Mapping the developing human immune system across organs

Single-cell genomics studies have decoded the immune cell composition of several human prenatal organs, but were limited in understanding the developing immune system as a distributed network across tissues. We profiled nine prenatal tissues combining single-cell RNA sequencing, antigen-receptor sequencing and spatial transcriptomics to reconstruct the developing human immune system. We revealed late acquisition of immune effector functions of myeloid and lymphoid cell subsets, and the maturation of monocytes and T cells prior to peripheral tissue seeding. We uncovered system-wide blood and immune cell development beyond primary hematopoietic organs, characterized human prenatal B1 cells, and shed light on the origin of unconventional T cells. Our atlas provides both valuable data resources and biological insights that will facilitate cell engineering, regenerative medicine and disease understanding.

Contact
Emma Dann
DOI
10.1126/science.abo0510
Release
12 May 2022
Lab
Teichmann Lab
Tissue
Fetal Bone Marrow, Fetal Gut, Fetal Kidney, Fetal Liver, Fetal Mesenteric Lymph Node, Fetal Skin, Fetal Spleen, Fetal Thymus, Organoids, Yolk Sac
Assay
10x 3' v2, 10x 5' v1, 10x 5' v2, Visium
Disease
None
Organism
Homo sapiens

scRNA-seq Datasets

Dataset
Tissue
Assay
Disease
Organism
Count
Fetal Bone Marrow
Fetal Gut
Fetal Kidney
Fetal Liver
Fetal Mesenteric Lymph Node
Fetal Skin
Fetal Spleen
Fetal Thymus
Yolk Sac
10x 5' v1
10x 3' v2
None
Homo sapiens
911873
Fetal Bone Marrow
Fetal Gut
Fetal Kidney
Fetal Liver
Fetal Mesenteric Lymph Node
Fetal Skin
Fetal Spleen
Fetal Thymus
Yolk Sac
10x 5' v1
10x 3' v2
None
Homo sapiens
593203
Fetal Bone Marrow
Fetal Gut
Fetal Kidney
Fetal Liver
Fetal Mesenteric Lymph Node
Fetal Skin
Fetal Spleen
Fetal Thymus
Yolk Sac
10x 5' v1
10x 3' v2
None
Homo sapiens
318670
Fetal Bone Marrow
Fetal Gut
Fetal Kidney
Fetal Liver
Fetal Mesenteric Lymph Node
Fetal Skin
Fetal Spleen
Fetal Thymus
Yolk Sac
10x 5' v1
10x 3' v2
None
Homo sapiens
149239
Fetal Bone Marrow
Fetal Gut
Fetal Kidney
Fetal Liver
Fetal Mesenteric Lymph Node
Fetal Skin
Fetal Spleen
Fetal Thymus
Yolk Sac
10x 5' v1
10x 3' v2
None
Homo sapiens
40422
Fetal Bone Marrow
Fetal Gut
Fetal Kidney
Fetal Liver
Fetal Mesenteric Lymph Node
Fetal Skin
Fetal Spleen
Fetal Thymus
Yolk Sac
10x 5' v1
10x 3' v2
None
Homo sapiens
218758
Fetal Bone Marrow
Fetal Gut
Fetal Kidney
Fetal Liver
Fetal Mesenteric Lymph Node
Fetal Skin
Fetal Spleen
Fetal Thymus
Yolk Sac
10x 5' v1
10x 3' v2
None
Homo sapiens
241950
Fetal Bone Marrow
Fetal Gut
Fetal Kidney
Fetal Liver
Fetal Mesenteric Lymph Node
Fetal Skin
Fetal Spleen
Fetal Thymus
Yolk Sac
10x 5' v1
10x 3' v2
None
Homo sapiens
174261

Spatial Datasets

Dataset
Tissue
Assay
Disease
Organism
Count
Fetal Liver
Visium
None
Homo sapiens
Fetal Thymus
Visium
None
Homo sapiens
Fetal Spleen
Visium
None
Homo sapiens

VDJ Datasets

Dataset
Tissue
Assay
Disease
Organism
Count
Fetal Bone Marrow
Fetal Gut
Fetal Kidney
Fetal Liver
Fetal Mesenteric Lymph Node
Fetal Skin
Fetal Spleen
Fetal Thymus
Yolk Sac
10x 5' v2
None
Homo sapiens
Fetal Bone Marrow
Fetal Gut
Fetal Kidney
Fetal Liver
Fetal Mesenteric Lymph Node
Fetal Skin
Fetal Spleen
Fetal Thymus
Yolk Sac
10x 5' v2
None
Homo sapiens
Fetal Bone Marrow
Fetal Gut
Fetal Kidney
Fetal Liver
Fetal Mesenteric Lymph Node
Fetal Skin
Fetal Spleen
Fetal Thymus
Yolk Sac
10x 5' v2
None
Homo sapiens

Reproducibility

Reproducibility is a major principle underpinning the scientific method. We make publicly available the raw data and analysis scripts associated with each collection.

Human Cell Atlas

Human Cell Atlas

Developmental

The Human Developmental Cell Atlas (HDCA) aims to generate a comprehensive profile of cell types and states present during development. This detailed study of development will be critical for understanding congenital and childhood disorders, as well as ageing.

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