1
|
de Boer RJ, Tesselaar K, Borghans JAM. Better safe than sorry: Naive T-cell dynamics in healthy ageing. Semin Immunol 2023; 70:101839. [PMID: 37716048 DOI: 10.1016/j.smim.2023.101839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/01/2023] [Accepted: 09/02/2023] [Indexed: 09/18/2023]
Abstract
It is well-known that the functioning of the immune system gradually deteriorates with age, and we are increasingly confronted with its consequences as the life expectancy of the human population increases. Changes in the T-cell pool are among the most prominent features of the changing immune system during healthy ageing, and changes in the naive T-cell pool in particular are generally held responsible for its gradual deterioration. These changes in the naive T-cell pool are thought to be due to involution of the thymus. It is commonly believed that the gradual loss of thymic output induces compensatory mechanisms to maintain the number of naive T cells at a relatively constant level, and induces a loss of diversity in the T-cell repertoire. Here we review the studies that support or challenge this widely-held view of immune ageing and discuss the implications for vaccination strategies.
Collapse
Affiliation(s)
- Rob J de Boer
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, the Netherlands
| | - Kiki Tesselaar
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - José A M Borghans
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands.
| |
Collapse
|
2
|
de Greef PC, Lanfermeijer J, Hendriks M, Cevirgel A, Vos M, Borghans JAM, van Baarle D, de Boer RJ. On the feasibility of using TCR sequencing to follow a vaccination response - lessons learned. Front Immunol 2023; 14:1210168. [PMID: 37520553 PMCID: PMC10374308 DOI: 10.3389/fimmu.2023.1210168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 06/26/2023] [Indexed: 08/01/2023] Open
Abstract
T cells recognize pathogens by their highly specific T-cell receptor (TCR), which can bind small fragments of an antigen presented on the Major Histocompatibility Complex (MHC). Antigens that are provided through vaccination cause specific T cells to respond by expanding and forming specific memory to combat a future infection. Quantification of this T-cell response could improve vaccine monitoring or identify individuals with a reduced ability to respond to a vaccination. In this proof-of-concept study we use longitudinal sequencing of the TCRβ repertoire to quantify the response in the CD4+ memory T-cell pool upon pneumococcal conjugate vaccination. This comes with several challenges owing to the enormous size and diversity of the T-cell pool, the limited frequency of vaccine-specific TCRs in the total repertoire, and the variation in sample size and quality. We defined quantitative requirements to classify T-cell expansions and identified critical parameters that aid in reliable analysis of the data. In the context of pneumococcal conjugate vaccination, we were able to detect robust T-cell expansions in a minority of the donors, which suggests that the T-cell response against the conjugate in the pneumococcal vaccine is small and/or very broad. These results indicate that there is still a long way to go before TCR sequencing can be reliably used as a personal biomarker for vaccine-induced protection. Nevertheless, this study highlights the importance of having multiple samples containing sufficient T-cell numbers, which will support future studies that characterize T-cell responses using longitudinal TCR sequencing.
Collapse
Affiliation(s)
- Peter C. de Greef
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
| | - Josien Lanfermeijer
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Marion Hendriks
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Alper Cevirgel
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Martijn Vos
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - José A. M. Borghans
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Debbie van Baarle
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Rob J. de Boer
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
| |
Collapse
|
3
|
Schrom E, Kinzig A, Forrest S, Graham AL, Levin SA, Bergstrom CT, Castillo-Chavez C, Collins JP, de Boer RJ, Doupé A, Ensafi R, Feldman S, Grenfell BT, Halderman JA, Huijben S, Maley C, Moses M, Perelson AS, Perrings C, Plotkin J, Rexford J, Tiwari M. Challenges in cybersecurity: Lessons from biological defense systems. Math Biosci 2023:109024. [PMID: 37270102 DOI: 10.1016/j.mbs.2023.109024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 04/27/2023] [Accepted: 05/20/2023] [Indexed: 06/05/2023]
Abstract
Defending against novel, repeated, or unpredictable attacks, while avoiding attacks on the 'self', are the central problems of both mammalian immune systems and computer systems. Both systems have been studied in great detail, but with little exchange of information across the different disciplines. Here, we present a conceptual framework for structured comparisons across the fields of biological immunity and cybersecurity, by framing the context of defense, considering different (combinations of) defensive strategies, and evaluating defensive performance. Throughout this paper, we pose open questions for further exploration. We hope to spark the interdisciplinary discovery of general principles of optimal defense, which can be understood and applied in biological immunity, cybersecurity, and other defensive realms.
Collapse
Affiliation(s)
- Edward Schrom
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, United States of America
| | - Ann Kinzig
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, United States of America
| | - Stephanie Forrest
- Biodesign Center for Biocomputation, Security and Society, Arizona State University, Tempe, AZ 85287, United States of America; School of Computing and Augmented Intelligence, Arizona State University, Tempe, AZ 85287, United States of America; Santa Fe Institute, Santa Fe, NM 87501, United States of America
| | - Andrea L Graham
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, United States of America; Santa Fe Institute, Santa Fe, NM 87501, United States of America
| | - Simon A Levin
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, United States of America.
| | - Carl T Bergstrom
- Department of Biology, University of Washington, Seattle, WA 98195, United States of America
| | - Carlos Castillo-Chavez
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287, United States of America
| | - James P Collins
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, United States of America
| | - Rob J de Boer
- Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Adam Doupé
- School of Computing and Augmented Intelligence, Arizona State University, Tempe, AZ 85287, United States of America; Center for Cybersecurity and Trusted Foundations, Global Security Initiative, Arizona State University, Tempe, AZ 85287, United States of America
| | - Roya Ensafi
- Department of Electrical Engineering and Computer Science, Computer Science and Engineering Division, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Stuart Feldman
- Schmidt Futures, New York, NY 10011, United States of America
| | - Bryan T Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, United States of America; Princeton School of Public and International Affairs, Princeton University, Princeton, NJ 08544, United States of America
| | - J Alex Halderman
- Department of Electrical Engineering and Computer Science, Computer Science and Engineering Division, University of Michigan, Ann Arbor, MI 48109, United States of America; Center for Computer Security and Society, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Silvie Huijben
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, United States of America
| | - Carlo Maley
- Arizona Cancer Evolution Center, Arizona State University, Tempe, AZ 85287, United States of America; Biodesign Center for Biocomputation, Security and Society, Arizona State University, Tempe, AZ 85287, United States of America
| | - Melanie Moses
- Department of Computer Science, University of New Mexico, Albuquerque, NM 87131, United States of America; Department of Biology, University of New Mexico, Albuquerque, NM 87131, United States of America; Santa Fe Institute, Santa Fe, NM 87501, United States of America
| | - Alan S Perelson
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America; Santa Fe Institute, Santa Fe, NM 87501, United States of America
| | - Charles Perrings
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, United States of America
| | - Joshua Plotkin
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, United States of America
| | - Jennifer Rexford
- Department of Computer Science, Princeton University, Princeton, NJ 08540, United States of America
| | - Mohit Tiwari
- Department of Electrical and Computer Engineering, University of Texas, Austin, TX 78712, United States of America
| |
Collapse
|
4
|
Schröter J, de Boer RJ. What explains the poor contraction of the viral load during paediatric HIV infection? J Theor Biol 2023; 570:111521. [PMID: 37164225 DOI: 10.1016/j.jtbi.2023.111521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 02/03/2023] [Accepted: 04/30/2023] [Indexed: 05/12/2023]
Abstract
An acute HIV infection in young children differs markedly from that in adults: Children have higher viral loads (VL), and a poor contraction to a setpoint VL that is not much lower than the peak VL. As a result, children progress faster towards AIDS in the absence of treatment. We used a classical ordinary differential equation model for viral infection dynamics to study why children have a lower viral contraction ratio than adults. We performed parameter sweeps to identify factors explaining the observed difference between children and adults. We grouped parameters associated with the host, the infection, or the immune response. Based on paediatric data available from datasets within the EPIICAL project (https://www.epiical.org/), we refuted that viral replication rates differ between young children and adults, and therefore these cannot be responsible for the low VL contraction ratios seen in children. The major differences in lowering VL contraction ratio resulted from sweeping the parameters linked to the immune response. Thus, we postulate that an "ineffective" (late and/or weak) immune response is the most parsimonious explanation for the higher setpoint VL in young children, and hence the reason for their fast disease progression.
Collapse
Affiliation(s)
- Juliane Schröter
- Theoretical Biology & Bioinformatics, Utrecht University, Utrecht, The Netherlands.
| | - Rob J de Boer
- Theoretical Biology & Bioinformatics, Utrecht University, Utrecht, The Netherlands
| |
Collapse
|
5
|
Schröter J, Borghans JAM, Bitter WM, van Dongen JJM, de Boer RJ. Age-Dependent Normalization Functions for T Lymphocytes in Healthy Individuals. J Immunol 2023:263658. [PMID: 37125851 DOI: 10.4049/jimmunol.2200520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 03/27/2023] [Indexed: 05/02/2023]
Abstract
Lymphocyte numbers naturally change through age. Normalization functions to account for this are sparse and mostly disregard measurements from children in which these changes are most prominent. In this study, we analyze 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 y). We fitted the data by a delayed exponential function and estimated parameters for each lymphocyte subset. Our modeling 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 obtain 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 before the total lymphocyte counts per microliter of blood start to change exponentially, and we find that T lymphocyte trajectories tend to increase during the first half a year of life. Thus, our study provides functions describing the general trajectories of T lymphocyte counts and percentages of the Dutch population. These functions provide important references to study T lymphocyte dynamics in disease, and they allow one to quantify losses and gains in longitudinal data, such as the CD4+ T cell decline in HIV-infected children and/or the rate of T cell recovery after the onset of treatment.
Collapse
Affiliation(s)
- Juliane Schröter
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, the Netherlands
| | - José A M Borghans
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - W Marieke Bitter
- Department of Immunology, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Rob J de Boer
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, the Netherlands
| |
Collapse
|
6
|
Mijnheer G, Servaas NH, Leong JY, Boltjes A, Spierings E, Chen P, Lai L, Petrelli A, Vastert S, de Boer RJ, Albani S, Pandit A, van Wijk F. Compartmentalization and persistence of dominant (regulatory) T cell clones indicates antigen skewing in juvenile idiopathic arthritis. eLife 2023; 12:79016. [PMID: 36688525 PMCID: PMC9995115 DOI: 10.7554/elife.79016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 01/20/2023] [Indexed: 01/24/2023] Open
Abstract
Autoimmune 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 clones were characterized by a high degree of sequence similarity, indicating the presence of TCR clusters responding to the same antigens. These data suggest that in localized autoimmune disease, there is autoantigen-driven expansion of both Teffector and Treg clones that are highly persistent and are (re)circulating. These dominant clones might represent interesting therapeutic targets.
