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Ye X, Shi T, Cui Y, Sakurai T. Interactive gene identification for cancer subtyping based on multi-omics clustering. Methods 2023; 211:61-67. [PMID: 36804215 DOI: 10.1016/j.ymeth.2023.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/06/2023] [Accepted: 02/12/2023] [Indexed: 02/17/2023] Open
Abstract
Recent advances in multi-omics databases offer the opportunity to explore complex systems of cancers across hierarchical biological levels. Some methods have been proposed to identify the genes that play a vital role in disease development by integrating multi-omics. However, the existing methods identify the related genes separately, neglecting the gene interactions that are related to the multigenic disease. In this study, we develop a learning framework to identify the interactive genes based on multi-omics data including gene expression. Firstly, we integrate different omics based on their similarities and apply spectral clustering for cancer subtype identification. Then, a gene co-expression network is construct for each cancer subtype. Finally, we detect the interactive genes in the co-expression network by learning the dense subgraphs based on the L1 prosperities of eigenvectors in the modularity matrix. We apply the proposed learning framework on a multi-omics cancer dataset to identify the interactive genes for each cancer subtype. The detected genes are examined by DAVID and KEGG tools for systematic gene ontology enrichment analysis. The analysis results show that the detected genes have relationships to cancer development and the genes in different cancer subtypes are related to different biological processes and pathways, which are expected to yield important references for understanding tumor heterogeneity and improving patient survival.
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Affiliation(s)
- Xiucai Ye
- Department of Computer Science, University of Tsukuba, Tsukuba 3058577, Japan.
| | - Tianyi Shi
- Tsukuba Life Science Innovation Program, University of Tsukuba, Tsukuba 3058577, Japan
| | - Yaxuan Cui
- Department of Computer Science, University of Tsukuba, Tsukuba 3058577, Japan
| | - Tetsuya Sakurai
- Department of Computer Science, University of Tsukuba, Tsukuba 3058577, Japan; Tsukuba Life Science Innovation Program, University of Tsukuba, Tsukuba 3058577, Japan
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2
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Dallari C, Innocenti R, Lenci E, Trabocchi A, Pavone FS, Credi C. Design and Synthesis of Novel Raman Reporters for Bioorthogonal SERS Nanoprobes Engineering. Int J Mol Sci 2022; 23:ijms23105573. [PMID: 35628383 PMCID: PMC9144405 DOI: 10.3390/ijms23105573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 11/16/2022] Open
Abstract
Surface-enhanced Raman spectroscopy (SERS) exploiting Raman reporter-labeled nanoparticles (RR@NPs) represents a powerful tool for the improvement of optical bio-assays due to RRs’ narrow peaks, SERS high sensitivity, and potential for multiplexing. In the present work, starting from low-cost and highly available raw materials such as cysteamine and substituted benzoic acids, novel bioorthogonal RRs, characterized by strong signal (103 counts with FWHM < 15 cm−1) in the biological Raman-silent region (>2000 cm−1), RRs are synthesized by implementing a versatile, modular, and straightforward method with high yields and requiring three steps lasting 18 h, thus overcoming the limitations of current reported procedures. The resulting RRs’ chemical structure has SH-pendant groups exploited for covalent conjugation to high anisotropic gold-NPs. RR@NPs constructs work as SERS nanoprobes demonstrating high colloidal stability while retaining NPs’ physical and vibrational properties, with a limit of detection down to 60 pM. RR@NPs constructs expose carboxylic moieties for further self-assembling of biomolecules (such as antibodies), conferring tagging capabilities to the SERS nanoprobes even in heterogeneous samples, as demonstrated with in vitro experiments by transmembrane proteins tagging in cell cultures. Finally, thanks to their non-overlapping spectra, we envision and preliminary prove the possibility of exploiting RR@NPs constructs simultaneously, aiming at improving current SERS-based multiplexing bioassays.
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Affiliation(s)
- Caterina Dallari
- European Laboratory for Non-Linear Spectroscopy, University of Florence, 50019 Sesto Fiorentino, Italy; (R.I.); (F.S.P.); (C.C.)
- Department of Physics, University of Florence, 50019 Sesto Fiorentino, Italy
- Correspondence:
| | - Riccardo Innocenti
- European Laboratory for Non-Linear Spectroscopy, University of Florence, 50019 Sesto Fiorentino, Italy; (R.I.); (F.S.P.); (C.C.)
| | - Elena Lenci
- Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy; (E.L.); (A.T.)
| | - Andrea Trabocchi
- Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy; (E.L.); (A.T.)
| | - Francesco Saverio Pavone
- European Laboratory for Non-Linear Spectroscopy, University of Florence, 50019 Sesto Fiorentino, Italy; (R.I.); (F.S.P.); (C.C.)
- Department of Physics, University of Florence, 50019 Sesto Fiorentino, Italy
- National Institute of Optics, National Research Council, 50019 Sesto Fiorentino, Italy
| | - Caterina Credi
- European Laboratory for Non-Linear Spectroscopy, University of Florence, 50019 Sesto Fiorentino, Italy; (R.I.); (F.S.P.); (C.C.)
- National Institute of Optics, National Research Council, 50019 Sesto Fiorentino, Italy
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3
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Yang Y, Tian S, Qiu Y, Zhao P, Zou Q. MDICC: novel method for multi-omics data integration and cancer subtype identification. Brief Bioinform 2022; 23:6569541. [PMID: 35437603 DOI: 10.1093/bib/bbac132] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/11/2022] [Accepted: 03/19/2022] [Indexed: 12/12/2022] Open
Abstract
Each type of cancer usually has several subtypes with distinct clinical implications, and therefore the discovery of cancer subtypes is an important and urgent task in disease diagnosis and therapy. Using single-omics data to predict cancer subtypes is difficult because genomes are dysregulated and complicated by multiple molecular mechanisms, and therefore linking cancer genomes to cancer phenotypes is not an easy task. Using multi-omics data to effectively predict cancer subtypes is an area of much interest; however, integrating multi-omics data is challenging. Here, we propose a novel method of multi-omics data integration for clustering to identify cancer subtypes (MDICC) that integrates new affinity matrix and network fusion methods. Our experimental results show the effectiveness and generalization of the proposed MDICC model in identifying cancer subtypes, and its performance was better than those of currently available state-of-the-art clustering methods. Furthermore, the survival analysis demonstrates that MDICC delivered comparable or even better results than many typical integrative methods.
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Affiliation(s)
- Ying Yang
- College of Mathematics and Statistics, Shenzhen University, 518000, China
| | - Sha Tian
- College of Mathematics and Statistics, Shenzhen University, 518000, China
| | - Yushan Qiu
- College of Mathematics and Statistics, Shenzhen University, 518000, China
| | - Pu Zhao
- College of Life and Health Sciences, Northeastern University, Shenyang, 110169, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, 610056, China
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4
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Carvalho RF, do Canto LM, Cury SS, Frøstrup Hansen T, Jensen LH, Rogatto SR. Drug Repositioning Based on the Reversal of Gene Expression Signatures Identifies TOP2A as a Therapeutic Target for Rectal Cancer. Cancers (Basel) 2021; 13:5492. [PMID: 34771654 PMCID: PMC8583090 DOI: 10.3390/cancers13215492] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/21/2021] [Accepted: 10/28/2021] [Indexed: 12/12/2022] Open
Abstract
Rectal cancer is a common disease with high mortality rates and limited therapeutic options. Here we combined the gene expression signatures of rectal cancer patients with the reverse drug-induced gene-expression profiles to identify drug repositioning candidates for cancer therapy. Among the predicted repurposable drugs, topoisomerase II inhibitors (doxorubicin, teniposide, idarubicin, mitoxantrone, and epirubicin) presented a high potential to reverse rectal cancer gene expression signatures. We showed that these drugs effectively reduced the growth of colorectal cancer cell lines closely representing rectal cancer signatures. We also found a clear correlation between topoisomerase 2A (TOP2A) gene copy number or expression levels with the sensitivity to topoisomerase II inhibitors. Furthermore, CRISPR-Cas9 and shRNA screenings confirmed that loss-of-function of the TOP2A has the highest efficacy in reducing cellular proliferation. Finally, we observed significant TOP2A copy number gains and increased expression in independent cohorts of rectal cancer patients. These findings can be translated into clinical practice to evaluate TOP2A status for targeted and personalized therapies based on topoisomerase II inhibitors in rectal cancer patients.
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Affiliation(s)
- Robson Francisco Carvalho
- Department of Clinical Genetics, University Hospital of Southern Denmark, 7100 Vejle, Denmark;
- Institute of Regional Health Research, University of Southern Denmark, 5230 Odense, Denmark
- Department of Functional and Structural Biology—Institute of Bioscience, São Paulo State University (UNESP), Botucatu 18618-689, Brazil;
| | - Luisa Matos do Canto
- Department of Clinical Genetics, University Hospital of Southern Denmark, 7100 Vejle, Denmark;
- Institute of Regional Health Research, University of Southern Denmark, 5230 Odense, Denmark
| | - Sarah Santiloni Cury
- Department of Functional and Structural Biology—Institute of Bioscience, São Paulo State University (UNESP), Botucatu 18618-689, Brazil;
| | - Torben Frøstrup Hansen
- Department of Oncology, University Hospital of Southern Denmark, 7100 Vejle, Denmark; (T.F.H.); (L.H.J.)
- Danish Colorectal Cancer Center South, 7100 Vejle, Denmark
| | - Lars Henrik Jensen
- Department of Oncology, University Hospital of Southern Denmark, 7100 Vejle, Denmark; (T.F.H.); (L.H.J.)
