Genome-wide exploration of reprogramming mechanisms using CRISPR/Cas9 and DamID technologies

使用 CRISPR/Cas9 和 DamID 技术对重编程机制进行全基因组探索

• 批准号: MR/N008715/1
• 负责人: Keisuke Kaji
• 金额: $ 411.14万
• 依托单位: University of Edinburgh
• 依托单位国家: 英国
• 项目类别: Fellowship
• 财政年份: 2016
• 资助国家: 英国
• 起止时间: 2016 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=MR%2FN008715%2F1
• 关键词: Genome; wide; exploration; reprogramming; mechanisms

In our body, skin cells generate only skin, muscle cells make only muscle, bone cells make only bone and so forth. However, our whole body was generated from a single cell, a fertilized egg, in the womb. This cell, the source of life, starts to divide just after fertilization and become 2 cells, 4 cells, 8 cells, 16 cells, continuing to divide and gradually form the body of an embryo. In the beginning of embryo development, until about 1 week after fertilization when the mass of cells still look like a ball, we have cells that can generate all ~300 different cell types which orchestrate the formation of our adult body. However, after this stage, cells in the womb start being specialized to generate specific cell types in the future body. The way cells start making commitments to a specialized cell in a body is often described as a ball rolling down a mountain. On the top of the mountain, the ball can go in to any valley at the bottom. However, once the ball drops from the top of the mountain, the valleys it can go to become restricted to the same side of the ridge. When the ball rolls down to a lower position of the mountain, choices of valleys to be able to travel down become more limited. Similarly, when a baby is born, cells in the body have very limited capacity to generate different cell types. The only way to keep cells with mulit-potential to generate all cell types is taking an embryo from the womb about 1 week after fertilization and put it in a plastic dish with nutrient rich liquid containing optimal conditions to prevent further specialization of the cells. These uncommitted cells that can make all cell types of the body are therefore called 'pluripotent stem cells', and because they arederived from an embryo they are called embryonic stem cells (ESCs). The general principles of development, whereby stem cells gradually and irreversibly become specialized, were re-written by a very simple experiment in 2006. A group of scientists found that any specialized cells can become uncommitted pluripotent cells like ESCs by artificially manipulating only 4 genes simultaneously. This trick that rewound the cells' biological time clock is called 'reprogramming' and the resulting artificially generated uncommitted cells are called 'induced pluripotent stem cells (iPSCs)'. The findings brought tremendous excitement to the stem cell and medical research community. iPSCs can be generated from any cell in the body (e.g. your skin cells) and in theory can be used for the production of any desired cell types for transplantation, drug screening, toxicology tests and so forth. At the moment, successful generation of iPSCs is not 100% efficient, the process of reprogramming takes over 1 month and is an expensive procedure. The technology is still far from delivering its merits to the society. In addition, surprisingly, we still do not know why the manipulation of only 4 genes can induce pluripotency, erasing the character of specialized cells. Therefore in this project we aim to illuminate molecular mechanism of reprogramming using state-of-the-art molecular biology techniques. In the first objective, we aim to reveal genes that are inhibitory or essential for efficient reprogramming. In the second objective, we will investigate how the manipulated 4 genes concisely and effectively execute the process of reprogramming. As an outcome of the project we expect to have strategies to generate iPSCs with higher success and in a shorter time period, and also better understanding how we can manipulate specialized cells and/or pluripotent cells to generate different specialized cells required for medical applications.

