Integration of single-cell transcriptomes and chromatin landscapes reveals regulatory programs driving pharyngeal organ development

Margaret E Magaletta,Fabian J Theis,René Maehr,Jack D Huey,Macrina Lobo,Eric M Kernfeld,Teagan J Parsons,Hananeh Aliee

doi:10.1038/s41467-022-28067-4

Abstract

Maldevelopment of the pharyngeal endoderm, an embryonic tissue critical for patterning of the pharyngeal region and ensuing organogenesis, ultimately contributes to several classes of human developmental syndromes and disorders. Such syndromes are characterized by a spectrum of phenotypes that currently cannot be fully explained by known mutations or genetic variants due to gaps in characterization of critical drivers of normal and dysfunctional development. Despite the disease-relevance of pharyngeal endoderm, we still lack a comprehensive and integrative view of the molecular basis and gene regulatory networks driving pharyngeal endoderm development. To close this gap, we apply transcriptomic and chromatin accessibility single-cell sequencing technologies to generate a multi-omic developmental resource spanning pharyngeal endoderm patterning to the emergence of organ-specific epithelia in the developing mouse embryo. We identify cell-type specific gene regulation, distill GRN models that define developing organ domains, and characterize the role of an immunodeficiency-associated forkhead box transcription factor.

Highlights

Maldevelopment of the pharyngeal endoderm, an embryonic tissue critical for patterning of the pharyngeal region and ensuing organogenesis, contributes to several classes of human developmental syndromes and disorders
While Gas[6] expression overlaps with Foxn[1] throughout the thymus organ domain, we find that Grhl[3] expression is largely restricted to the thymic medulla, which together with the single-cell transcriptomic analysis suggests mTEC specificity (Fig. 1f)
Unsupervised clustering on the network containing the top 200 regulators yielded 12 subnetworks (Fig. 4b, Supplementary Fig. 6, Supplementary Dataset 4), and we identified key transcription factors (TFs)-encoding genes of these modules including Pax[8] (Thyroid), Foxn[1], Pax[1], and Six[1] (Thymus), and Gcm[2], Gata[3], and Maf (Parathyroid) by ranking regulators according to their ability to explain coordinated variation within the pharyngeal endoderm data (Fig. 4c)

Summary

Introduction

Maldevelopment of the pharyngeal endoderm, an embryonic tissue critical for patterning of the pharyngeal region and ensuing organogenesis, contributes to several classes of human developmental syndromes and disorders. Despite the disease-relevance of pharyngeal endoderm, we still lack a comprehensive and integrative view of the molecular basis and gene regulatory networks driving pharyngeal endoderm development To close this gap, we apply transcriptomic and chromatin accessibility single-cell sequencing technologies to generate a multi-omic developmental resource spanning pharyngeal endoderm patterning to the emergence of organspecific epithelia in the developing mouse embryo. Disorders associated with defects in pharyngeal endoderm development are characterized by a spectrum of phenotypes ranging from craniofacial dysmorphia, heart deformities, and cognitive deficiencies to severe immune disorders and disrupted endocrine processes Such symptoms arise in part due to dysfunctions of the pharyngeal endoderm in organization of the pharyngeal region, and cell autonomous regulation of patterning and organogenesis[4,5,6,7,8,9]. We substantiate GRN model predictions by characterizing molecular and cellular impact of a perturbation targeting Foxn[1], which encodes a forkhead box DNA binding TF, resulting in developmental defects that underly primary immunodeficiency

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