell lines (GSE 48213) listed in the Gene Expression Omnibus database. Gene co-expression networks were used to construct and explore the biological function in hub modules using the weighted correlation network analysis algorithm method. Meanwhile, Gene ontology and KEGG pathway analysis were performed using Cytoscape plug-in ClueGo. The network of the key module was also constructed using Cytoscape. A total of 5000 genes were selected, 28 modules of co-expressed genes were identified from the gene co–expression network, one of which was found to be significantly associated with a subtype of BC lines. Functional enrichment analysis revealed that the brown module was mainly involved in the pathway of the autophagy, spliceosome, and mitophagy, the black module was mainly enriched in the pathway of colorectal cancer and pancreatic cancer, and genes in midnightblue module played critical roles in ribosome and regulation of lipolysis in adipocytes pathway. Three hub genes CBR3, SF3B6, and RHPN1 may play an important role in the development and malignancy of the disease. The findings of the present study could improve our understanding of the molecular pathogenesis of breast cancer.
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Zhai Y, Chen Y, Li Q, Zhang L. Exploration of the hub genes and miRNAs in lung adenocarcinoma. Oncol Lett 2019; 18:1713-1722. [PMID: 31423238 PMCID: PMC6607253 DOI: 10.3892/ol.2019.10478] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 05/14/2019] [Indexed: 01/01/2023] Open
Abstract
In order to investigate the oncogenic mechanisms of lung adenocarcinoma (LUAD), hub genes can be identified by constructing co-expression networks, and the potential linkages between hub genes, transcription factors (TFs) and microRNAs (miRNAs/miRs) can be visualized and identified. In the present study, a total of 12 co-expressed modules were constructed, and 9 of these were significantly correlated with clinical traits in LUAD. The differentially expressed genes and differentially expressed miRNAs were determined, and the targets of differentially expressed miRNA were identified from the hub genes or TFs. The results of the present study demonstrated that 10 hub genes and 12 TFs are the predicted targets for the 5 and 8 differentially expressed miRNAs, respectively. Genes in pink and red modules, which have a high correlation with the clinical trait of days to death, are significantly enriched in 'nucleosome assembly' and 'microtubule-based process', respectively. These results indicated that miR-206, miR-137, miR-153, hub genes and enriched TFs in the pink and red modules exert a potentially pivotal function in the development of LUAD.
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Affiliation(s)
- Yuanyuan Zhai
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, Inner Mongolia 010021, P.R. China
| | - Yingli Chen
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, Inner Mongolia 010021, P.R. China
| | - Qianzhong Li
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, Inner Mongolia 010021, P.R. China.,The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, Inner Mongolia 010070, P.R. China
| | - Luqiang Zhang
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, Inner Mongolia 010021, P.R. China
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Alexander-Dann B, Pruteanu LL, Oerton E, Sharma N, Berindan-Neagoe I, Módos D, Bender A. Developments in toxicogenomics: understanding and predicting compound-induced toxicity from gene expression data. Mol Omics 2018; 14:218-236. [PMID: 29917034 PMCID: PMC6080592 DOI: 10.1039/c8mo00042e] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/08/2018] [Indexed: 12/12/2022]
Abstract
The toxicogenomics field aims to understand and predict toxicity by using 'omics' data in order to study systems-level responses to compound treatments. In recent years there has been a rapid increase in publicly available toxicological and 'omics' data, particularly gene expression data, and a corresponding development of methods for its analysis. In this review, we summarize recent progress relating to the analysis of RNA-Seq and microarray data, review relevant databases, and highlight recent applications of toxicogenomics data for understanding and predicting compound toxicity. These include the analysis of differentially expressed genes and their enrichment, signature matching, methods based on interaction networks, and the analysis of co-expression networks. In the future, these state-of-the-art methods will likely be combined with new technologies, such as whole human body models, to produce a comprehensive systems-level understanding of toxicity that reduces the necessity of in vivo toxicity assessment in animal models.
