Stochastic competitive exclusion in the maintenance of the naïve T cell repertoire

Recognition of antigens by the adaptive immune system relies on a highly diverse T cell receptor repertoire. The mechanism that maintains this diversity is based on competition for survival stimuli; these stimuli depend upon weak recognition of self-antigens by the T cell antigen receptor. We study the dynamics of diversity maintenance as a stochastic competition process between a pair of T cell clonotypes that are similar in terms of the self-antigens they recognise. We formulate a bivariate continuous-time Markov process for the numbers of T cells belonging to the two clonotypes. We prove that the ultimate fate of both clonotypes is extinction and provide a bound on mean extinction times. We focus on the case where the two clonotypes exhibit negligible competition with other T cell clonotypes in the repertoire, since this case provides an upper bound on the mean extinction times. As the two clonotypes become more similar in terms of the self-antigens they recognise, one clonotype quickly becomes extinct in a process resembling classical competitive exclusion. We study the limiting probability distribution for the bivariate process, conditioned on non-extinction of both clonotypes. Finally, we derive deterministic equations for the number of cells belonging to each clonotype as well as a linear Fokker-Planck equation for the fluctuations about the deterministic stable steady state.     

Cutting edge: size and diversity of CD4+CD25high Foxp3+ regulatory T cell repertoire in humans: evidence for similarities and partial overlapping with CD4+CD25- T cells

Both differentiation and function of CD4+CD25(high) naturally arising regulatory T cells (Treg), which play a key role in the control of autoimmunity, are thought to depend on TCR specificity. In the present study, we comparatively measured the alphabetaTCR repertoire sizes of human peripheral blood Treg and CD4+CD25- T cells by using a methodology based on PCR amplification and sequencing analysis. We show that Treg use a large unrestricted alphabeta TCR repertoire, the size and diversity of which are closely similar to those of CD4+CD25- T cells, with a mean estimated size of 3.5 x 10(6) distinct alphabeta TCR vs 4.7 x 10(6) distinct alphabetaTCR for CD4+CD25- T cells. In addition, a 24% overlap between the repertoires of these two CD4+ subsets in the periphery is found. These data emphasize the intersection between naturally occurring Treg and effector T cell peripheral repertoires and provide new insights into the ontogeny of Treg in humans.     

The limiting conditional probability distribution in a stochastic model of T cell repertoire maintenance

The limiting conditional probability distribution (LCD) has been much studied in the field of mathematical biology, particularly in the context of epidemiology and the persistence of epidemics. However, it has not yet been applied to the immune system. One of the characteristic features of the T cell repertoire is its diversity. This diversity declines in old age, whence the concepts of extinction and persistence are also relevant to the immune system. In this paper we model T cell repertoire maintenance by means of a continuous-time birth and death process on the positive integers, where the origin is an absorbing state. We show that eventual extinction is guaranteed. The late-time behaviour of the process before extinction takes place is modelled by the LCD, which we prove always exists for the process studied here. In most cases, analytic expressions for the LCD cannot be computed but the probability distribution may be approximated by means of the stationary probability distributions of two related processes. We show how these approximations are related to the LCD of the original process and use them to study the LCD in two special cases. We also make use of the large N expansion to derive a further approximation to the LCD. The accuracy of the various approximations is then analysed.     

Fitness of cell-mediated immunity independent of repertoire diversity

Fitness of cell-mediated immunity is thought to depend on TCR diversity; however, this concept has not been tested formally. We tested the concept using JH(-/-) mice that lack B cells and have TCR Vbeta diversity <1% that of wild-type mice and quasimonoclonal (QM) mice with oligoclonal B cells and TCR Vbeta diversity 7% that of wild-type mice. Despite having a TCR repertoire contracted >99% and defective lymphoid organogenesis, JH(-/-) mice rejected H-Y-incompatible skin grafts as rapidly as wild-type mice. JH(-/-) mice exhibited T cell priming by peptide and delayed-type hypersensitivity, although these responses were less than normal owing either to TCR repertoire contraction or defective lymphoid organogenesis. QM mice with TCR diversity contracted >90%, and normal lymphoid organs rejected H-Y incompatible skin grafts as rapidly as wild type mice and exhibited normal T cell priming and normal delayed-type hypersensitivity reactions. QM mice also resisted Pneumocystis murina like wild-type mice. Thus, cell-mediated immunity can function normally despite contractions of TCR diversity >90% and possibly >99%.     

