Emergent Genome-Wide Control in Wildtype and Genetically Mutated Lipopolysaccarides-Stimulated Macrophages Masa Tsuchiya1,2.*, Vincent Piras1,2., Sangdun Choi3, Shizuo Akira4, Masaru Tomita1,2, Alessandro Giuliani5, Kumar Selvarajoo1,2.* 1 Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan, 2 Systems Biology Program, School of Media and Governance, Keio University, Fujisawa, Japan, 3 Department of Molecular Science and Technology, Ajou University, Suwon, Korea, 4 Department of Host Defense, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan, 5 Istituto Superiore di Sanita’, Environment and Health Department, Rome, Italy Abstract Large-scale gene expression studies have mainly focused on highly expressed and ‘discriminatory’ genes to decipher key regulatory processes. Biological responses are consequence of the concerted action of gene regulatory network, thus, limiting our attention to genes having the most significant variations is insufficient for a thorough understanding of emergent whole genome response. Here we comprehensively analyzed the temporal oligonucleotide microarray data of lipopolysaccharide (LPS) stimulated macrophages in 4 genotypes; wildtype, Myeloid Differentiation factor 88 (MyD88) knockout (KO), TIR-domain-containing adapter-inducing interferon-b (TRIF) KO and MyD88/TRIF double KO (DKO). Pearson correlations computed on the whole genome expression between different genotypes are extremely high (.0.98), indicating a strong co-regulation of the entire expression network. Further correlation analyses reveal genome-wide response is biphasic, i) acute-stochastic mode consisting of small number of sharply induced immune-related genes and ii) collective mode consisting of majority of weakly induced genes of diverse cellular processes which collectively adjust their expression level. Notably, temporal correlations of a small number of randomly selected genes from collective mode show scalability. Furthermore, in collective mode, the transition from large scatter in expression distributions for single ORFs to smooth linear lines emerges as an organizing principle when grouping of 50 ORFs and above. With this emergent behavior, the role of MyD88, TRIF and novel MyD88, TRIF-independent processes for gene induction can be linearly superposed to decipher quantitative whole genome differential control of transcriptional and mRNA decay machineries. Our work demonstrates genome-wide co-regulated responses subsequent to specific innate immune stimulus which have been largely neglected. Citation: Tsuchiya M, Piras V, Choi S, Akira S, Tomita M, et al. (2009) Emergent Genome-Wide Control in Wildtype and Genetically Mutated Lipopolysaccarides- Stimulated Macrophages. PLoS ONE 4(3): e4905. doi:10.1371/journal.pone.0004905 Editor: Peter Sommer, Institut Pasteur Korea, Republic of Korea Received January 13, 2009; Accepted February 19, 2009; Published March 20, 2009 Copyright: 2009 Tsuchiya et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was supported by Japan Science and Technology Agency/Core Research for Evolutional Science and Technology (JST CREST), Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT), Research fund by Yamagata Prefecture and Tsuruoka City, Japan. This work was also partly supported by the Korea Research Foundation Grant funded by the Korean Government (MOEHRD) (KRF-2006-311-C00482). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: tsuchiya@ttck.keio.ac.jp (MT); kumar@ttck.keio.ac.jp (KS) . These authors contributed equally to this work. Introduction The innate immune system utilizes pattern-recognition recep- tors (PRRs), present in phagocytes such as macrophages and dendritic cells, to recognize pathogen associated molecular patterns (PAMPs), such as lipopolysaccarides (LPS). LPS, which is found on the outer membrane of Gram-negative bacteria, through the Toll-like receptor (TLR) 4, triggers a cascade of signaling events initiated mainly by the MyD88- and TRIF- dependent pathways. This activates a number of common transcription factors including activator protein (AP)-1, nuclear factor–kB (NF-kB) and interferon regulatory factors (IRF)-3. As a result, a number of cytokines such as IL-1b and TNF-a, and type I interferons such as IFN-a and IFN-b are produced. These proinflammatory mediators activate helper T-cells for the onset of acquired immune defense where foreign intruders are eliminated and immunological memory is created [1–5]. These processes happen at a multi-cellular level implying the coordinated activities of many different tissues. Immunological responses are self-limiting, highly orchestrated systemic processes that if not precisely controlled can lead to major illnesses such as autoim- mune diseases, cardiovascular diseases and cancer [6–8]. Recent high throughput experimental technologies have enabled the comprehensive analysis of cellular response to a given stimulus. However, molecular immunology still largely follows the tradition of analyzing the snapshot of only a small number of specific statistically significant molecules’ response. Although analyzing statistically significant genes can help in the explanation of ‘local’ specific response, to grasp the global regulatory processes requires the comprehensive understanding of genome-wide response [9]. A previous high throughput study on LPS-stimulated murine macrophages (in wildtype, MyD88 KO, TRIF KO, and MyD88/ PLoS ONE | www.plosone.org 1 March 2009 | Volume 4 | Issue 3 | e4905