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Affiliation(s)
- Benjamin Alexander-Dann
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
| | - Lavinia Lorena Pruteanu
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
- Babeş-Bolyai University
, Institute for Doctoral Studies
,
1 Kogălniceanu Street
, Cluj-Napoca 400084
, Romania
- University of Medicine and Pharmacy “Iuliu Haţieganu”
, MedFuture Research Centre for Advanced Medicine
,
23 Marinescu Street/4-6 Pasteur Street
, Cluj-Napoca 400337
, Romania
| | - Erin Oerton
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
| | - Nitin Sharma
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
| | - Ioana Berindan-Neagoe
- University of Medicine and Pharmacy “Iuliu Haţieganu”
, MedFuture Research Centre for Advanced Medicine
,
23 Marinescu Street/4-6 Pasteur Street
, Cluj-Napoca 400337
, Romania
- University of Medicine and Pharmacy “Iuliu Haţieganu”
, Research Center for Functional Genomics
, Biomedicine and Translational Medicine
,
23 Marinescu Street
, Cluj-Napoca 400337
, Romania
- The Oncology Institute “Prof. Dr Ion Chiricuţă”
, Department of Functional Genomics and Experimental Pathology
,
34-36 Republicii Street
, Cluj-Napoca 400015
, Romania
| | - Dezső Módos
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
| | - Andreas Bender
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
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11
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Guo N, Zhang N, Yan L, Lian Z, Wang J, Lv F, Wang Y, Cao X. Weighted gene co‑expression network analysis in identification of key genes and networks for ischemic‑reperfusion remodeling myocardium. Mol Med Rep 2018; 18:1955-1962. [PMID: 29901145 PMCID: PMC6072198 DOI: 10.3892/mmr.2018.9161] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 03/07/2018] [Indexed: 11/14/2022] Open
Abstract
Acute myocardial infarction induces ventricular remodeling, which is implicated in dilated heart and heart failure. The pathogenical mechanism of myocardium remodeling remains to be elucidated. The aim of the present study was to identify key genes and networks for myocardium remodeling following ischemia-reperfusion (IR). First, the mRNA expression data from the National Center for Biotechnology Information database were downloaded to identify differences in mRNA expression of the IR heart at days 2 and 7. Then, weighted gene co-expression network analysis, hierarchical clustering, protein-protein interaction (PPI) network, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were used to identify key genes and networks for the heart remodeling process following IR. A total of 3,321 differentially expressed genes were identified during the heart remodeling process. A total of 6 modules were identified through gene co-expression network analysis. GO and KEGG analysis results suggested that each module represented a different biological function and was associated with different pathways. Finally, hub genes of each module were identified by PPI network construction. The present study revealed that heart remodeling following IR is a complicated process, involving extracellular matrix organization, neural development, apoptosis and energy metabolism. The dysregulated genes, including SRC proto-oncogene, non-receptor tyrosine kinase, discs large MAGUK scaffold protein 1, ATP citrate lyase, RAN, member RAS oncogene family, tumor protein p53, and polo like kinase 2, may be essential for heart remodeling following IR and may be used as potential targets for the inhibition of heart remodeling following acute myocardial infarction.