Collapse
Affiliation(s)
- Gerdien Mijnheer
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht UniversityUtrechtNetherlands
| | - Nila Hendrika Servaas
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht UniversityUtrechtNetherlands
| | - Jing Yao Leong
- Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, the AcademiaSingaporeSingapore
| | - Arjan Boltjes
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht UniversityUtrechtNetherlands
| | - Eric Spierings
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht UniversityUtrechtNetherlands
| | - Phyllis Chen
- Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, the AcademiaSingaporeSingapore
| | - Liyun Lai
- Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, the AcademiaSingaporeSingapore
| | - Alessandra Petrelli
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht UniversityUtrechtNetherlands
| | - Sebastiaan Vastert
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht UniversityUtrechtNetherlands
- Pediatric Immunology & Rheumatology, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht UniversityUtrechtNetherlands
| | - Rob J de Boer
- Theoretical Biology, Utrecht UniversityUtrechtNetherlands
| | - Salvatore Albani
- Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, the AcademiaSingaporeSingapore
| | - Aridaman Pandit
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht UniversityUtrechtNetherlands
| | - Femke van Wijk
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht UniversityUtrechtNetherlands
| |
Collapse
|
7
|
Swain AC, Borghans JA, de Boer RJ. Effect of cellular aging on memory T-cell homeostasis. Front Immunol 2022; 13:947242. [PMID: 36059495 PMCID: PMC9429809 DOI: 10.3389/fimmu.2022.947242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 07/07/2022] [Indexed: 11/23/2022] Open
Abstract
The fact that T-cell numbers remain relatively stable throughout life, and that T-cell proliferation rates increase during lymphopenia, has led to the consensus that T-cell numbers are regulated in a density-dependent manner. Competition for resources among memory T cells has been proposed to underlie this ‘homeostatic’ regulation. We first review how two classic models of resource competition affect the T-cell receptor (TCR) diversity of the memory T-cell pool. First, ‘global’ competition for cytokines leads to a skewed repertoire that tends to be dominated by the very first immune response. Second, additional ‘cognate’ competition for specific antigens results in a very diverse and stable memory T-cell pool, allowing every antigen to be remembered, which we therefore define as the ‘gold-standard’. Because there is limited evidence that memory T cells of the same specificity compete more strongly with each other than with memory T cells of different specificities, i.e., for ‘cognate’ competition, we investigate whether cellular aging could account for a similar level of TCR diversity. We define cellular aging as a declining cellular fitness due to reduced proliferation. We find that the gradual erosion of previous T-cell memories due to cellular aging allows for better establishment of novel memories and for a much higher level of TCR diversity compared to global competition. A small continual source (either from stem-cell-like memory T-cells or from naive T-cells due to repeated antigen exposure) improves the diversity of the memory T-cell pool, but remarkably, only in the cellular aging model. We further show that the presence of a source keeps the inflation of chronic memory responses in check by maintaining the immune memories to non-chronic antigens. We conclude that cellular aging along with a small source provides a novel and immunologically realistic mechanism to achieve and maintain the ‘gold-standard’ level of TCR diversity in the memory T-cell pool.
Collapse
Affiliation(s)
- Arpit C. Swain
- Theoretical Biology, Utrecht University, Utrecht, Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
- *Correspondence: Arpit C. Swain,
| | - José A.M. Borghans
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Rob J. de Boer
- Theoretical Biology, Utrecht University, Utrecht, Netherlands
| |
Collapse
|
8
|
Abstract
BACKGROUND Perinatally HIV-acquired infants benefit from an early antiretroviral treatment initiation. Thanks to a short viral exposure time, their immune system can be maintained or reconstituted, allowing a "normal" immune development. METHODS In this study, we mathematically modeled and quantified individual CD4+ T-cell reconstitution of a subset of 276 children who started treatment within 6 months of age and achieved sustained viral suppression. Considering natural age differences in CD4+ T-cell dynamics, we fitted distances to age-matched healthy reference values with a linear model approaching an asymptote. RESULTS Depleted CD4+ percentages (CD4%) and CD4+ counts (CD4ct) restored healthy levels during treatment. CD4ct recovered with a median rate of 4 cells/µL/d, and individual recovery rates were correlated negatively with their initial CD4ct. CD4 values at onset of treatment decrease with age, whereas recovery times and levels seem to be age-independent. CD4 recovery correlates positively with viral suppression, and the stabilization of CD4 levels usually occurs after viral suppression. CD4 levels stabilize within 3-13 months after treatment initiation. The recovery dynamics of the CD4% is comparable with those of the CD4ct. CONCLUSIONS In early-treated children with successful viral suppression, the CD4 depletion is typically mild and CD4+ T cells tend to "fully" recover in numbers.
Collapse
Affiliation(s)
- Juliane Schröter
- Theoretical Biology & Bioinformatics, Utrecht University, Utrecht, the Netherlands; and
| | - Anet J. N. Anelone
- Theoretical Biology & Bioinformatics, Utrecht University, Utrecht, the Netherlands; and
- Currently, School of Mathematics and Statistics, University of Sydney, Sydney, Australia
| | - Rob J. de Boer
- Theoretical Biology & Bioinformatics, Utrecht University, Utrecht, the Netherlands; and
| |
Collapse
|
9
|
Baliu-Piqué M, Drylewicz J, Zheng X, Borkner L, Swain AC, Otto SA, de Boer RJ, Tesselaar K, Cicin-Sain L, Borghans JAM. Turnover of Murine Cytomegalovirus-Expanded CD8 + T Cells Is Similar to That of Memory Phenotype T Cells and Independent of the Magnitude of the Response. J Immunol 2022; 208:799-806. [PMID: 35091435 DOI: 10.4049/jimmunol.2100883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 12/08/2021] [Indexed: 11/19/2022]
Abstract
The potential of memory T cells to provide protection against reinfection 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 Ag. 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 labeling and mathematical modeling, we found that the average production rates and expected lifespans of mouse CMV-specific CD8+ T cells are very similar to those of bulk memory-phenotype CD8+ T cells. Even CMV-specific inflationary CD8+ T cell responses that differ 3-fold in size were found to turn over at similar rates.
Collapse
Affiliation(s)
- Mariona Baliu-Piqué
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Julia Drylewicz
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Xiaoyan Zheng
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Lisa Borkner
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Arpit C Swain
- Theoretical Biology, Utrecht University, Utrecht, The Netherlands; and
| | - Sigrid A Otto
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Rob J de Boer
- Theoretical Biology, Utrecht University, Utrecht, The Netherlands; and
| | - Kiki Tesselaar
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Luka Cicin-Sain
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany.,German Center for Infection Research, Partner Site, Hannover-Braunschweig, Germany
| | - José A M Borghans
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands;
| |
Collapse
|
10
|
van den Berg SPH, Derksen LY, Drylewicz J, Nanlohy NM, Beckers L, Lanfermeijer J, Gessel SN, Vos M, Otto SA, de Boer RJ, Tesselaar K, Borghans JAM, van Baarle D. Quantification of T-cell dynamics during latent cytomegalovirus infection in humans. PLoS Pathog 2021; 17:e1010152. [PMID: 34914799 PMCID: PMC8717968 DOI: 10.1371/journal.ppat.1010152] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 12/30/2021] [Accepted: 11/27/2021] [Indexed: 01/10/2023] Open
Abstract
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+ T-cells of CMV+ versus CMV- individuals was not solely explained by the presence of large, immunodominant CMV-specific CD8+ T-cell populations. The lifespans of circulating CMV-specific CD8+ T-cells did not differ significantly from those of bulk memory CD8+ T-cells, and the lifespans of bulk memory CD8+ T-cells did not differ significantly between CMV- and CMV+ individuals. Memory CD4+ T-cells of CMV+ individuals showed increased expression of late-stage differentiation markers and decreased Ki-67 expression. Overall, the expression of senescence markers on T-cell populations correlated positively with their expected in vivo lifespan. Together, this work suggests that i) large, immunodominant CMV-specific CD8+ T-cell populations do not explain the phenotypical differences between CMV+ and CMV- individuals, ii) CMV infection hardly affects the dynamics of the T-cell pool, and iii) large numbers of CMV-specific CD8+ T-cells are not due to longer lifespans of these cells.
Collapse
Affiliation(s)
- Sara P. H. van den Berg
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Lyanne Y. Derksen
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Julia Drylewicz
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Nening M. Nanlohy
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Lisa Beckers
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Josien Lanfermeijer
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Stephanie N. Gessel
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Martijn Vos
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Sigrid A. Otto
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Rob J. de Boer
- Theoretical Biology, Utrecht University, Utrecht, the Netherlands
| | - Kiki Tesselaar
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - José A. M. Borghans
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Debbie van Baarle
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| |
Collapse
|
11
|
Cosgrove J, Hustin LSP, de Boer RJ, Perié L. Hematopoiesis in numbers. Trends Immunol 2021; 42:1100-1112. [PMID: 34742656 DOI: 10.1016/j.it.2021.10.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/28/2021] [Accepted: 10/11/2021] [Indexed: 12/16/2022]
Abstract
Hematopoiesis is a dynamic process in which stem and progenitor cells give rise to the ~1013 blood and immune cells distributed throughout the human body. We argue that a quantitative description of hematopoiesis can help consolidate existing data, identify knowledge gaps, and generate new hypotheses. Here, we review known numbers in murine and, where possible, human hematopoiesis, and consolidate murine numbers into a set of reference values. We present estimates of cell numbers, division and differentiation rates, cell size, and macromolecular composition for each hematopoietic cell type. We also propose guidelines to improve the reporting of measurements and highlight areas in which quantitative data are lacking. Overall, we show how quantitative approaches can be used to understand key properties of hematopoiesis.
Collapse
Affiliation(s)
- Jason Cosgrove
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France
| | - Lucie S P Hustin
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France
| | - Rob J de Boer
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
| | - Leïla Perié
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France.
| |
Collapse
|
12
|
Castro M, de Boer RJ. The limitations, dangers, and benefits of simple methods for testing identifiability. PLoS Comput Biol 2021; 17:e1009425. [PMID: 34648494 PMCID: PMC8516191 DOI: 10.1371/journal.pcbi.1009425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/06/2021] [Indexed: 11/19/2022] Open
Abstract
In their Commentary paper, Villaverde and Massonis (On testing structural identifiability by a simple scaling method: relying on scaling symmetries can be misleading) have commented on our paper in which we proposed a simple scaling method to test structural identifiability. Our scaling invariance method (SIM) tests for scaling symmetries only, and Villaverde and Massonis correctly show the SIM may fail to detect identifiability problems when a model has other types of symmetries. We agree with the limitations raised by these authors but, also, we emphasize that the method is still valuable for its applicability to a wide variety of models, its simplicity, and even as a tool to introduce the problem of identifiability to investigators with little training in mathematics.
Collapse
Affiliation(s)
- Mario Castro
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain
- Instituto de Investigación Tecnológica (IIT), Universidad Pontificia Comillas, Madrid, Spain
| | - Rob J. de Boer
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
| |
Collapse
|
13
|
Weigelin B, den Boer AT, Wagena E, Broen K, Dolstra H, de Boer RJ, Figdor CG, Textor J, Friedl P. Cytotoxic T cells are able to efficiently eliminate cancer cells by additive cytotoxicity. Nat Commun 2021; 12:5217. [PMID: 34471116 PMCID: PMC8410835 DOI: 10.1038/s41467-021-25282-3] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 07/19/2021] [Indexed: 02/07/2023] Open
Abstract
Lethal hit delivery by cytotoxic T lymphocytes (CTL) towards B lymphoma cells occurs as a binary, "yes/no" process. In non-hematologic solid tumors, however, CTL often fail to kill target cells during 1:1 conjugation. Here we describe a mechanism of "additive cytotoxicity" by which time-dependent integration of sublethal damage events, delivered by multiple CTL transiting between individual tumor cells, mediates effective elimination. Reversible sublethal damage includes perforin-dependent membrane pore formation, nuclear envelope rupture and DNA damage. Statistical modeling reveals that 3 serial hits delivered with decay intervals below 50 min discriminate between tumor cell death or survival after recovery. In live melanoma lesions in vivo, sublethal multi-hit delivery is most effective in interstitial tissue where high CTL densities and swarming support frequent serial CTL-tumor cell encounters. This identifies CTL-mediated cytotoxicity by multi-hit delivery as an incremental and tunable process, whereby accelerating damage magnitude and frequency may improve immune efficacy.
Collapse
Affiliation(s)
- Bettina Weigelin
- Department of Cell Biology, RIMLS, Radboud University Medical Center, Nijmegen, The Netherlands.
- David H. Koch Center for Applied Research of Genitourinary Cancers, Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Preclinical Imaging and Radiopharmacy, Eberhard Karls University, Tübingen, Germany.
