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Integrated scRNA-seq identifies human postnatal thymus seeding progenitors and regulatory dynamics of differentiating immature thymocytes

Marieke Lavaert, Kai Ling Liang (UGent) , Niels Vandamme (UGent) , Jong-Eun Park, Juliette Roels (UGent) , Monica S. Kowalczyk, Bo Li, Orr Ashenberg, Marcin Tabaka, Danielle Dionne, et al.
(2020) IMMUNITY. 52(6). p.1088-1104.e6
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Abstract
During postnatal life, thymopoiesis depends on the continuous colonization of the thymus by bone-marrow-derived hematopoietic progenitors that migrate through the bloodstream. The current understanding of the nature of thymic immigrants is largely based on data from pre-clinical models. Here, we employed single-cell RNA sequencing (scRNA-seq) to examine the immature postnatal thymocyte population in humans. Integration of bone marrow and peripheral blood precursor datasets identified two putative thymus seeding progenitors that varied in expression of CD7; CD10; and the homing receptors CCR7, CCR9, and ITGB7. Whereas both precursors supported T cell development, only one contributed to intrathymic dendritic cell (DC) differentiation, predominantly of plasmacytoid dendritic cells. Trajectory inference delineated the transcriptional dynamics underlying early human T lineage development, enabling prediction of transcription factor (TF) modules that drive stage-specific steps of human T cell development. This comprehensive dataset defines the expression signature of immature human thymocytes and provides a resource for the further study of human thymopoiesis.
Keywords
Immunology, Immunology and Allergy, Infectious Diseases, KILLER-CELL DEVELOPMENT, T-CELL, NATURAL-KILLER, LINEAGE COMMITMENT, IN-VITRO, HEMATOPOIETIC PROGENITORS, DENDRITIC CELLS, B-CELLS, EXPRESSION, INNATE

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MLA
Lavaert, Marieke, et al. “Integrated ScRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature Thymocytes.” IMMUNITY, vol. 52, no. 6, 2020, pp. 1088-1104.e6, doi:10.1016/j.immuni.2020.03.019.
APA
Lavaert, M., Liang, K. L., Vandamme, N., Park, J.-E., Roels, J., Kowalczyk, M. S., … Taghon, T. (2020). Integrated scRNA-seq identifies human postnatal thymus seeding progenitors and regulatory dynamics of differentiating immature thymocytes. IMMUNITY, 52(6), 1088-1104.e6. https://doi.org/10.1016/j.immuni.2020.03.019
Chicago author-date
Lavaert, Marieke, Kai Ling Liang, Niels Vandamme, Jong-Eun Park, Juliette Roels, Monica S. Kowalczyk, Bo Li, et al. 2020. “Integrated ScRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature Thymocytes.” IMMUNITY 52 (6): 1088-1104.e6. https://doi.org/10.1016/j.immuni.2020.03.019.
Chicago author-date (all authors)
Lavaert, Marieke, Kai Ling Liang, Niels Vandamme, Jong-Eun Park, Juliette Roels, Monica S. Kowalczyk, Bo Li, Orr Ashenberg, Marcin Tabaka, Danielle Dionne, Timothy L. Tickle, Michal Slyper, Orit Rozenblatt-Rosen, Bart Vandekerckhove, Georges Leclercq, Aviv Regev, Pieter Van Vlierberghe, Martin Guilliams, Sarah A. Teichmann, Yvan Saeys, and Tom Taghon. 2020. “Integrated ScRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature Thymocytes.” IMMUNITY 52 (6): 1088-1104.e6. doi:10.1016/j.immuni.2020.03.019.
Vancouver
1.
Lavaert M, Liang KL, Vandamme N, Park J-E, Roels J, Kowalczyk MS, et al. Integrated scRNA-seq identifies human postnatal thymus seeding progenitors and regulatory dynamics of differentiating immature thymocytes. IMMUNITY. 2020;52(6):1088-1104.e6.
IEEE
[1]
M. Lavaert et al., “Integrated scRNA-seq identifies human postnatal thymus seeding progenitors and regulatory dynamics of differentiating immature thymocytes,” IMMUNITY, vol. 52, no. 6, pp. 1088-1104.e6, 2020.
@article{8661089,
  abstract     = {{During postnatal life, thymopoiesis depends on the continuous colonization of the thymus by bone-marrow-derived hematopoietic progenitors that migrate through the bloodstream. The current understanding of the nature of thymic immigrants is largely based on data from pre-clinical models. Here, we employed single-cell RNA sequencing (scRNA-seq) to examine the immature postnatal thymocyte population in humans. Integration of bone marrow and peripheral blood precursor datasets identified two putative thymus seeding progenitors that varied in expression of CD7; CD10; and the homing receptors CCR7, CCR9, and ITGB7. Whereas both precursors supported T cell development, only one contributed to intrathymic dendritic cell (DC) differentiation, predominantly of plasmacytoid dendritic cells. Trajectory inference delineated the transcriptional dynamics underlying early human T lineage development, enabling prediction of transcription factor (TF) modules that drive stage-specific steps of human T cell development. This comprehensive dataset defines the expression signature of immature human thymocytes and provides a resource for the further study of human thymopoiesis.}},
  author       = {{Lavaert, Marieke and Liang, Kai Ling and Vandamme, Niels and Park, Jong-Eun and Roels, Juliette and Kowalczyk, Monica S. and Li, Bo and Ashenberg, Orr and Tabaka, Marcin and Dionne, Danielle and Tickle, Timothy L. and Slyper, Michal and Rozenblatt-Rosen, Orit and Vandekerckhove, Bart and Leclercq, Georges and Regev, Aviv and Van Vlierberghe, Pieter and Guilliams, Martin and Teichmann, Sarah A. and Saeys, Yvan and Taghon, Tom}},
  issn         = {{1074-7613}},
  journal      = {{IMMUNITY}},
  keywords     = {{Immunology,Immunology and Allergy,Infectious Diseases,KILLER-CELL DEVELOPMENT,T-CELL,NATURAL-KILLER,LINEAGE COMMITMENT,IN-VITRO,HEMATOPOIETIC PROGENITORS,DENDRITIC CELLS,B-CELLS,EXPRESSION,INNATE}},
  language     = {{eng}},
  number       = {{6}},
  pages        = {{1088--1104.e6}},
  title        = {{Integrated scRNA-seq identifies human postnatal thymus seeding progenitors and regulatory dynamics of differentiating immature thymocytes}},
  url          = {{http://doi.org/10.1016/j.immuni.2020.03.019}},
  volume       = {{52}},
  year         = {{2020}},
}
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