sanket rane | Maharaja Sayajirao University of Baroda (original) (raw)
Papers by sanket rane
eLife, Jun 9, 2022
Naive CD4 and CD8 T cells are cornerstones of adaptive immunity, but the dynamics of their establ... more Naive CD4 and CD8 T cells are cornerstones of adaptive immunity, but the dynamics of their establishment early in life and how their kinetics change as they mature following release from the thymus are poorly understood. Further, due to the diverse signals implicated in naive T cell survival, it has been a long-held and conceptually attractive view that they are sustained by active homeostatic control as thymic activity wanes. Here we use multiple modelling and experimental approachesto identify a unified model of naive CD4 and CD8 T cell population dynamics in mice, across their lifespan. We infer that both subsets divide rarely and progressively increase their survival capacity with cell age. Strikingly, this simple model is able to describe naive CD4 T cell dynamics throughout life. In contrast, we find that newly generated naive CD8 T cells are lost more rapidly during the first 3-4 weeks of life, likely due to increased recruitment into memory. We find no evidence for elevated division rates in neonates, or for feedback regulation of naive T cell numbers at any age. We show how confronting mathematical models with diverse datasets can reveal a quantitative and remarkably simple picture of naive T cell dynamics in mice from birth into old age. Editor's evaluation This paper challenges the widely held view that the number of naive T-cells in our body is regulated through homeostatic feedback mechanisms, meaning that cells divide more frequently-or live longer-when cell numbers are low. The arguments in favor of this homeostatic regulation rely on cross-sectional data, which fail to distinguish between the effects of host age, cell age, and cell numbers, each of which separately may influence the dynamics of cells. Using a set of mathematical models and experimental data sets, this paper manages to tear these factors apart and reports that in mice there is no feedback regulation of naive T-cell numbers.
bioRxiv (Cold Spring Harbor Laboratory), Dec 11, 2019
Follicular mature (FM) and germinal centre (GC) B cells underpin humoral immunity but the dynamic... more Follicular mature (FM) and germinal centre (GC) B cells underpin humoral immunity but the dynamics of their generation and maintenance are not clearly defined. Here we exploited a fate-mapping system in mice that tracks B cells as they develop into peripheral subsets, together with a cell division fate reporter mouse and mathematical models. We find that FM cells are kinetically homogeneous, recirculate freely, continually replenished from transitional populations, and self-renew rarely. In contrast, GC B cell lineages persist for weeks with rapid turnover and site-specific dynamics. Those in the spleen derive from transitional cells and are kinetically homogeneous, while those in lymph nodes derive from FM B cells and comprise both transient and persistent clones. These differences likely derive from the nature of antigen exposure at the different sites. Our integrative approach also reveals how the host environment drives cell-extrinsic, age-related changes in B cell homeostasis.
Immunology, Jan 13, 2019
We have previously demonstrated co‐receptor level‐associated functional heterogeneity in apparent... more We have previously demonstrated co‐receptor level‐associated functional heterogeneity in apparently homogeneous naive peripheral CD4 T cells, dependent on MHC‐mediated tonic signals. Maturation pathways can differ between naive CD4 and naive CD8 cells, so we tested whether the latter showed similar co‐receptor level‐associated functional heterogeneity. We report that, when either polyclonal and T‐cell receptor (TCR)‐transgenic monoclonal peripheral naive CD8 T cells from young mice were separated into CD8hi and CD8lo subsets, CD8lo cells responded poorly, but CD8hi and CD8lo subsets of CD8 single‐positive (SP) thymocytes responded similarly. CD8lo naive CD8 T cells were smaller and showed lower levels of some cell‐surface molecules, but higher levels of the negative regulator CD5. In addition to the expected peripheral decline in CD8 levels on transferred naive CD8 T cells in wild‐type (WT) but not in MHC class I‐deficient recipient mice, short‐duration naive T‐cell–dendritic cell (DC) co‐cultures in vitro also caused co‐receptor down‐modulation in CD8 T cells but not in CD4 T cells. Constitutive pZAP70/pSyk and pERK levels ex vivo were lower in CD8lo naive CD8 T cells and dual‐specific phosphatase inhibition partially rescued their hypo‐responsiveness. Bulk mRNA sequencing showed major differences in the transcriptional landscapes of CD8hi and CD8lo naive CD8 T cells. CD8hi naive CD8 T cells showed enrichment of genes involved in positive regulation of cell cycle and survival. Our data show that naive CD8 T cells show major differences in their signaling, transcriptional and functional landscapes associated with subtly altered CD8 levels, consistent with the possibility of peripheral cellular aging.
