Taken together, these findings suggest that while selection for antigen specificity is known to be important, VDJ combination alone does not determine antigen specificity, in clinically healthy individuals

Taken together, these findings suggest that while selection for antigen specificity is known to be important, VDJ combination alone does not determine antigen specificity, in clinically healthy individuals. Segment usage, pairwise preferences, and selection on VDJ combinations in mice We conducted the same analysis on VD, DJ, and VJ pairs, and VDJ combinations, from C57BL/6 mice. antibodies, and T cells, which target infected or otherwise aberrant cells through their T cell receptors (TCRs). Both cell types have been of longstanding interest for their functions in vaccines, infections, and autoimmune diseases, as well as malignancy [1], [2]. Underlying these roles is the ability of B and T cells to generate a seemingly infinite quantity of different antigen specificities from your finite genetic material encoded in the germline genome. Several mechanisms are responsible for generating this diversity. The most fundamental is usually somatic recombination [3]. This is a combinatorial process in which any one of several gene segments from each of two or three sets of segments are recombined to form a single novel gene (a highly ordered and regulated process). Each antibody molecule is made up of the protein products of two such genes, called heavy chain and light chain. The heavy-chain gene is usually constructed, through somatic recombination, of three gene segments, called V, D, and J; you will find 56 V, 23 D, and 6 J segments in the human genome [4]. The sequence from your V-D to the D-J junction, spanning the entire D segment, is called complementarity determining region (CDR) NU2058 3 and encodes part of the heavy chain that makes physical contact with the antigen. It is the single most important determinant of an antibody’s antigen specificity [5], [6]. Hence detailed descriptions of CDR3 diversity are a prerequisite for understanding antibody responses to vaccines and infections and in autoimmunity in fine detailthe level of detail required for rational approaches to development of the next generation of diagnostics and therapeutics [1], [2]. There has been growing desire for using high throughput sequencing for describing antibodies [7], [8] and TCR [9], [10], [11], [12]. Recent studies have used sequencing to describe the antibody repertoire in zebrafish [13], to estimate the diversity of TCR in humans [12], and to monitor residual disease in leukemia patients [14]. The B cell repertoire in humans and mice has been the subject of a number of detailed studies, especially of antibody responses to numerous diseases, but not typically at the level offered by high-throughput sequencing [15], [16], [17], [18], [19], [20], [21]. Since the diversity of antibody sequences depends on VDJ recombination, a number of previous studies have investigated the diversity of VDJ joints expressed in response to specific infections, malignancies, and autoimmune diseases [15], [16], [17], [18], [19], [20], [21]. They NU2058 showed that for many exposures, genetically different individuals NU2058 produce antibodies with the same heavy- or light-chain V(D)J NU2058 combinations [22], [23], [24], [25]. This has been observed most often in antibody responses to bacterial polysaccharide antigens, which are of interest because they are the targets of protective and vaccine responses against infections by a number of medically important life-threatening bacteria, such as and type B, in which protective antibodies use V segment VH3-23, either J segment JH4 or JH6, and a D that results in a heavy-chain CDR3 NU2058 that contains the protein sequence GYGF/MD [26]. Studies have shown the presence of so-called public sequences [27] (overlap among the repertoires of different individuals), an unlikely occurrence if repertoires are shaped exclusively by chance. In this context, we sought to describe the baseline diversity of V, D, J, and CDR3 repertoires in Rabbit Polyclonal to URB1 antibody heavy-chain genes in human and mouse using high-throughput sequencing with particular attention to the functions of somatic recombination and positive and negative selection. Materials and Methods Using 454 sequencing [28], we sequenced antibody heavy-chain VDJ-rearranged genes from two.