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Affiliation(s)
- Nan Guo
- Department of Cardiology, Cangzhou Central Hospital, Hebei Medical University, Cangzhou, Hebei 061000, P.R. China
| | - Nan Zhang
- Department of Cardiology, Cangzhou Central Hospital, Hebei Medical University, Cangzhou, Hebei 061000, P.R. China
| | - Liqiu Yan
- Department of Cardiology, Cangzhou Central Hospital, Hebei Medical University, Cangzhou, Hebei 061000, P.R. China
| | - Zheng Lian
- Department of Cardiology, Cangzhou Central Hospital, Hebei Medical University, Cangzhou, Hebei 061000, P.R. China
| | - Jiawang Wang
- Department of Cardiology, Cangzhou Central Hospital, Hebei Medical University, Cangzhou, Hebei 061000, P.R. China
| | - Fengfeng Lv
- Department of Cardiology, Cangzhou Central Hospital, Hebei Medical University, Cangzhou, Hebei 061000, P.R. China
| | - Yunfei Wang
- Department of Cardiology, Cangzhou Central Hospital, Hebei Medical University, Cangzhou, Hebei 061000, P.R. China
| | - Xufen Cao
- Department of Cardiology, Cangzhou Central Hospital, Hebei Medical University, Cangzhou, Hebei 061000, P.R. China
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Zhang J, Wang Y, Jiang X, Chan HC. Cystic fibrosis transmembrane conductance regulator-emerging regulator of cancer. Cell Mol Life Sci 2018; 75:1737-1756. [PMID: 29411041 PMCID: PMC11105598 DOI: 10.1007/s00018-018-2755-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 12/27/2017] [Accepted: 01/17/2018] [Indexed: 12/11/2022]
Abstract
Mutations of cystic fibrosis transmembrane conductance regulator (CFTR) cause cystic fibrosis, the most common life-limiting recessive genetic disease among Caucasians. CFTR mutations have also been linked to increased risk of various cancers but remained controversial for a long time. Recent studies have begun to reveal that CFTR is not merely an ion channel but also an important regulator of cancer development and progression with multiple signaling pathways identified. In this review, we will first present clinical findings showing the correlation of genetic mutations or aberrant expression of CFTR with cancer incidence in multiple cancers. We will then focus on the roles of CFTR in fundamental cellular processes including transformation, survival, proliferation, migration, invasion and epithelial-mesenchymal transition in cancer cells, highlighting the signaling pathways involved. Finally, the association of CFTR expression levels with patient prognosis, and the potential of CFTR as a cancer prognosis indicator in human malignancies will be discussed.
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Affiliation(s)
- Jieting Zhang
- Faculty of Medicine, Epithelial Cell Biology Research Center, School of Biomedical Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, People's Republic of China
- Key Laboratory for Regenerative Medicine of the Ministry of Education of China, Faculty of Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, People's Republic of China
- School of Biomedical Sciences Core Laboratory, Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, People's Republic of China
| | - Yan Wang
- Faculty of Medicine, Epithelial Cell Biology Research Center, School of Biomedical Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, People's Republic of China
- Key Laboratory for Regenerative Medicine of the Ministry of Education of China, Faculty of Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, People's Republic of China
- School of Biomedical Sciences Core Laboratory, Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, People's Republic of China
| | - Xiaohua Jiang
- Faculty of Medicine, Epithelial Cell Biology Research Center, School of Biomedical Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, People's Republic of China.
- Key Laboratory for Regenerative Medicine of the Ministry of Education of China, Faculty of Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, People's Republic of China.
- School of Biomedical Sciences Core Laboratory, Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, People's Republic of China.
| | - Hsiao Chang Chan
- Faculty of Medicine, Epithelial Cell Biology Research Center, School of Biomedical Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, People's Republic of China.
- Key Laboratory for Regenerative Medicine of the Ministry of Education of China, Faculty of Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, People's Republic of China.
- School of Biomedical Sciences Core Laboratory, Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, People's Republic of China.
- Sichuan University-The Chinese University of Hong Kong Joint Laboratory for Reproductive Medicine, West China Second University Hospital, Chengdu, People's Republic of China.
