PI3K signaling specifies proximal-distal fate by driving a developmental gene regulatory network in SOX9+ mouse lung progenitors.
PI3K signaling specifies proximal-distal fate by driving a developmental gene regulatory network in SOX9+ mouse lung progenitors.
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PI3K信号通过驱动SOX9+小鼠肺祖细胞中的发育基因调控网络来决定近端 - 远端命运。
DOI：
10.7554/elife.67954
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发表时间：
2022-08-17
期刊：
影响因子：
7.7
通讯作者：
Morrisey, Edward E.
中科院分区：
文献类型：
--
作者：
Khattar, Divya;Fernandes, Sharlene;Snowball, John;Guo, Minzhe;Gillen, Matthew C.;Jain, Suchi Singh;Sinner, Debora;Zacharias, William;Swarr, Daniel T.;Morrisey, Edward E.
关键词：
发育中的呼吸芽的尖端是重要的祖细胞的家园，这些祖细胞以SOX 9和ID 2的表达为标志。在胚胎发育早期（E13.5之前），SOX 9+祖细胞是多能的，产生气道和肺泡上皮细胞，但在发育后期是肺泡上皮细胞的选择性祖细胞。转录因子，包括Sox 9，Etv 5，Irx，Mycn和Foxp 1/2在复杂的基因调控网络中相互作用，以控制SOX 9+祖细胞的增殖和分化。这些转录因子和其他信号通路控制染色质状态以建立和维持细胞类型身份的分子机制尚未明确。在此，我们分析了小鼠胚胎发育过程中SOX 9+上皮祖细胞（EPCs）的配对基因表达（RNA-Seq）和染色质可及性（ATAC-Seq）数据。在E11.5和E16.5之间观察到染色质可及性的广泛变化，特别是在远端顺式调节元件（例如增强子）处。基因调控网络（GRN）推断鉴定了一个共同的SOX 9+祖细胞GRN，暗示磷酸肌醇3-激酶（PI 3 K）信号转导参与SOX 9+祖细胞的发育调控。与该模型一致，小鼠中发育中的肺上皮中PI 3 K信号传导的条件性消融导致S 0X 9 + EPC群体的扩增和气道上皮细胞分化受损。这些数据表明，PI 3 K信号传导是肺器官发生过程中上皮模式化所需的，并强调了成对RNA和ATAC序列在定义发育中的调控网络中的组合能力。研究肺部如何发育有助于我们了解和治疗通常具有破坏性的肺部疾病。这包括像囊性纤维化这样的疾病，它是由一个人的遗传密码中的拼写错误引起的。然而，并非所有的肺部疾病都涉及突变。许多其他疾病，无论是成人还是儿童，都是由肺发育过程中的基因未能在某个时候打开或关闭引起的。DNA被各种蛋白质包围，这些蛋白质将DNA包装成一种被称为染色质的压缩结构。细胞可以通过改变染色质内遗传密码的紧密排列来控制哪些基因被打开或关闭。染色质可及性的变化，也称为“表观遗传”变化，是发育的正常部分，并引导细胞在器官成熟时从事特定的工作或身份。然而，这是如何发生在发育中的肺是知之甚少。在这里，Khattar，Fernandes等人着手确定染色质可及性如何影响肺内衬组织的发育，重点是一组产生蛋白SOX 9的祖细胞。这些细胞最初在早期肺的尖端发现，在那里它们继续发育成整个成熟器官的细胞。最初的实验使用大规模的遗传技术来同时测量从小鼠肺部提取的祖细胞中的基因活性和染色质可及性。Khattar，Fernandes等人然后能够预测基于哪些基因被未包装的染色质包围来塑造肺衬里的信号通路，并确定负责这些表观遗传变化的蛋白质。这包括参与许多细胞过程的信号传导途径磷脂酰肌醇3激酶（PI 3 K）。在小鼠中进行的其他实验证实，PI 3 K通路在肺发育的早期就变得活跃，并一直保持到成年。相比之下，缺乏编码PI 3 K途径关键部分的基因的小鼠具有缺陷的肺，无法形成适当的衬里。这项研究中产生的数据将为未来研究表观遗传变化如何驱动正常肺发育提供重要资源。Khattar，Fernandes等人希望这些知识将有助于研究人员更好地了解人类肺部疾病的原因，并确定已经可用的“表观遗传药物”，这些药物可以重新用于治疗这些疾病。
The tips of the developing respiratory buds are home to important progenitor cells marked by the expression of SOX9 and ID2. Early in embryonic development (prior to E13.5), SOX9+progenitors are multipotent, generating both airway and alveolar epithelium, but are selective progenitors of alveolar epithelial cells later in development. Transcription factors, including Sox9, Etv5, Irx, Mycn, and Foxp1/2 interact in complex gene regulatory networks to control proliferation and differentiation of SOX9+progenitors. Molecular mechanisms by which these transcription factors and other signaling pathways control chromatin state to establish and maintain cell-type identity are not well-defined. Herein, we analyze paired gene expression (RNA-Seq) and chromatin accessibility (ATAC-Seq) data from SOX9+ epithelial progenitor cells (EPCs) during embryonic development in Mus musculus. Widespread changes in chromatin accessibility were observed between E11.5 and E16.5, particularly at distal cis-regulatory elements (e.g. enhancers). Gene regulatory network (GRN) inference identified a common SOX9+ progenitor