HCA Data Explorer

CD90 marks a mesenchymal program in human thymic epithelial cells in vitro and in vivo

Updated September 15, 2022

Thymic epithelium is critical for the structural integrity of the thymus and for T cell development. Within the fully formed thymus, large numbers of hematopoietic cells shape the thymic epithelium into a scaffold-like structure which bears little similarity to classical epithelial layers, such as those observed in the skin, intestine or pancreas. Here, we show that human thymic epithelial cells (TECs) possess an epithelial identity that also incorporates the expression of mesenchymal cell associated genes, whose expression levels vary between medullary and cortical TECs (m/cTECs). Using pluripotent stem cell (PSC) differentiation systems, we identified a unique population of cells that co-expressed the master TEC transcription factor FOXN1, as well as the epithelial associated marker EPCAM and the mesenchymal associated gene CD90. Using the same serum free culture conditions, we also observed co-expression of EPCAM and CD90 on cultured TECs derived from neonatal human thymus in vitro. Single cell RNA-sequencing revealed these cultured TECs possessed an immature mTEC phenotype and expressed epithelial and mesenchymal associated genes, such as EPCAM, CLDN4, CD90 and COL1A1. Importantly, flow cytometry and single cell RNA-sequencing analysis further confirmed the presence of an EPCAM+CD90+ population in the CD45- fraction of neonatal human thymic stromal cells in vivo. Using the human thymus cell atlas, we found that cTECs displayed more pronounced mesenchymal characteristics than mTECs during embryonic development. Collectively, these results suggest human TECs possess a hybrid gene expression program comprising both epithelial and mesenchymal elements, and provide a basis for the further exploration of thymus development from primary tissues and from the in vitro differentiation of PSCs. Overall design: This dataset includes RNA samples from three independent donors as biological replicates. For each donor, we sequenced mRNA isolated from four fractions of cells based on the expression of EPCAM and CD104, as well as samples representing unsorted cells.

Jacky Y LiMurdoch Children’s Research Instituteysl270796@gmail.com
Jacky Y Li (Experimental Scientist)1
1Murdoch Children’s Research Institute
Rachel Schwartz

To reference this project, please use the following link:

https://explore.data.humancellatlas.org/projects/a1312f9a-01ef-40a7-89bf-9091ca76a03a
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Analysis Portals

None

Project Label

CD90MarksMesenchymalProgram

Species

Homo sapiens

Sample Type

specimens

Anatomical Entity

thymus

Organ Part

Unspecified

Selected Cell Types

stromal cell

Disease Status (Specimen)

normal

Disease Status (Donor)

Abnormal heart morphology

Development Stage

infant stage

Library Construction Method

10x 3' v3

Nucleic Acid Source

single cell

Paired End

false

Analysis Protocol

analysis_protocol_1

File Format

3 file formats

Cell Count Estimate

17.1k

Donor Count

4
fastq.gz16 file(s)tar1 file(s)xlsx1 file(s)