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, Tübingen, Germany.
| | | | - Esther Wagena
- Department of Cell Biology, RIMLS, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Kelly Broen
- Department of Laboratory Medicine - Laboratory of Hematology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Harry Dolstra
- Department of Laboratory Medicine - Laboratory of Hematology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rob J de Boer
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
| | - Carl G Figdor
- Department of Tumor Immunology, RIMLS, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Johannes Textor
- Department of Tumor Immunology, RIMLS, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Peter Friedl
- Department of Cell Biology, RIMLS, Radboud University Medical Center, Nijmegen, The Netherlands.
- David H. Koch Center for Applied Research of Genitourinary Cancers, Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Cancer Genomics Centre Netherlands (CGC.nl), Utrecht, The Netherlands.
| |
Collapse
|
14
|
Wortel IMN, Niculescu I, Kolijn PM, Gov NS, de Boer RJ, Textor J. Local actin dynamics couple speed and persistence in a cellular Potts model of cell migration. Biophys J 2021; 120:2609-2622. [PMID: 34022237 PMCID: PMC8390880 DOI: 10.1016/j.bpj.2021.04.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 03/24/2021] [Accepted: 04/14/2021] [Indexed: 12/28/2022] Open
Abstract
Cell migration is astoundingly diverse. Molecular signatures, cell-cell interactions, and environmental structures each play their part in shaping cell motion, yielding numerous morphologies and migration modes. Nevertheless, in recent years, a simple unifying law was found to describe cell migration across many different cell types and contexts: faster cells turn less frequently. This universal coupling between speed and persistence (UCSP) was explained by retrograde actin flow from front to back, but it remains unclear how this mechanism generalizes to cells with complex shapes and cells migrating in structured environments, which may not have a well-defined front-to-back orientation. Here, we present an in-depth characterization of an existing cellular Potts model, in which cells polarize dynamically from a combination of local actin dynamics (stimulating protrusions) and global membrane tension along the perimeter (inhibiting protrusions). We first show that the UCSP emerges spontaneously in this model through a cross talk of intracellular mechanisms, cell shape, and environmental constraints, resembling the dynamic nature of cell migration in vivo. Importantly, we find that local protrusion dynamics suffice to reproduce the UCSP-even in cases in which no clear global, front-to-back polarity exists. We then harness the spatial nature of the cellular Potts model to show how cell shape dynamics limit both the speed and persistence a cell can reach and how a rigid environment such as the skin can restrict cell motility even further. Our results broaden the range of potential mechanisms underlying the speed-persistence coupling that has emerged as a fundamental property of migrating cells.
Collapse
Affiliation(s)
- Inge M N Wortel
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands; Data Science, Institute for Computing and Information Sciences, Radboud University, Nijmegen, the Netherlands.
| | - Ioana Niculescu
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Utrecht, the Netherlands
| | - P Martijn Kolijn
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Utrecht, the Netherlands
| | - Nir S Gov
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Rob J de Boer
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Utrecht, the Netherlands
| | - Johannes Textor
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands; Data Science, Institute for Computing and Information Sciences, Radboud University, Nijmegen, the Netherlands.
| |
Collapse
|
15
|
Baliu-Piqué M, van Hoeven V, Drylewicz J, van der Wagen LE, Janssen A, Otto SA, van Zelm MC, de Boer RJ, Kuball J, Borghans JA, Tesselaar K. Cell-density independent increased lymphocyte production and loss rates post-autologous HSCT. eLife 2021; 10:59775. [PMID: 33538246 PMCID: PMC7886352 DOI: 10.7554/elife.59775] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 02/03/2021] [Indexed: 12/18/2022] Open
Abstract
Lymphocyte numbers need to be quite tightly regulated. It is generally assumed that lymphocyte production and lifespan increase homeostatically when lymphocyte numbers are low and, vice versa, return to normal once cell numbers have normalized. This widely accepted concept is largely based on experiments in mice, but is hardly investigated in vivo in humans. Here we quantified lymphocyte production and loss rates in vivo in patients 0.5–1 year after their autologous hematopoietic stem cell transplantation (autoHSCT). We indeed found that the production rates of most T- and B-cell subsets in autoHSCT-patients were two to eight times higher than in healthy controls, but went hand in hand with a threefold to ninefold increase in cell loss rates. Both rates also did not normalize when cell numbers did. This shows that increased lymphocyte production and loss rates occur even long after autoHSCT and can persist in the face of apparently normal cell numbers.
Collapse
Affiliation(s)
- Mariona Baliu-Piqué
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Vera van Hoeven
- Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Julia Drylewicz
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | | | - Anke Janssen
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Sigrid A Otto
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Menno C van Zelm
- Department of Immunology and Pathology, Monash University and Alfred Hospital, Melbourne, Australia
| | - Rob J de Boer
- Theoretical Biology, Utrecht University, Utrecht, Netherlands
| | - Jürgen Kuball
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands.,Department of Hematology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Jose Am Borghans
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Kiki Tesselaar
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| |
Collapse
|
16
|
Schröter J, Anelone AJN, Yates AJ, de Boer RJ. Time to Viral Suppression in Perinatally HIV-Infected Infants Depends on the Viral Load and CD4 T-Cell Percentage at the Start of Treatment. J Acquir Immune Defic Syndr 2020; 83:522-529. [PMID: 31917752 PMCID: PMC7147397 DOI: 10.1097/qai.0000000000002291] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Interventions aiming for an HIV cure would benefit from rapid elimination of virus after the onset of antiretroviral therapy (ART), by keeping the latent HIV reservoir small. SETTING We investigated HIV suppression in 312 perinatally infected infants starting ART within 6 months after birth from the EPPICC (European Pregnancy and Paediatric HIV Cohort Collaboration). METHODS To better understand kinetic differences in HIV suppression among infants, we investigated their individual viral load (VL) decay dynamics. We identified VL decay patterns and determined times to viral suppression (TTS). For infants with strictly declining VLs (n = 188), we used parameter fitting methods to estimate baseline VLs, decay rates, and TTS. We subsequently identified the parameters determining TTS by linear modeling. RESULTS The majority of infants suppress HIV VL after the onset of ART. Some children experienced a long TTS due to an "erratic" VL decay pattern. We cannot exclude that this is partly due to treatment complications and subsequent treatment changes, but these children were characterized by significantly lower CD4 percentages (CD4%) at start of treatment compared with those with a "clean" VL decline. Focusing on this "clean" subset, the TTS could be predicted by mathematical modeling, and we identified baseline VL and CD4% as the major factors determining the TTS. CONCLUSIONS As VL steeply increases and CD4% constantly decreases in untreated HIV-infected infants, the progression of an HIV infection is largely determined by these 2 factors. To prevent a further disease progression, treatment should be initiated early after contracting HIV, which consequently shortens TTS.
Collapse
Affiliation(s)
- Juliane Schröter
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands; and
| | - Anet J N Anelone
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands; and
| | - Andrew J Yates
- Department of Pathology and Cell Biology, Columbia University, New York City, NY
| | - Rob J de Boer
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands; and
| | | |
Collapse
|
17
|
Silva-Cardoso SC, Tao W, Angiolilli C, Lopes AP, Bekker CPJ, Devaprasad A, Giovannone B, van Laar J, Cossu M, Marut W, Hack E, de Boer RJ, Boes M, Radstake TRDJ, Pandit A. CXCL4 Links Inflammation and Fibrosis by Reprogramming Monocyte-Derived Dendritic Cells in vitro. Front Immunol 2020; 11:2149. [PMID: 33042127 PMCID: PMC7527415 DOI: 10.3389/fimmu.2020.02149] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/07/2020] [Indexed: 12/25/2022] Open
Abstract
Fibrosis is a condition shared by numerous inflammatory diseases. Our incomplete understanding of the molecular mechanisms underlying fibrosis has severely hampered effective drug development. CXCL4 is associated with the onset and extent of fibrosis development in multiple inflammatory and fibrotic diseases. Here, we used monocyte-derived cells as a model system to study the effects of CXCL4 exposure on dendritic cell development by integrating 65 longitudinal and paired whole genome transcriptional and methylation profiles. Using data-driven gene regulatory network analyses, we demonstrate that CXCL4 dramatically alters the trajectory of monocyte differentiation, inducing a novel pro-inflammatory and pro-fibrotic phenotype mediated via key transcriptional regulators including CIITA. Importantly, these pro-inflammatory cells directly trigger a fibrotic cascade by producing extracellular matrix molecules and inducing myofibroblast differentiation. Inhibition of CIITA mimicked CXCL4 in inducing a pro-inflammatory and pro-fibrotic phenotype, validating the relevance of the gene regulatory network. Our study unveils that CXCL4 acts as a key secreted factor driving innate immune training and forming the long-sought link between inflammation and fibrosis.
Collapse
Affiliation(s)
- Sandra C Silva-Cardoso
- Center for Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands.,Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Weiyang Tao
- Center for Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands.,Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Chiara Angiolilli
- Center for Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands.,Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Ana P Lopes
- Center for Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands.,Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Cornelis P J Bekker
- Center for Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands.,Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Abhinandan Devaprasad
- Center for Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands.,Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Barbara Giovannone
- Department of Dermatology and Allergology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Jaap van Laar
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Marta Cossu
- Center for Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands.,Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Wioleta Marut
- Center for Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands.,Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Erik Hack
- Center for Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Rob J de Boer
- Theoretical Biology, Utrecht University, Utrecht, Netherlands
| | - Marianne Boes
- Center for Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands.,Department of Pediatrics, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Timothy R D J Radstake
- Center for Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands.,Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Aridaman Pandit
- Center for Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands.,Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| |
Collapse
|
18
|
de Greef PC, Oakes T, Gerritsen B, Ismail M, Heather JM, Hermsen R, Chain B, de Boer RJ. The naive T-cell receptor repertoire has an extremely broad distribution of clone sizes. eLife 2020; 9:e49900. [PMID: 32187010 PMCID: PMC7080410 DOI: 10.7554/elife.49900] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 03/03/2020] [Indexed: 12/24/2022] Open
Abstract
The clone size distribution of the human naive T-cell receptor (TCR) repertoire is an important determinant of adaptive immunity. We estimated the abundance of TCR sequences in samples of naive T cells from blood using an accurate quantitative sequencing protocol. We observe most TCR sequences only once, consistent with the enormous diversity of the repertoire. However, a substantial number of sequences were observed multiple times. We detect abundant TCR sequences even after exclusion of methodological confounders such as sort contamination, and multiple mRNA sampling from the same cell. By combining experimental data with predictions from models we describe two mechanisms contributing to TCR sequence abundance. TCRα abundant sequences can be primarily attributed to many identical recombination events in different cells, while abundant TCRβ sequences are primarily derived from large clones, which make up a small percentage of the naive repertoire, and could be established early in the development of the T-cell repertoire.