Frontiers in Immunology, Apr 5, 2019
Initiation of adaptive immunity involves distinct migratory cell populations coming together in a... more Initiation of adaptive immunity involves distinct migratory cell populations coming together in a highly dynamic and spatially organized process. However, we lack a detailed spatiotemporal map of these events due to our inability to track the fate of cells between anatomically distinct locations or functionally identify cell populations as migratory. We used photo-convertible transgenic mice (Kaede) to spatiotemporally track the fate and composition of the cell populations that leave the site of priming and enter the draining lymph node to initiate immunity. We show that following skin priming, the lymph node migratory population is principally composed of cells recruited to the site of priming, with a minor contribution from tissue resident cells. In combination with the YAe/Eα system, we also show that the majority of cells presenting antigen are CD103 + CD11b + dendritic cells that were recruited to the site of priming during the inflammatory response. This population has previously only been described in relation to mucosal tissues. Comprehensive phenotypic profiling of the cells migrating from the skin to the draining lymph node by mass cytometry revealed that in addition to dendritic cells, the migratory population also included CD4 + and CD8 + T cells, B cells, and neutrophils. Taking our complex spatiotemporal data set, we then generated a model of cell migration that quantifies and describes the dynamics of arrival, departure, and residence times of cells at the site of priming and in the draining lymph node throughout the time-course of the initiation of adaptive immunity. In addition, we have identified the mean migration time of migratory dendritic cells as they travel from the site of priming to the draining lymph node. These findings represent an unprecedented, detailed and quantitative map of cell dynamics and phenotypes during immunization, identifying where, when and which cells to target for immunomodulation in autoimmunity and vaccination strategies.
PLOS Biology, Oct 29, 2019
Thymic involution and proliferation of naive T cells both contribute to shaping the naive Tcell r... more Thymic involution and proliferation of naive T cells both contribute to shaping the naive Tcell repertoire as humans age, but a clear understanding of the roles of each throughout a human life span has been difficult to determine. By measuring nuclear bomb test-derived 14
PLOS Biology, Apr 11, 2018
The processes regulating peripheral naive T-cell numbers and clonal diversity remain poorly under... more The processes regulating peripheral naive T-cell numbers and clonal diversity remain poorly understood. Conceptually, homeostatic mechanisms must fall into the broad categories of neutral (simple random birth-death models), competition (regulation of cell numbers through quorum-sensing, perhaps via limiting shared resources), adaptation (involving cellintrinsic changes in homeostatic fitness, defined as net growth rate over time), or selection (involving the loss or outgrowth of cell populations deriving from intercellular variation in fitness). There may also be stably maintained heterogeneity within the naive T-cell pool. To distinguish between these mechanisms, we confront very general models of these processes with an array of experimental data, both new and published. While reduced competition for homeostatic stimuli may impact cell survival or proliferation in neonates or under moderate to severe lymphopenia, we show that the only mechanism capable of explaining multiple, independent experimental studies of naive CD4 + and CD8 + T-cell homeostasis in mice from young adulthood into old age is one of adaptation, in which cells act independently and accrue a survival or proliferative advantage continuously with their post-thymic age. However, aged naive T cells may also be functionally impaired, and so the accumulation of older cells via 'conditioning through experience' may contribute to reduced immune responsiveness in the elderly.