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13
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Wang W, Jiang W, Hou L, Duan H, Wu Y, Xu C, Tan Q, Li S, Zhang D. Weighted gene co-expression network analysis of expression data of monozygotic twins identifies specific modules and hub genes related to BMI. BMC Genomics 2017; 18:872. [PMID: 29132311 PMCID: PMC5683603 DOI: 10.1186/s12864-017-4257-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 11/01/2017] [Indexed: 02/08/2023] Open
Abstract
Background The therapeutic management of obesity is challenging, hence further elucidating the underlying mechanisms of obesity development and identifying new diagnostic biomarkers and therapeutic targets are urgent and necessary. Here, we performed differential gene expression analysis and weighted gene co-expression network analysis (WGCNA) to identify significant genes and specific modules related to BMI based on gene expression profile data of 7 discordant monozygotic twins. Results In the differential gene expression analysis, it appeared that 32 differentially expressed genes (DEGs) were with a trend of up-regulation in twins with higher BMI when compared to their siblings. Categories of positive regulation of nitric-oxide synthase biosynthetic process, positive regulation of NF-kappa B import into nucleus, and peroxidase activity were significantly enriched within GO database and NF-kappa B signaling pathway within KEGG database. DEGs of NAMPT, TLR9, PTGS2, HBD, and PCSK1N might be associated with obesity. In the WGCNA, among the total 20 distinct co-expression modules identified, coral1 module (68 genes) had the strongest positive correlation with BMI (r = 0.56, P = 0.04) and disease status (r = 0.56, P = 0.04). Categories of positive regulation of phospholipase activity, high-density lipoprotein particle clearance, chylomicron remnant clearance, reverse cholesterol transport, intermediate-density lipoprotein particle, chylomicron, low-density lipoprotein particle, very-low-density lipoprotein particle, voltage-gated potassium channel complex, cholesterol transporter activity, and neuropeptide hormone activity were significantly enriched within GO database for this module. And alcoholism and cell adhesion molecules pathways were significantly enriched within KEGG database. Several hub genes, such as GAL, ASB9, NPPB, TBX2, IL17C, APOE, ABCG4, and APOC2 were also identified. The module eigengene of saddlebrown module (212 genes) was also significantly correlated with BMI (r = 0.56, P = 0.04), and hub genes of KCNN1 and AQP10 were differentially expressed. Conclusion We identified significant genes and specific modules potentially related to BMI based on the gene expression profile data of monozygotic twins. The findings may help further elucidate the underlying mechanisms of obesity development and provide novel insights to research potential gene biomarkers and signaling pathways for obesity treatment. Further analysis and validation of the findings reported here are important and necessary when more sample size is acquired. Electronic supplementary material The online version of this article (10.1186/s12864-017-4257-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Weijing Wang
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, No. 38 Dengzhou Road, Shibei District, Qingdao, 266021, Shandong Province, People's Republic of China
| | - Wenjie Jiang
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, No. 38 Dengzhou Road, Shibei District, Qingdao, 266021, Shandong Province, People's Republic of China
| | - Lin Hou
- Department of Biochemistry, Medical College, Qingdao University, No. 38 Dengzhou Road, Shibei District, Qingdao, 266021, Shandong Province, People's Republic of China
| | - Haiping Duan
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, No. 38 Dengzhou Road, Shibei District, Qingdao, 266021, Shandong Province, People's Republic of China.,Qingdao Municipal Center for Disease Control and Prevention, No. 175 Shandong Road, Shibei District, Qingdao, 266033, Shandong Province, People's Republic of China
| | - Yili Wu
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, No. 38 Dengzhou Road, Shibei District, Qingdao, 266021, Shandong Province, People's Republic of China
| | - Chunsheng Xu
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, No. 38 Dengzhou Road, Shibei District, Qingdao, 266021, Shandong Province, People's Republic of China.,Qingdao Municipal Center for Disease Control and Prevention, No. 175 Shandong Road, Shibei District, Qingdao, 266033, Shandong Province, People's Republic of China.,Qingdao Institute of Preventive Medicine, No. 175 Shandong Road, Shibei District, Qingdao, 266033, Shandong Province, People's Republic of China
| | - Qihua Tan
- Epidemiology, Biostatistics and Bio-demography, Institute of Public Health, University of Southern Denmark, DK-5000, Odense C, Denmark.,Human Genetics, Institute of Clinical Research, University of Southern Denmark, DK-5000, Odense C, Denmark
| | - Shuxia Li
- Human Genetics, Institute of Clinical Research, University of Southern Denmark, DK-5000, Odense C, Denmark
| | - Dongfeng Zhang
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, No. 38 Dengzhou Road, Shibei District, Qingdao, 266021, Shandong Province, People's Republic of China.