Collapse
MESH Headings
- Adaptive Immunity
- Algorithms
- Antigens/immunology
- Clonal Evolution/genetics
- Computational Biology/methods
- High-Throughput Nucleotide Sequencing
- Humans
- Immunologic Memory
- Models, Biological
- Organ Specificity/genetics
- Organ Specificity/immunology
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- T-Lymphocyte Subsets/immunology
- T-Lymphocyte Subsets/metabolism
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- V(D)J Recombination
Collapse
Affiliation(s)
- Peter C de Greef
- Theoretical Biology and Bioinformatics, Utrecht UniversityUtrechtNetherlands
| | - Theres Oakes
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Bram Gerritsen
- Theoretical Biology and Bioinformatics, Utrecht UniversityUtrechtNetherlands
- Department of Pathology, Yale School of MedicineNew HavenUnited States
| | - Mazlina Ismail
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - James M Heather
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Rutger Hermsen
- Theoretical Biology and Bioinformatics, Utrecht UniversityUtrechtNetherlands
| | - Benjamin Chain
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Rob J de Boer
- Theoretical Biology and Bioinformatics, Utrecht UniversityUtrechtNetherlands
| |
Collapse
|
19
|
Doekes HM, de Boer RJ, Hermsen R. Toxin production spontaneously becomes regulated by local cell density in evolving bacterial populations. PLoS Comput Biol 2019; 15:e1007333. [PMID: 31469819 PMCID: PMC6742444 DOI: 10.1371/journal.pcbi.1007333] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 09/12/2019] [Accepted: 08/14/2019] [Indexed: 11/18/2022] Open
Abstract
The production of anticompetitor toxins is widespread among bacteria. Because production of such toxins is costly, it is typically regulated. In particular, many toxins are produced only when the local cell density is high. It is unclear which selection pressures shaped the evolution of density-dependent regulation of toxin production. Here, we study the evolution of toxin production, resistance and the response to a cell-density cue in a model of an evolving bacterial population with spatial structure. We present results for two growth regimes: (i) an undisturbed, fixed habitat in which only small fluctuations of cell density occur, and (ii) a serial-transfer regime with large fluctuations in cell density. We find that density-dependent toxin production can evolve under both regimes. However, the selection pressures driving the evolution of regulation differ. In the fixed habitat, regulation evolves because it allows cells to produce toxin only when opportunities for reproduction are highly limited (because of a high local cell density), and the effective fitness costs of toxin production are hence low. Under serial transfers, regulation evolves because it allows cells to switch from a fast-growing non-toxic phenotype when colonising a new habitat, to a slower-growing competitive toxic phenotype when the cell density increases. Colonies of such regulating cells rapidly expand into unoccupied space because their edges consist of fast-growing, non-toxin-producing cells, but are also combative because cells at the interfaces with competing colonies do produce toxin. Because under the two growth regimes different types of regulation evolve, our results underscore the importance of growth conditions in the evolution of social behaviour in bacteria. Bacteria live in microbial communities, in which they compete with many other microbes for nutrients and space. In this competitive environment, almost all known bacterial strains produce toxins that impair or kill other bacteria. This chemical warfare is thought to be one of the major factors shaping microbial diversity. Many toxins are produced only if the local density of bacteria is high. To achieve this, bacteria respond to cell-density cues: signalling molecules or other indicators of the presence of other cells. Here, we use a computational model to study the evolution of density-based regulation of toxin production in bacterial populations. We show that such regulation can arise under various growth conditions, and analyse the selection pressures driving its evolution. In particular, we find that if bacteria regularly need to colonise a new habitat, density-based regulation allows them to express a fast-growing, non-toxic phenotype when expanding into uncolonised territory, and a slower-growing, toxin-producing phenotype when competing with other strains. Colonies of regulating cells show a typical structure, with cells of the fast-growing, sensitive phenotype at their expanding edges, and toxin-producing cells in the colony interior and at interfaces between colonies.
Collapse
Affiliation(s)
- Hilje M. Doekes
- Theoretical Biology, Department of Biology, Utrecht University, Utrecht, the Netherlands
- * E-mail:
| | - Rob J. de Boer
- Theoretical Biology, Department of Biology, Utrecht University, Utrecht, the Netherlands
| | - Rutger Hermsen
- Theoretical Biology, Department of Biology, Utrecht University, Utrecht, the Netherlands
| |
Collapse
|
20
|
Borghans JAM, Tesselaar K, de Boer RJ. Current best estimates for the average lifespans of mouse and human leukocytes: reviewing two decades of deuterium-labeling experiments. Immunol Rev 2019; 285:233-248. [PMID: 30129193 DOI: 10.1111/imr.12693] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Deuterium is a non-toxic, stable isotope that can safely be administered to humans and mice to study their cellular turnover rates in vivo. It is incorporated into newly synthesized DNA strands during cell division, without interference with the kinetics of cells, and the accumulation and loss of deuterium in the DNA of sorted (sub-)populations of leukocytes can be used to estimate their cellular production rates and lifespans. In the past two decades, this powerful technology has been used to estimate the turnover rates of various types of leukocytes. Although it is the most reliable technique currently available to study leukocyte turnover, there are remarkable differences between the cellular turnover rates estimated by some of these studies. We have recently established that part of this variation is due to (a) difficulties in estimating deuterium availability in some deuterium-labeling studies, and (b) assumptions made by the mathematical models employed to fit the data. Being aware of these two problems, we here aim to approach a consensus on the life expectancies of different types of T cells, B cells, monocytes, and neutrophils in mice and men. We address remaining outstanding problems whenever appropriate and discuss for which immune subpopulations we currently have too little information to draw firm conclusions about their turnover.
Collapse
Affiliation(s)
- José A M Borghans
- Laboratory of Translational Immunology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Kiki Tesselaar
- Laboratory of Translational Immunology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Rob J de Boer
- Theoretical Biology & Bioinformatics, Utrecht, The Netherlands
| |
Collapse
|
21
|
Soekarjo KMW, Textor J, de Boer RJ. Local Attachment Explains Small World-like Properties of Fibroblastic Reticular Cell Networks in Lymph Nodes. J Immunol 2019; 202:3318-3325. [PMID: 30996001 DOI: 10.4049/jimmunol.1801016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 03/21/2019] [Indexed: 12/15/2022]
Abstract
Fibroblastic reticular cells (FRCs) form a cellular network that serves as the structural backbone of lymph nodes and facilitates lymphocyte migration. In mice, this FRC network has been found to have small-world properties. Using a model based on geographical preferential attachment, we simulated the formation of a variety of cellular networks and show that similar small-world properties robustly emerge under such natural conditions. By estimating the parameters of this model, we generated FRC network representations with realistic topological properties. We found that the topological properties change markedly when the network is expanded from a thin slice to a three-dimensional cube. Typical small-world properties were found to persist as network size was increased. The simulated networks were very similar to two-dimensional and three-dimensional lattice networks. According to the used metrics, these lattice networks also have small-world properties, indicating that lattice likeness is sufficient to become classified as a small-world network. Our results explain why FRC networks have small-world properties and provide a framework for simulating realistic FRC networks.
Collapse
Affiliation(s)
- Kasper M W Soekarjo
- Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH Utrecht, the Netherlands; and
| | - Johannes Textor
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, 6500 HB Nijmegen, the Netherlands
| | - Rob J de Boer
- Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH Utrecht, the Netherlands; and
| |
Collapse
|
22
|
Baliu-Piqué M, Verheij MW, Drylewicz J, Ravesloot L, de Boer RJ, Koets A, Tesselaar K, Borghans JAM. Short Lifespans of Memory T-cells in Bone Marrow, Blood, and Lymph Nodes Suggest That T-cell Memory Is Maintained by Continuous Self-Renewal of Recirculating Cells. Front Immunol 2018; 9:2054. [PMID: 30254637 PMCID: PMC6141715 DOI: 10.3389/fimmu.2018.02054] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 08/20/2018] [Indexed: 11/13/2022] Open
Abstract
Memory T-cells are essential to maintain long-term immunological memory. It is widely thought that the bone marrow (BM) plays an important role in the long-term maintenance of memory T-cells. There is controversy however on the longevity and recirculating kinetics of BM memory T-cells. While some have proposed that the BM is a reservoir for long-lived, non-circulating memory T-cells, it has also been suggested to be the preferential site for memory T-cell self-renewal. In this study, we used in vivo deuterium labeling in goats to simultaneously quantify the average turnover rates—and thereby expected lifespans—of memory T-cells from BM, blood and lymph nodes (LN). While the fraction of Ki-67 positive cells, a snapshot marker for recent cell division, was higher in memory T-cells from blood compared to BM and LN, in vivo deuterium labeling revealed no substantial differences in the expected lifespans of memory T-cells between these compartments. Our results support the view that the majority of memory T-cells in the BM are self-renewing as fast as those in the periphery, and are continuously recirculating between the blood, BM, and LN.
Collapse
Affiliation(s)
- Mariona Baliu-Piqué
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Myrddin W Verheij
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Julia Drylewicz
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Lars Ravesloot
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, Netherlands.,Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Rob J de Boer
- Theoretical Biology, Utrecht University, Utrecht, Netherlands
| | - Ad Koets
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, Netherlands.,Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Kiki Tesselaar
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - José A M Borghans
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| |
Collapse
|
23
|
Affiliation(s)
- Becca Asquith
- Department of Medicine, Imperial College London, London, UK
| | - Rob J de Boer
- Theoretical Biology and Bioinformatics, Utrecht University, the Netherlands
| |
Collapse
|
24
|
van Hoeven V, Drylewicz J, Westera L, den Braber I, Mugwagwa T, Tesselaar K, Borghans JAM, de Boer RJ. Dynamics of Recent Thymic Emigrants in Young Adult Mice. Front Immunol 2017; 8:933. [PMID: 28824653 PMCID: PMC5545745 DOI: 10.3389/fimmu.2017.00933] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 07/21/2017] [Indexed: 11/13/2022] Open
Abstract
The peripheral naive T-cell pool is generally thought to consist of a subpopulation of recent thymic emigrants (RTEs) and a subpopulation of mature naive (MN) T cells with different dynamics. Thymus transplantation and adoptive transfer studies in mice have provided contradicting results, with some studies suggesting that RTEs are relatively short-lived cells, while another study suggested that RTEs have a survival advantage. We here estimate the death rates of RTE and MN T cells by performing both thymus transplantations and deuterium labeling experiments in mice of at least 12 weeks old, an age at which the size of the T-cell pool has stabilized. For CD4+ T cells, we found the total loss rate from the RTE compartment (by death and maturation) to be fourfold faster than that of MN T cells. We estimate the death rate of CD4+ RTE to be 0.046 per day, which is threefold faster than the total loss rate from the MN T-cell compartment. For CD8+ T cells, we found no evidence for kinetic differences between RTE and MN T cells. Thus, our data support the notion that in young adult mice, CD4+ RTE are relatively short-lived cells within the naive CD4+ T-cell pool.
Collapse
Affiliation(s)
- Vera van Hoeven
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Julia Drylewicz
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht, Netherlands.,Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Utrecht, Netherlands
| | - Liset Westera
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Ineke den Braber
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Tendai Mugwagwa
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Utrecht, Netherlands
| | - Kiki Tesselaar
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - José A M Borghans
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Rob J de Boer
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Utrecht, Netherlands
| |
Collapse
|
25
|
Müller V, de Boer RJ, Bonhoeffer S, Szathmáry E. An evolutionary perspective on the systems of adaptive immunity. Biol Rev Camb Philos Soc 2017; 93:505-528. [PMID: 28745003 DOI: 10.1111/brv.12355] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 06/28/2017] [Accepted: 06/30/2017] [Indexed: 12/22/2022]
Abstract
We propose an evolutionary perspective to classify and characterize the diverse systems of adaptive immunity that have been discovered across all major domains of life. We put forward a new function-based classification according to the way information is acquired by the immune systems: Darwinian immunity (currently known from, but not necessarily limited to, vertebrates) relies on the Darwinian process of clonal selection to 'learn' by cumulative trial-and-error feedback; Lamarckian immunity uses templated targeting (guided adaptation) to internalize heritable information on potential threats; finally, shotgun immunity operates through somatic mechanisms of variable targeting without feedback. We argue that the origin of Darwinian (but not Lamarckian or shotgun) immunity represents a radical innovation in the evolution of individuality and complexity, and propose to add it to the list of major evolutionary transitions. While transitions to higher-level units entail the suppression of selection at lower levels, Darwinian immunity re-opens cell-level selection within the multicellular organism, under the control of mechanisms that direct, rather than suppress, cell-level evolution for the benefit of the individual. From a conceptual point of view, the origin of Darwinian immunity can be regarded as the most radical transition in the history of life, in which evolution by natural selection has literally re-invented itself. Furthermore, the combination of clonal selection and somatic receptor diversity enabled a transition from limited to practically unlimited capacity to store information about the antigenic environment. The origin of Darwinian immunity therefore comprises both a transition in individuality and the emergence of a new information system - the two hallmarks of major evolutionary transitions. Finally, we present an evolutionary scenario for the origin of Darwinian immunity in vertebrates. We propose a revival of the concept of the 'Big Bang' of vertebrate immunity, arguing that its origin involved a 'difficult' (i.e. low-probability) evolutionary transition that might have occurred only once, in a common ancestor of all vertebrates. In contrast to the original concept, we argue that the limiting innovation was not the generation of somatic diversity, but the regulatory circuitry needed for the safe operation of amplifiable immune responses with somatically acquired targeting. Regulatory complexity increased abruptly by genomic duplications at the root of the vertebrate lineage, creating a rare opportunity to establish such circuitry. We discuss the selection forces that might have acted at the origin of the transition, and in the subsequent stepwise evolution leading to the modern immune systems of extant vertebrates.