<p>Under the assumptions of pure density-dependent regulation of naive T-cell numbers (left... more <p>Under the assumptions of pure density-dependent regulation of naive T-cell numbers (left panels), or the adaptation model (right panels), we simulated recovery from different levels of naive CD4 T-cell depletion at age 200 d (upper panels) and recovery from 50% depletion at different host ages (lower panels). Simulations were performed using the model parameters estimated from the data in ref. [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003949#pbio.2003949.ref008" target="_blank">8</a>].</p
<p>For model comparison, only differences in AIC, not absolute values, are meaningful—these... more <p>For model comparison, only differences in AIC, not absolute values, are meaningful—these differences are shown relative to the best-fitting model, with larger numbers indicating lower support.</p
<p>The normalised age distributions of naive CD4 and CD8 T cells were generated using param... more <p>The normalised age distributions of naive CD4 and CD8 T cells were generated using parameters obtained from fits to the data from den Braber et al. [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003949#pbio.2003949.ref008" target="_blank">8</a>] (upper panels) and from the busulfan chimeras (lower panels). Different coloured curves denote different host ages. Distributions illustrate the preferential accumulation with longer-lived and/or more proliferative cell populations with host age. The discontinuity in the gradients at older cell ages derives from uncertainty in the precise form of the age distribution of cells at the beginning of the experiment. We proposed various forms for this distribution, and the parameters of each were estimated from the data. However, for all distributions we explored, the same U-shaped trend emerges over time.</p
<p>(A) Observed and predicted kinetics of loss of naive CD4 cells taken from young (2 mo) (... more <p>(A) Observed and predicted kinetics of loss of naive CD4 cells taken from young (2 mo) (solid circles and solid lines) and aged (24 mo) (open circles and dashed lines) donors, using the adaptation (blue line), incumbent (red lines), and selection (green lines) models. Data were taken from Fig 2C in ref. [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003949#pbio.2003949.ref014" target="_blank">14</a>]. Parameters were taken from the fits to the data from WT and Tx mice reported in ref. [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003949#pbio.2003949.ref008" target="_blank">8</a>] and from our busulfan chimera data (left and right panels, respectively). (B) Predicting the trend in the loss of donor cells from the naive CD4 pool over 15 d, using AND TCR transgenic naive T cells taken from donors of four different ages (left panel, data reproduced from Fig. 4E in ref. [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003949#pbio.2003949.ref014" target="_blank">14</a>]). The three panels to the right show the models’ predicted fold loss of polyclonal naive CD4 and CD8 T cells 15 d after adoptive transfer, from donors of the same ages used in the AND adoptive transfer experiment. Due to intrinsic differences in the survival rates of AND and polyclonal naive cells, the absolute levels of recovery differ substantially, but the predicted trends show that only the adaptation model is able to reproduce a consistent increase in recovery with donor age. As in panel A, these predictions were generated using model parameters obtained from fits to the data from the busulfan chimeras (solid circles) and from ref. [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003949#pbio.2003949.ref008" target="_blank">8</a>] (open circles). Data are provided in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003949#pbio.2003949.s004" target="_blank">S3 Data</a>. TCR, T-cell receptor; Tx, thymectomised; WT, wild-type.</p
<p>(A) A simple random birth–death model, with both processes occuring at rates that are co... more <p>(A) A simple random birth–death model, with both processes occuring at rates that are constant over time and identical for all cells. (B) A model of density-dependent homeostasis in which every cell’s homeostatic fitness declines equally with total population size, due to resource competition or other forms of quorum-sensing. (C) A model of adaptation in which every cell’s fitness increases progressively with its post-thymic age. We assume that post-thymic age is inherited by a dividing cell’s offspring. (D) A model in which T cells are generated with a distribution of intrinsic, constant, and heritable fitnesses. Over time, selection acts on this distribution. (E) A variant of the selection model, in which the naive pool comprises numerically stable, self-renewing ‘incumbent’ cells generated early in life and ‘displaceable’ cells that are continually replaced by new emigrants from the thymus.</p
<p>(A) The neutral model describes replete kinetics well but fails to capture the slow loss... more <p>(A) The neutral model describes replete kinetics well but fails to capture the slow loss of cells following thymectomy. (B) Comparing the density-dependent, adaptation, selection, and incumbent models using data from thymectomy onwards. (C) The same comparisons but using data from birth. Insets detail the growth of naive T-cell numbers in young mice. Data are provided in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003949#pbio.2003949.s002" target="_blank">S1 Data</a>. Tx, thymectomised; WT, wild-type.</p