在我们的身体里，皮肤细胞只生成皮肤，肌肉细胞只生成肌肉，骨细胞只生成骨骼，等等。然而，我们的整个身体都是由子宫中的一个细胞，一个受精卵产生的。这个细胞，生命的源泉，在受精后开始分裂，变成2个细胞，4个细胞，8个细胞，16个细胞，继续分裂，逐渐形成胚胎的身体。在胚胎发育的开始，直到受精后大约1周，当细胞团仍然看起来像一个球时，我们的细胞可以产生所有~300种不同的细胞类型，这些细胞类型协调我们成年身体的形成。然而，在这个阶段之后，子宫中的细胞开始专门化，以在未来的身体中产生特定的细胞类型。细胞开始向体内专门细胞做出承诺的方式通常被描述为一个从山上滚下来的球。在山顶上，球可以进入底部的任何山谷。然而，一旦球从山顶落下，它可以去的山谷就被限制在山脊的同一侧。当球滚到山的较低位置时，能够向下旅行的山谷的选择变得更加有限。同样，当婴儿出生时，体内细胞产生不同细胞类型的能力非常有限。保持具有多潜能的细胞产生所有细胞类型的唯一方法是在受精后约1周从子宫中取出胚胎，并将其放入含有营养丰富的液体的塑料盘中，该液体含有最佳条件以防止细胞的进一步特化。这些未定型的细胞可以制造身体的所有细胞类型，因此被称为“多能干细胞”，并且因为它们来自胚胎，所以被称为胚胎干细胞（ESC）。2006年，一个非常简单的实验改写了发育的一般原则，即干细胞逐渐且不可逆转地变得特化。一组科学家发现，任何特化细胞都可以通过同时人工操纵4个基因而成为像ESC这样的未定型多能细胞。这种逆转细胞生物钟的技巧被称为“重编程”，由此产生的人工生成的未定型细胞被称为“诱导多能干细胞（iPSCs）”。这些发现给干细胞和医学研究界带来了巨大的兴奋。iPSC可以从体内的任何细胞（例如皮肤细胞）中产生，理论上可以用于生产任何所需的细胞类型，用于移植，药物筛选，毒理学测试等。目前，成功产生iPSC并不是100%有效的，重编程的过程需要超过1个月，并且是一个昂贵的过程。这项技术还远远没有向社会提供它的优点。此外，令人惊讶的是，我们仍然不知道为什么只有4个基因的操作可以诱导多能性，消除特化细胞的特征。因此，在这个项目中，我们的目标是阐明重编程的分子机制，使用国家的最先进的分子生物学技术。在第一个目标中，我们的目标是揭示抑制性或有效重编程所必需的基因。在第二个目标中，我们将研究如何操纵的4个基因简洁而有效地执行重编程过程。作为该项目的成果，我们希望有策略在更短的时间内以更高的成功率产生iPSC，并更好地了解我们如何操纵特化细胞和/或多能细胞以产生医疗应用所需的不同特化细胞。

项目成果

B1 SINE-binding ZFP266 impedes mouse iPSC generation through suppression of chromatin opening mediated by reprogramming factors.

B1 SINE 结合 ZFP266 通过抑制重编程因子介导的染色质开放来阻碍小鼠 iPSC 的生成。

• DOI: 10.1038/s41467-023-36097-9
• 发表时间: 2023-01-30
• 期刊: NATURE COMMUNICATIONS
• 影响因子: 16.6
• 作者: Kaemena, Daniel F.;Yoshihara, Masahito;Beniazza, Meryam;Ashmore, James;Zhao, Suling;Bertenstam, Marten;Olariu, Victor;Katayama, Shintaro;Okita, Keisuke;Tomlinson, Simon R.;Yusa, Kosuke;Kaji, Keisuke
• 通讯作者: Kaji, Keisuke

Fine-Tuning Mybl2 Is Required for Proper Mesenchymal-to-Epithelial Transition during Somatic Reprogramming.

• DOI: 10.1016/j.celrep.2018.07.026
• 发表时间: 2018-08-07
• 期刊: Cell reports
• 影响因子: 8.8
• 作者: Ward C;Volpe G;Cauchy P;Ptasinska A;Almaghrabi R;Blakemore D;Nafria M;Kestner D;Frampton J;Murphy G;Buganim Y;Kaji K;García P
• 通讯作者: García P

CELLoGeNe - an Energy Landscape Framework for Logical Networks Controlling Cell Decisions

CELLoGeNe - 控制电池决策的逻辑网络的能源景观框架

• DOI: 10.1101/2022.02.09.479734
• 发表时间: 2022
• 作者: Andersson E

B1 SINE-binding ZFP266 impedes reprogramming through suppression of chromatin opening mediated by pioneering factors

• DOI: 10.1101/2022.01.04.474927
• 发表时间: 2022-01
• 期刊: bioRxiv
• 作者: Daniel F. Kaemena;Masahito Yoshihara;James Ashmore;Meryam Beniazza;Suling Zhao;Mårten Bertenstam;V. Olariu;S. Katayama;K. Okita;S. Tomlinson;K. Yusa;K. Kaji

Mapping transcription factor occupancy using minimal numbers of cells in vitro and in vivo.

• DOI: 10.1101/gr.227124.117
• 发表时间: 2018-04
• 期刊: Genome research
• 影响因子: 7
• 作者: Tosti L;Ashmore J;Tan BSN;Carbone B;Mistri TK;Wilson V;Tomlinson SR;Kaji K
• 通讯作者: Kaji K