- Danish Colorectal Cancer Center South, 7100 Vejle, Denmark
| | - Silvia Regina Rogatto
- Department of Clinical Genetics, University Hospital of Southern Denmark, 7100 Vejle, Denmark;
- Institute of Regional Health Research, University of Southern Denmark, 5230 Odense, Denmark
- Danish Colorectal Cancer Center South, 7100 Vejle, Denmark
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Yang B, Xin TT, Pang SM, Wang M, Wang YJ. Deep Subspace Mutual Learning For Cancer Subtypes Prediction. Bioinformatics 2021; 37:3715-3722. [PMID: 34478501 DOI: 10.1093/bioinformatics/btab625] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 07/26/2021] [Accepted: 09/01/2021] [Indexed: 12/11/2022] Open
Abstract
MOTIVATION Precise prediction of cancer subtypes is of significant importance in cancer diagnosis and treatment. Disease etiology is complicated existing at different omics levels, hence integrative analysis provides a very effective way to improve our understanding of cancer. RESULTS We propose a novel computational framework, named Deep Subspace Mutual Learning (DSML). DSML has the capability to simultaneously learn the subspace structures in each available omics data and in overall multi-omics data by adopting deep neural networks, which thereby facilitates the subtypes prediction via clustering on multi-level, single level, and partial level omics data. Extensive experiments are performed in five different cancers on three levels of omics data from The Cancer Genome Atlas. The experimental analysis demonstrates that DSML delivers comparable or even better results than many state-of-the-art integrative methods. AVAILABILITY An implementation and documentation of the DSML is publicly available at https://github.com/polytechnicXTT/Deep-Subspace-Mutual-Learning.git. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Bo Yang
- School of Computer Science, Xi'an Polytechnic University, Xi'an, 710048, China
| | - Ting-Ting Xin
- School of Computer Science, Xi'an Polytechnic University, Xi'an, 710048, China
| | - Shan-Min Pang
- School of Software Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Meng Wang
- School of Computer Science, Xi'an Polytechnic University, Xi'an, 710048, China
| | - Yi-Jie Wang
- School of Software Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
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6
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Choe EK, Lee S, Kim SY, Shivakumar M, Park KJ, Chai YJ, Kim D. Prognostic Effect of Inflammatory Genes on Stage I-III Colorectal Cancer-Integrative Analysis of TCGA Data. Cancers (Basel) 2021; 13:cancers13040751. [PMID: 33670198 PMCID: PMC7916934 DOI: 10.3390/cancers13040751] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/05/2021] [Accepted: 02/07/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Research interest in the role of inflammation in the progression and prognosis of colorectal cancer (CRC) is growing. In this study, we evaluated the expression and DNA methylation levels of inflammation-related genes in CRC tissues using the TCGA-COREAD dataset by integratively combining multi-omics features using machine learning. Statistical analysis was additionally performed to allow for interpretable, understandable, and clinically practical results. An integrative model combining expression, methylation, and clinical features had the highest performance. In multivariate analysis, the methylation levels of CEP250, RAB21, and TNPO3 were significantly associated with overall survival. Our study results implicate the importance of integrating expression and methylation information along with clinical information in the prediction of survival. CEP250, RAB21, and TNPO3 in the prediction model might have a crucial role in CRC prognosis and further improve our understanding of potential mechanisms linking inflammatory reactions and CRC progression. Abstract Background inflammatory status indicators have been reported as prognostic biomarkers of colorectal cancer (CRC). However, since inflammatory interactions with the colon involve various modes of action, the biological mechanism linking inflammation and CRC prognosis has not been fully elucidated. We comprehensively evaluated the predictive roles of the expression and methylation levels of inflammation-related genes for CRC prognosis and their pathophysiological associations. Method. An integrative analysis of 247 patients with stage I-III CRC from The Cancer Genome Atlas was conducted. Lasso-penalized Cox proportional hazards regression (Lasso-Cox) and statistical Cox proportional hazard regression (CPH) were used for the analysis. Results. Models to predict overall survival were designed with respective combinations of clinical variables, including age, sex, stage, gene expression, and methylation. An integrative model combining expression, methylation, and clinical features performed better (median C-index = 0.756) than the model with clinical features alone (median C-index = 0.726). Based on multivariate CPH with features from the best model, the methylation levels of CEP250, RAB21, and TNPO3 were significantly associated with overall survival. They did not share any biological process in functional networks. The 5-year survival rate was 29.8% in the low methylation group of CEP250 and 79.1% in the high methylation group (p < 0.001). Conclusion. Our study results implicate the importance of integrating expression and methylation information along with clinical information in the prediction of survival. CEP250, RAB21, and TNPO3 in the prediction model might have a crucial role in CRC prognosis and further improve our understanding of potential mechanisms linking inflammatory reactions and CRC progression.
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Affiliation(s)
- Eun Kyung Choe
- Department of Surgery, Seoul National University Hospital Healthcare System Gangnam Center, Seoul 06236, Korea;
- Department of Biostatistics, Epidemiology & Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6116, USA; (S.Y.K.); (M.S.)
- Department of Surgery, Seoul National University College of Medicine, Seoul 03080, Korea;
| | - Sangwoo Lee
- Department of Future Convergence, Cyber University of Korea, Seoul 03051, Korea;
| | - So Yeon Kim
- Department of Biostatistics, Epidemiology & Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6116, USA; (S.Y.K.); (M.S.)
- Department of Software and Computer Engineering, Ajou University, Suwon 16499, Korea
| | - Manu Shivakumar
- Department of Biostatistics, Epidemiology & Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6116, USA; (S.Y.K.); (M.S.)
| | - Kyu Joo Park
- Department of Surgery, Seoul National University College of Medicine, Seoul 03080, Korea;
| | - Young Jun Chai
- Department of Surgery, Seoul Metropolitan Government—Seoul National University Boramae Medical Center, Seoul 07061, Korea;
| | - Dokyoon Kim
- Department of Biostatistics, Epidemiology & Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6116, USA; (S.Y.K.); (M.S.)
- Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104-6116, USA
- Correspondence: ; Tel.: +1-215-573-5336
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Yang B, Zhang Y, Pang S, Shang X, Zhao X, Han M. Integrating Multi-Omic Data With Deep Subspace Fusion Clustering for Cancer Subtype Prediction. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:216-226. [PMID: 31689204 DOI: 10.1109/tcbb.2019.2951413] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
One type of cancer usually consists of several subtypes with distinct clinical implications, thus the cancer subtype prediction is an important task in disease diagnosis and therapy. Utilizing one type of data from molecular layers in biological system to predict is difficult to bridge the cancer genome to cancer phenotypes, since the genome is neither simple nor independent but rather complicated and dysregulated from multiple molecular mechanisms. Similarity Network Fusion (SNF) has been recently proposed to integrate diverse omics data for improving the understanding of tumorigenesis. SNF adopts Euclidean distance to measure the similarity between patients, which shows some limitations. In this article, we introduce a novel prediction technique as an extension of SNF, namely Deep Subspace Fusion Clustering (DSFC). DSFC utilizes auto-encoder and data self-expressiveness approaches to guide a deep subspace model, which can achieve effective expression of discriminative similarity between patients. As a result, the dissimilarity between inter-cluster is delivered and enhanced compactness of intra-cluster is achieved at the same time. The validity of DSFC is examined by extensive simulations over six different cancer through three levels omics data. The survival analysis demonstrates that DSFC delivers comparable or even better results than many state-of-the-art integrative methods.
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8
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Popova AA, Dietrich S, Huber W, Reischl M, Peravali R, Levkin PA. Miniaturized Drug Sensitivity and Resistance Test on Patient-Derived Cells Using Droplet-Microarray. SLAS Technol 2020; 26:274-286. [PMID: 32791934 DOI: 10.1177/2472630320934432] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Testing the sensitivity of patient-derived tumor cells ex vivo can potentially help determining the appropriate treatment for each patient and spot the development of resistance to a given therapy. The number of cells obtainable from a biopsy is, however, often insufficient for performing ex vivo tests in conventional microtiter plates. Here, we introduce a novel Droplet-Microarray platform based on a hydrophilic-superhydrophobic patterned surface that enables screenings using only 100 cells and 30 picomoles of a drug per individual nanoliter-sized droplet. We demonstrate that the dose-response of as few as 100 primary patient-derived chronic lymphocytic leukemia (CLL) cells to anticancer compounds on the Droplet-Microarray platform resembles the dose-response obtained in 384-well plates requiring 20,000 tumor cells per experiment. The extremely miniaturized Droplet-Microarray platform thus carries great potential for ex vivo drug sensitivity and resistance tests on patient-derived tumor cells and potentially for implementing such tests in medical practice of precision medicine.
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Affiliation(s)
- Anna A Popova
- Karlsruhe Institute of Technology, Institute of Chemical and Biological Systems, Eggenstein-Leopoldshafen, Germany
| | - Sascha Dietrich
- National Center for Tumor Diseases, Heidelberg, Germany.,Medizinische Klinik V, University Hospital of Heidelberg, Heidelberg, Germany.,European Molecular Biology Laboratories (EMBL), Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Wolfgang Huber
- European Molecular Biology Laboratories (EMBL), Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Markus Reischl
- Karlsruhe Institute of Technology, Institute for Automation and Applied Informatics, Eggenstein-Leopoldshafen, Germany
| | - Ravindra Peravali
- Karlsruhe Institute of Technology, Institute of Chemical and Biological Systems, Eggenstein-Leopoldshafen, Germany
| | - Pavel A Levkin
- Karlsruhe Institute of Technology, Institute of Chemical and Biological Systems, Eggenstein-Leopoldshafen, Germany.,Karlsruhe Institute of Technology, Institute of Organic Chemistry, Karlsruhe, Germany
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Popova AA, Levkin PA. Precision Medicine in Oncology: In Vitro Drug Sensitivity and Resistance Test (DSRT) for Selection of Personalized Anticancer Therapy. ADVANCED THERAPEUTICS 2020. [DOI: 10.1002/adtp.201900100] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Anna A. Popova
- Karlsruhe Institute of TechnologyInstitute of Toxicology and Genetics Hermann‐von‐Helmholtz‐Platz 1 76344 Eggenstein‐Leopoldshafen Germany
| | - Pavel A. Levkin
- Karlsruhe Institute of TechnologyInstitute of Toxicology and Genetics Hermann‐von‐Helmholtz‐Platz 1 76344 Eggenstein‐Leopoldshafen Germany
- Karlsruhe Institute of TechnologyInstitute of Organic Chemistry Fritz‐Haber Weg 6 76131 Karlsruhe Germany
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10
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Ullah MA, Sarkar B, Akter F. Prediction of biomarker signatures and therapeutic agents from blood sample against Pancreatic Ductal Adenocarcinoma (PDAC): A network-based study. INFORMATICS IN MEDICINE UNLOCKED 2020. [DOI: 10.1016/j.imu.2020.100346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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11
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Zhang A, Li A, He J, Wang M. LSCDFS-MKL: A multiple kernel based method for lung squamous cell carcinomas disease-free survival prediction with pathological and genomic data. J Biomed Inform 2019; 94:103194. [PMID: 31048071 DOI: 10.1016/j.jbi.2019.103194] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 04/14/2019] [Accepted: 04/29/2019] [Indexed: 11/18/2022]
Abstract
Lung squamous cell carcinoma (SCC) is a fatal disease in both male and female, for which current treatments are inadequate. Surgical resection is regarded as the cornerstone of treatment for patients with lung SCC, but even for the same stage patients, the wide spectrum of disease-free survival (DFS) times exits. Therefore, how to improve the DFS prediction performance of lung SCC becomes one major research area. In this study, we proposed a novel method called LSCDFS-MKL, which was on the basis of multiple kernel learning to predict DFS of lung SCC. In LSCDFS-MKL, we first efficiently integrated pathological images and genomic data (copy number aberration, gene expression, protein expression) from lung SCC. The results of LSCDFS-MKL between different types of data show that the features extracted from pathological images play an important role in DFS prediction of lung SCC. Then we compared our method LSCDFS-MKL with other existing methods and performance analysis indicates that LSCDFS-MKL has a significantly better performance than other prediction methods. After that, we applied the proposed method on different stage stratums and the performance demonstrates that LSCDFS-MKL remains efficient in DFS prediction of lung SCC patients. Finally, we performed LSCDFS-MKL on an independent validation dataset and the accuracy of DFS prediction achieves 100%, which is promising.
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Affiliation(s)
- Aoshuang Zhang
- School of Information Science and Technology, University of Science and Technology of China, 443 Huangshan Road, Hefei 230027, China.
| | - Ao Li
- School of Information Science and Technology, University of Science and Technology of China, 443 Huangshan Road, Hefei 230027, China; Research Centers for Biomedical Engineering, University of Science and Technology of China, 443 Huangshan Road, Hefei 230027, China.
| | - Jie He
- Department of Pathology, The First Affiliated Hospital of University of Science and Technology of China, Hefei 230031, China; Department of Pathology, Anhui Provincial Cancer Hospital, Hefei 230031, China.
| | - Minghui Wang
- School of Information Science and Technology, University of Science and Technology of China, 443 Huangshan Road, Hefei 230027, China; Research Centers for Biomedical Engineering, University of Science and Technology of China, 443 Huangshan Road, Hefei 230027, China.