Frontiers in Immunology, 2019
Initiation of adaptive immunity involves distinct migratory cell populations coming together in a... more Initiation of adaptive immunity involves distinct migratory cell populations coming together in a highly dynamic and spatially organized process. However, we lack a detailed spatiotemporal map of these events due to our inability to track the fate of cells between anatomically distinct locations or functionally identify cell populations as migratory. We used photo-convertible transgenic mice (Kaede) to spatiotemporally track the fate and composition of the cell populations that leave the site of priming and enter the draining lymph node to initiate immunity. We show that following skin priming, the lymph node migratory population is principally composed of cells recruited to the site of priming, with a minor contribution from tissue resident cells. In combination with the YAe/Eα system, we also show that the majority of cells presenting antigen are CD103 + CD11b + dendritic cells that were recruited to the site of priming during the inflammatory response. This population has previously only been described in relation to mucosal tissues. Comprehensive phenotypic profiling of the cells migrating from the skin to the draining lymph node by mass cytometry revealed that in addition to dendritic cells, the migratory population also included CD4 + and CD8 + T cells, B cells, and neutrophils. Taking our complex spatiotemporal data set, we then generated a model of cell migration that quantifies and describes the dynamics of arrival, departure, and residence times of cells at the site of priming and in the draining lymph node throughout the time-course of the initiation of adaptive immunity. In addition, we have identified the mean migration time of migratory dendritic cells as they travel from the site of priming to the draining lymph node. These findings represent an unprecedented, detailed and quantitative map of cell dynamics and phenotypes during immunization, identifying where, when and which cells to target for immunomodulation in autoimmunity and vaccination strategies.
Immunology, 2018
We have previously demonstrated co‐receptor level‐associated functional heterogeneity in apparent... more We have previously demonstrated co‐receptor level‐associated functional heterogeneity in apparently homogeneous naive peripheral CD4 T cells, dependent on MHC‐mediated tonic signals. Maturation pathways can differ between naive CD4 and naive CD8 cells, so we tested whether the latter showed similar co‐receptor level‐associated functional heterogeneity. We report that, when either polyclonal and T‐cell receptor (TCR)‐transgenic monoclonal peripheral naive CD8 T cells from young mice were separated into CD8hi and CD8lo subsets, CD8lo cells responded poorly, but CD8hi and CD8lo subsets of CD8 single‐positive (SP) thymocytes responded similarly. CD8lo naive CD8 T cells were smaller and showed lower levels of some cell‐surface molecules, but higher levels of the negative regulator CD5. In addition to the expected peripheral decline in CD8 levels on transferred naive CD8 T cells in wild‐type (WT) but not in MHC class I‐deficient recipient mice, short‐duration naive T‐cell–dendritic cell (...
PLoS biology, 2018
The processes regulating peripheral naive T-cell numbers and clonal diversity remain poorly under... more The processes regulating peripheral naive T-cell numbers and clonal diversity remain poorly understood. Conceptually, homeostatic mechanisms must fall into the broad categories of neutral (simple random birth-death models), competition (regulation of cell numbers through quorum-sensing, perhaps via limiting shared resources), adaptation (involving cell-intrinsic changes in homeostatic fitness, defined as net growth rate over time), or selection (involving the loss or outgrowth of cell populations deriving from intercellular variation in fitness). There may also be stably maintained heterogeneity within the naive T-cell pool. To distinguish between these mechanisms, we confront very general models of these processes with an array of experimental data, both new and published. While reduced competition for homeostatic stimuli may impact cell survival or proliferation in neonates or under moderate to severe lymphopenia, we show that the only mechanism capable of explaining multiple, ind...
Dynamics of cognate and non-cognate interactions during post-thymic survival of naïve CD4 (NCD4) ... more Dynamics of cognate and non-cognate interactions during post-thymic survival of naïve CD4 (NCD4) T lymphocytes in periphery may have distinct consequences on their function. It is not clear if there is any association between duration of peripheral residence of NCD4 T cells and their activation, proliferation and Effector functions. Alteration in phenotypic properties of NCD4 T cells owing to longer or shorter duration of peripheral residence also remains possible. Through our study, we are trying to understand the correlation between duration of peripheral residence and variations in phenotypic (CD4 levels) and functional properties of NCD4 T cells. We examined separated NCD4hi and NCD4lo subsets of mouse NCD4 cells. NCD4lo cells were smaller, had higher CD5 levels, responded poorly, were more Th2-skewed, with lower levels of the dual-specific phosphatase (DUSP)6-suppressing micro-RNA miR181a. Thymic NCD4lo and NCD4hi subsets did not show differences. Adoptive transfer-mediated par...