Collapse
Affiliation(s)
- Viktor Müller
- Parmenides Center for the Conceptual Foundations of Science, 82049 Pullach/Munich, Germany.,Department of Plant Systematics, Ecology and Theoretical Biology, Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary.,Evolutionary Systems Research Group, MTA Centre for Ecological Research, 8237 Tihany, Hungary
| | - Rob J de Boer
- Theoretical Biology, Department of Biology, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Sebastian Bonhoeffer
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zurich, 8092 Zurich, Switzerland
| | - Eörs Szathmáry
- Parmenides Center for the Conceptual Foundations of Science, 82049 Pullach/Munich, Germany.,Department of Plant Systematics, Ecology and Theoretical Biology, Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary.,Evolutionary Systems Research Group, MTA Centre for Ecological Research, 8237 Tihany, Hungary
| |
Collapse
|
26
|
Carrillo-Bustamante P, de Boer RJ, Keşmir C. Specificity of inhibitory KIRs enables NK cells to detect changes in an altered peptide environment. Immunogenetics 2017; 70:87-97. [PMID: 28695292 PMCID: PMC5775373 DOI: 10.1007/s00251-017-1019-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 06/20/2017] [Indexed: 12/12/2022]
Abstract
The activity of natural killer (NK) cells is tightly regulated by inhibitory and activating receptors. Inhibitory killer immunoglobulin-like receptors (iKIRs) survey the surface of target cells by monitoring the expression of human leukocyte antigen (HLA) class I. The binding of iKIRs has been shown to be sensitive to the peptides presented by HLA class I, implying that iKIRs have the ability to detect the changes in the repertoire of peptide-HLA class I complexes (pHLA), a process occurring during viral infection and in tumor cells. To study how the pHLA repertoire changes upon infection, and whether an iKIR is able to detect these changes, we study peptides eluted from cells prior and after infection with measles virus (MV). Remarkably, most changes in the repertoire of potential iKIR ligands are predicted to be caused by the altered expression of self-peptides. We show that an iKIR can detect these changes in the presented peptides only if it is sufficiently specific, e.g., if iKIRs can distinguish between different amino acids in the contact residues (e.g., position 7 and 8). Our analysis further indicates that one single iKIR per host is not sufficient to detect changes in the peptide repertoire, suggesting that a multigene family encoding for different iKIRs is required for successful peptide recognition.
Collapse
Affiliation(s)
- Paola Carrillo-Bustamante
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Utrecht, The Netherlands. .,Center for Modeling and Simulation in the Biosciences (BIOMS/IWR), Max Planck Institute, Heidelberg, Germany.
| | - Rob J de Boer
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Can Keşmir
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Utrecht, The Netherlands
| |
Collapse
|
27
|
Gadhamsetty S, Marée AFM, Beltman JB, de Boer RJ. A Sigmoid Functional Response Emerges When Cytotoxic T Lymphocytes Start Killing Fresh Target Cells. Biophys J 2017; 112:1221-1235. [PMID: 28355549 PMCID: PMC5375173 DOI: 10.1016/j.bpj.2017.02.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 02/01/2017] [Accepted: 02/03/2017] [Indexed: 11/19/2022] Open
Abstract
Cytotoxic T lymphocyte (CTL)-mediated killing involves the formation of a synapse with a target cell, followed by delivery of perforin and granzymes. Previously, we derived a general functional response for CTL killing while considering that CTLs form stable synapses (i.e., single-stage) and that the number of conjugates remains at steady state. However, the killing of target cells sometimes requires multiple engagements (i.e., multistage). To study how multistage killing and a lack of steady state influence the functional response, we here analyze a set of differential equations as well as simulations employing the cellular Potts model, in both cases describing CTLs that kill target cells. We find that at steady state the total killing rate (i.e., the number of target cells killed by all CTLs) is well described by the previously derived double saturation function. Compared to single-stage killing, the total killing rate during multistage killing saturates at higher CTL and target cell densities. Importantly, when the killing is measured before the steady state is approached, a qualitatively different functional response emerges for two reasons: First, the killing signal of each CTL gets diluted over several targets and because this dilution effect is strongest at high target cell densities; this can result in a peak in the dependence of the total killing rate on the target cell density. Second, the total killing rate exhibits a sigmoid dependence on the CTL density when killing is a multistage process, because it takes typically more than one CTL to kill a target. In conclusion, a sigmoid dependence of the killing rate on the CTLs during initial phases of killing may be indicative of a multistage killing process. Observation of a sigmoid functional response may thus arise from a dilution effect and is not necessarily due to cooperative behavior of the CTLs.
Collapse
Affiliation(s)
| | - Athanasius F M Marée
- Department of Computational and Systems Biology, John Innes Centre, Norwich, United Kingdom
| | - Joost B Beltman
- Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Rob J de Boer
- Theoretical Biology, Utrecht University, Utrecht, the Netherlands
| |
Collapse
|
28
|
Gadhamsetty S, Marée AFM, de Boer RJ, Beltman JB. Tissue Dimensionality Influences the Functional Response of Cytotoxic T Lymphocyte-Mediated Killing of Targets. Front Immunol 2017; 7:668. [PMID: 28123385 PMCID: PMC5225319 DOI: 10.3389/fimmu.2016.00668] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 12/19/2016] [Indexed: 11/13/2022] Open
Abstract
Cytotoxic T lymphocyte (CTL)-mediated killing of virus infections and tumors occurs over a wide range of conditions. The spatial environments in which CTLs encounter target cells vary from narrow vessels, to two-dimensional epithelial tissues, to densely populated 3-dimensional (3D) T cell areas within lymphoid tissues. How such spatial environments alter the functional response of CTL-mediated killing, i.e., how the killing efficiency depends on cell densities, is unclear. In this study, we perform cellular Potts model simulations in different spatial configurations to investigate how the dimensionality of the space affects the functional response of CTL-mediated killing. Irrespective of the spatial configuration, the function with separate saturation constants for CTL and for target cell densities that we previously proposed can in all cases describe the response, demonstrating its generality. However, the tissue dimensionality determines at which cell densities the killing rate starts to saturate. We show that saturation in a fully 3D environment is stronger than in a "flat" 3D environment, which is largely due to accompanying differences in the CTL-target encounter rates.
Collapse
Affiliation(s)
| | - Athanasius F M Marée
- Department of Computational and Systems Biology, John Innes Centre , Norwich , UK
| | - Rob J de Boer
- Theoretical Biology, Utrecht University , Utrecht , Netherlands
| | - Joost B Beltman
- Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University , Leiden , Netherlands
| |
Collapse
|
29
|
Abstract
Lymph nodes are meeting points for circulating immune cells. A network of reticular cells that ensheathe a mesh of collagen fibers crisscrosses the tissue in each lymph node. This reticular cell network distributes key molecules and provides a structure for immune cells to move around on. During infections, the network can suffer damage. A new study has now investigated the network's structure in detail, using methods from graph theory. The study showed that the network is remarkably robust to damage: it can still support immune responses even when half of the reticular cells are destroyed. This is a further important example of how network connectivity achieves tolerance to failure, a property shared with other important biological and nonbiological networks.
Collapse
Affiliation(s)
- Johannes Textor
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
- * E-mail:
| | - Judith N. Mandl
- Department of Physiology, McGill University, Montreal, Québec, Canada
| | - Rob J. de Boer
- Theoretical Biology, Utrecht University, Utrecht, The Netherlands
| |
Collapse
|
30
|
Gerritsen B, Pandit A, Andeweg AC, de Boer RJ. RTCR: a pipeline for complete and accurate recovery of T cell repertoires from high throughput sequencing data. Bioinformatics 2016; 32:3098-3106. [PMID: 27324198 PMCID: PMC5048062 DOI: 10.1093/bioinformatics/btw339] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 05/26/2016] [Indexed: 12/11/2022] Open
Abstract
Motivation: High Throughput Sequencing (HTS) has enabled researchers to probe the human T cell receptor (TCR) repertoire, which consists of many rare sequences. Distinguishing between true but rare TCR sequences and variants generated by polymerase chain reaction (PCR) and sequencing errors remains a formidable challenge. The conventional approach to handle errors is to remove low quality reads, and/or rare TCR sequences. Such filtering discards a large number of true and often rare TCR sequences. However, accurate identification and quantification of rare TCR sequences is essential for repertoire diversity estimation. Results: We devised a pipeline, called Recover TCR (RTCR), that accurately recovers TCR sequences, including rare TCR sequences, from HTS data (including barcoded data) even at low coverage. RTCR employs a data-driven statistical model to rectify PCR and sequencing errors in an adaptive manner. Using simulations, we demonstrate that RTCR can easily adapt to the error profiles of different types of sequencers and exhibits consistently high recall and high precision even at low coverages where other pipelines perform poorly. Using published real data, we show that RTCR accurately resolves sequencing errors and outperforms all other pipelines. Availability and Implementation: The RTCR pipeline is implemented in Python (v2.7) and C and is freely available at http://uubram.github.io/RTCR/along with documentation and examples of typical usage. Contact:b.gerritsen@uu.nl
Collapse
Affiliation(s)
- Bram Gerritsen
- Theoretical Biology and Bioinformatics, Utrecht University, 3584CH the Netherlands
| | - Aridaman Pandit
- Theoretical Biology and Bioinformatics, Utrecht University, 3584CH the Netherlands
| | - Arno C Andeweg
- Department of Viroscience, Rotterdam, Erasmus MC, 3000CA, the Netherlands
| | - Rob J de Boer
- Theoretical Biology and Bioinformatics, Utrecht University, 3584CH the Netherlands
| |
Collapse
|
31
|
Perié L, Duffy KR, Kok L, de Boer RJ, Schumacher TN. The Branching Point in Erythro-Myeloid Differentiation. Cell 2016; 163:1655-62. [PMID: 26687356 DOI: 10.1016/j.cell.2015.11.059] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 11/18/2015] [Accepted: 11/28/2015] [Indexed: 12/17/2022]
Abstract
Development of mature blood cell progenies from hematopoietic stem cells involves the transition through lineage-restricted progenitors. The first branching point along this developmental process is thought to separate the erythro-myeloid and lymphoid lineage fate by yielding two intermediate progenitors, the common myeloid and the common lymphoid progenitors (CMPs and CLPs). Here, we use single-cell lineage tracing to demonstrate that so-called CMPs are highly heterogeneous with respect to cellular output, with most individual CMPs yielding either only erythrocytes or only myeloid cells after transplantation. Furthermore, based on the labeling of earlier progenitors, we show that the divergence between the myeloid and erythroid lineage develops within multipotent progenitors (MPP). These data provide evidence for a model of hematopoietic branching in which multiple distinct lineage commitments occur in parallel within the MPP pool.
