Cytomegalovirus (CMV) infection has a major impact on the T-cell pool, which is thought to be ass... more Cytomegalovirus (CMV) infection has a major impact on the T-cell pool, which is thought to be associated with ageing of the immune system. The effect on the T-cell pool has been interpreted as an effect of CMV on non-CMV specific T-cells. However, it remains unclear whether the effect of CMV could simply be explained by the presence of large, immunodominant, CMV-specific memory CD8+ T-cell populations. These have been suggested to establish through gradual accumulation of long-lived cells. However, little is known about their maintenance. We investigated the effect of CMV infection on T-cell dynamics in healthy older adults, and aimed to unravel the mechanisms of maintenance of large numbers of CMV-specific CD8+ T-cells. We studied the expression of senescence, proliferation, and apoptosis markers and quantified the in vivo dynamics of CMV-specific and other memory T-cell populations using in vivo deuterium labelling. Increased expression of late-stage differentiation markers by CD8...
Proceedings of the National Academy of Sciences, 2008
In mice, recent thymic emigrants (RTEs) make up a large part of the naïve T cell pool and have be... more In mice, recent thymic emigrants (RTEs) make up a large part of the naïve T cell pool and have been suggested to be a distinct short-lived pool. In humans, however, the life span and number of RTEs are unknown. Although2H2O labeling in young mice showed high thymic-dependent daily naïve T cell production, long term up- and down-labeling with2H2O in human adults revealed a low daily production of naïve T cells. Using mathematical modeling, we estimated human naïve CD4 and CD8 T cell half-lives of 4.2 and 6.5 years, respectively, whereas memory CD4 and CD8 T cells had half-lives of 0.4 and 0.7 year. The estimated half-life of recently produced naïve T cells was much longer than these average half-lives. Thus, our data are incompatible with a substantial short-lived RTE population in human adults and suggest that the few naïve T cells that are newly produced are preferentially incorporated in the peripheral pool.
Our adaptive immune system has the remarkable ability to distinguish previously unseen foreign pe... more Our adaptive immune system has the remarkable ability to distinguish previously unseen foreign peptides from harmless self. This self-foreign discrimination was long thought to arise from the silencing of self-reactive T cells during negative selection in the thymus, but recent data show that negative selection is far from complete. Here we ask how a repertoire containing many self-reactive T cells can nevertheless discriminate self from foreign. We address this question using realistic-scale computational models of the T cell repertoire. Our models show that moderate T cell cross-reactivity automatically skews the post-selection repertoire towards peptides that differ systematically from self. But even when no systematic differences between self and foreign exist, discrimination remains possible if the peptides presented in the thymus are chosen in a way that minimizes the co-occurrence of similar, redundant self peptides. Thus, our model predicts that negative selection on a well-...
In this paper we present a model of the macrophage T lymphocyte interactions that generate an ant... more In this paper we present a model of the macrophage T lymphocyte interactions that generate an anti-tumor immune response. The model specifies i) induction of cytotoxic T lymphocytes, ii) antigen presentation by macrophages, which leads to iii) activation of helper T cells, and iv) production of lymphoid factors, which induce a) cytotoxic macrophages, b) T lymphocyte proliferation, and c) an inflammation reaction. Tumor escape mechanisms (suppression, antigenic heterogeneity) have been deliberately omitted from the model. This research combines hitherto unrelated or even contradictory data within the range of behavior of one model. In the model behavior, helper T cells play a crucial role: Tumors that differ minimally in antigenicity (i.e., helper reactivity) can differ markedly in rejectability. Immunization yields protection against tumor doses that would otherwise be lethal, because it increases the number of helper T cells. The magnitude of the cytotoxic effector cell response de...
ABSTRACTAutoimmune inflammation is characterized by tissue infiltration and expansion of antigen-... more ABSTRACTAutoimmune inflammation is characterized by tissue infiltration and expansion of antigen-specific T cells. Although this inflammation is often limited to specific target tissues, it remains yet to be explored whether distinct affected sites are infiltrated with the same, persistent T cell clones. Here we performed CyTOF analysis and T cell receptor (TCR) sequencing to study immune cell composition and (hyper-)expansion of circulating and joint-derived Tregs and non-Tregs in Juvenile Idiopathic Arthritis (JIA). We studied different joints affected at the same time, as well as over the course of relapsing-remitting disease. We found that the composition and functional characteristics of immune infiltrates are strikingly similar between joints within one patient, and observed a strong overlap between dominant T cell clones, especially Treg, of which some could also be detected in circulation and persisted over the course of relapsing remitting disease. Moreover, these T cell cl...