eLife, Jun 9, 2022
Naive CD4 and CD8 T cells are cornerstones of adaptive immunity, but the dynamics of their establ... more Naive CD4 and CD8 T cells are cornerstones of adaptive immunity, but the dynamics of their establishment early in life and how their kinetics change as they mature following release from the thymus are poorly understood. Further, due to the diverse signals implicated in naive T cell survival, it has been a long-held and conceptually attractive view that they are sustained by active homeostatic control as thymic activity wanes. Here we use multiple modelling and experimental approachesto identify a unified model of naive CD4 and CD8 T cell population dynamics in mice, across their lifespan. We infer that both subsets divide rarely and progressively increase their survival capacity with cell age. Strikingly, this simple model is able to describe naive CD4 T cell dynamics throughout life. In contrast, we find that newly generated naive CD8 T cells are lost more rapidly during the first 3-4 weeks of life, likely due to increased recruitment into memory. We find no evidence for elevated division rates in neonates, or for feedback regulation of naive T cell numbers at any age. We show how confronting mathematical models with diverse datasets can reveal a quantitative and remarkably simple picture of naive T cell dynamics in mice from birth into old age. Editor's evaluation This paper challenges the widely held view that the number of naive T-cells in our body is regulated through homeostatic feedback mechanisms, meaning that cells divide more frequently-or live longer-when cell numbers are low. The arguments in favor of this homeostatic regulation rely on cross-sectional data, which fail to distinguish between the effects of host age, cell age, and cell numbers, each of which separately may influence the dynamics of cells. Using a set of mathematical models and experimental data sets, this paper manages to tear these factors apart and reports that in mice there is no feedback regulation of naive T-cell numbers.
bioRxiv (Cold Spring Harbor Laboratory), Dec 11, 2019
Follicular mature (FM) and germinal centre (GC) B cells underpin humoral immunity but the dynamic... more Follicular mature (FM) and germinal centre (GC) B cells underpin humoral immunity but the dynamics of their generation and maintenance are not clearly defined. Here we exploited a fate-mapping system in mice that tracks B cells as they develop into peripheral subsets, together with a cell division fate reporter mouse and mathematical models. We find that FM cells are kinetically homogeneous, recirculate freely, continually replenished from transitional populations, and self-renew rarely. In contrast, GC B cell lineages persist for weeks with rapid turnover and site-specific dynamics. Those in the spleen derive from transitional cells and are kinetically homogeneous, while those in lymph nodes derive from FM B cells and comprise both transient and persistent clones. These differences likely derive from the nature of antigen exposure at the different sites. Our integrative approach also reveals how the host environment drives cell-extrinsic, age-related changes in B cell homeostasis.
Immunology, Jan 13, 2019
We have previously demonstrated co‐receptor level‐associated functional heterogeneity in apparent... more We have previously demonstrated co‐receptor level‐associated functional heterogeneity in apparently homogeneous naive peripheral CD4 T cells, dependent on MHC‐mediated tonic signals. Maturation pathways can differ between naive CD4 and naive CD8 cells, so we tested whether the latter showed similar co‐receptor level‐associated functional heterogeneity. We report that, when either polyclonal and T‐cell receptor (TCR)‐transgenic monoclonal peripheral naive CD8 T cells from young mice were separated into CD8hi and CD8lo subsets, CD8lo cells responded poorly, but CD8hi and CD8lo subsets of CD8 single‐positive (SP) thymocytes responded similarly. CD8lo naive CD8 T cells were smaller and showed lower levels of some cell‐surface molecules, but higher levels of the negative regulator CD5. In addition to the expected peripheral decline in CD8 levels on transferred naive CD8 T cells in wild‐type (WT) but not in MHC class I‐deficient recipient mice, short‐duration naive T‐cell–dendritic cell (DC) co‐cultures in vitro also caused co‐receptor down‐modulation in CD8 T cells but not in CD4 T cells. Constitutive pZAP70/pSyk and pERK levels ex vivo were lower in CD8lo naive CD8 T cells and dual‐specific phosphatase inhibition partially rescued their hypo‐responsiveness. Bulk mRNA sequencing showed major differences in the transcriptional landscapes of CD8hi and CD8lo naive CD8 T cells. CD8hi naive CD8 T cells showed enrichment of genes involved in positive regulation of cell cycle and survival. Our data show that naive CD8 T cells show major differences in their signaling, transcriptional and functional landscapes associated with subtly altered CD8 levels, consistent with the possibility of peripheral cellular aging.
