Multi-scale Dynamical Modeling of T Cell Development from an Early Thymic Progenitor State to Lineage Commitment
Olariu, Victor LU ; Yui, Mary A. ; Krupinski, Pawel LU ; Zhou, Wen ; Deichmann, Julia ; Andersson, Emil LU
; Rothenberg, Ellen V.
and Peterson, Carsten
LU
(2021)
In Cell Reports
34(2).
- Abstract
Intrathymic development of committed progenitor (pro)-T cells from multipotent hematopoietic precursors offers an opportunity to dissect the molecular circuitry establishing cell identity in response to environmental signals. This transition encompasses programmed shutoff of stem/progenitor genes, upregulation of T cell specification genes, proliferation, and ultimately commitment. To explain these features in light of reported cis-acting chromatin effects and experimental kinetic data, we develop a three-level dynamic model of commitment based upon regulation of the commitment-linked gene Bcl11b. The levels are (1) a core gene regulatory network (GRN) architecture from transcription factor (TF) perturbation data, (2) a stochastically... (More)
Intrathymic development of committed progenitor (pro)-T cells from multipotent hematopoietic precursors offers an opportunity to dissect the molecular circuitry establishing cell identity in response to environmental signals. This transition encompasses programmed shutoff of stem/progenitor genes, upregulation of T cell specification genes, proliferation, and ultimately commitment. To explain these features in light of reported cis-acting chromatin effects and experimental kinetic data, we develop a three-level dynamic model of commitment based upon regulation of the commitment-linked gene Bcl11b. The levels are (1) a core gene regulatory network (GRN) architecture from transcription factor (TF) perturbation data, (2) a stochastically controlled chromatin-state gate, and (3) a single-cell proliferation model validated by experimental clonal growth and commitment kinetic assays. Using RNA fluorescence in situ hybridization (FISH) measurements of genes encoding key TFs and measured bulk population dynamics, this single-cell model predicts state-switching kinetics validated by measured clonal proliferation and commitment times. The resulting multi-scale model provides a mechanistic framework for dissecting commitment dynamics.
(Less)
- author
- Olariu, Victor
LU
; Yui, Mary A.
; Krupinski, Pawel
LU
; Zhou, Wen
; Deichmann, Julia
; Andersson, Emil
LU
; Rothenberg, Ellen V.
and Peterson, Carsten
LU
- organization
- publishing date
- 2021
- type
- Contribution to journal
- publication status
- published
- subject
- keywords
- epigenetic modeling, experimental validations, kinetic measurements, population modeling, proliferation measurements, single-cell measurements, stochastic simulations, T cell development, transcriptional modeling
- in
- Cell Reports
- volume
- 34
- issue
- 2
- article number
- 108622
- publisher
- Cell Press
- external identifiers
-
- pmid:33440162
- scopus:85099137528
- ISSN
- 2211-1247
- DOI
- 10.1016/j.celrep.2020.108622
- language
- English
- LU publication?
- yes
- id
- 35632887-47ed-4bf8-ba30-c63daf56ee28
- date added to LUP
- 2021-01-19 11:36:10
- date last changed
- 2024-04-18 00:34:07
@article{35632887-47ed-4bf8-ba30-c63daf56ee28,
abstract = {{<p>Intrathymic development of committed progenitor (pro)-T cells from multipotent hematopoietic precursors offers an opportunity to dissect the molecular circuitry establishing cell identity in response to environmental signals. This transition encompasses programmed shutoff of stem/progenitor genes, upregulation of T cell specification genes, proliferation, and ultimately commitment. To explain these features in light of reported cis-acting chromatin effects and experimental kinetic data, we develop a three-level dynamic model of commitment based upon regulation of the commitment-linked gene Bcl11b. The levels are (1) a core gene regulatory network (GRN) architecture from transcription factor (TF) perturbation data, (2) a stochastically controlled chromatin-state gate, and (3) a single-cell proliferation model validated by experimental clonal growth and commitment kinetic assays. Using RNA fluorescence in situ hybridization (FISH) measurements of genes encoding key TFs and measured bulk population dynamics, this single-cell model predicts state-switching kinetics validated by measured clonal proliferation and commitment times. The resulting multi-scale model provides a mechanistic framework for dissecting commitment dynamics.</p>}},
author = {{Olariu, Victor and Yui, Mary A. and Krupinski, Pawel and Zhou, Wen and Deichmann, Julia and Andersson, Emil and Rothenberg, Ellen V. and Peterson, Carsten}},
issn = {{2211-1247}},
keywords = {{epigenetic modeling; experimental validations; kinetic measurements; population modeling; proliferation measurements; single-cell measurements; stochastic simulations; T cell development; transcriptional modeling}},
language = {{eng}},
number = {{2}},
publisher = {{Cell Press}},
series = {{Cell Reports}},
title = {{Multi-scale Dynamical Modeling of T Cell Development from an Early Thymic Progenitor State to Lineage Commitment}},
url = {{http://dx.doi.org/10.1016/j.celrep.2020.108622}},
doi = {{10.1016/j.celrep.2020.108622}},
volume = {{34}},
year = {{2021}},
}