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12
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Li M, Wu J, Ma M, Feng Z, Mi Z, Rong P, Liu D. Alkyne- and Nitrile-Anchored Gold Nanoparticles for Multiplex SERS Imaging of Biomarkers in Cancer Cells and Tissues. Nanotheranostics 2019; 3:113-119. [PMID: 30899639 PMCID: PMC6427935 DOI: 10.7150/ntno.30924] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 02/05/2019] [Indexed: 01/02/2023] Open
Abstract
Surface-enhanced Raman spectroscopy (SERS) has proven a powerful tool for multiplex detection and imaging due to its narrow peak width and high sensitivity. However, conventional SERS reporters are limited to thiolated compounds, which have limitations such as chemical stability and spectral overlap. Here, we used alkyne- and nitrile-bearing molecules to directly fabricate a set of SERS tags for multiplex imaging. The alkyne and nitrile groups act as both the anchoring points to interact with gold nanoparticle (AuNP) surfaces and the reporters exhibiting strong and nonoverlapping signals in the cellular Raman-silent region. The SERS tags were subsequently modified with different antibodies for multicolor imaging of cancer cells and human breast cancer tissues. The reporters have a simple and readily accessible structure, hence providing new opportunities to prepare SERS nanoprobes
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Affiliation(s)
- Mingmin Li
- College of Chemistry, Research Center for Analytical Sciences, State Key Laboratory of Medicinal Chemical Biology, and Tianjin Key Laboratory of Molecular Recognition and Biosensing, Nankai University, Tianjin 300071, China
| | - Jianzhen Wu
- Department of Radiology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Mengtian Ma
- Department of Radiology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Zhichao Feng
- Department of Radiology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Ze Mi
- Department of Radiology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Pengfei Rong
- Department of Radiology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Dingbin Liu
- College of Chemistry, Research Center for Analytical Sciences, State Key Laboratory of Medicinal Chemical Biology, and Tianjin Key Laboratory of Molecular Recognition and Biosensing, Nankai University, Tianjin 300071, China
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13
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El-Manzalawy Y, Hsieh TY, Shivakumar M, Kim D, Honavar V. Min-redundancy and max-relevance multi-view feature selection for predicting ovarian cancer survival using multi-omics data. BMC Med Genomics 2018; 11:71. [PMID: 30255801 PMCID: PMC6157248 DOI: 10.1186/s12920-018-0388-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Large-scale collaborative precision medicine initiatives (e.g., The Cancer Genome Atlas (TCGA)) are yielding rich multi-omics data. Integrative analyses of the resulting multi-omics data, such as somatic mutation, copy number alteration (CNA), DNA methylation, miRNA, gene expression, and protein expression, offer tantalizing possibilities for realizing the promise and potential of precision medicine in cancer prevention, diagnosis, and treatment by substantially improving our understanding of underlying mechanisms as well as the discovery of novel biomarkers for different types of cancers. However, such analyses present a number of challenges, including heterogeneity, and high-dimensionality of omics data. METHODS We propose a novel framework for multi-omics data integration using multi-view feature selection. We introduce a novel multi-view feature selection algorithm, MRMR-mv, an adaptation of the well-known Min-Redundancy and Maximum-Relevance (MRMR) single-view feature selection algorithm to the multi-view setting. RESULTS We report results of experiments using an ovarian cancer multi-omics dataset derived from the TCGA database on the task of predicting ovarian cancer survival. Our results suggest that multi-view models outperform both view-specific models (i.e., models trained and tested using a single type of omics data) and models based on two baseline data fusion methods. CONCLUSIONS Our results demonstrate the potential of multi-view feature selection in integrative analyses and predictive modeling from multi-omics data.
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Affiliation(s)
- Yasser El-Manzalawy
- Artificial Intelligence Research Laboratory, College of Information Sciences and Technology, Pennsylvania State University, University Park, PA, 16802, USA.,The Center for Big Data Analytics and Discovery Informatics, Pennsylvania State University, University Park, PA, 16802, USA.,The Clinical and Translational Sciences Institute, Pennsylvania State University, University Park, PA, 16802, USA
| | - Tsung-Yu Hsieh
- Artificial Intelligence Research Laboratory, College of Information Sciences and Technology, Pennsylvania State University, University Park, PA, 16802, USA.,School of Electrical Engineering and Computer Science, Pennsylvania State University, University Park, PA, 16802, USA.,The Center for Big Data Analytics and Discovery Informatics, Pennsylvania State University, University Park, PA, 16802, USA
| | - Manu Shivakumar
- Biomedical and Translational Informatics Institute, Geisinger Health System, Danville, PA, USA
| | - Dokyoon Kim
- Biomedical and Translational Informatics Institute, Geisinger Health System, Danville, PA, USA. .,The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA.
| | - Vasant Honavar
- Artificial Intelligence Research Laboratory, College of Information Sciences and Technology, Pennsylvania State University, University Park, PA, 16802, USA. .,The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA. .,School of Electrical Engineering and Computer Science, Pennsylvania State University, University Park, PA, 16802, USA. .,The Center for Big Data Analytics and Discovery Informatics, Pennsylvania State University, University Park, PA, 16802, USA. .,The Clinical and Translational Sciences Institute, Pennsylvania State University, University Park, PA, 16802, USA.
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14
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Kim D, Li R, Lucas A, Verma SS, Dudek SM, Ritchie MD. Using knowledge-driven genomic interactions for multi-omics data analysis: metadimensional models for predicting clinical outcomes in ovarian carcinoma. J Am Med Inform Assoc 2017; 24:577-587. [PMID: 28040685 DOI: 10.1093/jamia/ocw165] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 12/02/2016] [Indexed: 02/07/2023] Open
Abstract
It is common that cancer patients have different molecular signatures even though they have similar clinical features, such as histology, due to the heterogeneity of tumors. To overcome this variability, we previously developed a new approach incorporating prior biological knowledge that identifies knowledge-driven genomic interactions associated with outcomes of interest. However, no systematic approach has been proposed to identify interaction models between pathways based on multi-omics data. Here we have proposed such a novel methodological framework, called metadimensional knowledge-driven genomic interactions (MKGIs). To test the utility of the proposed framework, we applied it to an ovarian cancer dataset including multi-omics profiles from The Cancer Genome Atlas to predict grade, stage, and survival outcome. We found that each knowledge-driven genomic interaction model, based on different genomic datasets, contains different sets of pathway features, which suggests that each genomic data type may contribute to outcomes in ovarian cancer via a different pathway. In addition, MKGI models significantly outperformed the single knowledge-driven genomic interaction model. From the MKGI models, many interactions between pathways associated with outcomes were found, including the mitogen-activated protein kinase (MAPK) signaling pathway and the gonadotropin-releasing hormone (GnRH) signaling pathway, which are known to play important roles in cancer pathogenesis. The beauty of incorporating biological knowledge into the model based on multi-omics data is the ability to improve diagnosis and prognosis and provide better interpretability. Thus, determining variability in molecular signatures based on these interactions between pathways may lead to better diagnostic/treatment strategies for better precision medicine.
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Affiliation(s)
- Dokyoon Kim
- Biomedical and Translational Informatics, Geisinger Health System, Danville, Pennsylvania, USA.,Center for Systems Genomics, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Ruowang Li
- Center for Systems Genomics, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Anastasia Lucas
- Center for Systems Genomics, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Shefali S Verma
- Biomedical and Translational Informatics, Geisinger Health System, Danville, Pennsylvania, USA
| | - Scott M Dudek
- Center for Systems Genomics, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Marylyn D Ritchie
- Biomedical and Translational Informatics, Geisinger Health System, Danville, Pennsylvania, USA.,Center for Systems Genomics, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
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15
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Hanash S. The Wide World of Molecular Profiling for Tumor Classification. Clin Chem 2017; 64:743-744. [PMID: 29097505 DOI: 10.1373/clinchem.2017.273466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 04/27/2017] [Indexed: 11/06/2022]
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16
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Shivakumar M, Lee Y, Bang L, Garg T, Sohn KA, Kim D. Identification of epigenetic interactions between miRNA and DNA methylation associated with gene expression as potential prognostic markers in bladder cancer. BMC Med Genomics 2017; 10:30. [PMID: 28589857 PMCID: PMC5461531 DOI: 10.1186/s12920-017-0269-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Background One of the fundamental challenges in cancer is to detect the regulators of gene expression changes during cancer progression. Through transcriptional silencing of critical cancer-related genes, epigenetic change such as DNA methylation plays a crucial role in cancer. In addition, miRNA, another major component of epigenome, is also a regulator at the post-transcriptional levels that modulate transcriptome changes. However, a mechanistic role of synergistic interactions between DNA methylation and miRNA as epigenetic regulators on transcriptomic changes and its association with clinical outcomes such as survival have remained largely unexplored in cancer. Methods In this study, we propose an integrative framework to identify epigenetic interactions between methylation and miRNA associated with transcriptomic changes. To test the utility of the proposed framework, the bladder cancer data set, including DNA methylation, miRNA expression, and gene expression data, from The Cancer Genome Atlas (TCGA) was analyzed for this study. Results First, we found 120 genes associated with interactions between the two epigenomic components. Then, 11 significant epigenetic interactions between miRNA and methylation, which target E2F3, CCND1, UTP6, CDADC1, SLC35E3, METRNL, TPCN2, NACC2, VGLL4, and PTEN, were found to be associated with survival. To this end, exploration of TCGA bladder cancer data identified epigenetic interactions that are associated with survival as potential prognostic markers in bladder cancer. Conclusions Given the importance and prevalence of these interactions of epigenetic events in bladder cancer it is timely to understand further how different epigenetic components interact and influence each other. Electronic supplementary material The online version of this article (doi:10.1186/s12920-017-0269-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Manu Shivakumar
- Biomedical & Translational Informatics Institute, Geisinger Health System, Danville, PA, USA
| | - Younghee Lee
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Lisa Bang
- Biomedical & Translational Informatics Institute, Geisinger Health System, Danville, PA, USA
| | - Tullika Garg
- Mowad Urology Department, Geisinger Health System, Danville, PA, USA
| | - Kyung-Ah Sohn
- Department of Software and Computer Engineering, Ajou University, Suwon, South Korea.
| | - Dokyoon Kim
- Biomedical & Translational Informatics Institute, Geisinger Health System, Danville, PA, USA. .,The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA.
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17
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Paik ES, Choi HJ, Kim TJ, Lee JW, Kim BG, Bae DS, Choi CH. Molecular Signature for Lymphatic Invasion Associated with Survival of Epithelial Ovarian Cancer. Cancer Res Treat 2017; 50:461-473. [PMID: 28546526 PMCID: PMC5912145 DOI: 10.4143/crt.2017.104] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 05/09/2017] [Indexed: 01/02/2023] Open
Abstract
Purpose We aimed to develop molecular classifier that can predict lymphatic invasion and their clinical significance in epithelial ovarian cancer (EOC) patients. Materials and Methods We analyzed gene expression (mRNA, methylated DNA) in data from The Cancer Genome Atlas. To identify molecular signatures for lymphatic invasion, we found differentially expressed genes. The performance of classifier was validated by receiver operating characteristics analysis, logistic regression, linear discriminant analysis (LDA), and support vector machine (SVM). We assessed prognostic role of classifier using random survival forest (RSF) model and pathway deregulation score (PDS). For external validation,we analyzed microarray data from 26 EOC samples of Samsung Medical Center and curatedOvarianData database. Results We identified 21 mRNAs, and seven methylated DNAs from primary EOC tissues that predicted lymphatic invasion and created prognostic models. The classifier predicted lymphatic invasion well, which was validated by logistic regression, LDA, and SVM algorithm (C-index of 0.90, 0.71, and 0.74 for mRNA and C-index of 0.64, 0.68, and 0.69 for DNA methylation). Using RSF model, incorporating molecular data with clinical variables improved prediction of progression-free survival compared with using only clinical variables (p < 0.001 and p=0.008). Similarly, PDS enabled us to classify patients into high-risk and low-risk group, which resulted in survival difference in mRNA profiles (log-rank p-value=0.011). In external validation, gene signature was well correlated with prediction of lymphatic invasion and patients’ survival. Conclusion Molecular signature model predicting lymphatic invasion was well performed and also associated with survival of EOC patients.
