Nature:叹为观止!科学家对数万个小肠细胞进行了单细胞测序,绘制出了小肠立体百科全书

2017-11-15 代丝雨 奇点网

上周的《自然》杂志上,博德研究所(Broad Institute)研究团队发布了首个小肠细胞图谱!研究基于单细胞RNA测序(scRNA-seq),测定了共计53193个来自小鼠肠道和类肠器官细胞的表达图谱,带来了许多与以往认知不同的新发现,可谓是第一本立体的“小肠百科全书”。

我们将会看到我们所期望的东西,我们已知存在的东西。但我确信,除此以外,我们还会发现全新的东西。”

——桑格研究所细胞图谱团队负责人Mike Stubbington

1665年,罗伯特·胡克(Robert Hooke)凝视着显微镜下的软木,他看到了无数个像房间一样的小格子。作为第一个描述细胞的科学家,他一定会被人类现在试图完成的事情所震惊——我们将要使用强大的现代基因组学和细胞生物学工具,挨个端详人体中的数万亿个细胞。

2017年,来自全世界的顶级科学家公布了一项野心勃勃的计划——创建一个人类细胞图谱(Human Cell Atlas)。我们将破译出人体中每个细胞的类型和特性,建立健康人体细胞参考图;我们将通过它了解人体如何构成、人类为何生病;我们将拥有一个最新的复杂生物学模型,帮助我们提高研发的速度。

毫无疑问,我们会看到something new。

上周的《自然》杂志上,博德研究所(Broad Institute)研究团队发布了首个小肠细胞图谱!研究基于单细胞RNA测序(scRNA-seq),测定了共计53193个来自小鼠肠道和类肠器官细胞的表达图谱,带来了许多与以往认知不同的新发现,可谓是第一本立体的“小肠百科全书”。

〇划重点

①确定了小肠所有已知细胞、特定细胞亚群和罕见细胞的基因表达特征

②颠覆对肠内激素分泌的传统认知,重新定义了肠内分泌细胞的分类

③发现了两种新的簇细胞(Tuft Cell)亚型,分别与免疫和神经发育有关

④描述了小肠细胞对寄生虫和微生物感染感染模型,将为肠道疾病研究提供理论模型

研究团队由国际人类细胞图谱计划组委会联合主席、MIT生物学教授Aviv Regev博士,和马萨诸塞州综合医院消化科主任、临床胃肠病学家Ramnik Xavier博士领导。


本文通讯作者 Aviv Regev(左)和 Ramnik Xavier(右)

能够有如此开辟性的成果,还要得益于单细胞测序技术(scRNA-seq)。以往科学家们在研究细胞的时候,都是对一小块组织统一测序。这样得出的数据,不过是所有细胞的平均分,根本没办法体现每个细胞的“个性”。有很多虽然重要、但数量很少的RNA会被当成“最高分”或”最低分“去掉,根本进入不了科学家的视野。单细胞测序则允许科学家精确研究单个细胞的功能变化,每个细胞是什么样子根本就无所遁形!这项技术被《自然》杂志评为2013年年度技术。

“新技术给了我们机会,更详细地探究细胞和组织。”Aviv Regev博士这样说道,“新技术让我
们能够提出新的生物学问题,并审视过去的研究。” 


小肠细胞正在和寄生虫“战斗”

在详扒这本百科全书之前,奇点糕想先带大家回顾下小肠结构。

小肠是我们身体重要的消化器官,上接着胃下接着大肠,里面还居住着重要的房客肠道微生物。小肠有个十分特别的地方,它的内表面并不像一般的粘膜组织是光滑的,而是布满了“绒毛”,而且绒毛上还有更加微小的突起。这种特殊的结构使得小肠的内表面积一下扩大了六百倍,足足有200平方米!(奇点糕有点羡慕肠道菌了,住这么大的房子……哦,它们菌口也多,平衡了)

这么大的接触面积,使小肠有更多的空间去发挥功能。最基础的消化吸收就不说了,小肠同时还能分泌各种激素促进各种生理功能,甚至参加免疫反应。






小肠的结构

这么多的生理功能当然不是一种细胞能够实现的。小肠细胞家族很热闹,有负责营养吸收的肠上皮细胞(Enterocytes)、能分泌粘液保护其他成员的杯状细胞(Goblet cells)、分泌各种胃肠道激素的内分泌细胞(Enteroendocrine cells)、能产生抗菌肽的潘氏细胞(Paneth cells)、以及最近才走进我们视野的簇细胞(Tuft cells)等等。

