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Mehrpooya A, Saberi-Movahed F, Azizizadeh N, Rezaei-Ravari M, Saberi-Movahed F, Eftekhari M, Tavassoly I. High dimensionality reduction by matrix factorization for systems pharmacology. Brief Bioinform 2022; 23:bbab410. [PMID: 34891155 PMCID: PMC8898012 DOI: 10.1093/bib/bbab410] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 08/20/2021] [Accepted: 09/07/2021] [Indexed: 12/13/2022] Open
Abstract
The extraction of predictive features from the complex high-dimensional multi-omic data is necessary for decoding and overcoming the therapeutic responses in systems pharmacology. Developing computational methods to reduce high-dimensional space of features in in vitro, in vivo and clinical data is essential to discover the evolution and mechanisms of the drug responses and drug resistance. In this paper, we have utilized the matrix factorization (MF) as a modality for high dimensionality reduction in systems pharmacology. In this respect, we have proposed three novel feature selection methods using the mathematical conception of a basis for features. We have applied these techniques as well as three other MF methods to analyze eight different gene expression datasets to investigate and compare their performance for feature selection. Our results show that these methods are capable of reducing the feature spaces and find predictive features in terms of phenotype determination. The three proposed techniques outperform the other methods used and can extract a 2-gene signature predictive of a tyrosine kinase inhibitor treatment response in the Cancer Cell Line Encyclopedia.
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Affiliation(s)
- Adel Mehrpooya
- School of Mathematical Sciences, Science and Engineering Faculty, Queensland University of Technology (QUT), Brisbane, Australia
- Department of Computer Engineering, Faculty of Engineering, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Farid Saberi-Movahed
- Department of Applied Mathematics, Faculty of Sciences and Modern Technologies, Graduate University of Advanced Technology, Kerman, Iran
| | - Najmeh Azizizadeh
- Department of Applied Mathematics, Faculty of Mathematics and Computer, Shahid Bahonar University of Kerman, Iran
| | - Mohammad Rezaei-Ravari
- Department of Computer Engineering, Faculty of Engineering, Shahid Bahonar University of Kerman, Kerman, Iran
| | | | - Mahdi Eftekhari
- Department of Computer Engineering, Faculty of Engineering, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Iman Tavassoly
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY10029, USA
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Shang YK, Li C, Liu ZK, Kong LM, Wei D, Xu J, Wang ZL, Bian H, Chen ZN. System analysis of the regulation of the immune response by CD147 and FOXC1 in cancer cell lines. Oncotarget 2018; 9:12918-12931. [PMID: 29560120 PMCID: PMC5849184 DOI: 10.18632/oncotarget.24161] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 12/03/2017] [Indexed: 12/26/2022] Open
Abstract
CD147, encoded by BSG, is a highly glycosylated transmembrane protein that belongs to the immunological superfamily and expressed on the surface of many types of cancer cells. While CD147 is best known as a potent inducer of extracellular matrix metalloproteinases, it can also function as a key mediator of inflammatory and immune responses. To systematically elucidate the function of CD147 in cancer cells, we performed an analysis of genome-wide profiling across the Cancer Cell Line Encyclopedia (CCLE). We showed that CD147 mRNA expression was much higher than that of most other genes in cancer cell lines. CD147 varied widely across these cell lines, with the highest levels in the ovary (COLO704) and stomach (SNU668), intermediate levels in the lung (RERFLCKJ, NCIH596 and NCIH1651) and lowest levels in hematopoietic and lymphoid tissue (UT7, HEL9217, HEL and MHHCALL3) and the kidney (A704 and SLR20). Genome-wide analyses showed that CD147 expression was significantly negatively correlated with immune-related genes. Our findings implicated CD147 as a novel regulator of immune-related genes and suggest its important role as a master regulator of immune-related responses in cancer cell lines. We also found a high correlation between the expression of CD147 and FOXC1, and proved that CD147 was a direct transcriptional target of FOXC1. Our findings demonstrate that FOXC1 is a novel regulator of CD147 and confirms its role as a master regulator of the immune response.
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Affiliation(s)
- Yu-Kui Shang
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China.,State Key Laboratory of Cancer Biology, Cell Engineering Research Center and Department of Cell Biology, Fourth Military Medical University, Xi'an, 71032, China
| | - Can Li
- State Key Laboratory of Cancer Biology, Cell Engineering Research Center and Department of Cell Biology, Fourth Military Medical University, Xi'an, 71032, China
| | - Ze-Kun Liu
- State Key Laboratory of Cancer Biology, Cell Engineering Research Center and Department of Cell Biology, Fourth Military Medical University, Xi'an, 71032, China
| | - Ling-Min Kong
- State Key Laboratory of Cancer Biology, Cell Engineering Research Center and Department of Cell Biology, Fourth Military Medical University, Xi'an, 71032, China
| | - Ding Wei
- State Key Laboratory of Cancer Biology, Cell Engineering Research Center and Department of Cell Biology, Fourth Military Medical University, Xi'an, 71032, China
| | - Jing Xu
- State Key Laboratory of Cancer Biology, Cell Engineering Research Center and Department of Cell Biology, Fourth Military Medical University, Xi'an, 71032, China
| | - Zi-Ling Wang
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China
| | - Huijie Bian
- State Key Laboratory of Cancer Biology, Cell Engineering Research Center and Department of Cell Biology, Fourth Military Medical University, Xi'an, 71032, China
| | - Zhi-Nan Chen
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China.,State Key Laboratory of Cancer Biology, Cell Engineering Research Center and Department of Cell Biology, Fourth Military Medical University, Xi'an, 71032, China
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