Network, degeneracy and bow tie. Integrating paradigms and architectures to grasp the complexity of the immune system

Recently, the network paradigm, an application of graph theory to biology, has proven to be a powerful approach to gaining insights into biological complexity, and has catalyzed the advancement of systems biology. In this perspective and focusing on the immune system, we propose here a more comprehensive view to go beyond the concept of network. We start from the concept of degeneracy, one of the most prominent characteristic of biological complexity, defined as the ability of structurally different elements to perform the same function, and we show that degeneracy is highly intertwined with another recently-proposed organizational principle, i.e. 'bow tie architecture'. The simultaneous consideration of concepts such as degeneracy, bow tie architecture and network results in a powerful new interpretative tool that takes into account the constructive role of noise (stochastic fluctuations) and is able to grasp the major characteristics of biological complexity, i.e. the capacity to turn an apparently chaotic and highly dynamic set of signals into functional information

Detection of human antibodies using "convergent" combinatorial peptide libraries or "mixotopes" designed from a nonvariable antigen: application to the EBV viral capsid antigen p18.

International audienceWe have previously described the use of synthetic combinatorial "convergent" libraries, or "mixotopes" as immunogens or as antigens to represent naturally hypervariable sequences. The success of this approach suggests that such a mixture of closely related peptides could, at least in part, conveniently represent a nonvariable epitope during its multiple interactions with an antibody population. To address this possibility, we have designed from a non-variable immunodominant peptide of the EBV-viral capsid antigen of 18 kD (VCAp18) a series of three mixotopes containing from 65,000 to 16 million combinatorial sequences. The reactivity of VCAp18 and its three derived mixotopes was examined in ELISA towards a collection of 74 human sera from documented EBV-negative or EBV-positive donors, and analyzed in terms of sensitivity and specificity. Following the observation that the two least degenerated mixotopes could improve the sensitivity of detection of some sera of low reactivity for VCAp18, we decided to combine each mixotope with the VCAp18 peptide. In the case of the least degenerated mixotope in combination with VCAp18, sensitivity and specificity for immunoenzymatic EBV-serodiagnosis, were enhanced to 100%. Our results suggest that synthetic "convergent" combinatorial peptide libraries or "mixotopes," designed from nonvariable antigens, could be useful adjuncts to an antigenic single-sequence peptide in immunoenzymatic serodiagnosis.We have previously described the use of synthetic combinatorial "convergent" libraries, or "mixotopes" as immunogens or as antigens to represent naturally hypervariable sequences. The success of this approach suggests that such a mixture of closely related peptides could, at least in part, conveniently represent a nonvariable epitope during its multiple interactions with an antibody population. To address this possibility, we have designed from a non-variable immunodominant peptide of the EBV-viral capsid antigen of 18 kD (VCAp18) a series of three mixotopes containing from 65,000 to 16 million combinatorial sequences. The reactivity of VCAp18 and its three derived mixotopes was examined in ELISA towards a collection of 74 human sera from documented EBV-negative or EBV-positive donors, and analyzed in terms of sensitivity and specificity. Following the observation that the two least degenerated mixotopes could improve the sensitivity of detection of some sera of low reactivity for VCAp18, we decided to combine each mixotope with the VCAp18 peptide. In the case of the least degenerated mixotope in combination with VCAp18, sensitivity and specificity for immunoenzymatic EBV-serodiagnosis, were enhanced to 100%. Our results suggest that synthetic "convergent" combinatorial peptide libraries or "mixotopes," designed from nonvariable antigens, could be useful adjuncts to an antigenic single-sequence peptide in immunoenzymatic serodiagnosis

Positive role of macaque cytotoxic T lymphocytes during SIV infection: decrease of cellular viremia and increase of asymptomatic clinical period.

We have measured cellular viremia and observed clinical outcome of macaques from two cohorts, the first including 12 macaques infected by SIVmac251 and the second including 12 macaques immunized by lipopeptides and then challenged by SIVmac251. In the first cohort (SIV-infected macaques), 3 patterns of CTL responders were determined: high, low and non-responders. In the macaques belonging to pattern of low and non-responders, cellular viremia, measured by growing the virus from PBMC, was continuously high during the first 6 months after infection, and five macaques developed AIDS within 14.4+/-7.7 months. Conversely, in the six high-responder macaques, cellular viremia was constantly low and only one macaque developed AIDS at 19 months, the five others being alive at 24 months. After immunization with lipopeptides, 7/12 macaques showed CTL responses and among these, after SIV challenge, cellular viremia was continually low, and no disease was observed at 22 months of follow-up. Conversely, the five non-responder macaques displayed persistent high viremia and macaques developed AIDS within 12.6+/-2.9 months after SIV challenge. These data strongly suggest that the presence of cytotoxic responses is inversely correlated with cellular viremia and correlated with overall survival and thus is an important component of the immune response in vaccinated individuals. It supports the idea that a strengthening of the CTL responses, if possible, might be beneficial in HIV-infected human beings

Selection of virus variants and emergence of virus escape mutants after immunization with epitope vaccine

In this report, we assessed the evolution of the cytotoxic T-lymphocyte (CTL) response induced by an epitope vaccine, In two macaques immunized with a mixture of lipopeptides derived from simian immunodeficiency virus (SIV) Nef and Gag proteins, CTL responses were directed against the same, single epitope of the Nef protein (amino acids 128 to 137) presenting an alanine at position 136 (Nef 128-137/136A). However, after 5 months of SIV infection, peripheral blood mononuclear cells from both macaques lost their ability to be stimulated by autologous SIV-infected cells while still retaining their capacity to generate cytotoxic responses after specific Nef 128-137/136A peptide stimulation. The sequences of the pathogenic viral isolate used for the challenge showed a mixture of several variants. Within the Nef epitopic sequence from amino acids 128 to 137, 82% of viral variants expressed the epitopic peptide Nef 128-137/136A; the remaining variants presented a threonine at position 136 (Nef 128-137/136T), In contrast, sequence analysis of cloned proviral DNA obtained from both macaques 5 months after SN challenge showed a different pattern of quasi-species variants; 100% of clones presented a threonine at position 136 (Nef 128-137/136T), suggesting the disappearance of viral variants with an alanine at this position under antiviral pressure exerted by Nef 128-137/136A-specific CTLs. In addition, 12 months after SIV challenge, six: of eight clones from one macaque presented a glutamic acid at position 131 (Nef128-137/131E+136T), which was not found in the infecting isolate. Furthermore, CTLs generated very early after SIV challenge were able to Lyse cells sensitized with the Nef 128-137/136A epitope. In contrast, lysis was significantly less effective or even did not occur when either the selected peptide Nef 128-137/136T or the escape variant peptide Nef 128-137/131E+136T was used in a target cell sensitization assay. Dose analysis of peptides used to sensitize target cells as well as a major histocompatibility complex (MHC)-peptide stability assay suggested that the selected peptide Nef 128-137/136T has an altered capacity to bind to the MHC. These data suggest that CTL pressure leads to the selection of viral variants and to the emergence of escape mutants and supports the fact that immunization should elicit broad CTL responses