Lymphocyte numbers need to be quite tightly regulated. It is generally assumed that lymphocyte pr... more Lymphocyte numbers need to be quite tightly regulated. It is generally assumed that lymphocyte production and survival rates increase homeostatically when lymphocyte numbers decrease. This widely-accepted concept is largely based on experiments in mice. In humans, lymphocyte reconstitution usually occurs very slowly, which challenges the idea that density dependent homeostasis aids recovery from lymphopenia. Using in vivo deuterium labelling, we quantified lymphocyte production and survival rates in patients who underwent an autologous hematopoietic stem cell transplantation (autoHSCT). We indeed found that the production rates of most T-cell and B-cell subsets in autoHSCT-patients were 2 to 8-times higher than in healthy controls. These increased lymphocyte production rates went hand in hand with a 3 to 9-fold increase in cell loss rates, and both rates did not normalize when cell numbers did. This challenges the concept of homeostatic regulation of lymphocyte production and surviv...
Lymphocyte numbers naturally change through age. Normalisation functions to account for this are ... more Lymphocyte numbers naturally change through age. Normalisation functions to account for this are sparse, and mostly disregard measurements from children in which these changes are most prominent. In this study, we analyse cross-sectional numbers of mainly T-lymphocytes (CD3+, CD3+CD4+ and CD3+CD8+) and their subpopulations (naive and memory) from 673 healthy Dutch individuals ranging from infancy to adulthood (0-62 years). We fitted the data by a delayed exponential function and received parameter estimates for each lymphocyte subset. Our modelling approach follows general laboratory measurement procedures in which absolute cell counts of T-lymphocyte subsets are calculated from observed percentages within a reference population that is truly counted (typically the total lymphocyte count). Consequently, we receive one set of parameter estimates per T-cell subset representing both the trajectories of their counts and percentages. We allow for an initial time delay of half a year befo...
The potential of memory T-cells to provide protection against re-infection is beyond question. Ye... more The potential of memory T-cells to provide protection against re-infection is beyond question. Yet, it remains debated whether long-term T-cell memory is due to long-lived memory cells. There is ample evidence that blood-derived memory phenotype CD8+ T-cells maintain themselves through cell division, rather than through longevity of individual cells. It has recently been proposed, however, that there may be heterogeneity in the lifespans of memory T-cells, depending on factors such as exposure to cognate antigen. Cytomegalovirus (CMV) infection induces not only conventional, contracting T-cell responses, but also inflationary CD8+ T-cell responses, which are maintained at unusually high numbers, and are even thought to continue to expand over time. It has been proposed that such inflating T-cell responses result from the accumulation of relatively long-lived CMV-specific memory CD8+ T-cells. Using in vivo deuterium labelling and mathematical modelling, we found that the average prod...
Proceedings of the National Academy of Sciences, 2021
Significance The human body detects foreign pathogens by T cells with specific receptors. These a... more Significance The human body detects foreign pathogens by T cells with specific receptors. These are not directly encoded in the genome but generated in a random process that combines small gene segments into functional subunits of the receptor. The β -chain of the T cell receptor is normally composed of three such gene segments. Here we identify a group of T cells that lack the middle segment in their receptor sequence. We find that such sequences are mostly generated before birth, persist over a human lifetime, and, as a result, are excessively shared between individuals.
Treatment of human immunodeficiency virus type 1 (HIV-1) infection during the clinical latency ph... more Treatment of human immunodeficiency virus type 1 (HIV-1) infection during the clinical latency phase with drugs inhibiting reverse transcriptase (RT) reduces the HIV-1 RNA load and increases the CD4+ T-cell count. Typically, however, the virus evolves mutations in the RT gene that circumvent the drugs. We develop a mathematical model for this situation. The model distinguishes quiescent from activated CD4+ T cells, incorporates the fact that only activated cells can become productively infected by HIV-1, embodies empirical estimates for the drug resistance and the mutation frequency for each of the HIV-1 drug-resistant mutants, and assumes the antiviral immune response to remain constant over the course of the experiments. We analyze clinical data on the evolution of drug-resistant mutants for the RT inhibitors lamivudine and zidovudine. The results show that the evolutionary sequence of the drug-resistant mutants in both data sets is accounted for by our model, given that lamivudin...