Frontiers in Immunology, Apr 5, 2019
Initiation of adaptive immunity involves distinct migratory cell populations coming together in a... more Initiation of adaptive immunity involves distinct migratory cell populations coming together in a highly dynamic and spatially organized process. However, we lack a detailed spatiotemporal map of these events due to our inability to track the fate of cells between anatomically distinct locations or functionally identify cell populations as migratory. We used photo-convertible transgenic mice (Kaede) to spatiotemporally track the fate and composition of the cell populations that leave the site of priming and enter the draining lymph node to initiate immunity. We show that following skin priming, the lymph node migratory population is principally composed of cells recruited to the site of priming, with a minor contribution from tissue resident cells. In combination with the YAe/Eα system, we also show that the majority of cells presenting antigen are CD103 + CD11b + dendritic cells that were recruited to the site of priming during the inflammatory response. This population has previously only been described in relation to mucosal tissues. Comprehensive phenotypic profiling of the cells migrating from the skin to the draining lymph node by mass cytometry revealed that in addition to dendritic cells, the migratory population also included CD4 + and CD8 + T cells, B cells, and neutrophils. Taking our complex spatiotemporal data set, we then generated a model of cell migration that quantifies and describes the dynamics of arrival, departure, and residence times of cells at the site of priming and in the draining lymph node throughout the time-course of the initiation of adaptive immunity. In addition, we have identified the mean migration time of migratory dendritic cells as they travel from the site of priming to the draining lymph node. These findings represent an unprecedented, detailed and quantitative map of cell dynamics and phenotypes during immunization, identifying where, when and which cells to target for immunomodulation in autoimmunity and vaccination strategies.
PLOS Biology, Oct 29, 2019
Thymic involution and proliferation of naive T cells both contribute to shaping the naive Tcell r... more Thymic involution and proliferation of naive T cells both contribute to shaping the naive Tcell repertoire as humans age, but a clear understanding of the roles of each throughout a human life span has been difficult to determine. By measuring nuclear bomb test-derived 14
PLOS Biology, Apr 11, 2018
The processes regulating peripheral naive T-cell numbers and clonal diversity remain poorly under... more The processes regulating peripheral naive T-cell numbers and clonal diversity remain poorly understood. Conceptually, homeostatic mechanisms must fall into the broad categories of neutral (simple random birth-death models), competition (regulation of cell numbers through quorum-sensing, perhaps via limiting shared resources), adaptation (involving cellintrinsic changes in homeostatic fitness, defined as net growth rate over time), or selection (involving the loss or outgrowth of cell populations deriving from intercellular variation in fitness). There may also be stably maintained heterogeneity within the naive T-cell pool. To distinguish between these mechanisms, we confront very general models of these processes with an array of experimental data, both new and published. While reduced competition for homeostatic stimuli may impact cell survival or proliferation in neonates or under moderate to severe lymphopenia, we show that the only mechanism capable of explaining multiple, independent experimental studies of naive CD4 + and CD8 + T-cell homeostasis in mice from young adulthood into old age is one of adaptation, in which cells act independently and accrue a survival or proliferative advantage continuously with their post-thymic age. However, aged naive T cells may also be functionally impaired, and so the accumulation of older cells via 'conditioning through experience' may contribute to reduced immune responsiveness in the elderly.
