1
|
Abstract
Cancer is a genetic disease in which multiple genes are perturbed. Thus, information about the regulatory relationships between genes is necessary for the identification of biomarkers and therapeutic targets. In this review, methods for inference of gene regulatory networks (GRNs) from transcriptomics data that are used in cancer research are introduced. The methods are classified into three categories according to the analysis model. The first category includes methods that use pair-wise measures between genes, including correlation coefficient and mutual information. The second category includes methods that determine the genetic regulatory relationship using multivariate measures, which consider the expression profiles of all genes concurrently. The third category includes methods using supervised and integrative approaches. The supervised approach estimates the regulatory relationship using a supervised learning method that constructs a regression or classification model for predicting whether there is a regulatory relationship between genes with input data of gene expression profiles and class labels of prior biological knowledge. The integrative method is an expansion of the supervised method and uses more data and biological knowledge for predicting the regulatory relationship. Furthermore, simulation and experimental validation of the estimated GRNs are also discussed in this review. This review identified that most GRN inference methods are not specific for cancer transcriptome data, and such methods are required for better understanding of cancer pathophysiology. In addition, more systematic methods for validation of the estimated GRNs need to be developed in the context of cancer biology.
Collapse
|
2
|
Li YK, Hsu HM, Lin MC, Chang CW, Chu CM, Chang YJ, Yu JC, Chen CT, Jian CE, Sun CA, Chen KH, Kuo MH, Cheng CS, Chang YT, Wu YS, Wu HY, Yang YT, Lin C, Lin HC, Hu JM, Chang YT. Genetic co-expression networks contribute to creating predictive model and exploring novel biomarkers for the prognosis of breast cancer. Sci Rep 2021; 11:7268. [PMID: 33790307 PMCID: PMC8012617 DOI: 10.1038/s41598-021-84995-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 02/02/2021] [Indexed: 12/14/2022] Open
Abstract
Genetic co-expression network (GCN) analysis augments the understanding of breast cancer (BC). We aimed to propose GCN-based modeling for BC relapse-free survival (RFS) prediction and to discover novel biomarkers. We used GCN and Cox proportional hazard regression to create various prediction models using mRNA microarray of 920 tumors and conduct external validation using independent data of 1056 tumors. GCNs of 34 identified candidate genes were plotted in various sizes. Compared to the reference model, the genetic predictors selected from bigger GCNs composed better prediction models. The prediction accuracy and AUC of 3 ~ 15-year RFS are 71.0-81.4% and 74.6-78% respectively (rfm, ACC 63.2-65.5%, AUC 61.9-74.9%). The hazard ratios of risk scores of developing relapse ranged from 1.89 ~ 3.32 (p < 10-8) over all models under the control of the node status. External validation showed the consistent finding. We found top 12 co-expressed genes are relative new or novel biomarkers that have not been explored in BC prognosis or other cancers until this decade. GCN-based modeling creates better prediction models and facilitates novel genes exploration on BC prognosis.