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Affiliation(s)
- E Sun Paik
- Department of Obstetrics and Gynecology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hyun Jin Choi
- Department of Obstetrics and Gynecology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Tae-Joong Kim
- Department of Obstetrics and Gynecology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jeong-Won Lee
- Department of Obstetrics and Gynecology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Byoung-Gie Kim
- Department of Obstetrics and Gynecology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Duk-Soo Bae
- Department of Obstetrics and Gynecology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Chel Hun Choi
- Department of Obstetrics and Gynecology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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18
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Shi X, Banerjee S, Chen L, Hilakivi-Clarke L, Clarke R, Xuan J. CyNetSVM: A Cytoscape App for Cancer Biomarker Identification Using Network Constrained Support Vector Machines. PLoS One 2017; 12:e0170482. [PMID: 28122019 PMCID: PMC5266326 DOI: 10.1371/journal.pone.0170482] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 01/05/2017] [Indexed: 12/24/2022] Open
Abstract
One of the important tasks in cancer research is to identify biomarkers and build classification models for clinical outcome prediction. In this paper, we develop a CyNetSVM software package, implemented in Java and integrated with Cytoscape as an app, to identify network biomarkers using network-constrained support vector machines (NetSVM). The Cytoscape app of NetSVM is specifically designed to improve the usability of NetSVM with the following enhancements: (1) user-friendly graphical user interface (GUI), (2) computationally efficient core program and (3) convenient network visualization capability. The CyNetSVM app has been used to analyze breast cancer data to identify network genes associated with breast cancer recurrence. The biological function of these network genes is enriched in signaling pathways associated with breast cancer progression, showing the effectiveness of CyNetSVM for cancer biomarker identification. The CyNetSVM package is available at Cytoscape App Store and http://sourceforge.net/projects/netsvmjava; a sample data set is also provided at sourceforge.net.
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Affiliation(s)
- Xu Shi
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, Virginia, United States of America
| | - Sharmi Banerjee
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, Virginia, United States of America
| | - Li Chen
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Leena Hilakivi-Clarke
- Departments of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States of America
| | - Robert Clarke
- Departments of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States of America
| | - Jianhua Xuan
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, Virginia, United States of America
- * E-mail:
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Dong W, Zhang H, Yin X, Liu Y, Chen D, Liang X, Jin X, Lv J, Ma J, Tang K, Hu Z, Qin X, Huang B. Oral delivery of tumor microparticle vaccines activates NOD2 signaling pathway in ileac epithelium rendering potent antitumor T cell immunity. Oncoimmunology 2017; 6:e1282589. [PMID: 28405506 DOI: 10.1080/2162402x.2017.1282589] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 01/07/2017] [Accepted: 01/09/2017] [Indexed: 01/02/2023] Open
Abstract
Exploiting gut mucosal immunity to design new antitumor vaccination strategy remains unexplored. Tumor cell-derived microparticles (T-MP) are natural biomaterials that are capable of delivering tumor antigens and innate signals to dendritic cells (DC) for tumor-specific T cell immunity. Here, we show that T-MPs by oral vaccination route effectively access and activate mucosal epithelium, leading to subsequent antitumor T cell responses. Oral vaccination of T-MPs generated potent inhibitory effect against the growth of B16 melanoma and CT26 colon cancer in mice, which required both T cell and DC activation. T-MPs, once entering intestinal lumen, were mainly taken up by ileac intestinal epithelial cells (IEC), where T-MPs activated NOD2 and its downstream MAPK and NF-κB, leading to chemokine releasing, including CCL2, from IECs to attract CD103+ CD11c+ DCs. Furthermore, ileac IECs could transcytose T-MPs to the basolateral site, where T-MPs were captured by those DCs for cross-presentation of loaded antigen contents. Elucidating these molecular and cellular mechanisms highlights T-MPs as a novel antitumor oral vaccination strategy with great potential of clinical applications.
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Affiliation(s)
- Wenqian Dong
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing, China
| | - Huafeng Zhang
- Department of Biochemistry & Molecular Biology, Tongji Medical College, Huazhong University of Science & Technology , Wuhan, China
| | - Xiaonan Yin
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing, China
| | - Yuying Liu
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China; Clinical Immunology Center, Chinese Academy of Medical Sciences, Beijing, China
| | - Degao Chen
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing, China
| | - Xiaoyu Liang
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing, China
| | - Xun Jin
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing, China
| | - Jiadi Lv
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing, China
| | - Jingwei Ma
- Department of Biochemistry & Molecular Biology, Tongji Medical College, Huazhong University of Science & Technology , Wuhan, China
| | - Ke Tang
- Department of Biochemistry & Molecular Biology, Tongji Medical College, Huazhong University of Science & Technology , Wuhan, China
| | - Zhuowei Hu
- Molecular Immunology and Pharmacology Group, State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing, China
| | - Xiaofeng Qin
- Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China; Suzhou Institute of Systems Medicine, Suzhou, China
| | - Bo Huang
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China; Department of Biochemistry & Molecular Biology, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China; Clinical Immunology Center, Chinese Academy of Medical Sciences, Beijing, China
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20
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Hassanzadeh HR, Phan JH, Wang MD. A Multi-Modal Graph-Based Semi-Supervised Pipeline for Predicting Cancer Survival. PROCEEDINGS. IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE 2016; 2016:184-189. [PMID: 32655981 DOI: 10.1109/bibm.2016.7822516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cancer survival prediction is an active area of research that can help prevent unnecessary therapies and improve patient's quality of life. Gene expression profiling is being widely used in cancer studies to discover informative biomarkers that aid predict different clinical endpoint prediction. We use multiple modalities of data derived from RNA deep-sequencing (RNA-seq) to predict survival of cancer patients. Despite the wealth of information available in expression profiles of cancer tumors, fulfilling the aforementioned objective remains a big challenge, for the most part, due to the paucity of data samples compared to the high dimension of the expression profiles. As such, analysis of transcriptomic data modalities calls for state-of-the-art big-data analytics techniques that can maximally use all the available data to discover the relevant information hidden within a significant amount of noise. In this paper, we propose a pipeline that predicts cancer patients' survival by exploiting the structure of the input (manifold learning) and by leveraging the unlabeled samples using Laplacian support vector machines, a graph-based semi supervised learning (GSSL) paradigm. We show that under certain circumstances, no single modality per se will result in the best accuracy and by fusing different models together via a stacked generalization strategy, we may boost the accuracy synergistically. We apply our approach to two cancer datasets and present promising results. We maintain that a similar pipeline can be used for predictive tasks where labeled samples are expensive to acquire.
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Affiliation(s)
- Hamid Reza Hassanzadeh
- Department of Computational Science and Engineering, Georgia Institute of Technology Atlanta, Georgia 30332
| | - John H Phan
- Department of Biomedical Engineering Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332
| | - May D Wang
- Department of Biomedical Engineering Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332
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21
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Systems-level effects of ectopic galectin-7 reconstitution in cervical cancer and its microenvironment. BMC Cancer 2016; 16:680. [PMID: 27558259 PMCID: PMC4997669 DOI: 10.1186/s12885-016-2700-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 08/09/2016] [Indexed: 12/20/2022] Open
Abstract
Background Galectin-7 (Gal-7) is negatively regulated in cervical cancer, and appears to be a link between the apoptotic response triggered by cancer and the anti-tumoral activity of the immune system. Our understanding of how cervical cancer cells and their molecular networks adapt in response to the expression of Gal-7 remains limited. Methods Meta-analysis of Gal-7 expression was conducted in three cervical cancer cohort studies and TCGA. In silico prediction and bisulfite sequencing were performed to inquire epigenetic alterations. To study the effect of Gal-7 on cervical cancer, we ectopically re-expressed it in the HeLa and SiHa cervical cancer cell lines, and analyzed their transcriptome and SILAC-based proteome. We also examined the tumor and microenvironment host cell transcriptomes after xenotransplantation into immunocompromised mice. Differences between samples were assessed with the Kruskall-Wallis, Dunn’s Multiple Comparison and T tests. Kaplan–Meier and log-rank tests were used to determine overall survival. Results Gal-7 was constantly downregulated in our meta-analysis (p < 0.0001). Tumors with combined high Gal-7 and low galectin-1 expression (p = 0.0001) presented significantly better prognoses (p = 0.005). In silico and bisulfite sequencing assays showed de novo methylation in the Gal-7 promoter and first intron. Cells re-expressing Gal-7 showed a high apoptosis ratio (p < 0.05) and their xenografts displayed strong growth retardation (p < 0.001). Multiple gene modules and transcriptional regulators were modulated in response to Gal-7 reconstitution, both in cervical cancer cells and their microenvironments (FDR < 0.05 %). Most of these genes and modules were associated with tissue morphogenesis, metabolism, transport, chemokine activity, and immune response. These functional modules could exert the same effects in vitro and in vivo, even despite different compositions between HeLa and SiHa samples. Conclusions Gal-7 re-expression affects the regulation of molecular networks in cervical cancer that are involved in diverse cancer hallmarks, such as metabolism, growth control, invasion and evasion of apoptosis. The effect of Gal-7 extends to the microenvironment, where networks involved in its configuration and in immune surveillance are particularly affected. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2700-8) contains supplementary material, which is available to authorized users.
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22
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Shi X, Wang X, Shajahan A, Hilakivi-Clarke L, Clarke R, Xuan J. BMRF-MI: integrative identification of protein interaction network by modeling the gene dependency. BMC Genomics 2015; 16 Suppl 7:S10. [PMID: 26099273 PMCID: PMC4474537 DOI: 10.1186/1471-2164-16-s7-s10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Background Identification of protein interaction network is a very important step for understanding the molecular mechanisms in cancer. Several methods have been developed to integrate protein-protein interaction (PPI) data with gene expression data for network identification. However, they often fail to model the dependency between genes in the network, which makes many important genes, especially the upstream genes, unidentified. It is necessary to develop a method to improve the network identification performance by incorporating the dependency between genes. Results We proposed an approach for identifying protein interaction network by incorporating mutual information (MI) into a Markov random field (MRF) based framework to model the dependency between genes. MI is widely used in information theory to measure the uncertainty between random variables. Different from traditional Pearson correlation test, MI is capable of capturing both linear and non-linear relationship between random variables. Among all the existing MI estimators, we choose to use k-nearest neighbor MI (kNN-MI) estimator which is proved to have minimum bias. The estimated MI is integrated with an MRF framework to model the gene dependency in the context of network. The maximum a posterior (MAP) estimation is applied on the MRF-based model to estimate the network score. In order to reduce the computational complexity of finding the optimal network, a probabilistic searching algorithm is implemented. We further increase the robustness and reproducibility of the results by applying a non-parametric bootstrapping method to measure the confidence level of the identified genes. To evaluate the performance of the proposed method, we test the method on simulation data under different conditions. The experimental results show an improved accuracy in terms of subnetwork identification compared to existing methods. Furthermore, we applied our method onto real breast cancer patient data; the identified protein interaction network shows a close association with the recurrence of breast cancer, which is supported by functional annotation. We also show that the identified subnetworks can be used to predict the recurrence status of cancer patients by survival analysis. Conclusions We have developed an integrated approach for protein interaction network identification, which combines Markov random field framework and mutual information to model the gene dependency in PPI network. Improvements in subnetwork identification have been demonstrated with simulation datasets compared to existing methods. We then apply our method onto breast cancer patient data to identify recurrence related subnetworks. The experiment results show that the identified genes are enriched in the pathway and functional categories relevant to progression and recurrence of breast cancer. Finally, the survival analysis based on identified subnetworks achieves a good result of classifying the recurrence status of cancer patients.
