Shaping a stem cell into dozens of cell types: A single-cell epigenetic roadmap of planarian stem cell differentiation

将干细胞塑造成数十种细胞类型：涡虫干细胞分化的单细胞表观遗传路线图

• 批准号: MR/S007849/1
• 负责人: Jordi Solana
• 金额: $ 60.92万
• 依托单位: Oxford Brookes University
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2019
• 资助国家: 英国
• 起止时间: 2019 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=MR%2FS007849%2F1
• 关键词: Shaping; stem; cell; into; dozens

Pluripotent stem cells can differentiate into all adult cell types. Understanding how pluripotent stem cells differentiate into many different mature cell types is a key question for the biomedical and regenerative sciences. The regulation of gene activity is key for stem cells and differentiation. In the nucleus, histones and other molecules wrap the genetic material in a substance called chromatin. The accessibility of DNA within chromatin is of fundamental importance: chromatin "opens" to allow gene activity and "closes" to shut it down. Microscopy studies very early on showed that stem cells have relatively open chromatin while fully mature cells have large closed regions instead. We currently think that pluripotent stem cells achieve differentiation into many different cell types by opening and closing of different regions of their genomes in each type. In the last decade, we have made great advances to understand these opening and closing events in part thanks to the development of techniques that measure chromatin accessibility and interactions across the entire genome, and have elucidated the events that characterize differentiation to a few cell types in vitro. We have also discovered that alterations in these events often lead to cancer and disease. However, we still do not understand how pluripotent stem cells orchestrate their chromatin opening and closing events to unfold the differentiation programs of the myriad of mature cell types that make a complex adult organism.To tackle this question, I propose to measure chromatin interactions and accessibility at the single cell level in the planarian Schmidtea mediterranea, an ideal model organism through which we can investigate pluripotent stem cell differentiation in vivo. Freshwater planarians are invertebrates that, unlike us, have pluripotent stem cells as adults. They constantly differentiate into all cell types to replace damaged cells and to enable the remarkable planarian regeneration properties: each piece from a planarian can regenerate an entire adult in a matter of days. Recent technological advances of single-cell analysis together with the properties of planarians as a model organism enable this research now. We have already implemented single-cell approaches into planarians, resulting in the elucidation of the complete differentiation tree of planarian stem cells. Here I propose to use novel single-cell techniques to measure chromatin structure and accessibility in planarian cells. This will tell us which regions of the planarian DNA and chromatin open or close in every stage of differentiation to each of the major planarian mature cell types. We can also turn off several genes that are likely to be regulating this process and measure chromatin accessibility in these animals. Most of these genes are present in both humans and planarians and we know that stem cells from both need them to function both but we still ignore their precise mechanisms of action. By measuring how chromatin accessibility changes after turning them off we will understand which are the opening and closing events that they regulate and in which cell types they are important. This information will enable new strategies for human stem cell differentiation approaches and regenerative medicine by targeting those same genes. Altogether, this research will allow us to understand how stem cells reshape their chromatin to differentiate into multiple and different mature cell types.

多能干细胞可以分化成所有的成体细胞类型。了解多能干细胞如何分化成许多不同的成熟细胞类型是生物医学和再生科学的关键问题。基因活性的调节是干细胞和分化的关键。在细胞核中，组蛋白和其他分子将遗传物质包裹在一种称为染色质的物质中。染色质内DNA的可及性至关重要：染色质“打开”以允许基因活动，“关闭”以关闭基因活动。早期的显微镜研究表明，干细胞具有相对开放的染色质，而完全成熟的细胞则具有较大的封闭区域。我们目前认为，多能干细胞通过打开和关闭每种类型中基因组的不同区域来分化成许多不同的细胞类型。在过去的十年中，我们在理解这些开放和关闭事件方面取得了很大的进展，部分归功于测量整个基因组中染色质可及性和相互作用的技术的发展，并阐明了体外分化为几种细胞类型的特征事件。我们还发现，这些事件的改变往往会导致癌症和疾病。然而，我们仍然不明白多能干细胞如何协调其染色质开放和关闭事件，以展开无数成熟细胞类型的分化程序，使一个复杂的成年organis.To解决这个问题，我建议测量染色质的相互作用和可及性在单细胞水平上的涡虫Schmidtea mediterranea，一个理想的模型生物体，通过它我们可以研究体内多能干细胞分化。淡水真涡虫是一种无脊椎动物，与我们不同，它们在成年时具有多能干细胞。它们不断分化成各种类型的细胞，以取代受损的细胞，并使其具有非凡的再生特性：一只真涡虫的每一块细胞都可以在几天内再生出一个完整的成虫。单细胞分析的最新技术进展以及作为模式生物的真涡虫的特性使这项研究成为可能。我们已经实施了单细胞的方法到真涡虫，从而阐明了完整的分化树的真涡虫干细胞。在这里，我建议使用新的单细胞技术来测量染色质结构和可及性的涡虫细胞。这将告诉我们，在向每种主要的真涡虫成熟细胞类型分化的每个阶段，真涡虫DNA和染色质的哪些区域打开或关闭。我们还可以关闭几个可能调节这一过程的基因，并测量这些动物的染色质可及性。这些基因中的大多数存在于人类和真涡虫中，我们知道两者的干细胞都需要它们来发挥作用，但我们仍然忽略了它们的精确作用机制。通过测量关闭它们后染色质可及性的变化，我们将了解它们调节哪些开放和关闭事件以及它们在哪些细胞类型中很重要。这些信息将通过靶向这些相同的基因，为人类干细胞分化方法和再生医学提供新的策略。总而言之，这项研究将使我们了解干细胞如何重塑其染色质以分化成多种不同的成熟细胞类型。

项目成果

ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics.

• DOI: 10.1186/s13059-021-02302-5
• 发表时间: 2021-04-08
• 期刊: Genome biology
• 影响因子: 12.3
• 作者: García-Castro H;Kenny NJ;Iglesias M;Álvarez-Campos P;Mason V;Elek A;Schönauer A;Sleight VA;Neiro J;Aboobaker A;Permanyer J;Irimia M;Sebé-Pedrós A;Solana J
• 通讯作者: Solana J

ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics

ACME 解离：一种用于单细胞转录组学的多功能细胞固定-解离方法

• DOI: 10.1101/2020.05.26.117234
• 发表时间: 2020
• 作者: García-Castro H

Additional file 6 of ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics

ACME解离的附加文件6：一种用于单细胞转录组学的多功能细胞固定-解离方法

• DOI: 10.6084/m9.figshare.14385661
• 发表时间: 2021
• 作者: García-Castro H

Single-cell transcriptomics in planaria: new tools allow new insights into cellular and evolutionary features.

• DOI: 10.1042/bst20210825
• 发表时间: 2022-10-31
• 期刊: Biochemical Society transactions
• 影响因子: 3.9

Additional file 1 of ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics

ACME解离附加文件1：一种用于单细胞转录组学的多功能细胞固定-解离方法

• DOI: 10.6084/m9.figshare.14385646
• 发表时间: 2021
• 作者: García-Castro H