Size estimate of the alpha beta TCR repertoire of naive mouse splenocytes

The diversity of the T cell repertoire of mature T splenocytes is generated, in the thymus, by pairing of alpha and beta variable domains of the alpha beta TCR and by the rearrangements of various gene segments encoding these domains. In the periphery, it results from competition between various T cell subpopulations including recent thymic migrants and long-lived T cells. Quantitative data on the actual size of the T cell repertoire are lacking. Using PCR methods and extensive sequencing, we have measured for the first time the size of the TCR-alpha beta repertoire of naive mouse T splenocytes. There are 5-8 x 105 different nucleotide sequences of BV chains in the whole spleen of young adult mice. We have also determined the size of the BV repertoire in a subpopulation of AV2+ T splenocytes, which allows us to provide a minimum estimate of the alpha beta repertoire. We find that the mouse spleen harbors about 2 x 106 clones of about 10 cells each. This figure, although orders of magnitude smaller than the maximum theoretical diversity (estimated up to 1015), is still large enough to maintain a high functional diversity.     

A special repertoire of alpha:beta T cells in neonatal mice.

According to several functional criteria, the mature thymocytes of neonatal and adult mice are distinctly different. We wondered whether these differences in function might have a structural correlate: do neonates have a distinct repertoire of alpha:beta T cells? In this study, we have exploited the power of polymerase chain reaction technology to generate large numbers of T cell receptor sequences from sorted thymocyte populations from newborn and adult mice. The newborn-derived sequences show very few N nucleotide additions, usually the major source of diversity in T cell receptors. Most interestingly, the paucity of N insertions appears to be exaggerated by selection events that operate during T cell differentiation in the thymus. The significance of these results is largely: (i) that they parallel recent findings on the B cell repertoire in neonates, raising questions about the reactivities specified by such a special repertoire; and (ii) that they suggest a means to ''tag'' T cells exported perinatally, allowing one to test the premise that autoreactive T cells derive preferentially from the newborn repertoire.     

Longitudinal analysis of peripheral blood T cell receptor diversity in patients with systemic lupus erythematosus by next-generation sequencing

IntroductionT cells play an important role in the pathogenesis of systemic lupus erythematosus (SLE). Clonal expansion of T cells correlating with disease activity has been observed in peripheral blood (PB) of SLE subjects. Recently, next-generation sequencing (NGS) of the T cell receptor (TCR) β loci has emerged as a sensitive way to measure the T cell repertoire. In this study, we utilized NGS to assess whether changes in T cell repertoire diversity in PB of SLE patients correlate with or predict changes in disease activity.MethodsTotal RNA was isolated from the PB of 11 SLE patients. Each subject had three samples, collected at periods of clinical quiescence and at a flare. Twelve age-matched healthy controls (HC) were used for reference. NGS was used to profile the complementarity-determining region 3 (CDR3) of the rearranged TCR β loci.ResultsRelative to the HC, SLE patients (at quiescence) demonstrated a 2.2-fold reduction in repertoire diversity in a given PB volume (P <0.0002), a more uneven distribution of the repertoire (Gini coefficient, HC vs SLE, P = 0.015), and a trend toward increased percentage of expanded clones in the repertoire (clone size >1.0 %, HC vs SLE, P = 0.078). No significant correlation between the overall repertoire diversity and clinical disease activity was observed for most SLE patients with only two of eleven SLE patients showing a decreasing trend in repertoire diversity approaching the flare time point. We did not observe any overlap of CDR3 amino acid sequences or a preferential Vβ or Jβ gene usage among the top 100 expanded clones from all SLE patients. In both HC and SLE, the majority of the expanded clones were remarkably stable over time (HC = 5.5 ±0.5 months, SLE = 7.2 ±2.4 months).ConclusionsA significant decrease in T cell repertoire diversity was observed in PB of SLE patients compared to HC. However, in most SLE patients, repertoire diversity did not change significantly with increases in disease activity to a flare. Thus, without a priori knowledge of disease-specific clones, monitoring TCR repertoire in PB from SLE patients is not likely to be useful to predict changes in disease activity.

Electronic supplementary material

The online version of this article (doi:10.1186/s13075-015-0655-9) contains supplementary material, which is available to authorized users.     

