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Mansfeldt CB, Heavner GW, Rowe AR, Hayete B, Church BW, Richardson RE. Inferring Gene Networks for Strains of Dehalococcoides Highlights Conserved Relationships between Genes Encoding Core Catabolic and Cell-Wall Structural Proteins. PLoS One 2016; 11:e0166234. [PMID: 27829029 PMCID: PMC5102406 DOI: 10.1371/journal.pone.0166234] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 10/25/2016] [Indexed: 12/17/2022] Open
Abstract
The interpretation of high-throughput gene expression data for non-model microorganisms remains obscured because of the high fraction of hypothetical genes and the limited number of methods for the robust inference of gene networks. Therefore, to elucidate gene-gene and gene-condition linkages in the bioremediation-important genus Dehalococcoides, we applied a Bayesian inference strategy called Reverse Engineering/Forward Simulation (REFS™) on transcriptomic data collected from two organohalide-respiring communities containing different Dehalococcoides mccartyi strains: the Cornell University mixed community D2 and the commercially available KB-1® bioaugmentation culture. In total, 49 and 24 microarray datasets were included in the REFS™ analysis to generate an ensemble of 1,000 networks for the Dehalococcoides population in the Cornell D2 and KB-1® culture, respectively. Considering only linkages that appeared in the consensus network for each culture (exceeding the determined frequency cutoff of ≥ 60%), the resulting Cornell D2 and KB-1® consensus networks maintained 1,105 nodes (genes or conditions) with 974 edges and 1,714 nodes with 1,455 edges, respectively. These consensus networks captured multiple strong and biologically informative relationships. One of the main highlighted relationships shared between these two cultures was a direct edge between the transcript encoding for the major reductive dehalogenase (tceA (D2) or vcrA (KB-1®)) and the transcript for the putative S-layer cell wall protein (DET1407 (D2) or KB1_1396 (KB-1®)). Additionally, transcripts for two key oxidoreductases (a [Ni Fe] hydrogenase, Hup, and a protein with similarity to a formate dehydrogenase, “Fdh”) were strongly linked, generalizing a strong relationship noted previously for Dehalococcoides mccartyi strain 195 to multiple strains of Dehalococcoides. Notably, the pangenome array utilized when monitoring the KB-1® culture was capable of resolving signals from multiple strains, and the network inference engine was able to reconstruct gene networks in the distinct strain populations.
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Affiliation(s)
- Cresten B. Mansfeldt
- Department of Civil and Environmental Engineering, Cornell University, Ithaca, NY, United States of America
- * E-mail:
| | - Gretchen W. Heavner
- Department of Civil and Environmental Engineering, Cornell University, Ithaca, NY, United States of America
| | - Annette R. Rowe
- Field of Microbiology, Cornell University, Ithaca, NY, United States of America
| | - Boris Hayete
- GNS Healthcare. Cambridge, MA, United States of America
| | | | - Ruth E. Richardson
- Department of Civil and Environmental Engineering, Cornell University, Ithaca, NY, United States of America
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Cabanski M, Fields B, Boue S, Boukharov N, DeLeon H, Dror N, Geertz M, Guedj E, Iskandar A, Kogel U, Merg C, Peck MJ, Poussin C, Schlage WK, Talikka M, Ivanov NV, Hoeng J, Peitsch MC. Transcriptional profiling and targeted proteomics reveals common molecular changes associated with cigarette smoke-induced lung emphysema development in five susceptible mouse strains. Inflamm Res 2015; 64:471-86. [PMID: 25962837 PMCID: PMC4464601 DOI: 10.1007/s00011-015-0820-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 03/15/2015] [Accepted: 04/11/2015] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Mouse models are useful for studying cigarette smoke (CS)-induced chronic pulmonary pathologies such as lung emphysema. To enhance translation of large-scale omics data from mechanistic studies into pathophysiological changes, we have developed computational tools based on reverse causal reasoning (RCR). OBJECTIVE In the present study we applied a systems biology approach leveraging RCR to identify molecular mechanistic explanations of pathophysiological changes associated with CS-induced lung emphysema in susceptible mice. METHODS The lung transcriptomes of five mouse models (C57BL/6, ApoE (-/-) , A/J, CD1, and Nrf2 (-/-) ) were analyzed following 5-7 months of CS exposure. RESULTS We predicted 39 molecular changes mostly related to inflammatory processes including known key emphysema drivers such as NF-κB and TLR4 signaling, and increased levels of TNF-α, CSF2, and several interleukins. More importantly, RCR predicted potential molecular mechanisms that are less well-established, including increased transcriptional activity of PU.1, STAT1, C/EBP, FOXM1, YY1, and N-COR, and reduced protein abundance of ITGB6 and CFTR. We corroborated several predictions using targeted proteomic approaches, demonstrating increased abundance of CSF2, C/EBPα, C/EBPβ, PU.1, BRCA1, and STAT1. CONCLUSION These systems biology-derived candidate mechanisms common to susceptible mouse models may enhance understanding of CS-induced molecular processes underlying emphysema development in mice and their relevancy for human chronic obstructive pulmonary disease.
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Affiliation(s)
- Maciej Cabanski
- />Philip Morris International Research and Development, Philip Morris Products S.A, Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
- />Novartis Pharma AG, Novartis Institutes for Biomedical Research (NIBR), 4002 Basel, Switzerland
| | - Brett Fields
- />Selventa, One Alewife Center, Cambridge, MA 02140 USA
| | - Stephanie Boue
- />Philip Morris International Research and Development, Philip Morris Products S.A, Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | | | - Hector DeLeon
- />Philip Morris International Research and Development, Philip Morris Products S.A, Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Natalie Dror
- />Selventa, One Alewife Center, Cambridge, MA 02140 USA
| | - Marcel Geertz
- />Philip Morris International Research and Development, Philip Morris Products S.A, Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
- />Bayer Technology Services GmbH, 51368 Leverkusen, Germany
| | - Emmanuel Guedj
- />Philip Morris International Research and Development, Philip Morris Products S.A, Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Anita Iskandar
- />Philip Morris International Research and Development, Philip Morris Products S.A, Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Ulrike Kogel
- />Philip Morris International Research and Development, Philip Morris Products S.A, Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Celine Merg
- />Philip Morris International Research and Development, Philip Morris Products S.A, Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Michael J. Peck
- />Philip Morris International Research and Development, Philip Morris Products S.A, Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Carine Poussin
- />Philip Morris International Research and Development, Philip Morris Products S.A, Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Walter K. Schlage
- />Philip Morris International Research and Development, Philip Morris Products S.A, Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Marja Talikka
- />Philip Morris International Research and Development, Philip Morris Products S.A, Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Nikolai V. Ivanov
- />Philip Morris International Research and Development, Philip Morris Products S.A, Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Julia Hoeng
- />Philip Morris International Research and Development, Philip Morris Products S.A, Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Manuel C. Peitsch
- />Philip Morris International Research and Development, Philip Morris Products S.A, Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
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