Early emergence of T central memory precursors programs clonal dominance during chronic viral infection [bulkRNAseq]
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE157641 | GEO | 2020/09/09
REPOSITORIES: GEO
Similar Datasets
Project description:Chronic infection with cytomegalovirus (CMV) leads to long-term maintenance of extraordinarily large CMV-specific T cell populations. The magnitude of this so-called ‘memory inflation’ is thought to be mainly determined by the availability of antigenic stimuli during the chronic phase of infection. However, by mapping the long-term development of CD8+ T cell families derived from single naive precursors, we find that T cell fate decisions, taken during the acute phase of murine CMV infection, can alter the level of memory inflation by more than 1000-fold. Counterintuitively, a T cell family’s capacity for memory inflation is not determined by its initial clonal expansion. Instead, those rare T cell families that strongly dominate the chronic phase of infection show an early transcriptomic signature akin to that of established T central memory cells. Accordingly, a T cell family’s long-term dominance is best predicted by its early content of T central memory precursors, which later serve as a stem cell-like source for the antigen-driven maintenance of memory inflation.
2020-09-05 | GSE157501 | GEO
Project description:Cytomegalovirus (CMV) induces a uniquely robust and persistent T cell response, where the size of the antigen-specific population does not contract, but rather inflates during viral latency. It has been proposed that intermittent engagements of T cell receptors (TCRs) by viral antigens upon subclinical episodes of virus reactivation feed the inflation of CMV-specific memory cells, but evidence of TCR engagement has remained lacking. Nuclear factor of activated T cells (NFAT) is a family of transcription factors, where NFATc1, NFATc2 and NFATc3 are expressed in mature T lymphocytes, of which NFATc1 and NFATc2 are the dominating family members. In an in vivo model of mouse CMV (MCMV) infection of mice with genetic ablation of NFAT signaling, we show a selective impact of this defect in TCR signaling on the long-term inflation of MCMV-specific CD8 T cell responses, while the initial responses to acute infection remain largely maintained. NFATc1 ablation had an immediate effect, while ablation of both NFATs had the most profound influence. In presence of other lymphocytes, NFAT deficiency in T cells had no effect on virus replication or latency, but in adoptive immunotherapy of RAG2-deficient recipient mice, the lack of both NFAT molecules in solely transplanted CD8+ T cells uncovered their decreased antiviral efficacy. We characterized CD8 responses in absence of either or both NFAT molecules by transcriptome analyses and demonstrate that T cell-intrinsic NFAT is not necessary for CD8 T cell priming, but rather for their maturation towards effector memory and in particular the effector cells, which dominate the pool of inflationary cells.
2024-01-25 | GSE228527 | GEO
Project description:This a model from the article:
Dynamics of killer T cell inflation in viral infections.
Wodarz D, Sierro S, Klenerman P. J R Soc Interface
2007 Jun 22;4(14):533-43 17251133
,
Abstract:
Upon acute viral infection, a typical cytotoxic T lymphocyte (CTL) response is
characterized by a phase of expansion and contraction after which it settles at
a relatively stable memory level. Recently, experimental data from mice infected
with murine cytomegalovirus (MCMV) showed different and unusual dynamics. After
acute infection had resolved, some antigen specific CTL started to expand over
time despite the fact that no replicative virus was detectable. This phenomenon
has been termed as "CTL memory inflation". In order to examine the dynamics of
this system further, we developed a mathematical model analysing the impact of
innate and adaptive immune responses. According to this model, a potentially
important contributor to CTL inflation is competition between the specific CTL
response and an innate natural killer (NK) cell response. Inflation occurs most
readily if the NK cell response is more efficient than the CTL at reducing virus
load during acute infection, but thereafter maintains a chronic virus load which
is sufficient to induce CTL proliferation. The model further suggests that
weaker NK cell mediated protection can correlate with more pronounced CTL
inflation dynamics over time. We present experimental data from mice infected
with MCMV which are consistent with the theoretical predictions. This model
provides valuable information and may help to explain the inflation of CMV
specific CD8+T cells seen in humans as they age.
This model was taken from the CellML repository
and automatically converted to SBML.
The original model was:
Wodarz D, Sierro S, Klenerman P. (2007) - version=1.0
The original CellML model was created by:
Catherine Lloyd
c.lloyd@auckland.ac.nz
The University of Auckland
This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team.
To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication
for more information.
In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not..
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
2024-09-02 | BIOMD0000000688 | BioModels
Project description:This a model from the article:
Dynamics of killer T cell inflation in viral infections.