Collapse
Affiliation(s)
- Yuan-Kuei Li
- Division of Colorectal Surgery, Department of Surgery, Taoyuan Armed Forces General Hospital, Taoyuan, Taiwan.,Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, Taiwan
| | - Huan-Ming Hsu
- Division of General Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan.,Department of Surgery, Songshan Branch of Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan.,Department of Otolaryngology-Head and Neck Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, 11490, Taiwan
| | - Meng-Chiung Lin
- Division of Gastroenterology, Department of Medicine, Taichung Armed Forces General Hospital, Taichung, Taiwan
| | - Chi-Wen Chang
- School of Nursing, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan.,Department of Nursing, Chang Gung Memorial Hospital, Tao-Yuan, Taiwan
| | - Chi-Ming Chu
- Division of Medical Informatics, Department of Epidemiology, School of Public Health, National Defense Medical Center, Taipei, Taiwan.,Big Data Research Center, College of Medicine, Fu-Jen Catholic University, New Taipei City, Taiwan.,Department of Public Health, College of Medicine, Fu-Jen Catholic University, New Taipei City, Taiwan.,Department of Public Health, China Medical University, Taichung City, Taiwan.,Department of Healthcare Administration and Medical Informatics College of Health Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yu-Jia Chang
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Cell Physiology and Molecular Image Research Center, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Jyh-Cherng Yu
- Division of General Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Chien-Ting Chen
- Division of Medical Informatics, Department of Epidemiology, School of Public Health, National Defense Medical Center, Taipei, Taiwan
| | - Chen-En Jian
- Division of Medical Informatics, Department of Epidemiology, School of Public Health, National Defense Medical Center, Taipei, Taiwan
| | - Chien-An Sun
- Big Data Research Center, College of Medicine, Fu-Jen Catholic University, New Taipei City, Taiwan
| | - Kang-Hua Chen
- School of Nursing, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Nursing, Chang Gung Memorial Hospital, Tao-Yuan, Taiwan
| | - Ming-Hao Kuo
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan
| | - Chia-Shiang Cheng
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
| | - Ya-Ting Chang
- Division of Medical Informatics, Department of Epidemiology, School of Public Health, National Defense Medical Center, Taipei, Taiwan
| | - Yi-Syuan Wu
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
| | - Hao-Yi Wu
- Division of Medical Informatics, Department of Epidemiology, School of Public Health, National Defense Medical Center, Taipei, Taiwan
| | - Ya-Ting Yang
- Division of Medical Informatics, Department of Epidemiology, School of Public Health, National Defense Medical Center, Taipei, Taiwan
| | - Chen Lin
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, Taiwan.,Center for Biotechnology and Biomedical Engineering, National Central University, Taoyuan, Taiwan
| | - Hung-Che Lin
- Department of Otolaryngology-Head and Neck Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, 11490, Taiwan.,Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan.,Hualien Armed Forces General Hospital, Xincheng, Hualien, 97144, Taiwan
| | - Je-Ming Hu
- Department of Otolaryngology-Head and Neck Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, 11490, Taiwan.,Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan.,Division of Colorectal Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei City, Taiwan.,School of Medicine, National Defense Medical Center, Taipei City, Taiwan
| | - Yu-Tien Chang
- Division of Medical Informatics, Department of Epidemiology, School of Public Health, National Defense Medical Center, Taipei, Taiwan. .,Big Data Research Center, College of Medicine, Fu-Jen Catholic University, New Taipei City, Taiwan.
| |
Collapse
|
3
|
Ibragimova MK, Tsyganov MM, Slonimskaya EM, Litviakov NV. Aberrations of the number of copies (CNA) in the genome of luminal B breast tumor. BULLETIN OF SIBERIAN MEDICINE 2020. [DOI: 10.20538/1682-0363-2020-3-22-28] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- M. K. Ibragimova
- Саnсеr Rеsеаrсh Institute, Tomsk National Research Medical Center of Russian Academy of Sciences
| | - M. M. Tsyganov
- Саnсеr Rеsеаrсh Institute, Tomsk National Research Medical Center of Russian Academy of Sciences
| | | | - N. V. Litviakov
- Саnсеr Rеsеаrсh Institute, Tomsk National Research Medical Center of Russian Academy of Sciences
| |
Collapse
|
4
|
Khalyuzova MV, Litviakov NV, Takhauov RM, Isubakova DS, Usova TV, Bronikovskaya EV, Takhauova LR, Karpov AB. Delayed Changes in the Frequency of Unstable Chromosomal Aberrations and the CNA-Genetic Landscape of Blood Leukocytes in People Exposed to Long-Term Occupational Irradiation. BIOL BULL+ 2020. [DOI: 10.1134/s1062359019110049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