How competitive intransitivity and niche overlap affect spatial coexistence

Competitive intransitivity is mostly considered outside the main body of coexistence theories that rely primarily on the role of niche overlap and differentiation. How the interplay of competitive intransitivity and niche overlap jointly affects species coexistence has received little attention. Here, we consider a rock–paper–scissors competition system where interactions between species can represent the full spectra of transitive–intransitive continuum and niche overlap/differentiation under different levels of competition asymmetry. By comparing results from pair approximation that only considers interference competition between neighbouring cells in spatial lattices, with those under the mean-field assumption, we show that 1) species coexistence under transitive competition is only possible at high niche differentiation; 2) in communities with partial or pure intransitive interactions, high levels of niche overlap are not necessary to beget species extinction; and 3) strong spatial clustering can widen the condition for intransitive loops to facilitate species coexistence. The two mechanisms, competitive intransitivity and niche differentiation, can support species persistence and coexistence, either separately or in combination. Finally, the contribution of intransitive loops to species coexistence can be enhanced by strong local spatial correlations, modulated and maximised by moderate competition asymmetry. Our study, therefore, provides a bridge to link intransitive competition to other generic ecological theories of species coexistence.     

Effective adoptive therapy of tap-deficient lymphoma using diverse high avidity alloreactive T cells

High avidity for antigen and diversity of T cell receptor (TCR) repertoire are essential for effective immunity against cancer. We have previously created a transgenic mouse strain with increased TCR avidity in a diverse T cell population. In this report, we show that strong alloreactive responses of transgenic T cells against targets with low MHC class I expression can be used for effective adoptive transfer of tumor immunity in vivo. Alloreactive transgenic T cells could be an effective therapeutic approach counteracting tumor evasion of the immune system.     

Impact of ageing on the response and repertoire of influenza virus-specific CD4 T cells

Background

Ageing has been shown to reduce CD8 T cell repertoire diversity and immune responses against influenza virus infection in mice. In contrast, less is known about the impact of ageing on CD4 T cell repertoire diversity and immune response to influenza virus infection.

Results

The CD4 T cell response was followed after infection of young and aged C57BL/6 mice with influenza virus using a tetramer specific for an immunodominant MHC class II epitope of the influenza virus nucleoprotein. The appearance of virus-specific CD4 T cells in the lung airways of aged mice was delayed compared to young mice, but the overall peak number and cytokine secretion profile of responding CD4 T cells was not greatly perturbed. In addition, the T cell repertoire of responding cells, determined using T cell receptor Vβ analysis, failed to show the profound effect of age we previously described for CD8 T cells. The reduced impact of age on influenza-specific CD4 T cells was consistent with a reduced effect of age on the overall CD4 compared with the CD8 T cell repertoire in specific pathogen free mice. Aged mice that were thymectomized as young adults showed an enhanced loss of the epitope-specific CD4 T cell response after influenza virus infection compared with age-matched sham-thymectomized mice, suggesting that a reduced repertoire can contribute to impaired responsiveness.

Conclusions

The diversity of the CD4 T cell repertoire and response to influenza virus is not as profoundly impaired by ageing in C57BL/6 mice as previously shown for CD8 T cells. However, adult thymectomy enhanced the impact of ageing on the response. Understanding the impact of ageing on CD4 T cell responses to influenza virus infection is an important prerequisite for developing better vaccines for the elderly.

     

T cell repertoire development in humans with SCID after nonablative allogeneic marrow transplantation

Transplantation of HLA-identical or haploidentical T cell-depleted allogeneic bone marrow (BM) into SCID infants results in thymus-dependent T cell development in the recipients. Immunoscope analysis of the TCR V beta repertoire was performed on 15 SCID patients given BM transplants. Before and within the first 100 days after bone marrow transplantation (BMT), patients' PBMC displayed an oligoclonal or skewed T cell repertoire, low TCR excision circles (TREC) values, and a predominance of CD45RO(+) T cells. In contrast, the presence of high numbers of CD45RA(+) cells in the circulation of SCID patients >100 days post-BMT correlated with active T cell output by the thymus as revealed by high TREC values and a polyclonal T cell repertoire demonstrated by a Gaussian distribution of V beta-specific peaks. Ten years after BMT, we observed a decrease of the normal polyclonal T cell repertoire and an increase of a more skewed T cell repertoire. A decline of TREC levels and a decrease in the number of CD45RA(+) cells beyond 10 years after BMT was concomitant with the detection of oligoclonal CD3(+)CD8(+)CD45RO(+) cells. The switch from a polyclonal to a more skewed repertoire, observed in the CD3(+)CD8(+)CD45RO(+) T cell subset, is a phenomenon that occurs normally with decreased thymic output during aging, but not as rapidly as in this patient population. We conclude that a normal T cell repertoire develops in SCID patients as a result of thymic output and the repertoire remains highly diverse for the first 10 years after BMT. The TCR diversity positively correlates in these patients with TREC levels.     