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Kim D, Li R, Dudek SM, Ritchie MD. Predicting censored survival data based on the interactions between meta-dimensional omics data in breast cancer. J Biomed Inform 2015; 56:220-8. [PMID: 26048077 DOI: 10.1016/j.jbi.2015.05.019] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 05/15/2015] [Accepted: 05/27/2015] [Indexed: 12/27/2022]
Abstract
Evaluation of survival models to predict cancer patient prognosis is one of the most important areas of emphasis in cancer research. A binary classification approach has difficulty directly predicting survival due to the characteristics of censored observations and the fact that the predictive power depends on the threshold used to set two classes. In contrast, the traditional Cox regression approach has some drawbacks in the sense that it does not allow for the identification of interactions between genomic features, which could have key roles associated with cancer prognosis. In addition, data integration is regarded as one of the important issues in improving the predictive power of survival models since cancer could be caused by multiple alterations through meta-dimensional genomic data including genome, epigenome, transcriptome, and proteome. Here we have proposed a new integrative framework designed to perform these three functions simultaneously: (1) predicting censored survival data; (2) integrating meta-dimensional omics data; (3) identifying interactions within/between meta-dimensional genomic features associated with survival. In order to predict censored survival time, martingale residuals were calculated as a new continuous outcome and a new fitness function used by the grammatical evolution neural network (GENN) based on mean absolute difference of martingale residuals was implemented. To test the utility of the proposed framework, a simulation study was conducted, followed by an analysis of meta-dimensional omics data including copy number, gene expression, DNA methylation, and protein expression data in breast cancer retrieved from The Cancer Genome Atlas (TCGA). On the basis of the results from breast cancer dataset, we were able to identify interactions not only within a single dimension of genomic data but also between meta-dimensional omics data that are associated with survival. Notably, the predictive power of our best meta-dimensional model was 73% which outperformed all of the other models conducted based on a single dimension of genomic data. Breast cancer is an extremely heterogeneous disease and the high levels of genomic diversity within/between breast tumors could affect the risk of therapeutic responses and disease progression. Thus, identifying interactions within/between meta-dimensional omics data associated with survival in breast cancer is expected to deliver direction for improved meta-dimensional prognostic biomarkers and therapeutic targets.
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Affiliation(s)
- Dokyoon Kim
- Center for Systems Genomics, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Ruowang Li
- Center for Systems Genomics, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Scott M Dudek
- Center for Systems Genomics, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Marylyn D Ritchie
- Center for Systems Genomics, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA; Geisinger Health System, Danville, PA, USA.
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Zhou L, Wang R, Yao C, Li X, Wang C, Zhang X, Xu C, Zeng A, Zhao D, Zhang F. Single-band upconversion nanoprobes for multiplexed simultaneous in situ molecular mapping of cancer biomarkers. Nat Commun 2015; 6:6938. [PMID: 25907226 PMCID: PMC4423208 DOI: 10.1038/ncomms7938] [Citation(s) in RCA: 248] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 03/16/2015] [Indexed: 02/06/2023] Open
Abstract
The identification of potential diagnostic markers and target molecules among the plethora of tumour oncoproteins for cancer diagnosis requires facile technology that is capable of quantitatively analysing multiple biomarkers in tumour cells and tissues. Diagnostic and prognostic classifications of human tumours are currently based on the western blotting and single-colour immunohistochemical methods that are not suitable for multiplexed detection. Herein, we report a general and novel method to prepare single-band upconversion nanoparticles with different colours. The expression levels of three biomarkers in breast cancer cells were determined using single-band upconversion nanoparticles, western blotting and immunohistochemical technologies with excellent correlation. Significantly, the application of antibody-conjugated single-band upconversion nanoparticle molecular profiling technology can achieve the multiplexed simultaneous in situ biodetection of biomarkers in breast cancer cells and tissue specimens and produce more accurate results for the simultaneous quantification of proteins present at low levels compared with classical immunohistochemical technology.
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Affiliation(s)
- Lei Zhou
- Department of Chemistry and Laboratory of Advanced Materials, iChEm (Collaborative Innovation Center of Chemistry for Energy Materials), State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
| | - Rui Wang
- Department of Chemistry, iChEm (Collaborative Innovation Center of Chemistry for Energy Materials), State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
| | - Chi Yao
- Department of Chemistry, iChEm (Collaborative Innovation Center of Chemistry for Energy Materials), State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
| | - Xiaomin Li
- Department of Chemistry, iChEm (Collaborative Innovation Center of Chemistry for Energy Materials), State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
| | - Chengli Wang
- Department of Chemistry, iChEm (Collaborative Innovation Center of Chemistry for Energy Materials), State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
| | - Xiaoyan Zhang
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200011, China
| | - Congjian Xu
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200011, China
| | - Aijun Zeng
- Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Dongyuan Zhao
- Department of Chemistry, iChEm (Collaborative Innovation Center of Chemistry for Energy Materials), State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
| | - Fan Zhang
- Department of Chemistry, iChEm (Collaborative Innovation Center of Chemistry for Energy Materials), State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
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Chaudhary PM, Murthy RV, Yadav R, Kikkeri R. A rationally designed peptidomimetic biosensor for sialic acid on cell surfaces. Chem Commun (Camb) 2015; 51:8112-5. [PMID: 25868668 DOI: 10.1039/c5cc01662b] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have developed peptidomimetic sialic acid (Sia) biosensors using boronic acid and arginine groups on the peptide backbone. The designed peptides were conjugated to fluorescent streptavidin via biotin enabling the optical labeling of cells. This approach provides unique opportunities to detect Sia composition on the cell surfaces and filopodia.
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Affiliation(s)
- Preeti Madhukar Chaudhary
- Indian Institute of Science Education and Research, Dr. Homi Bhabbha Road, Pashan, Pune 411008, India.
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Shi X, Barnes RO, Chen L, Shajahan-Haq AN, Hilakivi-Clarke L, Clarke R, Wang Y, Xuan J. BMRF-Net: a software tool for identification of protein interaction subnetworks by a bagging Markov random field-based method. Bioinformatics 2015; 31:2412-4. [PMID: 25755273 DOI: 10.1093/bioinformatics/btv137] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 03/04/2015] [Indexed: 01/09/2023] Open
Abstract
UNLABELLED Identification of protein interaction subnetworks is an important step to help us understand complex molecular mechanisms in cancer. In this paper, we develop a BMRF-Net package, implemented in Java and C++, to identify protein interaction subnetworks based on a bagging Markov random field (BMRF) framework. By integrating gene expression data and protein-protein interaction data, this software tool can be used to identify biologically meaningful subnetworks. A user friendly graphic user interface is developed as a Cytoscape plugin for the BMRF-Net software to deal with the input/output interface. The detailed structure of the identified networks can be visualized in Cytoscape conveniently. The BMRF-Net package has been applied to breast cancer data to identify significant subnetworks related to breast cancer recurrence. AVAILABILITY AND IMPLEMENTATION The BMRF-Net package is available at http://sourceforge.net/projects/bmrfcjava/. The package is tested under Ubuntu 12.04 (64-bit), Java 7, glibc 2.15 and Cytoscape 3.1.0.
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Affiliation(s)
- Xu Shi
- Bradley Department of Electrical and Computer Engineering, Virginia Tech, Arlington, VA 22203, USA
| | - Robert O Barnes
- Bradley Department of Electrical and Computer Engineering, Virginia Tech, Arlington, VA 22203, USA
| | - Li Chen
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA and
| | - Ayesha N Shajahan-Haq
- Lombardi Comprehensive Cancer Center and Department of Oncology, Georgetown University, Washington, DC 20057, USA
| | - Leena Hilakivi-Clarke
- Lombardi Comprehensive Cancer Center and Department of Oncology, Georgetown University, Washington, DC 20057, USA
| | - Robert Clarke
- Lombardi Comprehensive Cancer Center and Department of Oncology, Georgetown University, Washington, DC 20057, USA
| | - Yue Wang
- Bradley Department of Electrical and Computer Engineering, Virginia Tech, Arlington, VA 22203, USA
| | - Jianhua Xuan
- Bradley Department of Electrical and Computer Engineering, Virginia Tech, Arlington, VA 22203, USA
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Podobed P, Pyle WG, Ackloo S, Alibhai FJ, Tsimakouridze EV, Ratcliffe WF, Mackay A, Simpson J, Wright DC, Kirby GM, Young ME, Martino TA. The day/night proteome in the murine heart. Am J Physiol Regul Integr Comp Physiol 2014; 307:R121-37. [PMID: 24789993 DOI: 10.1152/ajpregu.00011.2014] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Circadian rhythms are essential to cardiovascular health and disease. Temporal coordination of cardiac structure and function has focused primarily at the physiological and gene expression levels, but these analyses are invariably incomplete, not the least because proteins underlie many biological processes. The purpose of this study was to reveal the diurnal cardiac proteome and important contributions to cardiac function. The 24-h day-night murine cardiac proteome was assessed by two-dimensional difference in gel electrophoresis (2D-DIGE) and liquid chromatography-mass spectrometry. Daily variation was considerable, as ∼7.8% (90/1,147) of spots exhibited statistical changes at paired times across the 24-h light- (L) dark (D) cycle. JTK_CYCLE was used to investigate underlying diurnal rhythms in corresponding mRNA. We next revealed that disruption of the L:D cycle altered protein profiles and diurnal variation in cardiac function in Langendorff-perfused hearts, relative to the L:D cycle. To investigate the role of the circadian clock mechanism, we used cardiomyocyte clock mutant (CCM) mice. CCM myofilaments exhibited a loss of time-of-day-dependent maximal calcium-dependent ATP consumption, and altered phosphorylation rhythms. Moreover, the cardiac proteome was significantly altered in CCM hearts, especially enzymes regulating vital metabolic pathways. Lastly, we used a model of pressure overload cardiac hypertrophy to demonstrate the temporal proteome during heart disease. Our studies demonstrate that time of day plays a direct role in cardiac protein abundance and indicate a novel mechanistic contribution of circadian biology to cardiovascular structure and function.
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Miok V, Wilting SM, van de Wiel MA, Jaspers A, van Noort PI, Brakenhoff RH, Snijders PJF, Steenbergen RDM, van Wieringen WN. tigaR: integrative significance analysis of temporal differential gene expression induced by genomic abnormalities. BMC Bioinformatics 2014; 15:327. [PMID: 25278371 PMCID: PMC4288633 DOI: 10.1186/1471-2105-15-327] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 09/25/2014] [Indexed: 01/05/2023] Open
Abstract
Background To determine which changes in the host cell genome are crucial for cervical carcinogenesis, a longitudinal in vitro model system of HPV-transformed keratinocytes was profiled in a genome-wide manner. Four cell lines affected with either HPV16 or HPV18 were assayed at 8 sequential time points for gene expression (mRNA) and gene copy number (DNA) using high-resolution microarrays. Available methods for temporal differential expression analysis are not designed for integrative genomic studies. Results Here, we present a method that allows for the identification of differential gene expression associated with DNA copy number changes over time. The temporal variation in gene expression is described by a generalized linear mixed model employing low-rank thin-plate splines. Model parameters are estimated with an empirical Bayes procedure, which exploits integrated nested Laplace approximation for fast computation. Iteratively, posteriors of hyperparameters and model parameters are estimated. The empirical Bayes procedure shrinks multiple dispersion-related parameters. Shrinkage leads to more stable estimates of the model parameters, better control of false positives and improvement of reproducibility. In addition, to make estimates of the DNA copy number more stable, model parameters are also estimated in a multivariate way using triplets of features, imposing a spatial prior for the copy number effect. Conclusion With the proposed method for analysis of time-course multilevel molecular data, more profound insight may be gained through the identification of temporal differential expression induced by DNA copy number abnormalities. In particular, in the analysis of an integrative oncogenomics study with a time-course set-up our method finds genes previously reported to be involved in cervical carcinogenesis. Furthermore, the proposed method yields improvements in sensitivity, specificity and reproducibility compared to existing methods. Finally, the proposed method is able to handle count (RNAseq) data from time course experiments as is shown on a real data set. Electronic supplementary material The online version of this article (doi:10.1186/1471-2105-15-327) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Wessel N van Wieringen
- Department of Epidemiology and Biostatistics, VU University Medical Center, P,O, Box 7057, 1007 MB, Amsterdam, The Netherlands.
