两项研究展示了追溯胚胎细胞错综复杂历史的强大技术——并有望为癌症及其他疾病带来新见解。
Two studies demonstrate powerful techniques for retracing the byzantine histories of embryonic cells — and potentially revealing new insights into cancer and other diseases.
拼凑一份典型的家谱往往需要大量工作，但想象一下，如果你的家族成员不是几百个，而是数十亿个。这就是研究胚胎发育的科学家面临的挑战：他们深入探究源自单一祖先——受精卵——的细胞，这些细胞最终却形成了从皮肤到脑组织的一切。
Assembling a typical family tree can take a lot of work, but imagine if your family contained billions of members rather than hundreds. That’s the challenge facing researchers studying embryonic development, who delve into the cells that come from a sole ancestor — a fertilized egg — but form everything from skin to brain tissue.
本月发表的两项研究，代表了在单细胞层面上追溯这些错综复杂历史的能力迈出了重要一步。
Two studies published this month represent a major step toward being able to retrace these byzantine histories at a single-cell level of detail.
两项工作均采用了一种名为“碱基编辑”的系统，该系统能够在基因组特定位点插入特定的 DNA 标记。一旦这些标记被引入胚胎细胞，它们就会在发育中的细胞内保留下来。当细胞分裂时，产生的两个“子细胞”保留相同的基因组标记——但随后还会继续积累新的标记。这些新标记又会传给它们的后代，以此类推。
Both efforts employ a system known as prime editing, which makes it possible to insert specific DNA marks at defined sites in the genome. Once those are introduced into an embryonic cell, the sequences will be retained in the developing cell. When it divides, the two resulting “daughter cells” keep the same genomic marks — but will then go on to accumulate new ones as well. These are then also passed on to their descendants, and so on.
最终，DNA 测序揭示了每个胚胎细胞中积累的标记，使研究人员能够基于这些标记的模式，通过计算重建发育历史。
DNA sequencing ultimately reveals the accumulated marks in each embryonic cell and enables researchers to computationally reconstruct developmental history based on their patterns.
在最新的研究中，两个团队均使用胚胎期小鼠，并利用引导编辑技术插入由 DNA 的四种核苷酸字母（A、G、T 和 C）以不同组合构成的各种短序列。（即使是短序列也能产生大量多样性；例如，一个三核苷酸标记就能涵盖 64 种不同的组合。）何及其同事从受精卵出发，追踪了单个小鼠胚胎在发育 13.5 天后的细胞谱系——这已超过发育过程的一半，此时“已具备大多数器官等的基础”，他指出。
In the latest studies, both teams worked with embryonic mice and used prime editing to insert various short sequences comprising different combinations of the four nucleotide letters (A, G, T and C) that form DNA. (Even a short sequence can produce a lot of diversity; a three-nucleotide marker, for example, can encompass 64 different combinations.) He and colleagues started with a fertilized egg, tracing the cellular lineages in a single mouse embryo after 13½ days of development — more than halfway through the developmental process, when “you’ve got the basis of most organs and things like that,” he noted.
随后，他们构建了一棵庞大的家谱，追溯了近 130 万个细胞的系谱——仅占总数的 10%，但足以绘制出许多细胞和组织类型的起源。
They then assembled a massive family tree tracing the descent of nearly 1.3 million cells — only 10 percent of the total but sufficient to map the origins of many cell and tissue types.
第二项研究由马萨诸塞州怀特海德生物医学研究所的研究员乔纳森·韦斯曼领导，发表于《细胞》杂志，采用了一种名为 PEtracer 的替代性引导编辑方法。该分析的范围较窄——仅覆盖 2.5 天的发育窗口期——但包含了该时间跨度内的 16 个胚胎。在每个胚胎中，韦斯曼团队通常记录了近一半细胞的谱系，发现了一致的发育轨迹，这些轨迹确立了小鼠的整体体格蓝图，并导致心脏及其他器官的形成。
The second study, led by investigator Jonathan Weissman at the Whitehead Institute for Biomedical Research in Massachusetts and published in Cell, used an alternative prime-editing-based method called PEtracer. This analysis was narrower in scope — a 2½-day window of development — but included 16 embryos from across that span of time. Within each, Weissman’s group typically recorded the lineages of nearly half of the cells, finding consistent developmental trajectories that establish the mouse’s overall body plan and lead to the formation of the heart and other organs.
目前，这两种技术均无法完整捕捉胚胎发育的全貌，但这两项研究指明了一条清晰的前进道路。
Neither technique currently captures the whole picture of embryonic development, but the two studies suggest a clear road forward.
“拥有小鼠发育的那部‘电影’……仍在我们前方，但我更有信心我们将能实现这一目标，”申德尔说。这一谱系追踪工具箱同样可用于揭示许多疾病过程的演进，如肿瘤生长与转移。最终目标是利用这些发现，更好地理解人类身上发生的同类过程。
“Having that ‘movie’ of development of a mouse … is something that still lies ahead of us, but I feel much more confident we’re going to get there,” Shendure said. This same lineage-tracing toolbox could also be used to reveal how many disease processes unfold, such as tumor growth and metastasis. The goal is ultimately to utilize such findings to better understand the same processes in human beings.
基于 DNA Typewriter 和 PEtracer 的大规模谱系图谱可能还需要一段时间，才能让缺乏大量资金和技术资源的实验室也能使用。但这两个研究小组都已将其发表的数据公开在线，正如人类基因组计划 —— 一个由大型联盟主导、很快成为全球研究宝贵资源的宏大项目 —— Gagnon 乐观地认为，这些早期工作产生的参考资料将是一股上涨的潮水，托举起发育生物学领域的所有船只。
It may be some time before extensive lineage maps based on DNA Typewriter and PEtracer become accessible to labs without substantial financial and technical resources. But both research groups have made their published data available online, and as with the Human Genome Project — an immense consortium-led effort that soon became an invaluable resource for global research — Gagnon is optimistic that the reference material generated by these early efforts will be a tide that raises all boats in the developmental biology field.
“在我看来，这才是有趣的地方 —— 思考这类数据集如何赋能许多实验室的科学研究，”他说。
“For me, that’s the fun thing — trying to think of how these types of datasets empower science in many labs,” he said.