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De R, Whiteley M, Azad RK. A gene network-driven approach to infer novel pathogenicity-associated genes: application to Pseudomonas aeruginosa PAO1. mSystems 2023; 8:e0047323. [PMID: 37921470 PMCID: PMC10734507 DOI: 10.1128/msystems.00473-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 10/04/2023] [Indexed: 11/04/2023] Open
Abstract
IMPORTANCE We present here a new systems-level approach to decipher genetic factors and biological pathways associated with virulence and/or antibiotic treatment of bacterial pathogens. The power of this approach was demonstrated by application to a well-studied pathogen Pseudomonas aeruginosa PAO1. Our gene co-expression network-based approach unraveled known and unknown genes and their networks associated with pathogenicity in P. aeruginosa PAO1. The systems-level investigation of P. aeruginosa PAO1 helped identify putative pathogenicity and resistance-associated genetic factors that could not otherwise be detected by conventional approaches of differential gene expression analysis. The network-based analysis uncovered modules that harbor genes not previously reported by several original studies on P. aeruginosa virulence and resistance. These could potentially act as molecular determinants of P. aeruginosa PAO1 pathogenicity and responses to antibiotics.
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Affiliation(s)
- Ronika De
- Department of Biological Sciences, University of North Texas, Denton, Texas, USA
- BioDiscovery Institute, University of North Texas, Denton, Texas, USA
| | - Marvin Whiteley
- Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Emory-Children’s Cystic Fibrosis Center, Atlanta, Georgia, USA
| | - Rajeev K. Azad
- Department of Biological Sciences, University of North Texas, Denton, Texas, USA
- BioDiscovery Institute, University of North Texas, Denton, Texas, USA
- Department of Mathematics, University of North Texas, Denton, Texas, USA
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Qin ZX, Chen GZ, Yang QQ, Wu YJ, Sun CQ, Yang XM, Luo M, Yi CR, Zhu J, Chen WH, Liu Z. Cross-Platform Transcriptomic Data Integration, Profiling, and Mining in Vibrio cholerae. Microbiol Spectr 2023; 11:e0536922. [PMID: 37191528 PMCID: PMC10269641 DOI: 10.1128/spectrum.05369-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 04/24/2023] [Indexed: 05/17/2023] Open
Abstract
A large number of transcriptome studies generate important data and information for the study of pathogenic mechanisms of pathogens, including Vibrio cholerae. V. cholerae transcriptome data include RNA-seq and microarray: microarray data mainly include clinical human and environmental samples, and RNA-seq data mainly focus on laboratory processing conditions, including different stresses and experimental animals in vivo. In this study, we integrated the data sets of both platforms using Rank-in and the Limma R package normalized Between Arrays function, achieving the first cross-platform transcriptome data integration of V. cholerae. By integrating the entire transcriptome data, we obtained the profiles of the most active or silent genes. By transferring the integrated expression profiles into the weighted correlation network analysis (WGCNA) pipeline, we identified the important functional modules of V. cholerae in vitro stress treatment, gene manipulation, and in vitro culture as DNA transposon, chemotaxis and signaling, signal transduction, and secondary metabolic pathways, respectively. The analysis of functional module hub genes revealed the uniqueness of clinical human samples; however, under specific expression patterning, the Δhns, ΔoxyR1 strains, and tobramycin treatment group showed high expression profile similarity with human samples. By constructing a protein-protein interaction (PPI) interaction network, we discovered several unreported novel protein interactions within transposon functional modules. IMPORTANCE We used two techniques to integrate RNA-seq data for laboratory studies with clinical microarray data for the first time. The interactions between V. cholerae genes were obtained from a global perspective, as well as comparing the similarity between clinical human samples and the current experimental conditions, and uncovering the functional modules that play a major role under different conditions. We believe that this data integration can provide us with some insight and basis for elucidating the pathogenesis and clinical control of V. cholerae.
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Affiliation(s)
- Zi-Xin Qin
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Guo-Zhong Chen
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Qian-Qian Yang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ying-Jian Wu
- Department of Bioinformatics and Systems Biology, Huazhong University of Science and Technology College of Life Sciences and Technology, Wuhan, Hubei, China
| | - Chu-Qing Sun
- Department of Bioinformatics and Systems Biology, Huazhong University of Science and Technology College of Life Sciences and Technology, Wuhan, Hubei, China
| | - Xiao-Man Yang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Mei Luo
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Chun-Rong Yi
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jun Zhu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Wei-Hua Chen
- Department of Bioinformatics and Systems Biology, Huazhong University of Science and Technology College of Life Sciences and Technology, Wuhan, Hubei, China
| | - Zhi Liu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
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Im H, Lee JH, Choi SH. Independent Component Analysis Identifies the Modulons Expanding the Transcriptional Regulatory Networks of Enterohemorrhagic Escherichia coli. Front Microbiol 2022; 13:953404. [PMID: 35814713 PMCID: PMC9263587 DOI: 10.3389/fmicb.2022.953404] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 06/06/2022] [Indexed: 01/19/2023] Open
Abstract
The elucidation of the transcriptional regulatory networks (TRNs) of enterohemorrhagic Escherichia coli (EHEC) is critical to understand its pathogenesis and survival in the host. However, the analyses of current TRNs are still limited to comprehensively understand their target genes generally co-regulated under various conditions regardless of the genetic backgrounds. In this study, independent component analysis (ICA), a machine learning-based decomposition method, was used to decompose the large-scale transcriptome data of EHEC into the modulons, which contain the target genes of several TRNs. The locus of enterocyte effacement (LEE) and the Shiga toxin (Stx) modulons mainly consisted of the Ler regulon and the Stx prophage genes, respectively, confirming that ICA properly grouped the co-regulated major virulence genes of EHEC. Further investigation revealed that the LEE modulon contained the hypothetical Z0395 gene as a novel member of the Ler regulon, and the Stx modulon contained the thi and cus locus genes in addition to the Stx prophage genes. Correspondingly, the Stx prophage genes were also regulated by thiamine and copper ions known to control the thi and cus locus genes, respectively. The modulons effectively clustered the genes co-regulated regardless of the growth conditions and the genetic backgrounds of EHEC. The changed activities of the individual modulons successfully explained the differential expressions of the virulence and survival genes during the course of infection in bovines. Altogether, these results suggested that ICA of the large-scale transcriptome data can expand and enhance the current understanding of the TRNs of EHEC.
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Affiliation(s)
- Hanhyeok Im
- National Research Laboratory of Molecular Microbiology and Toxicology, Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Seoul National University, Seoul, South Korea
- Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Science, Seoul National University, Seoul, South Korea
| | - Ju-Hoon Lee
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Seoul National University, Seoul, South Korea
- Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Science, Seoul National University, Seoul, South Korea
- *Correspondence: Ju-Hoon Lee,
| | - Sang Ho Choi
- National Research Laboratory of Molecular Microbiology and Toxicology, Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Seoul National University, Seoul, South Korea
- Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Science, Seoul National University, Seoul, South Korea
- Sang Ho Choi,
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