Niche width impacts vertebrate diversification

Aim The size of the climatic niche of a species is a major factor determining its distribution and evolution. In particular, it has been proposed that niche width should be associated with the rate of species diversification. Here, we test whether species niche width affects the speciation and extinction rates of three main clades of vertebrates: amphibians, mammals and birds. Location Global. Methods We obtained the time‐calibrated phylogenies, IUCN conservation status, species distribution maps and climatic data for 2340 species of amphibians, 4563 species of mammals and 9823 species of birds. We computed the niche width for each species as the mean annual temperature across the species range. We estimated speciation, extinction and transition rates associated with lineages with either narrow (specialist) or wide (generalist) niches using phylogeny‐based birth–death models. We also tested if current conservation status was correlated with the niche width of species. Results We found higher net diversification rates in specialist species than in generalist species. This result was explained by both higher speciation rates (for the three taxonomic groups) and lower extinction rates (for mammals and birds only) in specialist than in generalist species. In contrast, current specialist species tended to be more threatened than generalist species. Main conclusions Our diversification analysis shows that the width of the climatic niche is strongly associated with diversification rates and may thus be a crucial factor for understanding the emergence of diversity patterns in vertebrates. The striking difference between our diversification results and current conservation status suggests that the current extinction process may be different from extinction rates estimated from the whole history of the group.     

Niche theory: New insights from an old paradigm

We apply a quantification of contemporary niche theory to several related topics of current interest: competition for alternative resources, the effect of consumers on those resources, and contemporary and evolutionary patterns at the community level attributable to the sequential colonization of resources and their consumers. Although the first topic is the traditional purview of niche theory, we believe that our model brings several issues into sharper focus than heretofore: The breadths of species' niches, overlap between them and the resulting interspecific effects all depend on the strategies by which competitors exploit heterogeneous environments. For our second application, we allow the alternative resources to be animate, and discover a positive relationship between predation and prey species diversity. Because we expect such a relationship for reasons that differ from those motivating the disturbance hypothesis, these ideas are easily distinguished. Finally, we consider the development of communities whose constituent populations behave according to the tenets of niche theory. Because successive trophic levels are colonized sequentially, patterns resulting from resource competition are replaced by those resulting from predation on consumers. For instance, consumer species-abundance distributions, which are uneven initially, become increasingly even during succession. Similar processes occur in evolutionary time, but the results have been reported as individual taxon cycles of invasion, accommodation and extinction or reinvasion. Niche theory suggests strategies and efficiencies of resource use that would facilitate invasion and prevent extinction. Though these last three are novel applications, the potential of this theory far exceeds them all. Moreover, the resulting insights augment the theory itself, increasing its general applicability. As a consequence of such feedback, niche theory may yet become a unifying concept in population biology.     

Resource partitioning among competing species—A coevolutionary approach

A reasonably general theory for predicting the outcome of coevolution among interacting species is developed. It is applied to a model for resource partitioning among competing species.Current theory for resource partitioning is based on derivations of a “limiting similarity”—i.e., a limit to how similar competitors can be to one another consistent with coexistence. This theory presumes there is a mechanism, perhaps invasion and extinction, which causes competitors to attain the limiting similarity. The view taken in this paper is that partitioning is an evolutionary compromise between pressures for character displacement and disadvantages inherent in the shift to different resource types.A set of principles is offered for the evolution of the parameters in ecological models. (1) For single population models natural selection causes the parameters ultimately to assume those values which produce the highest equilibrium population size. (2) For models of interacting populations, but without interspecific frequency-dependence, natural selection causes the parameters to assume values which produce either the highest or lowest equilibrium population size for any species depending on the sign of the “feedback” in the community obtained by deleting that species. (3) For models of interacting populations with interspecific frequency dependence natural selection leads to parameter values which produce intermediate equilibrium population sizes. A function called the conditional equilibrium population size is introduced. Provided (a) the mean fitness is a maximum in each species at a stable coevolutionary equilibrium and (b) there is negative density-dependence in each species then natural selection causes the parameters to assume values which produce the highest conditional equilibrium population size for each species.These coevolutionary principles, applied to a model for resource partitioning, entail that the niche separation between species relative to given niche widths, increases with the variety of available resources and decreases with the number of competing populations. Also, the evolution of character displacement between two species does not proceed far enough to maximize the equilibrium population sizes of the species involved. These results imply that the relationship between the niche overlap (of nearest neighbors) and species diversity is qualitatively different depending on whether the variety of resources at any place covaries with the species diversity there. Without covariation niche overlap increases with species diversity; with covariation overlap may decrease with species diversity. This study provides the beginning of a theory for the convergent evolution of community structure.     