5
|
Zhao Y, Wang Y, Zhu F, Zhang J, Ma X, Zhang D. Gene expression profiling revealed MCM3 to be a better marker than Ki67 in prognosis of invasive ductal breast carcinoma patients. Clin Exp Med 2020; 20:249-259. [PMID: 31980982 DOI: 10.1007/s10238-019-00604-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 12/30/2019] [Indexed: 12/11/2022]
Abstract
Invasive ductal carcinoma (IDC) is the most common breast cancer. Our study used gene microarray data to select differentially expressed genes between normal and IDC mammary tissues. From these, we selected genes related to the proliferation of tumor cells and compared their prognostic value with known biomarker Ki67 for IDC. Analysis of publicly available Gene Expression Omnibus (GEO) data revealed 24 differentially expressed genes (DEGs) in normal and 31 DEGS in IDC tissues that were used for further analyses. Gene chip analysis software was used to identify DEGs. DEG profiles were confirmed using quantitative PCR (qPCR). DEG functions where shown to be related to cell proliferation. We confirmed MCM3 expression using immunohistochemical staining in 45 IDC patients. The relationship between MCM3 expression and survival was investigated using Kaplan-Meier survival curves and Cox proportional hazard regression models. A total of 1307 differentially expressed genes were identified between IDC and normal tissues, which were enriched in 32 Gene Ontology (GO) terms and 9 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. qPCR demonstrated that both COL1A1 and MCM3 were significantly up-regulated in IDC tissues, of which only MCM3 was related to cell proliferation. Ki67 is closely associated with the tumor grade, ER status, PR status and HER2 status, while MCM3 was shown to relate to tumor size, lymph node, and PR status. There was significant association between survival and MCM3, but not for Ki67. High MCM3 expression demonstrated statistically significant associations with poor prognosis in IDC patients. Findings from the gene microarray data analysis confirmed that MCM3 is associated with the response to cell proliferation. MCM3 represents a better proliferation marker than Ki67 making it a valuable prognostic tool that is independent of ER and HER2 status.
Collapse
Affiliation(s)
- Yue Zhao
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
- Department of Urology, Xiang'an Hospital of Xiamen University, Xiamen, China
| | - Yimin Wang
- Department of Surgery, Harbin Medical University, Harbin, China
| | - Fudi Zhu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jiayu Zhang
- Department of Surgery, the Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Harbin, 150086, Heilongjiang, China
| | - Xiao Ma
- Department of Surgery, Jinan Maternal and Child Health Care Hospital, 2 Jianguo Xiaojing Third Road, Jinan, 250000, Shandong, China.
| | - Dongwei Zhang
- Department of Surgery, the Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Harbin, 150086, Heilongjiang, China.
| |
Collapse
|
6
|
Wang T, Zhang J, Huang K. Generalized gene co-expression analysis via subspace clustering using low-rank representation. BMC Bioinformatics 2019; 20:196. [PMID: 31074376 PMCID: PMC6509871 DOI: 10.1186/s12859-019-2733-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Background Gene Co-expression Network Analysis (GCNA) helps identify gene modules with potential biological functions and has become a popular method in bioinformatics and biomedical research. However, most current GCNA algorithms use correlation to build gene co-expression networks and identify modules with highly correlated genes. There is a need to look beyond correlation and identify gene modules using other similarity measures for finding novel biologically meaningful modules. Results We propose a new generalized gene co-expression analysis algorithm via subspace clustering that can identify biologically meaningful gene co-expression modules with genes that are not all highly correlated. We use low-rank representation to construct gene co-expression networks and local maximal quasi-clique merger to identify gene co-expression modules. We applied our method on three large microarray datasets and a single-cell RNA sequencing dataset. We demonstrate that our method can identify gene modules with different biological functions than current GCNA methods and find gene modules with prognostic values. Conclusions The presented method takes advantage of subspace clustering to generate gene co-expression networks rather than using correlation as the similarity measure between genes. Our generalized GCNA method can provide new insights from gene expression datasets and serve as a complement to current GCNA algorithms.
