Genomic, epigenomic, and biophysical cues controlling the emergence of the lung alveolus.
Genomic, epigenomic, and biophysical cues controlling the emergence of the lung alveolus.
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基因组、表观基因组和生物物理线索控制肺泡的出现。
DOI：
10.1126/science.abc3172
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发表时间：
2021-03-12
期刊：
影响因子：
--
通讯作者：
Morrisey EE
中科院分区：
文献类型：
--
作者：
Zepp JA;Morley MP;Loebel C;Kremp MM;Chaudhry FN;Basil MC;Leach JP;Liberti DC;Niethamer TK;Ying Y;Jayachandran S;Babu A;Zhou S;Frank DB;Burdick JA;Morrisey EE
肺泡是呼吸系统进行气体交换所需的功能单位。在过渡到出生时呼吸空气，生物物理力量被认为是塑造新兴的组织生态位。然而，驱动这些过程的细胞间信号传导仍然知之甚少。应用多模式的方法，我们确定肺泡1型（AT 1）上皮细胞作为一个独特的信号枢纽。谱系追踪表明，AT 1祖细胞与接受，施力，肌成纤维细胞在空间和时间的方式。通过单细胞染色质可及性和途径表达（SCAPE）分析，我们证明AT 1限制性配体是肌成纤维细胞和肺泡形成所必需的。这些研究表明，由生物物理和AT 1衍生的旁分泌信号介导的细胞命运的排列驱动了产后呼吸所需的广泛组织重塑。肺的肺泡区域在跨越生命的晚期胚胎和早期出生后阶段的时期中发育。在向空气呼吸过渡的过程中，发生了一系列复杂的事件，包括细胞增殖、表面活性剂产生和肺泡结构的形态发生，这一过程称为肺泡发生。这一关键时期建立了肺泡上皮、毛细血管内皮和成纤维细胞的空间排列，以产生气体交换龛。细胞室的时间和空间排列以及协调肺泡发育和成熟的细胞间信号传导仍然缺乏特征。此外，由于广泛的形态学变化，形状的肺泡龛，目前还不清楚在何种程度上亚组的肺泡间充质可以施加机械力，以促进正确的肺泡结构在出生后的早期发展。单细胞测序和新的遗传谱系追踪工具有助于阐明肺中所有三个细胞区室中的细胞异质性，特别值得注意的是肺间充质中的广泛异质性。我们试图整合这些新技术和工具来评估驱动肺泡生成的细胞间通讯。我们生成了发育中小鼠肺的单细胞RNA测序（scRNA-seq）图谱，其中包括来自胚胎和出生后阶段的七个时间点的上皮、内皮和间充质隔室。然后，我们分析了预测的配体和受体的相互作用，并确定肺泡1型上皮细胞（AT 1）作为一个独特的和高度富集的配体枢纽。这些配体的同源受体的表达在发育中的间充质细胞的亚群中受到限制。间充质祖细胞在空间上和转录上分离成表达Acta 2、Pdgfrb或Wnt 2的亚群。到胚胎第E15.5天，间充质祖细胞致力于在出生后肺中产生不同的成纤维细胞。我们通过scRNA-seq和谱系追踪表明，仅存在于出生后早期肺发育肺泡化期间的瞬时次级嵴肌成纤维细胞（SCMF）的祖细胞在空间和转录上与AT 1细胞祖细胞对齐。与其他肺泡成纤维细胞相比，我们表明，纯化的SCMF施加显着更大的牵引力离体，表明他们是一个功能专门的成纤维细胞谱系，可以重塑肺泡。接下来，为了鉴定调节细胞谱系身份的细胞间信号传导途径，我们检查了AT 1和SCMF的单细胞染色质可及性和途径表达（SCAPE）。我们确定Foxa和Tead转录因子作为几个AT 1衍生配体，包括Shh和Wnt配体的上游调节因子。相反，SCMF表现出开放的染色质与预测的Gli 1和Tcf靶基因，暗示Shh和Wnt途径在其发展和功能。为了在体内测试这些途径，我们产生了Wnt-配体分泌（Wls）和Shh的AT 1细胞特异性条件性敲除。从AT 1细胞中有条件地消融Shh导致SCMF细胞的损失和随后出生后肺中的肺泡简化。我们的研究整合了单细胞基因组学和遗传谱系追踪，以确定在远端肺发育和成熟过程中活跃的细胞间信号通路的空间和时间模式。这项工作的一个关键发现是，AT 1上皮细胞，以前认为主要提供薄的气体扩散界面与毛细血管内皮，也是一个重要的配体表达节点所需的适当的肺发育。这些观察结果表明，维持AT 1细胞的活力是至关重要的，以建立肺发育过程中的组织稳态。我们的整体安装成像和单细胞生物物理测量分析表明，AT 1相邻的间充质祖细胞占据解剖学上离散的区域，并在功能上专门塑造肺泡的复杂结构。间充质生物学的这些方面增加了越来越多的证据，强调不同成纤维细胞谱系的转录和功能异质性。AT 1细胞为肺泡发育提供细胞间信号。肺单细胞发育图谱揭示了肺泡1型（AT 1）上皮细胞中配体表达的富集特征。染色质可及性和整装成像鉴定发育中肺中AT 1和次级嵴肌成纤维细胞（SCMF）祖细胞的转录和空间对齐。AT 1衍生的Shh信号是施力SCMF的规范和产物所必需的。
The lung alveolus is the functional unit of the respiratory system required for gas exchange. During the transition to air breathing at birth, biophysical forces are thought to shape the emerging tissue niche. However, the intercellular signaling that drives these processes remain poorly understood. Applying a multimodal approach, we identify alveolar type 1 (AT1) epithelial cells as a distinct signaling hub. Lineage tracing demonstrates that AT1 progenitors align with receptive, force-exerting, myofibroblasts in a spatial and temporal manner. Through single cell chromatin accessibility and pathway expression (SCAPE) analysis, we demonstrate that AT1-restricted ligands are required for myofibroblasts and alveolar formation. These studies show that the alignment of cell fates, mediated by biophysical and AT1-derived paracrine signals, drives the extensive tissue remodeling required for postnatal respiration. The alveolar region of the lung develops in a period spanning the late embryonic and early post-natal stages of life. An intricate series of events including cellular proliferation, surfactant production and morphogenesis of the alveolar structure occur during the transition to air breathing, a process known as alveologenesis. This critical period establishes the spatial arrangement of alveolar epithelium, capillary endothelium and fibroblasts to generate the gas-exchange niche. The temporal and spatial alignment of cell compartments and the intercellular signaling that coordinates the development and maturation of the lung alveolus remain poorly characterized. Moreover, due to the extensive morphological changes that shape the alveolar niche, it is unclear the extent to which subsets of alveolar mesenchyme could exert mechanical force to promote correct alveolar architecture during early postnatal development. Single cell sequencing and new genetic lineage tracing tools have helped elucidate the cellular heterogeneity in all three cellular compartments in the lung, with extensive heterogeneity in the lung