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14
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Sun M, Sun T, He Z, Xiong B. Identification of two novel biomarkers of rectal carcinoma progression and prognosis via co-expression network analysis. Oncotarget 2017; 8:69594-69609. [PMID: 29050227 PMCID: PMC5642502 DOI: 10.18632/oncotarget.18646] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 05/22/2017] [Indexed: 12/16/2022] Open
Abstract
mRNA expression profiles provide important insights on a diversity of biological processes involved in rectal carcinoma (RC). Our aim was to comprehensively map complex interactions between the mRNA expression patterns and the clinical traits of RC. We employed the integrated analysis of five microarray datasets and The Cancer Genome Atlas rectal adenocarcinoma database to identify 2118 consensual differentially expressed genes (DEGs) in RC and adjacent normal tissue samples, and then applied weighted gene co-expression network analysis to parse DEGs and eight clinical traits in 66 eligible RC samples. A total of 16 co-expressed gene modules were identified. The green-yellow and salmon modules were most appropriate to the pathological stage (R = 0.36) and the overall survival (HR =13.534, P = 0.014), respectively. A diagnostic model of the five pathological stage hub genes (SCG3, SYP, CDK5R2, AP3B2, and RUNDC3A) provided a powerful classification accuracy between localized RC and non-localized RC. We also found increased Secretogranin III (SCG3) expression with higher pathological stage and poorer prognosis in the test and validation set. The increased Homer scaffolding protein 2 (HOMER2) expression with the favorable survival prediction efficiency significantly correlated with the markedly reduced overall survival of RC patients and the higher pathological stage during the test and validation set. Our findings indicate that the SCG3 and HOMER2 mRNA levels should be further evaluated as predictors of pathological stage and survival in patients with RC.
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Affiliation(s)
- Min Sun
- Department of Oncology, Zhongnan Hospital of Wuhan University, Hubei Key Laboratory of Tumor Biological Behaviors & Hubei Cancer Clinical Study Center, Wuhan 430071, P.R. China
| | - Taojiao Sun
- Department of Stomatology, Zhongnan Hospital of Wuhan University, Wuhan 430071, P.R. China
| | - Zhongshi He
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430071, P.R. China
| | - Bin Xiong
- Department of Oncology, Zhongnan Hospital of Wuhan University, Hubei Key Laboratory of Tumor Biological Behaviors & Hubei Cancer Clinical Study Center, Wuhan 430071, P.R. China
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Vella D, Zoppis I, Mauri G, Mauri P, Di Silvestre D. From protein-protein interactions to protein co-expression networks: a new perspective to evaluate large-scale proteomic data. EURASIP JOURNAL ON BIOINFORMATICS & SYSTEMS BIOLOGY 2017; 2017:6. [PMID: 28477207 PMCID: PMC5359264 DOI: 10.1186/s13637-017-0059-z] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 03/09/2017] [Indexed: 12/19/2022]
Abstract
The reductionist approach of dissecting biological systems into their constituents has been successful in the first stage of the molecular biology to elucidate the chemical basis of several biological processes. This knowledge helped biologists to understand the complexity of the biological systems evidencing that most biological functions do not arise from individual molecules; thus, realizing that the emergent properties of the biological systems cannot be explained or be predicted by investigating individual molecules without taking into consideration their relations. Thanks to the improvement of the current -omics technologies and the increasing understanding of the molecular relationships, even more studies are evaluating the biological systems through approaches based on graph theory. Genomic and proteomic data are often combined with protein-protein interaction (PPI) networks whose structure is routinely analyzed by algorithms and tools to characterize hubs/bottlenecks and topological, functional, and disease modules. On the other hand, co-expression networks represent a complementary procedure that give the opportunity to evaluate at system level including organisms that lack information on PPIs. Based on these premises, we introduce the reader to the PPI and to the co-expression networks, including aspects of reconstruction and analysis. In particular, the new idea to evaluate large-scale proteomic data by means of co-expression networks will be discussed presenting some examples of application. Their use to infer biological knowledge will be shown, and a special attention will be devoted to the topological and module analysis.