Collapse
Affiliation(s)
- Leïla Perié
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands; Institut Curie, PSL Research University, CNRS UMR168, 26 rue d'Ulm, 75005 Paris, France; Sorbonne Universités, UPMC Univ Paris 06, 4 place Jussieu, 75005 Paris, France.
| | - Ken R Duffy
- Hamilton Institute, Maynooth University, Maynooth, Co Kildare, Ireland
| | - Lianne Kok
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Rob J de Boer
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Ton N Schumacher
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands.
| |
Collapse
|
32
|
Ikeda H, Nakaoka S, de Boer RJ, Morita S, Misawa N, Koyanagi Y, Aihara K, Sato K, Iwami S. Quantifying the effect of Vpu on the promotion of HIV-1 replication in the humanized mouse model. Retrovirology 2016; 13:23. [PMID: 27086687 PMCID: PMC4834825 DOI: 10.1186/s12977-016-0252-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 03/15/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tetherin is an intrinsic anti-viral factor impairing the release of nascent HIV-1 particles from infected cells. Vpu, an HIV-1 accessory protein, antagonizes the anti-viral action of tetherin. Although previous studies using in vitro cell culture systems have revealed the molecular mechanisms of the anti-viral action of tetherin and the antagonizing action of Vpu against tetherin, it still remains unclear how Vpu affects the kinetics of HIV-1 replication in vivo. RESULTS To quantitatively assess the role of Vpu in viral replication in vivo, we analyzed time courses of experimental data with viral load and target cell levels in the peripheral blood of humanized mice infected with wild-type and vpu-deficient HIV-1. Our recently developed mathematical model describes the acute phase of this infection reasonably, and allowed us to estimate several parameters characterizing HIV-1 infection in mice. Using a technique of Bayesian parameter estimation, we estimate distributions of the basic reproduction number of wild-type and vpu-deficient HIV-1. This reveals that Vpu markedly increases the rate of viral replication in vivo. CONCLUSIONS Combining experiments with mathematical modeling, we provide an estimate for the contribution of Vpu to viral replication in humanized mice.
Collapse
Affiliation(s)
- Hiroki Ikeda
- Department of Biology, Faculty of Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, Fukuoka, 812-8581, Japan
| | - Shinji Nakaoka
- Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Rob J de Boer
- Theoretical Biology, Utrecht University, Utrecht, The Netherlands
| | - Satoru Morita
- Department of Mathematical and Systems Engineering, Shizuoka University, Shizuoka, Japan
| | - Naoko Misawa
- Laboratory of Viral Pathogenesis, Institute for Virus Research, Kyoto University, 53 Shogoinkawara-cho, Sakyo-ku, Kyoto, Kyoto, 606-8507, Japan
| | - Yoshio Koyanagi
- Laboratory of Viral Pathogenesis, Institute for Virus Research, Kyoto University, 53 Shogoinkawara-cho, Sakyo-ku, Kyoto, Kyoto, 606-8507, Japan
| | - Kazuyuki Aihara
- Institute of Industrial Science, The University of Tokyo, Tokyo, Japan.,Graduate School of Information Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Kei Sato
- Laboratory of Viral Pathogenesis, Institute for Virus Research, Kyoto University, 53 Shogoinkawara-cho, Sakyo-ku, Kyoto, Kyoto, 606-8507, Japan. .,CREST, JST, Saitama, Japan.
| | - Shingo Iwami
- Department of Biology, Faculty of Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, Fukuoka, 812-8581, Japan. .,CREST, JST, Saitama, Japan. .,PRESTO, JST, Saitama, Japan.
| |
Collapse
|
33
|
Drylewicz J, Vrisekoop N, Mugwagwa T, de Boer AB, Otto SA, Hazenberg MD, Tesselaar K, de Boer RJ, Borghans JAM. Reconciling Longitudinal Naive T-Cell and TREC Dynamics during HIV-1 Infection. PLoS One 2016; 11:e0152513. [PMID: 27010200 PMCID: PMC4806918 DOI: 10.1371/journal.pone.0152513] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 03/15/2016] [Indexed: 12/14/2022] Open
Abstract
Naive T cells in untreated HIV-1 infected individuals have a reduced T-cell receptor excision circle (TREC) content. Previous mathematical models have suggested that this is due to increased naive T-cell division. It remains unclear, however, how reduced naive TREC contents can be reconciled with a gradual loss of naive T cells in HIV-1 infection. We performed longitudinal analyses in humans before and after HIV-1 seroconversion, and used a mathematical model to investigate which processes could explain the observed changes in naive T-cell numbers and TRECs during untreated HIV-1 disease progression. Both CD4+ and CD8+ naive T-cell TREC contents declined biphasically, with a rapid loss during the first year and a much slower loss during the chronic phase of infection. While naive CD8+ T-cell numbers hardly changed during follow-up, naive CD4+ T-cell counts continually declined. We show that a fine balance between increased T-cell division and loss in the peripheral naive T-cell pool can explain the observed short- and long-term changes in TRECs and naive T-cell numbers, especially if T-cell turnover during the acute phase is more increased than during the chronic phase of infection. Loss of thymic output, on the other hand, does not help to explain the biphasic loss of TRECs in HIV infection. The observed longitudinal changes in TRECs and naive T-cell numbers in HIV-infected individuals are most likely explained by a tight balance between increased T-cell division and death, suggesting that these changes are intrinsically linked in HIV infection.
Collapse
Affiliation(s)
- Julia Drylewicz
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
- Theoretical Biology & Bioinformatics, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Nienke Vrisekoop
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Tendai Mugwagwa
- Theoretical Biology & Bioinformatics, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Anne Bregje de Boer
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sigrid A. Otto
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Mette D. Hazenberg
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Kiki Tesselaar
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rob J. de Boer
- Theoretical Biology & Bioinformatics, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - José A. M. Borghans
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
- * E-mail:
| |
Collapse
|
34
|
Abstract
Highly active antiretroviral therapy (ART) has successfully turned Human immunodeficiency virus type 1 (HIV-1) from a deadly pathogen into a manageable chronic infection. ART is a lifelong therapy which is both expensive and toxic, and HIV can become resistant to it. An alternative to lifelong ART is gene therapy that targets the CCR5 co-receptor and creates a population of genetically modified host cells that are less susceptible to viral infection. With generic mathematical models we show that gene therapy that only targets the CCR5 co-receptor fails to suppress HIV-1 (which is in agreement with current data). We predict that the same gene therapy can be markedly improved if it is combined with a suicide gene that is only expressed upon HIV-1 infection.
Collapse
Affiliation(s)
- Aridaman Pandit
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, 3584CH, The Netherlands
| | - Rob J de Boer
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, 3584CH, The Netherlands
| |
Collapse
|
35
|
Ariotti S, Beltman JB, Borsje R, Hoekstra ME, Halford WP, Haanen JBAG, de Boer RJ, Schumacher TNM. Subtle CXCR3-Dependent Chemotaxis of CTLs within Infected Tissue Allows Efficient Target Localization. J Immunol 2015; 195:5285-95. [PMID: 26525288 DOI: 10.4049/jimmunol.1500853] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 10/02/2015] [Indexed: 11/19/2022]
Abstract
It is well established how effector T cells exit the vasculature to enter the peripheral tissues in which an infection is ongoing. However, less is known regarding how CTLs migrate toward infected cells after entry into peripheral organs. Recently, it was shown that the chemokine receptor CXCR3 on T cells has an important role in their ability to localize infected cells and to control vaccinia virus infection. However, the search strategy of T cells for virus-infected targets has not been investigated in detail and could involve chemotaxis toward infected cells, chemokinesis (i.e., increased motility) combined with CTL arrest when targets are detected, or both. In this study, we describe and analyze the migration of CTLs within HSV-1-infected epidermis in vivo. We demonstrate that activated T cells display a subtle distance-dependent chemotaxis toward clusters of infected cells and confirm that this is mediated by CXCR3 and its ligands. Although the chemotactic migration is weak, computer simulations based on short-term experimental data, combined with subsequent long-term imaging indicate that this behavior is crucial for efficient target localization and T cell accumulation at effector sites. Thus, chemotactic migration of effector T cells within peripheral tissue forms an important factor in the speed with which T cells are able to arrive at sites of infection.
Collapse
Affiliation(s)
- Silvia Ariotti
- Division of Immunology, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Joost B Beltman
- Division of Immunology, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH Utrecht, the Netherlands; Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, the Netherlands; and
| | - Rianne Borsje
- Division of Immunology, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Mirjam E Hoekstra
- Division of Immunology, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - William P Halford
- Department of Medical Microbiology, Immunology and Cell Biology, Southern Illinois University School of Medicine, Springfield, IL 62794
| | - John B A G Haanen
- Division of Immunology, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Rob J de Boer
- Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Ton N M Schumacher
- Division of Immunology, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands;
| |
Collapse
|
36
|
Niculescu I, Textor J, de Boer RJ. Crawling and Gliding: A Computational Model for Shape-Driven Cell Migration. PLoS Comput Biol 2015; 11:e1004280. [PMID: 26488304 PMCID: PMC4619082 DOI: 10.1371/journal.pcbi.1004280] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 04/10/2015] [Indexed: 11/21/2022] Open
Abstract
Cell migration is a complex process involving many intracellular and extracellular factors, with different cell types adopting sometimes strikingly different morphologies. Modeling realistically behaving cells in tissues is computationally challenging because it implies dealing with multiple levels of complexity. We extend the Cellular Potts Model with an actin-inspired feedback mechanism that allows small stochastic cell rufflings to expand to cell protrusions. This simple phenomenological model produces realistically crawling and deforming amoeboid cells, and gliding half-moon shaped keratocyte-like cells. Both cell types can migrate randomly or follow directional cues. They can squeeze in between other cells in densely populated environments or migrate collectively. The model is computationally light, which allows the study of large, dense and heterogeneous tissues containing cells with realistic shapes and migratory properties. Cell migration is involved in vital processes like morphogenesis, regeneration and immune system responses, but can also play a central role in pathological processes like metastasization. Computational models have been successfully employed to explain how single cells migrate, and to study how diverse cell-cell interactions contribute to tissue level behavior. However, there are few models that implement realistic cell shapes in multicellular simulations. The method we present here is able to reproduce two different types of motile cells—amoeboid and keratocyte-like cells. Amoeboid cells are highly motile and deform frequently; many cells can act amoeboid in certain circumstances e.g., immune system cells, epithelial cells, individually migrating cancer cells. Keratocytes are (fish) epithelial cells which are famous for their ability to preserve their shape and direction when migrating individually; during wound healing, keratocytes migrate collectively, in sheets, to the site needing reepithelialization. Our method is computationally simple, improves the realism of multicellular simulations and can help assess the tissue level impact of specific cell shapes. For example, it can be employed to study the tissue scanning strategies of leukocytes, the circumstances in which cancer cells adopt amoeboid migration strategies, or the collective migration of keratocytes.
