Public, private and non-specific antibodies induced by non-cytopathic viral infections

Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing

BACKGROUND

V(D)J recombinations in lymphocytes are essential for immunological diversity. They are also useful markers of pathologies. In leukemia, they are used to quantify the minimal residual disease during patient follow-up. However, the full breadth of lymphocyte diversity is not fully understood.

RESULTS

We propose new algorithms that process high-throughput sequencing (HTS) data to extract unnamed V(D)J junctions and gather them into clones for quantification. This analysis is based on a seed heuristic and is fast and scalable because in the first phase, no alignment is performed with germline database sequences. The algorithms were applied to TR γ HTS data from a patient with acute lymphoblastic leukemia, and also on data simulating hypermutations. Our methods identified the main clone, as well as additional clones that were not identified with standard protocols.

CONCLUSIONS

The proposed algorithms provide new insight into the analysis of high-throughput sequencing data for leukemia, and also to the quantitative assessment of any immunological profile. The methods described here are implemented in a C++ open-source program called Vidjil.

Control of B cells expressing naturally occurring autoantibodies

Naturally occurring autoantibodies (NAbs) are typically polyreactive, bind with low affinity to a discrete set of autoantigens and are encoded by variable region genes in germline configuration. They differ from disease-associated autoantibodies (autoAb), which are mostly monoreactive, somatically mutated and of high affinities. Structure-function studies have shown that polyreactivity of NAbs relies on the somatically generated complementarity determining region, CDR3, of the heavy chain. This finding suggested that NAb-producing B cells were positively selected from the pre-immune B-cell repertoire. The biological significance of this selection remains, however, unclear. Data originating mainly from transgenic mice have shown that mature NAb-producing B cells are frequently ignorant toward their antigen, possibly due to their low affinity, though active tolerance mechanisms are not excluded. An important issue is whether NAb-producing B cells constitute the pool from which pathologic auto Ab emerge after autoantigen-driven maturation. We summarize results obtained in mouse models, showing that some infectious agents are able to induce an autoantigen-driven activation of certain NAb-producing B cells. However direct proof that selection by autoantigen may lead to somatic hypermutation are still lacking. Other data tend to suggest that pathologic auto Abs may derive from non-autoimmune B cells that have diversified by somatic hypermutation of their variable region genes.

High-resolution description of antibody heavy-chain repertoires in humans

Antibodies' protective, pathological, and therapeutic properties result from their considerable diversity. This diversity is almost limitless in potential, but actual diversity is still poorly understood. Here we use deep sequencing to characterize the diversity of the heavy-chain CDR3 region, the most important contributor to antibody binding specificity, and the constituent V, D, and J segments that comprise it. We find that, during the stepwise D-J and then V-DJ recombination events, the choice of D and J segments exert some bias on each other; however, we find the choice of the V segment is essentially independent of both. V, D, and J segments are utilized with different frequencies, resulting in a highly skewed representation of VDJ combinations in the repertoire. Nevertheless, the pattern of segment usage was almost identical between two different individuals. The pattern of V, D, and J segment usage and recombination was insufficient to explain overlap that was observed between the two individuals' CDR3 repertoires. Finally, we find that while there are a near-infinite number of heavy-chain CDR3s in principle, there are about 3–9 million in the blood of an adult human being.

Viral persistence redirects CD4 T cell differentiation toward T follicular helper cells

Persistent virus infection drives follicular T helper cell differentiation.

CD4 T cell responses are crucial to prevent and control viral infection; however, virus-specific CD4 T cell activity is considered to be rapidly lost during many persistent viral infections. This is largely caused by the fact that during viral persistence CD4 T cells do not produce the classical Th1 cytokines associated with control of acute viral infections. Considering that CD4 T cell help is critical for both CD8 T cell and B cell functions, it is unclear how CD4 T cells can lose responsiveness but continue to sustain long-term control of persistent viral replication. We now demonstrate that CD4 T cell function is not extinguished as a result of viral persistence. Instead, viral persistence and prolonged T cell receptor stimulation progressively redirects CD4 T cell development away from the Th1 response induced during an acute infection toward T follicular helper cells. Importantly, this sustained CD4 T cell functionality is critical to maintain immunity and ultimately aid in the control of persistent viral infection.

Characterization of Anti-HCV Antibodies in IL-10-Treated Patients

There is limited information on the direct role of the neutralizing antibody responses against hepatitis C virus (HCV) infection or methodologies to study them. Previously we have demonstrated that interleukin-10 (IL-10) administered to chronic hepatitis patients led to a decrease in disease activity, but an increase in HCV viral burden. The mechanism behind this is unknown. The objective of this study was to examine the antibody response in IL-10-treated patients. To establish a neutralization antibody assay, HCV-positive and HCV-negative sera were collected and incubated with HCV strain JFH-1 particles before culture with Huh 7.5 cells. Viral replication was measured a week later by either indirect immunofluorescence assay (iIFA) or real-time reverse transcriptase polymerase chain reaction (RT-PCR). After validation of the methodology, the sera from 30 previously-described subjects of a group previously treated with IL-10 were tested for the neutralization capacity of their antibodies. The amount of total anti-HCV antibody in the sera was also measured by direct staining of HCV full-length replicon cells. With this validated neutralization assay for anti-HCV antibodies we found that HCV-neutralizing antibodies are universally present, but with significantly different titers. In patients who were treated with IL-10, the total anti-HCV antibody titers appear to be constant, but with significantly decreased antibody neutralization activity. Our study validates an assay to quantitatively determine the presence and strength of HCV-specific neutralizing antibodies. We have found that IL-10-treated patients have significantly lower HCV antibodies, but maintain the total anti-HCV antibody titer, suggesting a novel mechanism by which IL-10 treatment increases viral load in patients.

Adaptive immunity to Lymphocytic choriomeningitis virus: new insights into antigenic determinants

Lymphocytic choriomeningitis virus (LCMV) is one of the most studied infectious disease models in mice. Human infection with LCMV can result in severe disease, ranging from aseptic meningitis in immunocompetent individuals, hydrocephalus, chorioretinitis or microcephaly in fetal infection, or to a highly lethal outcome in immunosuppressed individuals. This review examines recent advances in our understanding of the adaptive immune response to LCMV and how the cell-mediated and humoral immune responses contribute to protective immunity. New insights into the antigenicity of the LCMV proteome and the complexity of the cell-mediated immune response are addressed. We also discuss state-of-the-art approaches for T-cell epitope discovery in murine and human backgrounds and their recent application to LCMV. New findings regarding CD4+ T-cell dysregulation during chronic LCMV infection, and potential avenues for the treatment of chronic viral infection through modulation of the programmed cell death-1 receptor and/or IL-10 signaling pathways, are also evaluated.