mesenchyme of particular note. We sought to integrate these new technologies and tools to assess the cell-cell communication that drives alveolar generation. We generated a single cell RNA-sequencing (scRNA-seq) atlas of the developing mouse lung which included epithelial, endothelial and mesenchymal compartments from seven timepoints spanning embryonic and post-natal stages. We then analyzed predicted ligand and receptor interactions and identified the alveolar type 1 epithelial cell (AT1) as a unique and highly enriched hub of ligands. The expression of cognate receptors for these ligands were restricted in subsets of developing mesenchymal cells. Mesenchymal progenitors are spatially and transcriptionally segregated into Acta2, Pdgfrb or Wnt2 expressing subsets. By embryonic day E15.5 the mesenchymal progenitors are committed to generating distinct fibroblasts in the post-natal lung. We show by scRNA-seq and lineage tracing that the progenitors for the transient secondary crest myofibroblast (SCMF), which exists only during the early post-natal alveolarization period of lung development, is spatially and transcriptionally aligned with the AT1 cell progenitors. Compared to other alveolar fibroblasts we show that purified SCMF exert significantly more traction force ex vivo, indicating that they are a functionally specialized fibroblast lineage that can remodel the alveolus. Next, to identify intercellular signaling pathways that regulate cell lineage identity, we examined the single cell chromatin accessibility and pathway expression (SCAPE) of the AT1 and SCMF. We identify Foxa and Tead transcription factors as upstream regulators of several AT1-derived ligands including Shh and Wnt ligands. Conversely, SCMFs exhibit open chromatin with predicted Gli1 and Tcf target genes, implicating Shh and Wnt pathways in their development and function. To test these pathways in vivo, we generated AT1-cell specific conditional knockouts for Wnt-ligand secretion (Wls) and Shh. Conditional ablation of Shh from AT1 cells results in a loss of SCMF cells and subsequent alveolar simplification in the post-natal lung. Our studies integrated single-cell genomics and genetic lineage tracing, to identify the spatial and temporal patterning of intercellular signaling pathways that are active during the development and maturation of the distal lung. A key finding from this work is that the AT1 epithelial cell, previously thought to primarily provide the thin gas-diffusible interface with the capillary endothelium, is also a crucial ligand expressing node required for proper lung development. These observations suggest that maintaining the viability of the AT1 cell is paramount to establish tissue homeostasis during lung development. Our whole-mount imaging and single cell biophysical measurement assays demonstrate that AT1 adjacent mesenchymal progenitors occupy anatomically discrete regions and are functionally specialized to mold the intricate architecture of the lung alveolus. These aspects of mesenchymal biology add to growing evidence underscoring the transcriptional and functional heterogeneity that underlies distinct fibroblast lineages. AT1 cells provide intercellular cues for alveolar development. A lung single cell developmental atlas reveals an enriched signature of ligand expression in alveolar type 1 (AT1) epithelial cells. Chromatin accessibility and whole-mount imaging identify the transcriptional and spatial alignment of AT1 and the secondary crest myofibroblast (SCMF) progenitors in the developing lung. The AT1-derived Shh signal is required for specification and outgrowth of the force-exerting SCMF.
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影响因子：
64.8
作者：
Gillich A;Zhang F;Farmer CG;Travaglini KJ;Tan SY;Gu M;Zhou B;Feinstein JA;Krasnow MA;Metzger RJ
通讯作者：
Metzger RJ
影响因子：
2.7
作者：
Branchfield K;Li R;Lungova V;Verheyden JM;McCulley D;Sun X
通讯作者：
Sun X
影响因子：
64.8
作者：
Peng T;Frank DB;Kadzik RS;Morley MP;Rathi KS;Wang T;Zhou S;Cheng L;Lu MM;Morrisey EE
通讯作者：
Morrisey EE
影响因子：
5.2
作者：
Moiseenko, Alena;Kheirollahi, Vahid;Bellusci, Saverio
通讯作者：
Bellusci, Saverio
影响因子：
16.6
作者：
Alanis, Denise Martinez;Chang, Daniel R.;Akiyama, Haruhiko;Krasnow, Mark A.;Chen, Jichao
通讯作者：
Chen, Jichao