Collapse
Affiliation(s)
- Ioana Niculescu
- Theoretical Biology & Bioinformatics, Utrecht University, The Netherlands
| | - Johannes Textor
- Theoretical Biology & Bioinformatics, Utrecht University, The Netherlands
| | - Rob J de Boer
- Theoretical Biology & Bioinformatics, Utrecht University, The Netherlands
| |
Collapse
|
37
|
Ahmed R, Westera L, Drylewicz J, Elemans M, Zhang Y, Kelly E, Reljic R, Tesselaar K, de Boer RJ, Macallan DC, Borghans JAM, Asquith B. Reconciling Estimates of Cell Proliferation from Stable Isotope Labeling Experiments. PLoS Comput Biol 2015; 11:e1004355. [PMID: 26437372 PMCID: PMC4593553 DOI: 10.1371/journal.pcbi.1004355] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 05/26/2015] [Indexed: 01/01/2023] Open
Abstract
Stable isotope labeling is the state of the art technique for in vivo quantification of lymphocyte kinetics in humans. It has been central to a number of seminal studies, particularly in the context of HIV-1 and leukemia. However, there is a significant discrepancy between lymphocyte proliferation rates estimated in different studies. Notably, deuterated 2H2-glucose (D2-glucose) labeling studies consistently yield higher estimates of proliferation than deuterated water (D2O) labeling studies. This hampers our understanding of immune function and undermines our confidence in this important technique. Whether these differences are caused by fundamental biochemical differences between the two compounds and/or by methodological differences in the studies is unknown. D2-glucose and D2O labeling experiments have never been performed by the same group under the same experimental conditions; consequently a direct comparison of these two techniques has not been possible. We sought to address this problem. We performed both in vitro and murine in vivo labeling experiments using identical protocols with both D2-glucose and D2O. This showed that intrinsic differences between the two compounds do not cause differences in the proliferation rate estimates, but that estimates made using D2-glucose in vivo were susceptible to difficulties in normalization due to highly variable blood glucose enrichment. Analysis of three published human studies made using D2-glucose and D2O confirmed this problem, particularly in the case of short term D2-glucose labeling. Correcting for these inaccuracies in normalization decreased proliferation rate estimates made using D2-glucose and slightly increased estimates made using D2O; thus bringing the estimates from the two methods significantly closer and highlighting the importance of reliable normalization when using this technique. Stable isotope labeling is used to quantify the rate at which living cells proliferate and die in humans. It has been central to a number of seminal studies, particularly in viral infections such as HIV-1, and leukemia. However, different labels (deuterated water or deuterated glucose) yield different estimates for the rate of cell proliferation and loss; this hampers our understanding and weakens our confidence in this important technique. We performed in vitro and in vivo experiments as well as a new analysis of existing data to directly compare the two labels. This reveals that a major source of the discrepancy lies in the difficulty of assessing deuterated glucose availability. We reconcile published studies and provide recommendations to avoid this problem in the future.
Collapse
Affiliation(s)
- Raya Ahmed
- Institute for Infection and Immunity, St. George’s, University of London, London, United Kingdom
| | - Liset Westera
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Julia Drylewicz
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
- Theoretical Biology & Bioinformatics, Utrecht University, The Netherlands
| | - Marjet Elemans
- Department of Medicine, Imperial College, London, United Kingdom
| | - Yan Zhang
- Institute for Infection and Immunity, St. George’s, University of London, London, United Kingdom
| | - Elizabeth Kelly
- Institute for Infection and Immunity, St. George’s, University of London, London, United Kingdom
| | - Rajko Reljic
- Institute for Infection and Immunity, St. George’s, University of London, London, United Kingdom
| | - Kiki Tesselaar
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rob J. de Boer
- Theoretical Biology & Bioinformatics, Utrecht University, The Netherlands
| | - Derek C. Macallan
- Institute for Infection and Immunity, St. George’s, University of London, London, United Kingdom
| | - José A. M. Borghans
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Becca Asquith
- Department of Medicine, Imperial College, London, United Kingdom
- * E-mail:
| |
Collapse
|
38
|
Perié L, Duffy KR, de Boer RJ, Schumacher T. Common myeloid progenitors are made up of distinct subpopulations that either yield erythrocytes or myeloid cells. Exp Hematol 2015. [DOI: 10.1016/j.exphem.2015.06.227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
39
|
Gadhamsetty S, Beltman JB, de Boer RJ. What do mathematical models tell us about killing rates during HIV-1 infection? Immunol Lett 2015; 168:1-6. [PMID: 26279491 DOI: 10.1016/j.imlet.2015.07.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/15/2015] [Accepted: 07/31/2015] [Indexed: 10/23/2022]
Abstract
Over the past few decades the extent to which cytotoxic T lymphocytes (CTLs) control human immunodeficiency virus (HIV) replication has been studied extensively, yet their role and mode of action remain controversial. In some studies, CTLs were found to kill a large fraction of the productively infected cells relative to the viral cytopathicity, whereas in others CTLs were suggested to kill only a small fraction of infected cells. In this review, we compile published estimates of CTL-mediated death rates, and examine whether these studies permit determining the rate at which CTLs kill HIV-1 infected cells. We highlight potential misinterpretations of the CTL-killing rates from the escape rates of mutants, and from perturbations of the steady state viral load during chronic infection. Our major conclusion is that CTL-mediated killing rates remain unknown. But contrary to current consensus, we argue that killing rates higher than one per day are perfectly consistent with the experimental data, which would imply that the majority of the productively infected cells could still die from CTL-mediated killing rather than from viral cytopathicity.
Collapse
Affiliation(s)
- Saikrishna Gadhamsetty
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Joost B Beltman
- Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Rob J de Boer
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| |
Collapse
|
40
|
Carrillo-Bustamante P, Kesmir C, de Boer RJ. Can Selective MHC Downregulation Explain the Specificity and Genetic Diversity of NK Cell Receptors? Front Immunol 2015; 6:311. [PMID: 26136746 PMCID: PMC4468891 DOI: 10.3389/fimmu.2015.00311] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 06/01/2015] [Indexed: 11/26/2022] Open
Abstract
Natural killer (NK) cells express inhibiting receptors (iNKRs), which specifically bind MHC-I molecules on the surface of healthy cells. When the expression of MHC-I on the cell surface decreases, which might occur during certain viral infections and cancer, iNKRs lose inhibiting signals and the infected cells become target for NK cell activation (missing-self detection). Although the detection of MHC-I deficient cells can be achieved by conserved receptor-ligand interactions, several iNKRs are encoded by gene families with a remarkable genetic diversity, containing many haplotypes varying in gene content and allelic polymorphism. So far, the biological function of this expansion within the NKR cluster has remained poorly understood. Here, we investigate whether the evolution of diverse iNKRs genes can be driven by a specific viral immunoevasive mechanism: selective MHC downregulation. Several viruses, including EBV, CMV, and HIV, decrease the expression of MHC-I to escape from T cell responses. This downregulation does not always affect all MHC loci in the same way, as viruses target particular MHC molecules. To study the selection pressure of selective MHC downregulation on iNKRs, we have developed an agent-based model simulating an evolutionary scenario of hosts infected with herpes-like viruses, which are able to selectively downregulate the expression of MHC-I molecules on the cell surface. We show that iNKRs evolve specificity and, depending on the similarity of MHC alleles within each locus and the differences between the loci, they can specialize to a particular MHC-I locus. The easier it is to classify an MHC allele to its locus, the lower the required diversity of the NKRs. Thus, the diversification of the iNKR cluster depends on the locus specific MHC structure.
Collapse
Affiliation(s)
- Paola Carrillo-Bustamante
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University , Utrecht , Netherlands
| | - Can Kesmir
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University , Utrecht , Netherlands
| | - Rob J de Boer
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University , Utrecht , Netherlands
| |
Collapse
|
41
|
Carrillo-Bustamante P, Keşmir C, de Boer RJ. A Coevolutionary Arms Race between Hosts and Viruses Drives Polymorphism and Polygenicity of NK Cell Receptors. Mol Biol Evol 2015; 32:2149-60. [PMID: 25911231 PMCID: PMC4833080 DOI: 10.1093/molbev/msv096] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Natural killer cell receptors (NKRs) monitor the expression of major histocompatibility class I (MHC-I) and stress molecules to detect unhealthy tissue, such as infected or tumor cells. The NKR gene family shows a remarkable genetic diversity, containing several genes encoding receptors with activating and inhibiting signaling, and varying in gene content and allelic polymorphism. The expansion of the NKR genes is species-specific, with different species evolving alternative expanded NKR genes, which encode structurally different proteins, yet perform comparable functions. So far, the biological function of this expansion within the NKR cluster has remained poorly understood. To study the evolution of NKRs, we have developed an agent-based model implementing a coevolutionary scenario between hosts and herpes-like viruses that are able to evade the immune response by downregulating the expression of MHC-I on the cell surface. We show that hosts evolve specific inhibitory NKRs, specialized to particular MHC-I alleles in the population. Viruses in our simulations readily evolve proteins mimicking the MHC molecules of their host, even in the absence of MHC-I downregulation. As a result, the NKR locus becomes polygenic and polymorphic, encoding both specific inhibiting and activating receptors to optimally protect the hosts from coevolving viruses.
Collapse
Affiliation(s)
- Paola Carrillo-Bustamante
- Theoretical Biology & Bioinformatics, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Can Keşmir
- Theoretical Biology & Bioinformatics, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Rob J de Boer
- Theoretical Biology & Bioinformatics, Department of Biology, Utrecht University, Utrecht, The Netherlands
| |
Collapse
|
42
|
Westera L, van Hoeven V, Drylewicz J, Spierenburg G, van Velzen JF, de Boer RJ, Tesselaar K, Borghans JAM. Lymphocyte maintenance during healthy aging requires no substantial alterations in cellular turnover. Aging Cell 2015; 14:219-27. [PMID: 25627171 PMCID: PMC4364834 DOI: 10.1111/acel.12311] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2014] [Indexed: 12/19/2022] Open
Abstract
In healthy humans, lymphocyte populations are maintained at a relatively constant size throughout life, reflecting a balance between lymphocyte production and loss. Given the profound immunological changes that occur during healthy aging, including a significant decline in T-cell production by the thymus, lymphocyte maintenance in the elderly is generally thought to require homeostatic alterations in lymphocyte dynamics. Surprisingly, using in vivo2H2O labeling, we find similar dynamics of most lymphocyte subsets between young adult and elderly healthy individuals. As the contribution of thymic output to T-cell production is only minor from young adulthood onward, compensatory increases in peripheral T-cell division rates are not required to maintain the T-cell pool, despite a tenfold decline in thymic output. These fundamental insights will aid the interpretation of further research into aging and clinical conditions related to disturbed lymphocyte dynamics.
Collapse
Affiliation(s)
- Liset Westera
- Laboratory of Translational Immunology; Department of Immunology; University Medical Center Utrecht; Lundlaan 6 3584 EA Utrecht The Netherlands
| | - Vera van Hoeven
- Laboratory of Translational Immunology; Department of Immunology; University Medical Center Utrecht; Lundlaan 6 3584 EA Utrecht The Netherlands
| | - Julia Drylewicz
- Laboratory of Translational Immunology; Department of Immunology; University Medical Center Utrecht; Lundlaan 6 3584 EA Utrecht The Netherlands
- Theoretical Biology and Bioinformatics; Department of Biology; Utrecht University; Padualaan 8 3584 CH Utrecht The Netherlands
| | - Gerrit Spierenburg
- Laboratory of Translational Immunology; Department of Immunology; University Medical Center Utrecht; Lundlaan 6 3584 EA Utrecht The Netherlands
| | - Jeroen F. van Velzen
- Laboratory of Translational Immunology; Department of Immunology; University Medical Center Utrecht; Lundlaan 6 3584 EA Utrecht The Netherlands
| | - Rob J. de Boer
- Theoretical Biology and Bioinformatics; Department of Biology; Utrecht University; Padualaan 8 3584 CH Utrecht The Netherlands
| | - Kiki Tesselaar
- Laboratory of Translational Immunology; Department of Immunology; University Medical Center Utrecht; Lundlaan 6 3584 EA Utrecht The Netherlands
| | - José A. M. Borghans
- Laboratory of Translational Immunology; Department of Immunology; University Medical Center Utrecht; Lundlaan 6 3584 EA Utrecht The Netherlands
| |
Collapse
|
43
|
van Dorp CH, van Boven M, de Boer RJ. Immuno-epidemiological modeling of HIV-1 predicts high heritability of the set-point virus load, while selection for CTL escape dominates virulence evolution. PLoS Comput Biol 2014; 10:e1003899. [PMID: 25522184 PMCID: PMC4270429 DOI: 10.1371/journal.pcbi.1003899] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 09/07/2014] [Indexed: 02/07/2023] Open
Abstract
It has been suggested that HIV-1 has evolved its set-point virus load to be optimized for transmission. Previous epidemiological models and studies into the heritability of set-point virus load confirm that this mode of adaptation within the human population is feasible. However, during the many cycles of replication between infection of a host and transmission to the next host, HIV-1 is under selection for escape from immune responses, and not transmission. Here we investigate with computational and mathematical models how these two levels of selection, within-host and between-host, are intertwined. We find that when the rate of immune escape is comparable to what has been observed in patients, immune selection within hosts is dominant over selection for transmission. Surprisingly, we do find high values for set-point virus load heritability, and argue that high heritability estimates can be caused by the 'footprints' left by differing hosts' immune systems on the virus.
