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

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Updated February 14, 2025

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 precursors 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. Overall design: Single cell transcriptional libraries were generated from CD34+ human post-natal thymocyte samples using the 10X Genomics Chromium 3’ sequencing V2 kit.

Tom TaghonGhent University

Integrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature Thymocytes. (Official HCA Publication)

Marieke Lavaert1
Kai Ling Liang1
Niels Vandamme2
Jong-Eun Park3
Juliette Roels1
Monica S Kowalczyk4
Bo Li4
Orr Ashenberg4
Marcin Tabaka4
Danielle Dionne4
Timothy L Tickle4
Michal Slyper4
Orit Rozenblatt-Rosen4
Bart Vandekerckhove1
Georges Leclercq1
Aviv Regev4
Pieter Van Vlierberghe5
Martin Guilliams2
Sarah A Teichmann3
Yvan Saeys2
Tom Taghon (Principal Investigator)1
1Ghent University
2VIB Center for Inflammation Research
3Wellcome Sanger Institute, Wellcome Genome Campus
4Broad Institute of Harvard and MIT
5Cancer Research Institute Ghent (CRIG), Ghent University
Ray Stefancsik

To reference this project, please use the following link:

https://explore.data.humancellatlas.org/projects/dbd836cf-bfc2-41f0-9834-41cc6c0b235a
None
GEO Series Accessions:
INSDC Project Accessions:
INSDC Study Accessions:

Atlas

None

Analysis Portals

CZ CELLxGENE
CZ CELLxGENE

Project Label

LavaertHumanThymus

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

5 development stages

Library Construction Method

4 library construction methods

Nucleic Acid Source

single cell

Paired End

false

Analysis Protocol

analysis _protocol1

File Format

2 file formats

Cell Count Estimate

70.0k

Donor Count

10
fastq25 file(s)tar1 file(s)
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