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Wang L, Xiao Y, Ping Y, Li J, Zhao H, Li F, Hu J, Zhang H, Deng Y, Tian J, Li X. Integrating multi-omics for uncovering the architecture of cross-talking pathways in breast cancer. PLoS One 2014; 9:e104282. [PMID: 25137136 PMCID: PMC4138095 DOI: 10.1371/journal.pone.0104282] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 07/07/2014] [Indexed: 12/21/2022] Open
Abstract
Cross-talk among abnormal pathways widely occurs in human cancer and generally leads to insensitivity to cancer treatment. Moreover, alterations in the abnormal pathways are not limited to single molecular level. Therefore, we proposed a strategy that integrates a large number of biological sources at multiple levels for systematic identification of cross-talk among risk pathways in cancer by random walk on protein interaction network. We applied the method to multi-Omics breast cancer data from The Cancer Genome Atlas (TCGA), including somatic mutation, DNA copy number, DNA methylation and gene expression profiles. We identified close cross-talk among many known cancer-related pathways with complex change patterns. Furthermore, we identified key genes (linkers) bridging these cross-talks and showed that these genes carried out consistent biological functions with the linked cross-talking pathways. Through identification of leader genes in each pathway, the architecture of cross-talking pathways was built. Notably, we observed that linkers cooperated with leaders to form the fundamentation of cross-talk of pathways which play core roles in deterioration of breast cancer. As an example, we observed that KRAS showed a direct connection to numerous cancer-related pathways, such as MAPK signaling pathway, suggesting that it may be a central communication hub. In summary, we offer an effective way to characterize complex cross-talk among disease pathways, which can be applied to other diseases and provide useful information for the treatment of cancer.
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Affiliation(s)
- Li Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yanyan Ping
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jing Li
- Department of Ultrasonic medicine, The 1st Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, China
| | - Hongying Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Feng Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jing Hu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hongyi Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yulan Deng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jiawei Tian
- Department of Ultrasonic medicine, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, China
- * E-mail: (JT); (XL)
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- * E-mail: (JT); (XL)
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Kim D, Joung JG, Sohn KA, Shin H, Park YR, Ritchie MD, Kim JH. Knowledge boosting: a graph-based integration approach with multi-omics data and genomic knowledge for cancer clinical outcome prediction. J Am Med Inform Assoc 2014; 22:109-20. [PMID: 25002459 PMCID: PMC4433357 DOI: 10.1136/amiajnl-2013-002481] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Objective Cancer can involve gene dysregulation via multiple mechanisms, so no single level of genomic data fully elucidates tumor behavior due to the presence of numerous genomic variations within or between levels in a biological system. We have previously proposed a graph-based integration approach that combines multi-omics data including copy number alteration, methylation, miRNA, and gene expression data for predicting clinical outcome in cancer. However, genomic features likely interact with other genomic features in complex signaling or regulatory networks, since cancer is caused by alterations in pathways or complete processes. Methods Here we propose a new graph-based framework for integrating multi-omics data and genomic knowledge to improve power in predicting clinical outcomes and elucidate interplay between different levels. To highlight the validity of our proposed framework, we used an ovarian cancer dataset from The Cancer Genome Atlas for predicting stage, grade, and survival outcomes. Results Integrating multi-omics data with genomic knowledge to construct pre-defined features resulted in higher performance in clinical outcome prediction and higher stability. For the grade outcome, the model with gene expression data produced an area under the receiver operating characteristic curve (AUC) of 0.7866. However, models of the integration with pathway, Gene Ontology, chromosomal gene set, and motif gene set consistently outperformed the model with genomic data only, attaining AUCs of 0.7873, 0.8433, 0.8254, and 0.8179, respectively. Conclusions Integrating multi-omics data and genomic knowledge to improve understanding of molecular pathogenesis and underlying biology in cancer should improve diagnostic and prognostic indicators and the effectiveness of therapies.
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Affiliation(s)
- Dokyoon Kim
- Division of Biomedical Informatics, Seoul National University Biomedical Informatics (SNUBI), Seoul National University College of Medicine, Seoul, Korea Department of Biochemistry and Molecular Biology, Center for Systems Genomics, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Je-Gun Joung
- Division of Biomedical Informatics, Seoul National University Biomedical Informatics (SNUBI), Seoul National University College of Medicine, Seoul, Korea Translational Bioinformatics Lab (TBL), Samsung Genome Institute (SGI), Samsung Medical Center, Seoul, Korea
| | - Kyung-Ah Sohn
- Division of Biomedical Informatics, Seoul National University Biomedical Informatics (SNUBI), Seoul National University College of Medicine, Seoul, Korea Department of Information and Computer Engineering, Ajou University, Suwon, Korea
| | - Hyunjung Shin
- Department of Industrial and Information Systems Engineering, Ajou University, Suwon, Korea
| | - Yu Rang Park
- Division of Biomedical Informatics, Seoul National University Biomedical Informatics (SNUBI), Seoul National University College of Medicine, Seoul, Korea Department of Biomedical Informatics, Asan Medical Center, Seoul, Korea
| | - Marylyn D Ritchie
- Department of Biochemistry and Molecular Biology, Center for Systems Genomics, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Ju Han Kim
- Division of Biomedical Informatics, Seoul National University Biomedical Informatics (SNUBI), Seoul National University College of Medicine, Seoul, Korea Systems Biomedical Informatics Research Center, Seoul National University, Seoul, Korea
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Kim D, Shin H, Sohn KA, Verma A, Ritchie MD, Kim JH. Incorporating inter-relationships between different levels of genomic data into cancer clinical outcome prediction. Methods 2014; 67:344-53. [PMID: 24561168 DOI: 10.1016/j.ymeth.2014.02.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Revised: 01/25/2014] [Accepted: 02/07/2014] [Indexed: 01/06/2023] Open
Abstract
In order to improve our understanding of cancer and develop multi-layered theoretical models for the underlying mechanism, it is essential to have enhanced understanding of the interactions between multiple levels of genomic data that contribute to tumor formation and progression. Although there exist recent approaches such as a graph-based framework that integrates multi-omics data including copy number alteration, methylation, gene expression, and miRNA data for cancer clinical outcome prediction, most of previous methods treat each genomic data as independent and the possible interplay between them is not explicitly incorporated to the model. However, cancer is dysregulated by multiple levels in the biological system through genomic, epigenomic, transcriptomic, and proteomic level. Thus, genomic features are likely to interact with other genomic features in the different genomic levels. In order to deepen our knowledge, it would be desirable to incorporate such inter-relationship information when integrating multi-omics data for cancer clinical outcome prediction. In this study, we propose a new graph-based framework that integrates not only multi-omics data but inter-relationship between them for better elucidating cancer clinical outcomes. In order to highlight the validity of the proposed framework, serous cystadenocarcinoma data from TCGA was adopted as a pilot task. The proposed model incorporating inter-relationship between different genomic features showed significantly improved performance compared to the model that does not consider inter-relationship when integrating multi-omics data. For the pair between miRNA and gene expression data, the model integrating miRNA, for example, gene expression, and inter-relationship between them with an AUC of 0.8476 (REI) outperformed the model combining miRNA and gene expression data with an AUC of 0.8404. Similar results were also obtained for other pairs between different levels of genomic data. Integration of different levels of data and inter-relationship between them can aid in extracting new biological knowledge by drawing an integrative conclusion from many pieces of information collected from diverse types of genomic data, eventually leading to more effective screening strategies and alternative therapies that may improve outcomes.
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Affiliation(s)
- Dokyoon Kim
- Seoul National University Biomedical Informatics (SNUBI), Div. of Biomedical Informatics, Seoul National University College of Medicine, Seoul 110799, Republic of Korea; Center for Systems Genomics, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.
| | - Hyunjung Shin
- Department of Industrial & Information Systems Engineering, Ajou University, San 5, Wonchun-dong, Yeoungtong-gu, 443-749 Suwon, Republic of Korea.
| | - Kyung-Ah Sohn
- Department of Information and Computer Engineering, Ajou University, Suwon 443-749, Republic of Korea.
| | - Anurag Verma
- Center for Systems Genomics, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.
| | - Marylyn D Ritchie
- Center for Systems Genomics, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.
| | - Ju Han Kim
- Seoul National University Biomedical Informatics (SNUBI), Div. of Biomedical Informatics, Seoul National University College of Medicine, Seoul 110799, Republic of Korea; Systems Biomedical Informatics Research Center, Seoul National University, Seoul 110799, Republic of Korea.
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Ye B, Gagnon A, Mok SC. Recent technical strategies to identify diagnostic biomarkers for ovarian cancer. Expert Rev Proteomics 2014; 4:121-31. [PMID: 17288520 DOI: 10.1586/14789450.4.1.121] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Ovarian cancer is the fifth leading cause of cancer deaths among North American women. Regrettably, there is currently no reliable circulating biomarker that can detect ovarian cancer in its early stages. The CA125 biomarker is very useful for treatment response monitoring, but its sensitivity is very low for early detection. Thus, there is an urgent need for the identification of new circulating biomarkers/panel of biomarkers that could be used to diagnose ovarian cancer before it becomes clinically detectable and advanced. Unfortunately, the strategies used in the past years to identify such biomarkers have not led to any outstanding candidate. This review summarizes the different approaches used in the last decade and suggests which strategies should be adopted in the near future in order to lead to the successful identification of new ovarian cancer diagnostic biomarkers.
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Affiliation(s)
- Bin Ye
- Harvard Medical School, Department of Obstetrics & Gynecology, Brigham & Women's Hospital, Dana-Farber Harvard Cancer Center, Boston, MA 02115, USA.
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Kang Y. Functional genomic analysis of cancer metastasis: biologic insights and clinical implications. Expert Rev Mol Diagn 2014; 5:385-95. [PMID: 15934815 DOI: 10.1586/14737159.5.3.385] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Metastasis, the spread of cancer from primary tumors to distant vital organs, has devastating consequences. Lack of effective tools to study this complex problem has hindered the development of accurate prognostic methods and effective treatments for metastatic cancer. In the postgenomic era, the application of genomic profiling methods to the analysis of clinical metastasis samples and animal metastasis models has revolutionized the field of metastasis research. This article reviews recent breakthroughs in the functional genomic analysis of metastasis. In addition, its impacts on our understanding of the molecular basis of metastasis and on clinical practice are discussed.
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Affiliation(s)
- Yibin Kang
- Princeton University Department of Molecular Biology, Princeton, NJ 08544, USA.