Collapse
Affiliation(s)
- Tongxin Wang
- Department of Computer Science, Indiana University Bloomington, Bloomington, 47408, IN, USA
| | - Jie Zhang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, 46202, IN, USA
| | - Kun Huang
- Department of Medicine, Indiana University School of Medicine, Indianapolis, 46202, IN, USA. .,Regenstrief Institute, Indianapolis, 46202, IN, USA.
| |
Collapse
|
7
|
In-Silico Integration Approach to Identify a Key miRNA Regulating a Gene Network in Aggressive Prostate Cancer. Int J Mol Sci 2018; 19:ijms19030910. [PMID: 29562723 PMCID: PMC5877771 DOI: 10.3390/ijms19030910] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 03/15/2018] [Accepted: 03/16/2018] [Indexed: 12/12/2022] Open
Abstract
Like other cancer diseases, prostate cancer (PC) is caused by the accumulation of genetic alterations in the cells that drives malignant growth. These alterations are revealed by gene profiling and copy number alteration (CNA) analysis. Moreover, recent evidence suggests that also microRNAs have an important role in PC development. Despite efforts to profile PC, the alterations (gene, CNA, and miRNA) and biological processes that correlate with disease development and progression remain partially elusive. Many gene signatures proposed as diagnostic or prognostic tools in cancer poorly overlap. The identification of co-expressed genes, that are functionally related, can identify a core network of genes associated with PC with a better reproducibility. By combining different approaches, including the integration of mRNA expression profiles, CNAs, and miRNA expression levels, we identified a gene signature of four genes overlapping with other published gene signatures and able to distinguish, in silico, high Gleason-scored PC from normal human tissue, which was further enriched to 19 genes by gene co-expression analysis. From the analysis of miRNAs possibly regulating this network, we found that hsa-miR-153 was highly connected to the genes in the network. Our results identify a four-gene signature with diagnostic and prognostic value in PC and suggest an interesting gene network that could play a key regulatory role in PC development and progression. Furthermore, hsa-miR-153, controlling this network, could be a potential biomarker for theranostics in high Gleason-scored PC.
Collapse
|
8
|
Litviakov NV, Cherdyntseva NV, Tsyganov MM, Slonimskaya EM, Ibragimova MK, Kazantseva PV, Kzhyshkowska J, Choinzonov EL. Deletions of multidrug resistance gene loci in breast cancer leads to the down-regulation of its expression and predict tumor response to neoadjuvant chemotherapy. Oncotarget 2016; 7:7829-41. [PMID: 26799285 PMCID: PMC4884957 DOI: 10.18632/oncotarget.6953] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 12/05/2015] [Indexed: 01/10/2023] Open
Abstract
Neoadjuvant chemotherapy (NAC) is intensively used for the treatment of primary breast cancer. In our previous studies, we reported that clinical tumor response to NAC is associated with the change of multidrug resistance (MDR) gene expression in tumors after chemotherapy. In this study we performed a combined analysis of MDR gene locus deletions in tumor DNA, MDR gene expression and clinical response to NAC in 73 BC patients. Copy number variations (CNVs) in biopsy specimens were tested using high-density microarray platform CytoScanTM HD Array (Affymetrix, USA). 75%–100% persons having deletions of MDR gene loci demonstrated the down-regulation of MDR gene expression. Expression of MDR genes was 2–8 times lower in patients with deletion than in patients having no deletion only in post-NAC tumors samples but not in tumor tissue before chemotherapy. All patients with deletions of ABCB1 ABCB 3 ABCC5 gene loci – 7q21.1, 6p21.32, 3q27 correspondingly, and most patients having deletions in ABCC1 (16p13.1), ABCC2 (10q24), ABCG1 (21q22.3), ABCG2 (4q22.1), responded favorably to NAC. The analysis of all CNVs, including both amplification and deletion showed that the frequency of 13q14.2 deletion was 85% among patients bearing tumor with the deletion at least in one MDR gene locus versus 9% in patients with no deletions. Differences in the frequency of 13q14.2 deletions between the two groups were statistically significant (p = 2.03 ×10−11, Fisher test, Bonferroni-adjusted p = 1.73 × 10−8). In conclusion, our study for the first time demonstrates that deletion MDR gene loci can be used as predictive marker for tumor response to NAC.