GRN, implicating phosphoinositide 3-kinase (PI3K) signaling in the developmental regulation of SOX9+ progenitor cells. Consistent with this model, conditional ablation of PI3K signaling in the developing lung epithelium in mouse resulted in an expansion of the SOX9+ EPC population and impaired airway epithelial cell differentiation. These data demonstrate that PI3K signaling is required for epithelial patterning during lung organogenesis, and emphasize the combinatorial power of paired RNA and ATAC seq in defining regulatory networks in development. Studying how lungs develop has helped us understand and treat often-devastating lung diseases. This includes diseases like cystic fibrosis which result from spelling mistakes known as mutations in a person’s genetic code. However, not all lung diseases involve mutations. Many other diseases, in both adults and children, are caused by genes failing to switch on or off at some point during lung development. DNA is surrounded by various proteins which package it into a compressed structure known as chromatin. Cells can control which genes are turned on or off by modifying how tightly packed parts of the genetic code are within chromatin. Changes in chromatin accessibility, also known as ‘epigenetic’ changes, are a normal part of development, and guide cells towards specific jobs or identities as an organ matures. However, how this happens in the developing lung is poorly understood. Here, Khattar, Fernandes et al. set out to determine how chromatin accessibility shapes development of the tissue lining the lungs, focusing on a group of progenitor cells which produce the protein SOX9. These cells are initially found at the tips of the early lung, where they go on to develop into the cells that line the whole of the mature organ. Initial experiments used large-scale genetic techniques to measure gene activity and chromatin accessibility simultaneously in progenitor cells extracted from the lungs of mice. Khattar, Fernandes et al. were then able to predict the signaling pathways that shape the lung lining based on which genes were surrounded by unpacked chromatin, and determine the proteins responsible for these epigenetic changes. This included the signaling pathway Phosphatidylinositol 3 kinase (PI3K) which is involved in a number of cellular processes. Additional experiments in mice confirmed that the PI3K pathway became active very early in lung development and remained so until adulthood. In contrast, mice lacking a gene that codes for a key part of the PI3K pathway had defective lungs which failed to develop a proper lining. The data generated in this study will provide an important resource for future studies investigating how epigenetic changes drive normal lung development. Khattar, Fernandes et al. hope that this knowledge will help researchers to better understand the cause of human lung diseases, and identify already available ‘epigenetic drugs’ which could be repurposed to treat them.
影响因子：
3.7
作者：
Carter E;Miron-Buchacra G;Goldoni S;Danahay H;Westwick J;Watson ML;Tosh D;Ward SG
通讯作者：
Ward SG