HCA Data Explorer

Integrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature Thymocytes

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Updated October 10, 2023

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 na- ture 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 pre- cursors supported T cell development, only one contributed to intrathymic dendritic cell (DC) differentiation, predominantly of plasmacytoid dendritic cells. Trajectory inference delineated the transcriptional dynamics un- derlying 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 signa- ture of immature human thymocytes and provides a resource for the further study of human thymopoiesis.

Tom TaghonGhent Universitytom.taghon@ugent.be
Bo Li1
Niels Vandamme2
Sarah Teichmann3
Marcin Tabaka1
Timothy Tickle1
Kai Ling Liang4
Orit Rozenblatt-Rosen5
Orr Ashenberg1
Juliette Roels4
Yvan Saeys4
Monica Kowalczyk1
Pieter Van Vlierberghe6
Danielle Dionne7
Michal Slyper5
Martin Guilliams4
Georges Leclercq6
Marieke Lavaert4
Aviv Regev5
Jong-Eun Park8
Bart Vandekerckhove6
Tom Taghon4
1Broad Institute of MIT and Harvard
2VIB Center for Inflammation Research
3Wellcome Sanger Institute
4Ghent University
5Genentech
6Cancer Research Institute Ghent (CRIG), Ghent University
7Klarman Cell Observatory, Broad Institute
8Wellcome Sanger Institute, Wellcome Genome Campus
None

To reference this project, please use the following link:

https://explore.data.humancellatlas.org/projects/dbd836cf-bfc2-41f0-9834-41cc6c0b235a

Supplementary links are provided by contributors and represent items such as additional data which can’t be hosted here; code that was used to analyze this data; or tools and visualizations associated with this specific dataset.

1.https://cellxgene.cziscience.com/collections/83ed3be8-4cb9-43e6-9aaa-3fbbf5d1bd3a
GEO Series Accessions:INSDC Study Accessions:INSDC Project Accessions:

Analysis Portals

CZ CELLxGENECZ CELLxGENE

Project Label

IntegratedscRNA-SeqIdentifiesHumanPostnatalThymusS

Species

Homo sapiens

Sample Type

specimens

Anatomical Entity

thymus

Organ Part

thymus

Selected Cell Types

thymocyte

Disease Status (Specimen)

Unspecified

Disease Status (Donor)

congenital heart disease

Development Stage

4 development stages

Library Construction Method

2 library construction methods

Nucleic Acid Source

single cell

Paired End

false

File Format

fastq

Cell Count Estimate

72.3k

Donor Count

5
fastq25 file(s)