Collapse
Affiliation(s)
- Nikolai V Litviakov
- Laboratory of Oncovirology, Tomsk Cancer Research Institute, Tomsk, Russian Federation.,Laboratory of Translational Cell and Molecular Biomedicine, National Research Tomsk State University, Tomsk, Russian Federation
| | - Nadezhda V Cherdyntseva
- Laboratory of Translational Cell and Molecular Biomedicine, National Research Tomsk State University, Tomsk, Russian Federation.,Laboratory of Molecular Oncology and Immunology, Tomsk Cancer Research Institute, Tomsk, Russian Federation
| | - Matvey M Tsyganov
- Laboratory of Oncovirology, Tomsk Cancer Research Institute, Tomsk, Russian Federation.,Laboratory of Translational Cell and Molecular Biomedicine, National Research Tomsk State University, Tomsk, Russian Federation
| | - Elena M Slonimskaya
- Department of General Oncology, Tomsk Cancer Research Institute, Tomsk, Russian Federation
| | - Marina K Ibragimova
- Laboratory of Oncovirology, Tomsk Cancer Research Institute, Tomsk, Russian Federation
| | - Polina V Kazantseva
- Department of General Oncology, Tomsk Cancer Research Institute, Tomsk, Russian Federation
| | - Julia Kzhyshkowska
- Laboratory of Translational Cell and Molecular Biomedicine, National Research Tomsk State University, Tomsk, Russian Federation.,Department of Innate Immunity and Tolerance, Institute of Transfusion Medicine and Immunology, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Eugeniy L Choinzonov
- Department of Head and Neck Cancer, Tomsk Cancer Research Institute, Tomsk, Russian Federation
| |
Collapse
|
9
|
Jinawath N, Bunbanjerdsuk S, Chayanupatkul M, Ngamphaiboon N, Asavapanumas N, Svasti J, Charoensawan V. Bridging the gap between clinicians and systems biologists: from network biology to translational biomedical research. J Transl Med 2016; 14:324. [PMID: 27876057 PMCID: PMC5120462 DOI: 10.1186/s12967-016-1078-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 11/08/2016] [Indexed: 01/22/2023] Open
Abstract
With the wealth of data accumulated from completely sequenced genomes and other high-throughput experiments, global studies of biological systems, by simultaneously investigating multiple biological entities (e.g. genes, transcripts, proteins), has become a routine. Network representation is frequently used to capture the presence of these molecules as well as their relationship. Network biology has been widely used in molecular biology and genetics, where several network properties have been shown to be functionally important. Here, we discuss how such methodology can be useful to translational biomedical research, where scientists traditionally focus on one or a small set of genes, diseases, and drug candidates at any one time. We first give an overview of network representation frequently used in biology: what nodes and edges represent, and review its application in preclinical research to date. Using cancer as an example, we review how network biology can facilitate system-wide approaches to identify targeted small molecule inhibitors. These types of inhibitors have the potential to be more specific, resulting in high efficacy treatments with less side effects, compared to the conventional treatments such as chemotherapy. Global analysis may provide better insight into the overall picture of human diseases, as well as identify previously overlooked problems, leading to rapid advances in medicine. From the clinicians’ point of view, it is necessary to bridge the gap between theoretical network biology and practical biomedical research, in order to improve the diagnosis, prevention, and treatment of the world’s major diseases.
Collapse
Affiliation(s)
- Natini Jinawath
- Integrative Computational BioScience (ICBS) Center, Mahidol University, Nakhon Pathom, Thailand.,Program in Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Sacarin Bunbanjerdsuk
- Program in Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Maneerat Chayanupatkul
- Department of Physiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Division of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Nuttapong Ngamphaiboon
- Medical Oncology Unit, Department of Medicine Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Nithi Asavapanumas
- Department of Physiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Jisnuson Svasti
- Integrative Computational BioScience (ICBS) Center, Mahidol University, Nakhon Pathom, Thailand.,Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand.,Laboratory of Biochemistry, Chulabhorn Research Institute, Bangkok, Thailand
| | - Varodom Charoensawan
- Integrative Computational BioScience (ICBS) Center, Mahidol University, Nakhon Pathom, Thailand. .,Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand. .,Systems Biology of Diseases Research Unit, Faculty of Science, Mahidol University, Bangkok, Thailand.