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Kim D, Li R, Dudek SM, Ritchie MD. ATHENA: Identifying interactions between different levels of genomic data associated with cancer clinical outcomes using grammatical evolution neural network. BioData Min 2013; 6:23. [PMID: 24359638 PMCID: PMC3912499 DOI: 10.1186/1756-0381-6-23] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 11/27/2013] [Indexed: 12/19/2022] Open
Abstract
Background Gene expression profiles have been broadly used in cancer research as a diagnostic or prognostic signature for the clinical outcome prediction such as stage, grade, metastatic status, recurrence, and patient survival, as well as to potentially improve patient management. However, emerging evidence shows that gene expression-based prediction varies between independent data sets. One possible explanation of this effect is that previous studies were focused on identifying genes with large main effects associated with clinical outcomes. Thus, non-linear interactions without large individual main effects would be missed. The other possible explanation is that gene expression as a single level of genomic data is insufficient to explain the clinical outcomes of interest since cancer can be dysregulated by multiple alterations through genome, epigenome, transcriptome, and proteome levels. In order to overcome the variability of diagnostic or prognostic predictors from gene expression alone and to increase its predictive power, we need to integrate multi-levels of genomic data and identify interactions between them associated with clinical outcomes. Results Here, we proposed an integrative framework for identifying interactions within/between multi-levels of genomic data associated with cancer clinical outcomes using the Grammatical Evolution Neural Networks (GENN). In order to demonstrate the validity of the proposed framework, ovarian cancer data from TCGA was used as a pilot task. We found not only interactions within a single genomic level but also interactions between multi-levels of genomic data associated with survival in ovarian cancer. Notably, the integration model from different levels of genomic data achieved 72.89% balanced accuracy and outperformed the top models with any single level of genomic data. Conclusions Understanding the underlying tumorigenesis and progression in ovarian cancer through the global view of interactions within/between different levels of genomic data is expected to provide guidance for improved prognostic biomarkers and individualized therapies.
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Affiliation(s)
| | | | | | - Marylyn D Ritchie
- Center for Systems Genomics, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park PA, USA.
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Sohn KA, Kim D, Lim J, Kim JH. Relative impact of multi-layered genomic data on gene expression phenotypes in serous ovarian tumors. BMC SYSTEMS BIOLOGY 2013; 7 Suppl 6:S9. [PMID: 24521303 PMCID: PMC3906601 DOI: 10.1186/1752-0509-7-s6-s9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background The emerging multi-layers of genomic data have provided unprecedented opportunities for cancer research, especially for the association study between gene expressions and other types of genomic features. No previous approaches, however, provide an adequate statistical framework for or global analysis on the relative impact of different genomic feature layers to gene expression phenotypes. Methods We propose an integrative statistical framework based on a sparse regression to model the impact of multi-layered genomic features on gene expression traits. The proposed approach can be regarded as an integrative expression Quantitative Traits Loci approach in which not only the genetic variations of SNPs or copy number variations but also other features in both genomic and epigenomic levels are used to explain the expression of genes. To highlight the validity of the proposed approach, the TCGA ovarian cancer dataset was analysed as a pilot task. Results The analysis shows that our integrative approach has consistently superior power in predicting gene expression levels compared to that from each single data type-based analysis. Moreover, the proposed method has the advantage of producing a substantially reduced number of spurious associations. We provide an interesting characterization of genes in terms of its genomic association patterns. Important genomic features reported in previous ovarian cancer research are successfully identified as major hubs in the resulting association network between heterogeneous types of genomic features and genes. Conclusions In this paper, we model the gene expression phenotypes with respect to multiple different types of genomic data in an integrative framework. Our analysis reveals the global view on the relative contribution of different genomic feature types to gene expression phenotypes in ovarian cancer.
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Kim D, Shin H, Joung JG, Lee SY, Kim JH. Intra-relation reconstruction from inter-relation: miRNA to gene expression. BMC SYSTEMS BIOLOGY 2013; 7 Suppl 3:S8. [PMID: 24521265 PMCID: PMC3852212 DOI: 10.1186/1752-0509-7-s3-s8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
BACKGROUND In computational biology, a novel knowledge has been obtained mostly by identifying 'intra-relation,' the relation between entities on a specific biological level such as from gene expression or from microRNA (miRNA) and many such researches have been successful. However, intra-relations are not fully explaining complex cancer mechanisms because the inter-relation information between different levels of genomic data is missing, e.g. miRNA and its target genes. The 'inter-relation' between different levels of genomic data can be constructed from biological experimental data as well as genomic knowledge. METHODS Previously, we have proposed a graph-based framework that integrates with multi-layers of genomic data, copy number alteration, DNA methylation, gene expression, and miRNA expression, for the cancer clinical outcome prediction. However, the limitation of previous work was that we integrated with multi-layers of genomic data without considering of inter-relationship information between genomic features. In this paper, we propose a new integrative framework that combines genomic dataset from gene expression and genomic knowledge from inter-relation between miRNA and gene expression for the clinical outcome prediction as a pilot study. RESULTS In order to demonstrate the validity of the proposed method, the prediction of short-term/long-term survival for 82 patients in glioblastoma multiforme (GBM) was adopted as a base task. Based on our results, the accuracy of our predictive model increases because of incorporation of information fused over genomic dataset from gene expression and genomic knowledge from inter-relation between miRNA and gene expression. CONCLUSIONS In the present study, the intra-relation of gene expression was reconstructed from inter-relation between miRNA and gene expression for prediction of short-term/long-term survival of GBM patients. Our finding suggests that the utilization of external knowledge representing miRNA-mediated regulation of gene expression is substantially useful for elucidating the cancer phenotype.
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Affiliation(s)
- Dokyoon Kim
- Seoul National University Biomedical Informatics (SNUBI), Div. of Biomedical Informatics, Seoul National University College of Medicine, Seoul 110799, Korea
- Systems Biomedical Informatics Research Center, Seoul National University, Seoul 110799, Korea
- Center for Systems Genomics, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Hyunjung Shin
- Department of Industrial Engineering, Ajou University, San 5, Wonchun-dong, Yeoungtong-gu, 443-749, Suwon, Korea
| | - Je-Gun Joung
- Seoul National University Biomedical Informatics (SNUBI), Div. of Biomedical Informatics, Seoul National University College of Medicine, Seoul 110799, Korea
- Systems Biomedical Informatics Research Center, Seoul National University, Seoul 110799, Korea
- Translational Bioinformatics Lab (TBL), Samsung Genome Institute (SGI), Samsung Medical Center, Seoul, Korea
| | - Su-Yeon Lee
- Seoul National University Biomedical Informatics (SNUBI), Div. of Biomedical Informatics, Seoul National University College of Medicine, Seoul 110799, Korea
- Systems Biomedical Informatics Research Center, Seoul National University, Seoul 110799, Korea
| | - Ju Han Kim
- Seoul National University Biomedical Informatics (SNUBI), Div. of Biomedical Informatics, Seoul National University College of Medicine, Seoul 110799, Korea
- Systems Biomedical Informatics Research Center, Seoul National University, Seoul 110799, Korea
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Sun L, Wang S, Li K, Meng D. Analysis of cascading failure in gene networks. Front Genet 2012; 3:292. [PMID: 23248647 PMCID: PMC3521958 DOI: 10.3389/fgene.2012.00292] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 11/26/2012] [Indexed: 12/13/2022] Open
Abstract
It is an important subject to research the functional mechanism of cancer-related genes make in formation and development of cancers. The modern methodology of data analysis plays a very important role for deducing the relationship between cancers and cancer-related genes and analyzing functional mechanism of genome. In this research, we construct mutual information networks using gene expression profiles of glioblast and renal in normal condition and cancer conditions. We investigate the relationship between structure and robustness in gene networks of the two tissues using a cascading failure model based on betweenness centrality. Define some important parameters such as the percentage of failure nodes of the network, the average size-ratio of cascading failure, and the cumulative probability of size-ratio of cascading failure to measure the robustness of the networks. By comparing control group and experiment groups, we find that the networks of experiment groups are more robust than that of control group. The gene that can cause large scale failure is called structural key gene. Some of them have been confirmed to be closely related to the formation and development of glioma and renal cancer respectively. Most of them are predicted to play important roles during the formation of glioma and renal cancer, maybe the oncogenes, suppressor genes, and other cancer candidate genes in the glioma and renal cancer cells. However, these studies provide little information about the detailed roles of identified cancer genes.
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Affiliation(s)
- Longxiao Sun
- College of Information Science and Engineering, Shandong University of Science and Technology Qingdao, China
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Synergistic effect of different levels of genomic data for cancer clinical outcome prediction. J Biomed Inform 2012; 45:1191-8. [DOI: 10.1016/j.jbi.2012.07.008] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Revised: 06/20/2012] [Accepted: 07/19/2012] [Indexed: 11/23/2022]
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39
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Chen L, Xuan J, Riggins RB, Wang Y, Clarke R. Identifying protein interaction subnetworks by a bagging Markov random field-based method. Nucleic Acids Res 2012; 41:e42. [PMID: 23161673 PMCID: PMC3553975 DOI: 10.1093/nar/gks951] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Identification of differentially expressed subnetworks from protein–protein interaction (PPI) networks has become increasingly important to our global understanding of the molecular mechanisms that drive cancer. Several methods have been proposed for PPI subnetwork identification, but the dependency among network member genes is not explicitly considered, leaving many important hub genes largely unidentified. We present a new method, based on a bagging Markov random field (BMRF) framework, to improve subnetwork identification for mechanistic studies of breast cancer. The method follows a maximum a posteriori principle to form a novel network score that explicitly considers pairwise gene interactions in PPI networks, and it searches for subnetworks with maximal network scores. To improve their robustness across data sets, a bagging scheme based on bootstrapping samples is implemented to statistically select high confidence subnetworks. We first compared the BMRF-based method with existing methods on simulation data to demonstrate its improved performance. We then applied our method to breast cancer data to identify PPI subnetworks associated with breast cancer progression and/or tamoxifen resistance. The experimental results show that not only an improved prediction performance can be achieved by the BMRF approach when tested on independent data sets, but biologically meaningful subnetworks can also be revealed that are relevant to breast cancer and tamoxifen resistance.
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Affiliation(s)
- Li Chen
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA
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40
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Zdobnova TA, Stremovskiy OA, Lebedenko EN, Deyev SM. Self-assembling complexes of quantum dots and scFv antibodies for cancer cell targeting and imaging. PLoS One 2012; 7:e48248. [PMID: 23133578 PMCID: PMC3484990 DOI: 10.1371/journal.pone.0048248] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 09/21/2012] [Indexed: 01/25/2023] Open
Abstract
Semiconductor quantum dots represent a novel class of fluorophores with unique physical and chemical properties which could enable a remarkable broadening of the current applications of fluorescent imaging and optical diagnostics. Complexes of quantum dots and antibodies are promising visualising agents for fluorescent detection of selective biomarkers overexpressed in tumor tissues. Here we describe the construction of self-assembling fluorescent complexes of quantum dots and anti-HER1 or anti-HER2/neu scFv antibodies and their interactions with cultured tumor cells. A binding strategy based on a very specific non-covalent interaction between two proteins, barnase and barstar, was used to connect quantum dots and the targeting antibodies. Such a strategy allows combining the targeting and visualization functions simply by varying the corresponding modules of the fluorescent complex.
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Affiliation(s)
- Tatiana A Zdobnova
- Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia.
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41
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Comparative analysis of algorithms for integration of copy number and expression data. Nat Methods 2012; 9:351-5. [PMID: 22327835 DOI: 10.1038/nmeth.1893] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Accepted: 01/06/2012] [Indexed: 12/15/2022]
Abstract
Chromosomal instability is a hallmark of cancer, and genes that display abnormal expression in aberrant chromosomal regions are likely to be key players in tumor progression. Identifying such driver genes reliably requires computational methods that can integrate genome-scale data from several sources. We compared the performance of ten algorithms that integrate copy-number and transcriptomics data from 15 head and neck squamous cell carcinoma cell lines, 129 lung squamous cell carcinoma primary tumors and simulated data. Our results revealed clear differences between the methods in terms of sensitivity and specificity as well as in their performance in small and large sample sizes. Results of the comparison are available at http://csbi.ltdk.helsinki.fi/cn2gealgo/.
