Correlates of immune-mediated protection to most viral and cancer vaccines are still unknown. This impedes the development of novel vaccines to incurable diseases such as HIV and cancer. In this study, we have used functional genomics and polychromatic flow cytometry to define the signature of the immune response to the yellow fever (YF) vaccine 17D (YF17D) in a cohort of 40 volunteers followed for up to 1 yr after vaccination. We show that immunization with YF17D leads to an integrated immune response that includes several effector arms of innate immunity, including complement, the inflammasome, and interferons, as well as adaptive immunity as shown by an early T cell response followed by a brisk and variable B cell response. Development of these responses is preceded, as demonstrated in three independent vaccination trials and in a novel in vitro system of primary immune responses (modular immune in vitro construct [MIMIC] system), by the coordinated up-regulation of transcripts for specific transcription factors, including STAT1, IRF7, and ETS2, which are upstream of the different effector arms of the immune response. These results clearly show that the immune response to a strong vaccine is preceded by coordinated induction of master transcription factors that lead to the development of a broad, polyfunctional, and persistent immune response that integrates all effector cells of the immune system.

Advances in molecular biological, analytical and computational technologies are enabling us to systematically investigate the complex molecular processes underlying biological systems. In particular, using high-throughput gene expression assays, we are able to measure the output of the gene regulatory network. We aim here to review datamining and modeling approaches for conceptualizing and unraveling the functional relationships implicit in these datasets. Clustering of co-expression profiles allows us to infer shared regulatory inputs and functional pathways. We discuss various aspects of clustering, ranging from distance measures to clustering algorithms and multiple-cluster memberships. More advanced analysis aims to infer causal connections between genes directly, i.e. who is regulating whom and how. We discuss several approaches to the problem of reverse engineering of genetic networks, from discrete Boolean networks, to continuous linear and non-linear models. We conclude that the combination of predictive modeling with systematic experimental verification will be required to gain a deeper insight into living organisms, therapeutic targeting and bioengineering.

It is not understood how immune inflammation influences the pathogenesis of severe acute respiratory syndrome (SARS). One area of strong controversy is the role of interferon (IFN) responses in the natural history of SARS.The fact that the majority of SARS patients recover after relatively moderate illness suggests that the prevailing notion of deficient type I IFN-mediated immunity, with hypercytokinemia driving a poor clinical course, is oversimplified. We used proteomic and genomic technology to systematically analyze host innate and adaptive immune responses of 40 clinically well-described patients with SARS during discrete phases of illness from the onset of symptoms to discharge or a fatal outcome. A novel signature of high IFN-␣, IFN-␥, and IFN-stimulated chemokine levels, plus robust antiviral IFN-stimulated gene (ISG) expression, accompanied early SARS sequelae. As acute illness progressed, SARS patients entered a crisis phase linked to oxygen saturation profiles. The majority of SARS patients resolved IFN responses at crisis and expressed adaptive immune genes. In contrast, patients with poor outcomes showed deviated ISG and immunoglobulin gene expression levels, persistent chemokine levels, and deficient anti-SARS spike antibody production. We contend that unregulated IFN responses during acute-phase SARS may culminate in a malfunction of the switch from innate immunity to adaptive immunity. The potential for the use of the gene signatures we describe in this study to better assess the immunopathology and clinical management of severe viral infections, such as SARS and avian influenza (H5N1), is therefore worth careful examination.Severe acute respiratory syndrome coronavirus (SARS CoV) causes a spectrum of disease ranging from flu-like symptoms and viral pneumonia to acute respiratory distress syndrome and fatal outcomes (14,16,23,31,41). The mechanisms by which SARS CoV causes severe illness in humans are largely unknown. SARS CoV takes hold in the airways and other organs via its main putative receptor, angiotensin-converting enzyme 2 (ACE2), expressed on many cell types, including pneumocytes, enterocytes, and endothelial cells (19,25,32). SARS CoV appears to evade innate immunity during the first 10 days of infection during a period of widespread inflammation and steadily increasing viral load (39, 52). The consequent immune inflammation and hypercytokinemia, or "cytokine storm," during the course of SARS has been illustrated (22,27,33,37,51), but the molecular and cellular basis of how SARS CoV impacts host defense, resulting in a poor prognosis, is not understood. One particular area of controversy is the role of interferon (IFN) responses in human host immune responses against SARS CoV.Type I IFNs, such as IFN-␣ and -␤, are critical to innate immune responses against viral and other microbial infections and act in concert with IFN-␥ in the activation of antiviral IFN-stimulated genes (ISGs) and the immunomodulation of innate and adaptive immunity (3,36,42,48). It has been proposed that deficie...

We used reverse transcription-coupled PCR to produce a high-resolution temporal map of f luctuations in mRNA expression of 112 genes during rat central nervous system development, focusing on the cervical spinal cord. The data provide a temporal gene expression ''fingerprint'' of spinal cord development based on major families of inter-and intracellular signaling genes. By using distance matrices for the pair-wise comparison of these 112 temporal gene expression patterns as the basis for a cluster analysis, we found five basic ''waves'' of expression that characterize distinct phases of development. The results suggest functional relationships among the genes f luctuating in parallel. We found that genes belonging to distinct functional classes and gene families clearly map to particular expression profiles. The concepts and data analysis discussed herein may be useful in objectively identifying coherent patterns and sequences of events in the complex genetic signaling network of development. Functional genomics approaches such as this may have applications in the elucidation of complex developmental and degenerative disorders.The complexity of living organisms poses a challenge to biologists: considering the rapid accumulation of vast amounts of data in the fields of molecular and cell biology, how can we begin to organize these data into a coherent functional whole? To understand the nature of complex biological processes, such as development, we must determine the specific gene expression patterns and biochemical interactions within an organism but, equally important, seek out the organizing principles that allow them to function in a coherent way. Herein, we present a practical experimental-computational strategy that may allow us to advance our understanding of the nature of the complex self-organizing process underlying mammalian central nervous system (CNS) development.As a first step in this approach, we have addressed the question of whether the temporal expression patterns of large numbers of genes exhibit some degree of order across a tissue, in this case, the developing cervical spinal cord. Further, we are interested in forming hypotheses concerning possible functional relationships between gene families, by examining their patterns of expression over the course of development.The differentiation and maintenance of a cell phenotype may be viewed as the product of a system of well-coordinated interactions, with some cell types influencing the development of others. Therefore, we have taken a systems approach to CNS development in which the tissue is treated as a whole. In vivo gene expression patterns characteristic of stem cells, pluripotent progenitor cells, and mature neurons and glia should be reflected in the patterns of gene expression obtained at different developmental time points.Ongoing genome sequencing projects are based on the concept that proteins mediating the functions of organisms are strictly determined by the structure and activity of the genes that encode them. Data from g...