| |
Collapse
|
10
|
Han Z, Zhang J, Sun G, Liu G, Huang K. A matrix rank based concordance index for evaluating and detecting conditional specific co-expressed gene modules. BMC Genomics 2016; 17 Suppl 7:519. [PMID: 27556416 PMCID: PMC5001231 DOI: 10.1186/s12864-016-2912-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Gene co-expression network analysis (GCNA) is widely adopted in bioinformatics and biomedical research with applications such as gene function prediction, protein-protein interaction inference, disease markers identification, and copy number variance discovery. Currently there is a lack of rigorous analysis on the mathematical condition for which the co-expressed gene module should satisfy. METHODS In this paper, we present a linear algebraic based Centralized Concordance Index (CCI) for evaluating the concordance of co-expressed gene modules from gene co-expression network analysis. The CCI can be used to evaluate the performance for co-expression network analysis algorithms as well as for detecting condition specific co-expression modules. We applied CCI in detecting lung tumor specific gene modules. RESULTS AND DISCUSSION Simulation showed that CCI is a robust indicator for evaluating the concordance of a group of co-expressed genes. The application to lung cancer datasets revealed interesting potential tumor specific genetic alterations including CNVs and even hints for gene-fusion. Deeper analysis required for understanding the molecular mechanisms of all such condition specific co-expression relationships. CONCLUSION The CCI can be used to evaluate the performance for co-expression network analysis algorithms as well as for detecting condition specific co-expression modules. It is shown to be more robust to outliers and interfering modules than density based on Pearson correlation coefficients.
Collapse
Affiliation(s)
- Zhi Han
- College of Computer and Control Engineering, Nankai University, Tianjin, China
- College of Software, Nankai University, Tianjin, China
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH USA
| | - Jie Zhang
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH USA
- The CCC Biomedical Informatics Shared Resource, The Ohio State University, Columbus, OH USA
| | - Guoyuan Sun
- College of Computer and Control Engineering, Nankai University, Tianjin, China
- College of Software, Nankai University, Tianjin, China
| | - Gang Liu
- College of Computer and Control Engineering, Nankai University, Tianjin, China
- College of Software, Nankai University, Tianjin, China
| | - Kun Huang
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH USA
- The CCC Biomedical Informatics Shared Resource, The Ohio State University, Columbus, OH USA
| |
Collapse
|
11
|
Abdelmotelb AM, Rose-Zerilli MJ, Barton SJ, Holgate ST, Walls AF, Holloway JW. Alpha-tryptase gene variation is associated with levels of circulating IgE and lung function in asthma. Clin Exp Allergy 2015; 44:822-30. [PMID: 24372627 PMCID: PMC4282335 DOI: 10.1111/cea.12259] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 11/20/2013] [Accepted: 11/27/2013] [Indexed: 12/31/2022]
Abstract
Background Tryptase, a major secretory product of human mast cells has been implicated as a key mediator of allergic inflammation. Genetic variation in the tryptases is extensive, and α-tryptase, an allelic variant of the more extensively studied β-tryptase, is absent in substantial numbers of the general population. The degree to which α-tryptase expression may be associated with asthma has not been studied. We have investigated the α-tryptase gene copy number variation and its potential associations with phenotypes of asthma. Objectives Caucasian families (n = 341) with at least two asthmatic siblings (n = 1350) were genotyped for the α-tryptase alleles, using high-resolution melting assays. Standards for the possible α-/β-tryptase ratios were constructed by cloning α-and β-tryptase PCR products to generate artificial templates. Association analysis of asthma affection status and related phenotypes [total and allergen-specific serum IgE, bronchial hyperresponsiveness to methacholine, forced expiratory volume in 1s (FEV1) and atopy and asthma severity scores] was undertaken using family-based association tests (FBAT). Results Four consistent melting patterns for the α-tryptase genotype were identified with alleles carrying null, one or two copies of the α-tryptase allele. Possessing one copy of α-tryptase was significantly associated with lower serum levels of total and dust mite-specific IgE levels and higher FEV1 measurements, while two copies were related to higher serum concentrations of total and dust mite-specific IgE and greater atopy severity scores. Conclusions and Clinical Relevance Associations of α-tryptase copy number with serum IgE levels, atopy scores and bronchial function may reflect roles for tryptases in regulating IgE production and other processes in asthma.