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42
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Abstract
Personalized medicine is based on intraspecies differences. It is axiomatic that small differences in genetic make-up can result in dramatic differences in response to drugs or disease. To express this in more general terms: in any given complex system, small changes in initial conditions can result in dramatically different outcomes. Despite human variability and intraspecies variation in other species, nonhuman species are still the primary model for ascertaining data for humans. We call this practice into question and conclude that human-based research should be the primary means for obtaining data about human diseases and responses to drugs.
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Affiliation(s)
| | - Andre Menache
- Americans For Medical Advancement, 2251 Refugio Rd, Goleta, CA 93117, USA
| | - Mark J Rice
- Department of Anesthesiology, University of Florida College of Medicine, PO Box 100254, Gainesville, FL 32610-0254, USA
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43
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Bünger S, Haug U, Kelly FM, Klempt-Giessing K, Cartwright A, Posorski N, Dibbelt L, Fitzgerald SP, Bruch HP, Roblick UJ, von Eggeling F, Brenner H, Habermann JK. Toward standardized high-throughput serum diagnostics: multiplex-protein array identifies IL-8 and VEGF as serum markers for colon cancer. ACTA ACUST UNITED AC 2011; 16:1018-26. [PMID: 21807963 DOI: 10.1177/1087057111414894] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Development and progression of colon cancer may be related to cytokines. Cytokines with diagnostic value have been identified individually but have not been implemented into clinical praxis. Using a multiplex protein array, the authors explore a panel of cytokines simultaneously and compared its performance to carcinoembryonic antigen (CEA) and carbohydrate antigen 19-9 (CA 19-9). Serum concentrations of 12 cytokines were simultaneously determined by multiplex biochip technology in 50 colon cancer patients and 50 healthy controls. Serum levels of interleukin-8 (IL-8) and CEA were significantly higher in cancer patients than in healthy controls. Areas under the receiver operating characteristic curves (AUCs) were largest for IL-8, followed by CEA, vascular endothelial growth factor (VEGF), and CA 19-9. Analyses regarding marker combinations showed an advantage over single marker performance for CEA, VEGF, and CA 19-9 but not for IL-8. Multiplex biochip array technology represents a practical tool in cytokine and cancer research when simultaneous determination of different biomarkers is of interest. The results suggest that the assessment of IL-8, CEA, VEGF, and possibly CA 19-9 serum levels could be useful for colon cancer screening with the potential of also detecting early stage tumors. Further validation studies using these and additional markers on a multiplex array format are encouraged.
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Affiliation(s)
- Stefanie Bünger
- Laboratory for Surgical Research, Department of Surgery, University of Lübeck, Germany
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44
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Hongzhan H, Shukla HD, Cathy W, Satya S. Challenges and solutions in proteomics. Curr Genomics 2011; 8:21-8. [PMID: 18645629 PMCID: PMC2474689 DOI: 10.2174/138920207780076910] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2006] [Revised: 12/10/2006] [Accepted: 12/15/2006] [Indexed: 11/22/2022] Open
Abstract
The accelerated growth of proteomics data presents both opportunities and challenges. Large-scale proteomic profiling of biological samples such as cells, organelles or biological fluids has led to discovery of numerous key and novel proteins involved in many biological/disease processes including cancers, as well as to the identification of novel disease biomarkers and potential therapeutic targets. While proteomic data analysis has been greatly assisted by the many bioinformatics tools developed in recent years, a careful analysis of the major steps and flow of data in a typical highthroughput analysis reveals a few gaps that still need to be filled to fully realize the value of the data. To facilitate functional and pathway discovery for large-scale proteomic data, we have developed an integrated proteomic expression analysis system, iProXpress, which facilitates protein identification using a comprehensive sequence library and functional interpretation using integrated data. With its modular design, iProXpress complements and can be integrated with other software in a proteomic data analysis pipeline. This novel approach to complex biological questions involves the interrogation of multiple data sources, thereby facilitating hypothesis generation and knowledge discovery from the genomic-scale studies and fostering disease diagnosis and drug development.
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Affiliation(s)
- Huang Hongzhan
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington DC, USA
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45
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Balestrieri C, Vanoni M, Hautaniemi S, Alberghina L, Chiaradonna F. Integrative transcriptional analysis between human and mouse cancer cells provides a common set of transformation associated genes. Biotechnol Adv 2011; 30:16-29. [PMID: 21736933 DOI: 10.1016/j.biotechadv.2011.06.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Revised: 06/13/2011] [Accepted: 06/13/2011] [Indexed: 12/26/2022]
Abstract
Mouse functional genomics is largely used to investigate relevant aspects of mammalian physiology and pathology. To which degree mouse models may offer accurate representations of molecular events underlining human diseases such as cancer is not yet fully established. Herein we compare gene expression signatures between a set of human cancer cell lines (NCI-60 cell collection) and a mouse cellular model of oncogenic K-ras dependent transformation in order to identify their closeness at the transcriptional level. The results of our integrative and comparative analysis show that in both species as compared to normal cells or tissues the transformation process involves the activation of a transcriptional response. Furthermore, the cellular mouse model of K-ras dependent transformation has a good degree of similarity with several human cancer cell lines and in particular with cell lines containing oncogenic Ras mutations. Moreover both species have similar genetic signatures that are associated to the same altered cellular pathways (e.g. Spliceosome and Proteasome) or to deregulation of the same genes (e.g. cyclin D1, AHSA1 and HNRNPD) detected in the comparison between cancer cells versus normal cells or tissues. In summary, we report one of the first in-depth analysis of global gene expression profiles of a K-ras dependent mouse cell model of transformation and a large collection of human cancer cells as compared to their normal counterparts. Taken together our findings show a strong correlation in the transcriptional and pathway alteration responses between the two species, therefore validating the use of the mouse model as an appropriate tool to investigate human cancer, and indicating that the comparative analysis, as described here, offers a useful approach to identify cancer-specific gene signatures.
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Affiliation(s)
- C Balestrieri
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy.
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46
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Nagel JHA, Peeters JK, Smid M, Sieuwerts AM, Wasielewski M, de Weerd V, Trapman-Jansen AMAC, van den Ouweland A, Brüggenwirth H, van IJcken WFJ, Klijn JGM, van der Spek PJ, Foekens JA, Martens JWM, Schutte M, Meijers-Heijboer H. Gene expression profiling assigns CHEK2 1100delC breast cancers to the luminal intrinsic subtypes. Breast Cancer Res Treat 2011; 132:439-48. [DOI: 10.1007/s10549-011-1588-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Accepted: 05/11/2011] [Indexed: 12/24/2022]
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47
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Koschmieder A, Zimmermann K, Trissl S, Stoltmann T, Leser U. Tools for managing and analyzing microarray data. Brief Bioinform 2011; 13:46-60. [PMID: 21422065 DOI: 10.1093/bib/bbr010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The microarray-based analysis of gene expression has become a workhorse for biomedical research. Managing the amount and diversity of data that such experiments produce is a task that must be supported by appropriate software tools, which led to the creation of literally hundreds of systems. In consequence, choosing the right tool for a given project is difficult even for the expert. We report on the results of a survey encompassing 78 of such tools, of which 22 were inspected in detail and seven were tested hands-on. We report on our experiences with a focus on completeness of functionality, ease-of-use, and necessary effort for installation and maintenance. Thereby, our survey provides a valuable guideline for any project considering the use of a microarray data management system. It reveals which tasks are covered by mature tools and also shows that important requirements, especially in the area of integrated analysis of different experimental data, are not yet met satisfyingly by existing systems.
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Affiliation(s)
- André Koschmieder
- Department of Computer Science, Humboldt-Universität zu Berlin, Rudower Chaussee 25, 12489 Berlin, Germany.
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48
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Uziely B, Turm H, Maoz M, Cohen I, Maly B, Bar-Shavit R. Par genes: molecular probes to pathological assessment in breast cancer progression. PATHOLOGY RESEARCH INTERNATIONAL 2011; 2011:178265. [PMID: 21318117 PMCID: PMC3035039 DOI: 10.4061/2011/178265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Accepted: 01/04/2011] [Indexed: 01/21/2023]
Abstract
Taking the issue of tumor categorization a step forward and
establish molecular imprints to accompany histopathological
assessment is a challenging task. This is important since often
patients with similar clinical and pathological tumors may respond
differently to a given treatment. Protease-activated receptor-1
(PAR1), a G protein-coupled receptor (GPCR),
is the first member
of the mammalian PAR family consisting of four genes. PAR1 and
PAR2 play a central role in breast cancer. The release of
N-terminal peptides during activation and the exposure of a
cryptic internal ligand in PARs, endow these receptors with the
opportunity to serve as a “mirror-image”
index reflecting the level of cell surface PAR1&2-in body fluids. It is possible to
use the levels of PAR-released peptide in patients and
accordingly determine the choice of treatment. We have both
identified PAR1 C-tail as a scaffold site for the immobilization
of signaling partners, and the critical minimal binding site. This
binding region may be used for future therapeutic modalities in
breast cancer, since abrogation of the binding inhibits PAR1
induced breast cancer. Altogether, both PAR1 and PAR2 may serve as
molecular probes for breast cancer diagnosis and valuable targets
for therapy.
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Affiliation(s)
- Beatrice Uziely
- Departments of Oncology, Hadassah-University Hospital P.O. Box 12000, Jerusalem 91120, Israel
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49
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Hu ZZ, Huang H, Wu CH, Jung M, Dritschilo A, Riegel AT, Wellstein A. Omics-based molecular target and biomarker identification. Methods Mol Biol 2011; 719:547-71. [PMID: 21370102 PMCID: PMC3742302 DOI: 10.1007/978-1-61779-027-0_26] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Genomic, proteomic, and other omic-based approaches are now broadly used in biomedical research to facilitate the understanding of disease mechanisms and identification of molecular targets and biomarkers for therapeutic and diagnostic development. While the Omics technologies and bioinformatics tools for analyzing Omics data are rapidly advancing, the functional analysis and interpretation of the data remain challenging due to the inherent nature of the generally long workflows of Omics experiments. We adopt a strategy that emphasizes the use of curated knowledge resources coupled with expert-guided examination and interpretation of Omics data for the selection of potential molecular targets. We describe a downstream workflow and procedures for functional analysis that focus on biological pathways, from which molecular targets can be derived and proposed for experimental validation.
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Affiliation(s)
- Zhang-Zhi Hu
- Lombardi Cancer Center, Georgetown University, Washington, DC, USA.
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50
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Sparano JA, Fazzari M, Kenny PA. Clinical application of gene expression profiling in breast cancer. Surg Oncol Clin N Am 2010; 19:581-606. [PMID: 20620929 DOI: 10.1016/j.soc.2010.03.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Breast cancer is a heterogeneous disease associated with variable clinical outcomes and response to therapy. Classic clinicopathologic factors associated with outcome include anatomic features associated with prognosis (eg, tumor size, number of positive regional lymph nodes) and biologic features associated with prognosis and/or predictive of response to specific therapies, usually by evaluating protein expression by immunohistochemistry (eg, estrogen and/or progesterone receptors) or amplification of a single gene (eg, HER2/neu). Gene expression profiling evaluating thousands of genes is now feasible, and has facilitated the development of multiparameter assays that may identify breast cancer subtypes associated with distinct clinical outcomes that were not previously recognized, or provide more accurate information about prognosis or response to specific therapies than may be provided by classic clinicopathologic features alone. Several multiparameter gene expression assays are commercially available, and additional assays are being developed that will facilitate more accurate therapeutic individualization.
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Affiliation(s)
- Joseph A Sparano
- Department of Medicine and Oncology, Albert Einstein College of Medicine, Montefiore Medical Center, 1825 Eastchester Road, Bronx, NY 10461, USA.
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