Forty first-trimester human hearts were studied to lay groundwork for further studies of the mechanisms underlying congenital heart defects. We first sampled 49,227 cardiac nuclei from three fetuses at 8.6, 9.0, and 10.7 post-conceptional weeks (pcw) for single-nucleus RNA sequencing, enabling the distinction of six classes comprising 21 cell types. Improved resolution led to the identification of previously unappreciated cardiomyocyte populations and minority autonomic and lymphatic endothelial transcriptomes, among others. After integration with 5-7 pcw heart single-cell RNA-sequencing data, we identified a human cardiomyofibroblast progenitor preceding the diversification of cardiomyocyte and stromal lineages. Spatial transcriptomic analysis (six Visium sections from two additional hearts) was aided by deconvolution, and key spatial markers validated on sectioned and whole hearts in two- and three-dimensional space and over time. Altogether, anatomical-positional features, including innervation, conduction and subdomains of the atrioventricular septum, translate latent molecular identity into specialized cardiac functions. This atlas adds unprecedented spatial and temporal resolution to the characterization of human-specific aspects of early heart formation.

Keywords:
Human development, Cardiac, Deconvolution, Single-nucleus RNA-sequencing, Spatial transcriptomics, Light-sheet microscopy
Subjects:
Cardiovascular development and regeneration

Author contributions

Conceptualization: H.C.E., S.Z.; Data curation: C.D.B., S.K., M.H., C.H., S.R., A.B., H.C.E.; Formal analysis: C.D.B., Y.X., S.K., A.B., S.Z., H.C.E.; Funding acquisition: I.V., A.C., S.Z.; Investigation: C.D.B., Y.X., S.K., M.H., C.M., Y.G., A.L., S.Z., H.C.E.; Methodology: C.D.B., Y.X., S.K., M.H., C.H., M.M., Y.G., A.L., I.V., S.M.-G., A.C., A.B., S.Z., H.C.E.; Project administration: S.M.-G., A.C., S.Z., H.C.E.; Resources: M.H., M.M., W.S., S.M.-G., A.C., S.Z., H.C.E.; Software: C.D.B., Y.X., S.K., C.H., A.L., A.B., H.C.E.; Supervision: S.Z., H.C.E.; Validation: C.D.B., M.H., H.C.E.; Visualization: C.D.B., Y.X., M.H., C.H., S.R., A.L., I.V., S.Z., H.C.E.; Writing – original draft: C.D.B., Y.X., S.K., A.B., S.Z., H.C.E.; Writing – review & editing: C.D.B., Y.X., C.H., Y.G., A.L., S.M.-G., A.B., S.Z., H.C.E.

Funding

This work was supported by the Institut National de la Santé et de la Recherche Médicale (INSERM) Programme Transversale ‘HuDeCA, France (M.H., Y.G., A.C., S.M.-G., S.Z., H.C.E.), and a grant ‘MoThARD’ from the Association Française contre les Myopathies (S.K., A.B., S.Z., H.C.E.). C.D.B. is supported by a grant from the Fondation pour la Recherche Médicale, France (ARF202209015768). Y.X. was supported by the National Key Research and Development Program of China (2024YFF1207500), the National Natural Science Foundation of China (23DAA01060 and 32470703), and the Shanghai Pujiang Program (23PJ1408900). This publication is part of the Human Cell Atlas (https://www.humancellatlas.org/publications/).

Data availability

Sequencing data, images and snRNAseq matrices are available from the Gene Expression Omnibus (GEO) under accession number GSE283967; code from https://github.com/BAUDOTlab/Human_fetal_heart_atlas; movies, large images and high-resolution gross anatomy images are available from Figshare at https://figshare.com/projects/Multi-modal_refinement_of_the_human_heart_atlas_during_the_first_gestational_trimester/213151. Some images are reproduced at the Human Developmental Biology Resource (UK) fetal cardiac anatomy website (https://bit.ly/HumanFetalHeart).

The people behind the papers

This article has an associated ‘The people behind the papers’ interview with some of the authors.

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