Collapse
Affiliation(s)
- A M Abdelmotelb
- Clinical and Experimental Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK; Faculty of Medicine, Tanta University, Tanta, Egypt
| | | | | | | | | | | |
Collapse
|
12
|
Li L, Lian B, Li C, Li W, Li J, Zhang Y, He X, Li Y, Xie L. Integrative analysis of transcriptional regulatory network and copy number variation in intrahepatic cholangiocarcinoma. PLoS One 2014; 9:e98653. [PMID: 24897108 PMCID: PMC4045758 DOI: 10.1371/journal.pone.0098653] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Accepted: 05/06/2014] [Indexed: 01/02/2023] Open
Abstract
Background Transcriptional regulatory network (TRN) is used to study conditional regulatory relationships between transcriptional factors and genes. However few studies have tried to integrate genomic variation information such as copy number variation (CNV) with TRN to find causal disturbances in a network. Intrahepatic cholangiocarcinoma (ICC) is the second most common hepatic carcinoma with high malignancy and poor prognosis. Research about ICC is relatively limited comparing to hepatocellular carcinoma, and there are no approved gene therapeutic targets yet. Method We first constructed TRN of ICC (ICC-TRN) using forward-and-reverse combined engineering method, and then integrated copy number variation information with ICC-TRN to select CNV-related modules and constructed CNV-ICC-TRN. We also integrated CNV-ICC-TRN with KEGG signaling pathways to investigate how CNV genes disturb signaling pathways. At last, unsupervised clustering method was applied to classify samples into distinct classes. Result We obtained CNV-ICC-TRN containing 33 modules which were enriched in ICC-related signaling pathways. Integrated analysis of the regulatory network and signaling pathways illustrated that CNV might interrupt signaling through locating on either genomic sites of nodes or regulators of nodes in a signaling pathway. In the end, expression profiles of nodes in CNV-ICC-TRN were used to cluster the ICC patients into two robust groups with distinct biological function features. Conclusion Our work represents a primary effort to construct TRN in ICC, also a primary effort to try to identify key transcriptional modules based on their involvement of genetic variations shown by gene copy number variations (CNV). This kind of approach may bring the traditional studies of TRN based only on expression data one step further to genetic disturbance. Such kind of approach can easily be extended to other disease samples with appropriate data.
Collapse
Affiliation(s)
- Ling Li
- School of Life Sciences and Technology, Tongji University, Shanghai, P.R.China
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, P.R.China
| | - Baofeng Lian
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, P.R.China
- School of Life Sciences and Technology, Shanghai Jiaotong University, Shanghai, P.R.China
| | - Chao Li
- Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P.R.China
| | - Wei Li
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, P.R.China
| | - Jing Li
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, P.R.China
| | - Yuannv Zhang
- Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P.R.China
| | - Xianghuo He
- Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P.R.China
| | - Yixue Li
- School of Life Sciences and Technology, Tongji University, Shanghai, P.R.China
- School of Life Sciences and Technology, Shanghai Jiaotong University, Shanghai, P.R.China
- Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P.R.China
- * E-mail: (LX); (YL)
| | - Lu Xie
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, P.R.China
- * E-mail: (LX); (YL)
| |
Collapse
|
13
|
Wolf DM, Lenburg ME, Yau C, Boudreau A, van ‘t Veer LJ. Gene co-expression modules as clinically relevant hallmarks of breast cancer diversity. PLoS One 2014; 9:e88309. [PMID: 24516633 PMCID: PMC3917875 DOI: 10.1371/journal.pone.0088309] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 01/06/2014] [Indexed: 12/25/2022] Open
Abstract