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Affiliation(s)
- Danila Vella
- Institute for Biomedical Technologies - National Research Council (ITB-CNR), 93 Fratelli Cervi, Segrate, Milan, Italy.,Department of Computer Science, Systems and Communication DiSCo, University of Milano-Bicocca, 336 Viale Sarca, Milan, Italy
| | - Italo Zoppis
- Department of Computer Science, Systems and Communication DiSCo, University of Milano-Bicocca, 336 Viale Sarca, Milan, Italy
| | - Giancarlo Mauri
- Department of Computer Science, Systems and Communication DiSCo, University of Milano-Bicocca, 336 Viale Sarca, Milan, Italy
| | - Pierluigi Mauri
- Institute for Biomedical Technologies - National Research Council (ITB-CNR), 93 Fratelli Cervi, Segrate, Milan, Italy
| | - Dario Di Silvestre
- Institute for Biomedical Technologies - National Research Council (ITB-CNR), 93 Fratelli Cervi, Segrate, Milan, Italy.
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Tian F, Zhao J, Fan X, Kang Z. Weighted gene co-expression network analysis in identification of metastasis-related genes of lung squamous cell carcinoma based on the Cancer Genome Atlas database. J Thorac Dis 2017; 9:42-53. [PMID: 28203405 PMCID: PMC5303106 DOI: 10.21037/jtd.2017.01.04] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 10/20/2016] [Indexed: 11/06/2022]
Abstract
BACKGROUND Lung squamous cell carcinoma (lung SCC) is a common type of malignancy. Its pathogenesis mechanism of tumor development is unclear. The aim of this study was to identify key genes for diagnosis biomarkers in lung SCC metastasis. METHODS We searched and downloaded mRNA expression data and clinical data from The Cancer Genome Atlas (TCGA) database to identify differences in mRNA expression of primary tumor tissues from lung SCC with and without metastasis. Gene co-expression network analysis, protein-protein interaction (PPI) network, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and quantitative real-time polymerase chain reactions (qRT-PCR) were used to explore the biological functions of the identified dysregulated genes. RESULTS Four hundred and eighty-two differentially expressed genes (DEGs) were identified between lung SCC with and without metastasis. Nineteen modules were identified in lung SCC through weighted gene co-expression network analysis (WGCNA). Twenty-three DEGs and 26 DEGs were significantly enriched in the respective pink and black module. KEGG pathway analysis displayed that 26 DEGs in the black module were significantly enriched in bile secretion pathway. Forty-nine DEGs in the two gene co-expression module were used to construct PPI network. CFTR in the black module was the hub protein, had the connectivity with 182 genes. The results of qRT-PCR displayed that FIGF, SFTPD, DYNLRB2 were significantly down-regulated in the tumor samples of lung SCC with metastasis and CFTR, SCGB3A2, SSTR1, SCTR, ROPN1L had the down-regulation tendency in lung SCC with metastasis compared to lung SCC without metastasis. CONCLUSIONS The dysregulated genes including CFTR, SCTR and FIGF might be involved in the pathology of lung SCC metastasis and could be used as potential diagnosis biomarkers or therapeutic targets for lung SCC.
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Affiliation(s)
- Feng Tian
- Department of Respiratory Medicine, Linyi People’s Hospital, Linyi 276000, China
| | - Jinlong Zhao
- Department of Thoracic Surgery, Linyi People’s Hospital, Linyi 276000, China
| | - Xinlei Fan
- Department of Internal Medicine, Shandong Medical College, Linyi 276000, China
| | - Zhenxing Kang
- Department of Respiratory Medicine, The Third People’s Hospital of Linyi, Linyi 276000, China
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