Collapse
Affiliation(s)
- Christiaan H. van Dorp
- Theoretical Biology and Bioinformatics, Universiteit Utrecht, Utrecht, The Netherlands
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- * E-mail:
| | - Michiel van Boven
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Rob J. de Boer
- Theoretical Biology and Bioinformatics, Universiteit Utrecht, Utrecht, The Netherlands
| |
Collapse
|
44
|
Textor J, Henrickson SE, Mandl JN, von Andrian UH, Westermann J, de Boer RJ, Beltman JB. Random migration and signal integration promote rapid and robust T cell recruitment. PLoS Comput Biol 2014; 10:e1003752. [PMID: 25102014 PMCID: PMC4125054 DOI: 10.1371/journal.pcbi.1003752] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 06/13/2014] [Indexed: 01/27/2023] Open
Abstract
To fight infections, rare T cells must quickly home to appropriate lymph nodes (LNs), and reliably localize the antigen (Ag) within them. The first challenge calls for rapid trafficking between LNs, whereas the second may require extensive search within each LN. Here we combine simulations and experimental data to investigate which features of random T cell migration within and between LNs allow meeting these two conflicting demands. Our model indicates that integrating signals from multiple random encounters with Ag-presenting cells permits reliable detection of even low-dose Ag, and predicts a kinetic feature of cognate T cell arrest in LNs that we confirm using intravital two-photon data. Furthermore, we obtain the most reliable retention if T cells transit through LNs stochastically, which may explain the long and widely distributed LN dwell times observed in vivo. Finally, we demonstrate that random migration, both between and within LNs, allows recruiting the majority of cognate precursors within a few days for various realistic infection scenarios. Thus, the combination of two-scale stochastic migration and signal integration is an efficient and robust strategy for T cell immune surveillance.
Collapse
Affiliation(s)
- Johannes Textor
- Theoretical Biology & Bioinformatics, Utrecht University, Utrecht, The Netherlands
| | - Sarah E. Henrickson
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Judith N. Mandl
- Lymphocyte Biology Section, National Insitutes of Health, Bethesda, Maryland, United States of America
| | - Ulrich H. von Andrian
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, United States of America
| | | | - Rob J. de Boer
- Theoretical Biology & Bioinformatics, Utrecht University, Utrecht, The Netherlands
| | - Joost B. Beltman
- Theoretical Biology & Bioinformatics, Utrecht University, Utrecht, The Netherlands
- Division of Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| |
Collapse
|
45
|
Pandit A, de Boer RJ. Reliable reconstruction of HIV-1 whole genome haplotypes reveals clonal interference and genetic hitchhiking among immune escape variants. Retrovirology 2014; 11:56. [PMID: 24996694 PMCID: PMC4227095 DOI: 10.1186/1742-4690-11-56] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 06/24/2014] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Following transmission, HIV-1 evolves into a diverse population, and next generation sequencing enables us to detect variants occurring at low frequencies. Studying viral evolution at the level of whole genomes was hitherto not possible because next generation sequencing delivers relatively short reads. RESULTS We here provide a proof of principle that whole HIV-1 genomes can be reliably reconstructed from short reads, and use this to study the selection of immune escape mutations at the level of whole genome haplotypes. Using realistically simulated HIV-1 populations, we demonstrate that reconstruction of complete genome haplotypes is feasible with high fidelity. We do not reconstruct all genetically distinct genomes, but each reconstructed haplotype represents one or more of the quasispecies in the HIV-1 population. We then reconstruct 30 whole genome haplotypes from published short sequence reads sampled longitudinally from a single HIV-1 infected patient. We confirm the reliability of the reconstruction by validating our predicted haplotype genes with single genome amplification sequences, and by comparing haplotype frequencies with observed epitope escape frequencies. CONCLUSIONS Phylogenetic analysis shows that the HIV-1 population undergoes selection driven evolution, with successive replacement of the viral population by novel dominant strains. We demonstrate that immune escape mutants evolve in a dependent manner with various mutations hitchhiking along with others. As a consequence of this clonal interference, selection coefficients have to be estimated for complete haplotypes and not for individual immune escapes.
Collapse
Affiliation(s)
- Aridaman Pandit
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Rob J de Boer
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| |
Collapse
|
46
|
Carrillo-Bustamante P, Keşmir C, de Boer RJ. Quantifying the Protection of Activating and Inhibiting NK Cell Receptors during Infection with a CMV-Like Virus. Front Immunol 2014; 5:20. [PMID: 24523722 PMCID: PMC3906586 DOI: 10.3389/fimmu.2014.00020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 01/15/2014] [Indexed: 11/16/2022] Open
Abstract
The responsiveness of natural killer (NK) cells is controlled by balancing signals from activating and inhibitory receptors. The most important ligands of inhibitory NK cell receptors are the highly polymorphic major histocompatibility complex (MHC) class I molecules, which allow NK cells to screen the cellular health of target cells. Although these inhibitory receptor–ligand interactions have been well characterized, the ligands for most activating receptors are still unknown. The mouse cytomegalovirus (MCMV) represents a helpful model to study NK cell-driven immune responses. Many studies have demonstrated that CMV infection can be controlled by NK cells via their activating receptors, but the exact contribution of the different signaling potential (i.e., activating vs. inhibiting) remains puzzling. In this study, we have developed a probabilistic model, which predicts the optimal specificity of inhibitory and activating NK cell receptors needed to offer the best protection against a CMV-like virus. We confirm our analytical predictions with an agent-based model of an evolving host population. Our analysis quantifies the degree of protection of each receptor type, revealing that mixed haplotypes (i.e., haplotypes composed of activating and inhibiting receptors) are most protective against CMV-like viruses, and that the protective effect depends on the number of MHC loci per individual.
Collapse
Affiliation(s)
- Paola Carrillo-Bustamante
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University , Utrecht , Netherlands
| | - Can Keşmir
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University , Utrecht , Netherlands
| | - Rob J de Boer
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University , Utrecht , Netherlands
| |
Collapse
|
47
|
Carrillo-Bustamante P, Keşmir C, de Boer RJ. Virus encoded MHC-like decoys diversify the inhibitory KIR repertoire. PLoS Comput Biol 2013; 9:e1003264. [PMID: 24130473 PMCID: PMC3794908 DOI: 10.1371/journal.pcbi.1003264] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 08/23/2013] [Indexed: 11/19/2022] Open
Abstract
Natural killer (NK) cells are circulating lymphocytes that play an important role in the control of viral infections and tumors. Their functions are regulated by several activating and inhibitory receptors. A subset of these receptors in human NK cells are the killer immunoglobulin-like receptors (KIRs), which interact with the highly polymorphic MHC class I molecules. One important function of NK cells is to detect cells that have down-regulated MHC expression (missing-self). Because MHC molecules have non polymorphic regions, their expression could have been monitored with a limited set of monomorphic receptors. Surprisingly, the KIR family has a remarkable genetic diversity, the function of which remains poorly understood. The mouse cytomegalovirus (MCMV) is able to evade NK cell responses by coding "decoy" molecules that mimic MHC class I. This interaction was suggested to have driven the evolution of novel NK cell receptors. Inspired by the MCMV system, we develop an agent-based model of a host population infected with viruses that are able to evolve MHC down-regulation and decoy molecules. Our simulations show that specific recognition of MHC class I molecules by inhibitory KIRs provides excellent protection against viruses evolving decoys, and that the diversity of inhibitory KIRs will subsequently evolve as a result of the required discrimination between host MHC molecules and decoy molecules.
Collapse
Affiliation(s)
- Paola Carrillo-Bustamante
- Theoretical Biology & Bioinformatics, Department of Biology, Utrecht University, Utrecht, The Netherlands
- * E-mail:
| | - Can Keşmir
- Theoretical Biology & Bioinformatics, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Rob J. de Boer
- Theoretical Biology & Bioinformatics, Department of Biology, Utrecht University, Utrecht, The Netherlands
| |
Collapse
|
48
|
Miedema F, Hazenberg MD, Tesselaar K, van Baarle D, de Boer RJ, Borghans JAM. Immune activation and collateral damage in AIDS pathogenesis. Front Immunol 2013; 4:298. [PMID: 24133492 PMCID: PMC3783946 DOI: 10.3389/fimmu.2013.00298] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 09/09/2013] [Indexed: 12/17/2022] Open
Abstract
In the past decade, evidence has accumulated that human immunodeficiency virus (HIV)-induced chronic immune activation drives progression to AIDS. Studies among different monkey species have shown that the difference between pathological and non-pathological infection is determined by the response of the immune system to the virus, rather than its cytopathicity. Here we review the current understanding of the various mechanisms driving chronic immune activation in HIV infection, the cell types involved, its effects on HIV-specific immunity, and how persistent inflammation may cause AIDS and the wide spectrum of non-AIDS related pathology. We argue that therapeutic relief of inflammation may be beneficial to delay HIV-disease progression and to reduce non-AIDS related pathological side effects of HIV-induced chronic immune stimulation.
Collapse
Affiliation(s)
- Frank Miedema
- Department of Immunology, University Medical Center Utrecht , Utrecht , Netherlands
| | | | | | | | | | | |
Collapse
|
49
|
van Deutekom HWM, Wijnker G, de Boer RJ. The rate of immune escape vanishes when multiple immune responses control an HIV infection. J Immunol 2013; 191:3277-86. [PMID: 23940274 DOI: 10.4049/jimmunol.1300962] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
During the first months of HIV infection, the virus typically evolves several immune escape mutations. These mutations are found in epitopes in viral proteins and reduce the impact of the CD8⁺ T cells specific for these epitopes. Recent data show that only a subset of the epitopes escapes, that most of these escapes evolve early, and that the rate of immune escape slows down considerably. To investigate why the evolution of immune escape slows down over the time of infection, we have extended a consensus mathematical model to allow several immune responses to control the virus together. In the extended model, most escapes also occur early, and the immune escape rate becomes small later, and typically only a minority of the epitopes escape. We show that escaping one of the many immune responses provides little advantage after viral setpoint has been approached because the total killing rate hardly depends on the breadth of the immune response. If the breadth of the immune response slowly wanes during disease progression, the model predicts an increase in the rate of immune escape at late stages of infection. Overall, the most striking prediction of the model is that HIV evolves a small number of immune escapes, in both relative and absolute terms, when the CTL immune response is broad.
Collapse
|
50
|
Abstract
Spatial patterns of the hormone auxin are important drivers of plant development. The observed feedback between the active, directed transport that generates auxin patterns and the auxin distribution that influences transport orientation has rendered this a popular subject for modelling studies. Here we propose a new mathematical framework for the analysis of polar auxin transport and present a detailed mathematical analysis of published models. We show that most models allow for self-organised patterning for similar biological assumptions, and find that the pattern generated is typically unidirectional, unless additional assumptions or mechanisms are incorporated. Our analysis thus suggests that current models cannot explain the bidirectional fountain-type patterns found in plant meristems in a fully self-organised manner, and we discuss future research directions to address the gaps in our understanding of auxin transport mechanisms.
Collapse
Affiliation(s)
- Klaartje van Berkel
- Molecular Genetics Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | | | | | | |
Collapse
|