Co-expression modules are groups of genes with highly correlated expression patterns. In cancer, differences in module activity potentially represent the heterogeneity of phenotypes important in carcinogenesis, progression, or treatment response. To find gene expression modules active in breast cancer subpopulations, we assembled 72 breast cancer-related gene expression datasets containing ∼5,700 samples altogether. Per dataset, we identified genes with bimodal expression and used mixture-model clustering to ultimately define 11 modules of genes that are consistently co-regulated across multiple datasets. Functionally, these modules reflected estrogen signaling, development/differentiation, immune signaling, histone modification, ERBB2 signaling, the extracellular matrix (ECM) and stroma, and cell proliferation. The Tcell/Bcell immune modules appeared tumor-extrinsic, with coherent expression in tumors but not cell lines; whereas most other modules, interferon and ECM included, appeared intrinsic. Only four of the eleven modules were represented in the PAM50 intrinsic subtype classifier and other well-established prognostic signatures; although the immune modules were highly correlated to previously published immune signatures. As expected, the proliferation module was highly associated with decreased recurrence-free survival (RFS). Interestingly, the immune modules appeared associated with RFS even after adjustment for receptor subtype and proliferation; and in a multivariate analysis, the combination of Tcell/Bcell immune module down-regulation and proliferation module upregulation strongly associated with decreased RFS. Immune modules are unusual in that their upregulation is associated with a good prognosis without chemotherapy and a good response to chemotherapy, suggesting the paradox of high immune patients who respond to chemotherapy but would do well without it. Other findings concern the ECM/stromal modules, which despite common themes were associated with different sites of metastasis, possibly relating to the “seed and soil” hypothesis of cancer dissemination. Overall, co-expression modules provide a high-level functional view of breast cancer that complements the “cancer hallmarks” and may form the basis for improved predictors and treatments.
Collapse
Affiliation(s)
- Denise M. Wolf
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
| | - Marc E. Lenburg
- Department of Medicine, Section of Computational Biomedicine, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Christina Yau
- Department of Surgery, University of California San Francisco, San Francisco, California, United States of America
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Aaron Boudreau
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Laura J. van ‘t Veer
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America
| |
Collapse
|
14
|
Essaghir A, Demoulin JB. A minimal connected network of transcription factors regulated in human tumors and its application to the quest for universal cancer biomarkers. PLoS One 2012; 7:e39666. [PMID: 22761861 PMCID: PMC3382591 DOI: 10.1371/journal.pone.0039666] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Accepted: 05/25/2012] [Indexed: 12/19/2022] Open
Abstract
A universal cancer biomarker candidate for diagnosis is supposed to distinguish, within a broad range of tumors, between healthy and diseased patients. Recently published studies have explored the universal usefulness of some biomarkers in human tumors. In this study, we present an integrative approach to search for potential common cancer biomarkers. Using the TFactS web-tool with a catalogue of experimentally established gene regulations, we could predict transcription factors (TFs) regulated in 305 different human cancer cell lines covering a large panel of tumor types. We also identified chromosomal regions having significant copy number variation (CNV) in these cell lines. Within the scope of TFactS catalogue, 88 TFs whose activity status were explained by their gene expressions and CNVs were identified. Their minimal connected network (MCN) of protein-protein interactions forms a significant module within the human curated TF proteome. Functional analysis of the proteins included in this MCN revealed enrichment in cancer pathways as well as inflammation. The ten most central proteins in MCN are TFs that trans-regulate 157 known genes encoding secreted and transmembrane proteins. In publicly available collections of gene expression data from 8,525 patient tissues, 86 genes were differentially regulated in cancer compared to inflammatory diseases and controls. From TCGA cancer gene expression data sets, 50 genes were significantly associated to patient survival in at least one tumor type. Enrichment analysis shows that these genes mechanistically interact in common cancer pathways. Among these cancer biomarker candidates, TFRC, MET and VEGFA are commonly amplified genes in tumors and their encoded proteins stained positive in more than 80% of malignancies from public databases. They are linked to angiogenesis and hypoxia, which are common in cancer. They could be interesting for further investigations in cancer diagnostic strategies.
Collapse
Affiliation(s)
- Ahmed Essaghir
- de Duve institute, Université Catholique de Louvain, Brussels, Belgium.
| | | |
Collapse
|