Cytomegalovirus (CMV) infection has a major impact on the T-cell pool, which is thought to be ass... more Cytomegalovirus (CMV) infection has a major impact on the T-cell pool, which is thought to be associated with ageing of the immune system. The effect on the T-cell pool has been interpreted as an effect of CMV on non-CMV specific T-cells. However, it remains unclear whether the effect of CMV could simply be explained by the presence of large, immunodominant, CMV-specific memory CD8+ T-cell populations. These have been suggested to establish through gradual accumulation of long-lived cells. However, little is known about their maintenance. We investigated the effect of CMV infection on T-cell dynamics in healthy older adults, and aimed to unravel the mechanisms of maintenance of large numbers of CMV-specific CD8+ T-cells. We studied the expression of senescence, proliferation, and apoptosis markers and quantified the in vivo dynamics of CMV-specific and other memory T-cell populations using in vivo deuterium labelling. Increased expression of late-stage differentiation markers by CD8...
Proceedings of the National Academy of Sciences, 2008
In mice, recent thymic emigrants (RTEs) make up a large part of the naïve T cell pool and have be... more In mice, recent thymic emigrants (RTEs) make up a large part of the naïve T cell pool and have been suggested to be a distinct short-lived pool. In humans, however, the life span and number of RTEs are unknown. Although2H2O labeling in young mice showed high thymic-dependent daily naïve T cell production, long term up- and down-labeling with2H2O in human adults revealed a low daily production of naïve T cells. Using mathematical modeling, we estimated human naïve CD4 and CD8 T cell half-lives of 4.2 and 6.5 years, respectively, whereas memory CD4 and CD8 T cells had half-lives of 0.4 and 0.7 year. The estimated half-life of recently produced naïve T cells was much longer than these average half-lives. Thus, our data are incompatible with a substantial short-lived RTE population in human adults and suggest that the few naïve T cells that are newly produced are preferentially incorporated in the peripheral pool.
Our adaptive immune system has the remarkable ability to distinguish previously unseen foreign pe... more Our adaptive immune system has the remarkable ability to distinguish previously unseen foreign peptides from harmless self. This self-foreign discrimination was long thought to arise from the silencing of self-reactive T cells during negative selection in the thymus, but recent data show that negative selection is far from complete. Here we ask how a repertoire containing many self-reactive T cells can nevertheless discriminate self from foreign. We address this question using realistic-scale computational models of the T cell repertoire. Our models show that moderate T cell cross-reactivity automatically skews the post-selection repertoire towards peptides that differ systematically from self. But even when no systematic differences between self and foreign exist, discrimination remains possible if the peptides presented in the thymus are chosen in a way that minimizes the co-occurrence of similar, redundant self peptides. Thus, our model predicts that negative selection on a well-...
In this paper we present a model of the macrophage T lymphocyte interactions that generate an ant... more In this paper we present a model of the macrophage T lymphocyte interactions that generate an anti-tumor immune response. The model specifies i) induction of cytotoxic T lymphocytes, ii) antigen presentation by macrophages, which leads to iii) activation of helper T cells, and iv) production of lymphoid factors, which induce a) cytotoxic macrophages, b) T lymphocyte proliferation, and c) an inflammation reaction. Tumor escape mechanisms (suppression, antigenic heterogeneity) have been deliberately omitted from the model. This research combines hitherto unrelated or even contradictory data within the range of behavior of one model. In the model behavior, helper T cells play a crucial role: Tumors that differ minimally in antigenicity (i.e., helper reactivity) can differ markedly in rejectability. Immunization yields protection against tumor doses that would otherwise be lethal, because it increases the number of helper T cells. The magnitude of the cytotoxic effector cell response de...
ABSTRACTAutoimmune inflammation is characterized by tissue infiltration and expansion of antigen-... more ABSTRACTAutoimmune inflammation is characterized by tissue infiltration and expansion of antigen-specific T cells. Although this inflammation is often limited to specific target tissues, it remains yet to be explored whether distinct affected sites are infiltrated with the same, persistent T cell clones. Here we performed CyTOF analysis and T cell receptor (TCR) sequencing to study immune cell composition and (hyper-)expansion of circulating and joint-derived Tregs and non-Tregs in Juvenile Idiopathic Arthritis (JIA). We studied different joints affected at the same time, as well as over the course of relapsing-remitting disease. We found that the composition and functional characteristics of immune infiltrates are strikingly similar between joints within one patient, and observed a strong overlap between dominant T cell clones, especially Treg, of which some could also be detected in circulation and persisted over the course of relapsing remitting disease. Moreover, these T cell cl...