<p>Under the assumptions of pure density-dependent regulation of naive T-cell numbers (left... more <p>Under the assumptions of pure density-dependent regulation of naive T-cell numbers (left panels), or the adaptation model (right panels), we simulated recovery from different levels of naive CD4 T-cell depletion at age 200 d (upper panels) and recovery from 50% depletion at different host ages (lower panels). Simulations were performed using the model parameters estimated from the data in ref. [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003949#pbio.2003949.ref008" target="_blank">8</a>].</p
<p>For model comparison, only differences in AIC, not absolute values, are meaningful—these... more <p>For model comparison, only differences in AIC, not absolute values, are meaningful—these differences are shown relative to the best-fitting model, with larger numbers indicating lower support.</p
<p>The normalised age distributions of naive CD4 and CD8 T cells were generated using param... more <p>The normalised age distributions of naive CD4 and CD8 T cells were generated using parameters obtained from fits to the data from den Braber et al. [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003949#pbio.2003949.ref008" target="_blank">8</a>] (upper panels) and from the busulfan chimeras (lower panels). Different coloured curves denote different host ages. Distributions illustrate the preferential accumulation with longer-lived and/or more proliferative cell populations with host age. The discontinuity in the gradients at older cell ages derives from uncertainty in the precise form of the age distribution of cells at the beginning of the experiment. We proposed various forms for this distribution, and the parameters of each were estimated from the data. However, for all distributions we explored, the same U-shaped trend emerges over time.</p
<p>(A) Observed and predicted kinetics of loss of naive CD4 cells taken from young (2 mo) (... more <p>(A) Observed and predicted kinetics of loss of naive CD4 cells taken from young (2 mo) (solid circles and solid lines) and aged (24 mo) (open circles and dashed lines) donors, using the adaptation (blue line), incumbent (red lines), and selection (green lines) models. Data were taken from Fig 2C in ref. [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003949#pbio.2003949.ref014" target="_blank">14</a>]. Parameters were taken from the fits to the data from WT and Tx mice reported in ref. [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003949#pbio.2003949.ref008" target="_blank">8</a>] and from our busulfan chimera data (left and right panels, respectively). (B) Predicting the trend in the loss of donor cells from the naive CD4 pool over 15 d, using AND TCR transgenic naive T cells taken from donors of four different ages (left panel, data reproduced from Fig. 4E in ref. [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003949#pbio.2003949.ref014" target="_blank">14</a>]). The three panels to the right show the models’ predicted fold loss of polyclonal naive CD4 and CD8 T cells 15 d after adoptive transfer, from donors of the same ages used in the AND adoptive transfer experiment. Due to intrinsic differences in the survival rates of AND and polyclonal naive cells, the absolute levels of recovery differ substantially, but the predicted trends show that only the adaptation model is able to reproduce a consistent increase in recovery with donor age. As in panel A, these predictions were generated using model parameters obtained from fits to the data from the busulfan chimeras (solid circles) and from ref. [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003949#pbio.2003949.ref008" target="_blank">8</a>] (open circles). Data are provided in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003949#pbio.2003949.s004" target="_blank">S3 Data</a>. TCR, T-cell receptor; Tx, thymectomised; WT, wild-type.</p
<p>(A) A simple random birth–death model, with both processes occuring at rates that are co... more <p>(A) A simple random birth–death model, with both processes occuring at rates that are constant over time and identical for all cells. (B) A model of density-dependent homeostasis in which every cell’s homeostatic fitness declines equally with total population size, due to resource competition or other forms of quorum-sensing. (C) A model of adaptation in which every cell’s fitness increases progressively with its post-thymic age. We assume that post-thymic age is inherited by a dividing cell’s offspring. (D) A model in which T cells are generated with a distribution of intrinsic, constant, and heritable fitnesses. Over time, selection acts on this distribution. (E) A variant of the selection model, in which the naive pool comprises numerically stable, self-renewing ‘incumbent’ cells generated early in life and ‘displaceable’ cells that are continually replaced by new emigrants from the thymus.</p
<p>(A) The neutral model describes replete kinetics well but fails to capture the slow loss... more <p>(A) The neutral model describes replete kinetics well but fails to capture the slow loss of cells following thymectomy. (B) Comparing the density-dependent, adaptation, selection, and incumbent models using data from thymectomy onwards. (C) The same comparisons but using data from birth. Insets detail the growth of naive T-cell numbers in young mice. Data are provided in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003949#pbio.2003949.s002" target="_blank">S1 Data</a>. Tx, thymectomised; WT, wild-type.</p
Frontiers in Immunology, 2019
Initiation of adaptive immunity involves distinct migratory cell populations coming together in a... more Initiation of adaptive immunity involves distinct migratory cell populations coming together in a highly dynamic and spatially organized process. However, we lack a detailed spatiotemporal map of these events due to our inability to track the fate of cells between anatomically distinct locations or functionally identify cell populations as migratory. We used photo-convertible transgenic mice (Kaede) to spatiotemporally track the fate and composition of the cell populations that leave the site of priming and enter the draining lymph node to initiate immunity. We show that following skin priming, the lymph node migratory population is principally composed of cells recruited to the site of priming, with a minor contribution from tissue resident cells. In combination with the YAe/Eα system, we also show that the majority of cells presenting antigen are CD103 + CD11b + dendritic cells that were recruited to the site of priming during the inflammatory response. This population has previously only been described in relation to mucosal tissues. Comprehensive phenotypic profiling of the cells migrating from the skin to the draining lymph node by mass cytometry revealed that in addition to dendritic cells, the migratory population also included CD4 + and CD8 + T cells, B cells, and neutrophils. Taking our complex spatiotemporal data set, we then generated a model of cell migration that quantifies and describes the dynamics of arrival, departure, and residence times of cells at the site of priming and in the draining lymph node throughout the time-course of the initiation of adaptive immunity. In addition, we have identified the mean migration time of migratory dendritic cells as they travel from the site of priming to the draining lymph node. These findings represent an unprecedented, detailed and quantitative map of cell dynamics and phenotypes during immunization, identifying where, when and which cells to target for immunomodulation in autoimmunity and vaccination strategies.