Wodarz D, Sierro S, Klenerman P. J R Soc Interface
2007 Jun 22;4(14):533-43 17251133
,
Abstract:
Upon acute viral infection, a typical cytotoxic T lymphocyte (CTL) response is
characterized by a phase of expansion and contraction after which it settles at
a relatively stable memory level. Recently, experimental data from mice infected
with murine cytomegalovirus (MCMV) showed different and unusual dynamics. After
acute infection had resolved, some antigen specific CTL started to expand over
time despite the fact that no replicative virus was detectable. This phenomenon
has been termed as "CTL memory inflation". In order to examine the dynamics of
this system further, we developed a mathematical model analysing the impact of
innate and adaptive immune responses. According to this model, a potentially
important contributor to CTL inflation is competition between the specific CTL
response and an innate natural killer (NK) cell response. Inflation occurs most
readily if the NK cell response is more efficient than the CTL at reducing virus
load during acute infection, but thereafter maintains a chronic virus load which
is sufficient to induce CTL proliferation. The model further suggests that
weaker NK cell mediated protection can correlate with more pronounced CTL
inflation dynamics over time. We present experimental data from mice infected
with MCMV which are consistent with the theoretical predictions. This model
provides valuable information and may help to explain the inflation of CMV
specific CD8+T cells seen in humans as they age.
This model was taken from the CellML repository
and automatically converted to SBML.
The original model was:
Wodarz D, Sierro S, Klenerman P. (2007) - version=1.0
The original CellML model was created by:
Catherine Lloyd
c.lloyd@auckland.ac.nz
The University of Auckland
This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team.
To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication
for more information.
In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not..
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
2024-09-02 | BIOMD0000000687 | BioModels
Project description:This a model from the article:
Dynamics of killer T cell inflation in viral infections.
Wodarz D, Sierro S, Klenerman P. J R Soc Interface
2007 Jun 22;4(14):533-43 17251133
,
Abstract:
Upon acute viral infection, a typical cytotoxic T lymphocyte (CTL) response is
characterized by a phase of expansion and contraction after which it settles at
a relatively stable memory level. Recently, experimental data from mice infected
with murine cytomegalovirus (MCMV) showed different and unusual dynamics. After
acute infection had resolved, some antigen specific CTL started to expand over
time despite the fact that no replicative virus was detectable. This phenomenon
has been termed as "CTL memory inflation". In order to examine the dynamics of
this system further, we developed a mathematical model analysing the impact of
innate and adaptive immune responses. According to this model, a potentially
important contributor to CTL inflation is competition between the specific CTL
response and an innate natural killer (NK) cell response. Inflation occurs most
readily if the NK cell response is more efficient than the CTL at reducing virus
load during acute infection, but thereafter maintains a chronic virus load which
is sufficient to induce CTL proliferation. The model further suggests that
weaker NK cell mediated protection can correlate with more pronounced CTL
inflation dynamics over time. We present experimental data from mice infected
with MCMV which are consistent with the theoretical predictions. This model
provides valuable information and may help to explain the inflation of CMV
specific CD8+T cells seen in humans as they age.
This model was taken from the CellML repository
and automatically converted to SBML.
The original model was:
Wodarz D, Sierro S, Klenerman P. (2007) - version=1.0
The original CellML model was created by:
Catherine Lloyd
c.lloyd@auckland.ac.nz
The University of Auckland
This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team.
To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication
for more information.
In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not..
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
2024-09-02 | BIOMD0000000686 | BioModels
Project description:Reconstitution of cytomegalovirus (CMV)-specific immunity following transplant remains a primary clinical objective to prevent CMV disease, and adoptive immunotherapy of CMV-specific T cells can be an effective therapeutic approach. Due to the persistence of CMV, most CMV-specific CD8+ T cells become terminally differentiated effector cells (TEFF). However, a minor subset retains a memory phenotype (TM). Interestingly, recent studies suggest that CMV-specific CD8+ T cells with different phenotypes may have different abilities to reconstitute sustained immunity following transfer. The immunology of human CMV (HCMV) infections is reflected in the mouse model of MCMV infection. We found that HCMV- and MCMV-specific T cells displayed shared genetic programs, validating the MCMV model for studies of CMV-specific T cells in vivo. After transfer, the proliferative capacity of MCMV-specific TM cells was vastly superior to TEFF cells. Strikingly, TM cells expanded and established sustained and diverse T cell populations even after multiple challenges. Although both TEFF and TM cells could protect Rag-/- mice, only TM cells could consistently survive after transfer into immune replete, latently infected recipients and respond if recipient immunity was lost. These data show that CMV-specific TM cells retain memory function during persistent infection and can re-establish CMV immunity when necessary. C57BL/6 mice were infected intraperitoneally (i.p.) with MCMV strain MW97.01 between 6-16 weeks of age. Splenocytes were isolated from chronically-infected mice and co-stained with three PE-conjugated tetramers loaded with the antigenic peptides from M38, m139 and IE3, all of which promote memory inflation. Cells were then stained with fluorescently conjugated antibodies and sorted on a MoFlo cell sorter. Naïve CD8+ cells were identified as CD44lo. MCMV-specific T cells were identified as CD8+, CD44hi and tetramer binding and then further segregated into memory and effector cells subsets by their expression of KLRG1 and CD127.