在这次的研究中,研究者一口气分析了五万多个细胞,而且在前人研究发现的已知标志的基础上,继续寻找新的标志物,最终成功确定了各个类型细胞和它们在不同成熟阶段的特定表达标志,还成功描述了超级稀有的M细胞!有趣的是,小肠内的细胞分布并不是均匀的,不同类型的肠细胞在不同的区域发挥着不同的功能。例如,在靠近胃的区域,表达促进进食的饥饿素(ghrelin)[3]的细胞就更多;相反,靠近大肠区域的细胞则多是表达能控制食欲的YY肽[4]。


分析不同标志物观察到的细胞分布

利用这些数据,研究者发现了两种以前无法识别的簇细胞亚型。簇细胞是小肠内的一类能感受化学信号的细胞[5],最近有研究认为它们在防御寄生虫感染中有关键作用[6]。新发现的两种簇细胞亚型,其中一种能够表达生成素(Tslp,能促进免疫细胞成熟)和白细胞共同抗原CD45,另一种则与神经发育相关。这可是第一次在造血系统以外的细胞上发现CD45!

除此以外,研究者还提出了新的小肠内分泌细胞分类标准。以往科学家们认为,小肠内的一种内分泌细胞只能分泌一种激素。但是研究者发现,实际上这些细胞还是很多才多艺的,一种内分泌细胞实际上可以分泌多种激素,难怪以前有些研究对不上呢!他们根据分泌激素的种类,提出了新的分类法,为以后研究提供了更详细的理论依据。


纵轴为新分类细胞,横轴为所分泌激素,图注为原分类

拍完了小肠细胞的“证件照”,“生活照”也不能放过,毕竟人体可是动态的,小肠时刻要面对着外来病原体的威胁。研究者采用了沙门氏菌(Salmonella enterica)和多形螺旋线虫(Heligmosomoides polygyrus)两种经典模型,分别模拟了小肠细胞对病原菌和寄生虫的反应。

面对病原体的入侵,小肠细胞可算是用尽了全身力气抵抗。研究者观察到了一些保护基因表达的上调,多种抗菌肽的表达增加,原本不表达抗菌肽的细胞也无师自通地学会了这项技能。在感染过程中,小肠细胞的组成也有变化,包括潘氏细胞在内的一些细胞数量增加、干细胞和未成熟细胞数减少,这和以前的研究也是相符的[7]。部分细胞还会针对病原体,产生特异性的表达改变,这是从来没有被观察到的。


定位!无所遁形!

原本肉眼都看不见的细胞,现在一个一个清楚排列在眼前,我们能够看清楚它们的任何一个”小动作“,想想都觉得刺激!而且这种模型是动态的,可以用来测试各种生理、病理和药理过程,这对研究者来说是多么大的一个好消息啊!

“肠道上皮同时联系着免疫系统和肠道菌群,它是细胞反应的关键所在,了解肠道在健康和疾病情况下的生理反应是非常重要的。”本项研究的第一作者,博士后研究生Moshe Biton这样说道。

掌握了这些数据,研究者将会立刻开展更多的研究,包括在克罗恩病、结肠炎、胃肠癌、食物过敏等多种条件下,肠细胞基因表达和结构功能的变化,这将会让我们更加了解这些疾病,或许很快就会有应对它们的新方法出现了!

原始出处:Adam L. Haber, Moshe Biton,  Noga Rogel, et al. A single-cell survey of the small intestinal epithelium. Nature. 08 November 2017

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    2018-09-13 仁医06
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    2018-10-02 一叶知秋
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    2017-12-03 jyzxjiangqin

    小肠细胞的单细胞测序.

    0

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    2017-11-25 jyzxjiangqin

    科学家对数万个小肠细胞测序.

    0

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    2017-11-15 lyh994

    非常了不起的工作

    0

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    2017-11-15 刘煜

    谢谢分享.阅读

    0

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    2017-11-15 yjs木玉

    好好好好好好好好就

    0

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