Immunology, 2018
We have previously demonstrated co‐receptor level‐associated functional heterogeneity in apparent... more We have previously demonstrated co‐receptor level‐associated functional heterogeneity in apparently homogeneous naive peripheral CD4 T cells, dependent on MHC‐mediated tonic signals. Maturation pathways can differ between naive CD4 and naive CD8 cells, so we tested whether the latter showed similar co‐receptor level‐associated functional heterogeneity. We report that, when either polyclonal and T‐cell receptor (TCR)‐transgenic monoclonal peripheral naive CD8 T cells from young mice were separated into CD8hi and CD8lo subsets, CD8lo cells responded poorly, but CD8hi and CD8lo subsets of CD8 single‐positive (SP) thymocytes responded similarly. CD8lo naive CD8 T cells were smaller and showed lower levels of some cell‐surface molecules, but higher levels of the negative regulator CD5. In addition to the expected peripheral decline in CD8 levels on transferred naive CD8 T cells in wild‐type (WT) but not in MHC class I‐deficient recipient mice, short‐duration naive T‐cell–dendritic cell (...
PLoS biology, 2018
The processes regulating peripheral naive T-cell numbers and clonal diversity remain poorly under... more The processes regulating peripheral naive T-cell numbers and clonal diversity remain poorly understood. Conceptually, homeostatic mechanisms must fall into the broad categories of neutral (simple random birth-death models), competition (regulation of cell numbers through quorum-sensing, perhaps via limiting shared resources), adaptation (involving cell-intrinsic changes in homeostatic fitness, defined as net growth rate over time), or selection (involving the loss or outgrowth of cell populations deriving from intercellular variation in fitness). There may also be stably maintained heterogeneity within the naive T-cell pool. To distinguish between these mechanisms, we confront very general models of these processes with an array of experimental data, both new and published. While reduced competition for homeostatic stimuli may impact cell survival or proliferation in neonates or under moderate to severe lymphopenia, we show that the only mechanism capable of explaining multiple, ind...
Dynamics of cognate and non-cognate interactions during post-thymic survival of naïve CD4 (NCD4) ... more Dynamics of cognate and non-cognate interactions during post-thymic survival of naïve CD4 (NCD4) T lymphocytes in periphery may have distinct consequences on their function. It is not clear if there is any association between duration of peripheral residence of NCD4 T cells and their activation, proliferation and Effector functions. Alteration in phenotypic properties of NCD4 T cells owing to longer or shorter duration of peripheral residence also remains possible. Through our study, we are trying to understand the correlation between duration of peripheral residence and variations in phenotypic (CD4 levels) and functional properties of NCD4 T cells. We examined separated NCD4hi and NCD4lo subsets of mouse NCD4 cells. NCD4lo cells were smaller, had higher CD5 levels, responded poorly, were more Th2-skewed, with lower levels of the dual-specific phosphatase (DUSP)6-suppressing micro-RNA miR181a. Thymic NCD4lo and NCD4hi subsets did not show differences. Adoptive transfer-mediated par...