2015-01-28 | E-GEOD-61927 | biostudies-arrayexpress
Project description:Following exposure to vaccines, antigen-specific CD8+ T-cell responses develop as long-term memory pools. Novel vaccine strategies based on adenoviral vectors, e.g. those developed for HCV, are able to induce and sustain substantial CD8+ T-cell populations. How such populations evolve following vaccination remains to be defined at a transcriptional level. We addressed the transcriptional regulation of divergent CD8+ T-cell memory pools induced by an adenoviral vector encoding a model antigen (beta-galactosidase). We observe transcriptional profiles that mimic those following infection with persistent pathogens, murine and human cytomegalovirus (CMV). Key transcriptional hallmarks include up-regulation of homing receptors, and anti-apoptotic pathways, driven by conserved networks of transcription factors, including T-bet (TBX21). In humans, a novel adenovirus vaccine induced similar CMV-like phenotypes and underlying transcription factor regulation. These data clarify the core features of CD8+ T-cell memory following vaccination with adenovirus vectors and indicate a conserved pathway for memory development shared with persistent herpesviruses. Total RNA was extracted from sorted memory CD8 T cells induce by CMV and adenoviral vectors, and naïve CD8 cells
2015-09-23 | E-GEOD-73314 | biostudies-arrayexpress
Project description:Gamma Delta (gd) T cells play unique protective roles in different settings of acute and chronic infections. However, what they respond to and how they function in the acute versus chronic phases of the same infection remains unclear. It is well documented that cytolytic gd T cells that express Vg9Vd2 TCRs and respond to phosphoantigens (pAgs) expand in acute Mycobacterium tuberculosis (Mtb) infection in humans. However, most infections with Mtb manifest as a chronic, clinically asymptomatic state. While past work indicates that gd T cells contribute to Mtb infection control, their response during this phase of Mtb infection is not well understood. Here, we analyze peripheral blood gd T cells from a South African adolescent cohort and show that a unique CD8+ gd T cell subset with features of “memory inflation” expand in chronic Mtb infection.
2022-10-31 | GSE216652 | GEO
Project description:Here we studied the transcriptional profile of virus specific CD8 T cells to gain molecular insights in CD8 T cell functionality in HIV infection. HIV- and CMV-specific CD8 T cells were isolated from HIV infected individuals participating in the Amsterdam Cohort Studies (HIV progressors, long-term non-progressors (LTNP; HLA-B*57 and non-HLA-B*57) and individuals carrying the MAVS minor genotype) and CMV seropositive blood donors (BD). The transcription profile of HIV-specific CD8 T cells of LTNP groups was associated with increased protein/RNA metabolism pathways, indicating that immune control of HIV infection in these individuals is associated with increased functionality. In contrast, CMV-specific CD8 T cells from progressors showed increased expression of genes related to effector functions and suggests recent CMV reactivation. Our study provides novel insights into molecular mechanisms involved in HIV and CMV control in chronic HIV infection.
2024-10-09 | GSE197333 | GEO
Project description:The avidity of the T-cell receptor (TCR) for antigenic peptides presented by the MHC (pMHC) on cells is an essential parameter for efficient T cell-mediated immunity. Yet, whether the TCR-ligand avidity can drive the clonal evolution of virus antigen-specific CD8 T cells, and how this process is determined in latent Cytomegalovirus (CMV)- against Epstein-Barr virus (EBV)-mediated infection remains largely unknown. Here, we quantified monomeric TCR-pMHC dissociation rates on CMV- and EBV-specific individual TCR-alpha-beta clonotypes and polyclonal CD8 T cell populations in healthy donors over a follow-up time of 15-18 years. Within CMV/pp65-specific T cell repertoires, a progressive contraction of clonotypes with high TCR-pMHC avidity and low CD8 binding dependency was observed, leading to an overall avidity decline during long-term antigen exposure. We identified a unique transcriptional signature preferentially expressed by high-avidity CMV/pp65-specific T cell clonotypes, including the inhibitory receptor LILRB1. Interestingly, T cell clonotypes of high-avidity showed higher LILRB1 expression than the low-avidity ones and LILRB1 blockade moderately increased T cell proliferation. Similar findings were made for CD8 T cell repertoires specific for the CMV/IE-1 epitope. There was a gradual in vivo loss of high-avidity T cells with time for both CMV specificities, corresponding to virus-specific CD8 T cells expressing enhanced LILRB1 levels. In sharp contrast, the EBV/BMFL1-specific T cell clonal composition and distribution, once established, displayed an exceptional stability, unrelated to TCR-pMHC binding avidity or LILRB1 expression. Together, these findings reveal an overall long-term avidity decline of CMV- but not EBV-specific T cell clonal repertoires, highlighting the differing role played by TCR-ligand avidity over the course of these two latent herpesvirus infections. Our data suggest that the inhibitor receptor LILRB1 potentially restricts the clonal expansion of high-avidity CMV-specific T cell clonotypes during latent infection. We propose that the mechanisms regulating the long-term outcome of CMV- and EBV-specific memory CD8 T cell clonotypes in humans are distinct.
2023-11-15 | GSE246111 | GEO