Lymphocyte numbers need to be quite tightly regulated. It is generally assumed that lymphocyte pr... more Lymphocyte numbers need to be quite tightly regulated. It is generally assumed that lymphocyte production and survival rates increase homeostatically when lymphocyte numbers decrease. This widely-accepted concept is largely based on experiments in mice. In humans, lymphocyte reconstitution usually occurs very slowly, which challenges the idea that density dependent homeostasis aids recovery from lymphopenia. Using in vivo deuterium labelling, we quantified lymphocyte production and survival rates in patients who underwent an autologous hematopoietic stem cell transplantation (autoHSCT). We indeed found that the production rates of most T-cell and B-cell subsets in autoHSCT-patients were 2 to 8-times higher than in healthy controls. These increased lymphocyte production rates went hand in hand with a 3 to 9-fold increase in cell loss rates, and both rates did not normalize when cell numbers did. This challenges the concept of homeostatic regulation of lymphocyte production and surviv...
Lymphocyte numbers naturally change through age. Normalisation functions to account for this are ... more Lymphocyte numbers naturally change through age. Normalisation functions to account for this are sparse, and mostly disregard measurements from children in which these changes are most prominent. In this study, we analyse cross-sectional numbers of mainly T-lymphocytes (CD3+, CD3+CD4+ and CD3+CD8+) and their subpopulations (naive and memory) from 673 healthy Dutch individuals ranging from infancy to adulthood (0-62 years). We fitted the data by a delayed exponential function and received parameter estimates for each lymphocyte subset. Our modelling approach follows general laboratory measurement procedures in which absolute cell counts of T-lymphocyte subsets are calculated from observed percentages within a reference population that is truly counted (typically the total lymphocyte count). Consequently, we receive one set of parameter estimates per T-cell subset representing both the trajectories of their counts and percentages. We allow for an initial time delay of half a year befo...
The potential of memory T-cells to provide protection against re-infection is beyond question. Ye... more The potential of memory T-cells to provide protection against re-infection is beyond question. Yet, it remains debated whether long-term T-cell memory is due to long-lived memory cells. There is ample evidence that blood-derived memory phenotype CD8+ T-cells maintain themselves through cell division, rather than through longevity of individual cells. It has recently been proposed, however, that there may be heterogeneity in the lifespans of memory T-cells, depending on factors such as exposure to cognate antigen. Cytomegalovirus (CMV) infection induces not only conventional, contracting T-cell responses, but also inflationary CD8+ T-cell responses, which are maintained at unusually high numbers, and are even thought to continue to expand over time. It has been proposed that such inflating T-cell responses result from the accumulation of relatively long-lived CMV-specific memory CD8+ T-cells. Using in vivo deuterium labelling and mathematical modelling, we found that the average prod...
Proceedings of the National Academy of Sciences, 2021
Significance The human body detects foreign pathogens by T cells with specific receptors. These a... more Significance The human body detects foreign pathogens by T cells with specific receptors. These are not directly encoded in the genome but generated in a random process that combines small gene segments into functional subunits of the receptor. The β -chain of the T cell receptor is normally composed of three such gene segments. Here we identify a group of T cells that lack the middle segment in their receptor sequence. We find that such sequences are mostly generated before birth, persist over a human lifetime, and, as a result, are excessively shared between individuals.
Treatment of human immunodeficiency virus type 1 (HIV-1) infection during the clinical latency ph... more Treatment of human immunodeficiency virus type 1 (HIV-1) infection during the clinical latency phase with drugs inhibiting reverse transcriptase (RT) reduces the HIV-1 RNA load and increases the CD4+ T-cell count. Typically, however, the virus evolves mutations in the RT gene that circumvent the drugs. We develop a mathematical model for this situation. The model distinguishes quiescent from activated CD4+ T cells, incorporates the fact that only activated cells can become productively infected by HIV-1, embodies empirical estimates for the drug resistance and the mutation frequency for each of the HIV-1 drug-resistant mutants, and assumes the antiviral immune response to remain constant over the course of the experiments. We analyze clinical data on the evolution of drug-resistant mutants for the RT inhibitors lamivudine and zidovudine. The results show that the evolutionary sequence of the drug-resistant mutants in both data sets is accounted for by our model, given that lamivudin...
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Papers by Rob J de Boer