The influence of age on T cell generation and TCR diversity

The ability to mount protective immune responses depends on the diversity of T cells. T cell diversity may be compromised by the declining thymic output of new T cells. The aging process imposes a threat to diversity, because thymic function deteriorates. In this study we have examined the relationship between thymic production, homeostatic T cell proliferation and TCR beta-chain diversity in young (approximately 25 years), middle-aged ( approximately 60 years), and elderly adults (approximately 75 years). TCR excision circles (TREC) as a marker of thymic output exponentially decreased by >95% between 25 and 60 years of age. The frequency of Ki67(+) cycling CD4 T cells remained steady, and surprisingly, the diversity of the naive CD4 T cell repertoire was maintained at approximately 2 x 10(7) different TCR beta-chains. After the age of 70 years, TRECs only slightly declined, but homeostatic proliferation doubled. The diversity of the T cell pool drastically contracted to 200,000 TCR beta-chains. Also, the phenotypic distinction between naive and memory CD4 T cells became fuzzy. The collapse in CD4 T cell diversity during the seventh and eighth decades indicates substantial T cell loss and implies that therapeutic measures to improve vaccine responses will have to include strategies for T cell replenishment.     

A framework for estimating niche metrics using the resemblance between qualitative resources

Despite the central importance of the niche concept for the ecological theory, current methods to quantify the species niche from qualitative resources, such as food or habitat types, remain insufficiently developed. Classically, information theory and diversity measures have formed the toolbox used for calculating resource niche metrics on species preference data for a set of qualitative resources. We provide a comprehensive framework that extends these classical approaches by incorporating the resemblance between resources into the calculation of resource niche metrics. This does not only allow estimation of the niche centre, breadth, overlap and displacement with greater accuracy, but also makes the estimates less influenced by the way the resources are subdivided. In addition, all niche metrics can be calculated while taking into account the variation in resource availability, and confidence intervals can be obtained by bootstrapping. We illustrate the utility of the framework with an analysis of dietary preferences in feral pigeons Columba livia.     

Cancer of the gastrointestinal tract results in a restricted T-cell repertoire dependent upon tumor differentiation

We investigated the influence of tumor tissue differentiation on the diversity of TCR repertoire. CDR3 spectratypes of CD4⁺ and CD8⁺ T cell subsets were analyzed from 27 patients with gastrointestinal tract tumors exhibiting varying degrees of differentiation. A CDR3 spectratype complexity scoring system was used to quantify the diversity of TCR repertoire. Each patient was matched with an age-matched healthy group to control for age variability. Results show that the complexity scores (TCR repertoire diversity) have a significant correlation with the degree of tumor differentiation, which provides useful information for understanding immune response in cancer patients.     

Immune remodeling: lessons from repertoire alterations during chronological aging and in immune-mediated disease

Immunological studies of aging and of patients with chronic immune-mediated diseases document overlap of immune phenotypes. Here, the term "immune remodeling" refers to these phenotypes that are indicative of biological processes of deterioration and repair. This concept is explored through lessons from studies about the changes in the T-cell repertoire and the functional diversity of otherwise oligoclonal, senescent T cells. Immune remodeling suggests a gradual process that occurs throughout life. However, similar but more drastic remodeling occurs disproportionately among young patients with chronic disease. In this article, I propose that immune remodeling is a beneficial adaptation of aging to promote healthy survival beyond reproductive performance, but acute remodeling poses risk of premature exhaustion of the immune repertoire and, thus, is detrimental in young individuals.