Using planarians and single cell transcriptomics to study cell type evolution

动物和其他多细胞生物是由细胞组成的，这些细胞可以分为不同的“细胞类型”。细胞类型在进化过程中通常是高度保守的：例如，所有两侧对称的动物似乎都有肌肉细胞。这些细胞似乎是从它们最后一个共同祖先的细胞类型进化而来的。这是由它们的结构成分之间的相似性以及它们共同的基因调控所支持的。在大多数动物中，不仅肌肉，神经元、表皮和其他细胞类型似乎都是保守的，然而，我们也知道，有些细胞类型在某些组中没有明显的等价物。例如，脊椎动物免疫细胞（例如B细胞或T细胞）的同源物难以在非脊椎动物类型中鉴定。这种细胞类型的多样性是如何在进化过程中出现的？所有动物都有相同的细胞类型吗？或者，新的细胞类型在进化中频繁出现吗？细胞类型是仅在门之间不同，还是在同一门内也不同？已经提出了几种细胞类型进化的模型。例如，细胞类型可能由于原始细胞类型的复制而出现。然后，其中一个复制的类型专注于不同的功能，而另一个保持原始功能。这方面的一个描述的例子是鱼类中的一种电感受器细胞，它已经从毛细胞多样化。其他作者提出，一组新基因的新表达可以导致新细胞类型的产生。例如，细胞可以在压力下表达一些基因以实现新的功能，但是如果这种表达变得不依赖于压力，它就会产生一种新的细胞类型。最终，细胞类型进化和新细胞类型出现的机制在很大程度上是未知的。这主要是由于缺乏对他们进行剖析的技术。细胞类型通常通过标记（蛋白质或RNA）来识别，但这些在许多物种中是未知的。因此，细胞类型的比较一直极具挑战性。然而，近年来，一种称为单细胞转录组学（scRNA-seq）的新技术使我们能够研究细胞的基因表达谱，从而通过无偏数学方法对细胞类型进行分类。使用scRNA-seq，我们可以对数千个单个细胞的单个mRNA进行测序。这使我们能够将它们分类，因为它们表达不同的mRNA。单细胞转录组学已经应用于广泛的动物，因此将彻底改变我们对细胞类型进化的理解。即使利用单细胞转录组学方法，比较高度不同的物种（即来自不同动物群体）也是具有挑战性的，因为纯粹的系统发育距离阻碍了跨物种等同基因的鉴定。为了开始揭开细胞类型进化之谜，我建议比较密切相关的物种。这是一种很有前途的方法，可以首先开发细胞类型的计算比较，然后了解物种之间的差异。我们预计它们将共享大量的细胞类型，这将使我们能够微调用于比较的数学算法。Planarians是进行这项研究的一个特殊模型，因为它们可以不断产生所有成年细胞类型。因此，在这里，我建议通过scRNA-seq研究一组涡虫物种，然后确定它们共享的细胞类型，以及任何谱系特异性细胞类型，并通过功能研究分析它们的差异。然后，我们将研究相似性，并通过抑制它们背后的基因来剖析差异。这将照亮研究其他动物群体中细胞类型进化的方式，并导致对细胞类型的理解，这是所有多细胞生物的基石。

Animals and other multicellular organisms are made of cells that can be classified into different "cell types". Often cell types are deeply conserved in evolution: for instance, all bilaterian animals seem to have muscle cells. These seem to have evolved from a cell type present in their last common ancestor. This is supported by the resemblance between their structural components but also their common gene regulation. Not only muscle, but also neurons, epidermis and other cell types seem to be conserved in most animals.However, we also know that there are cell types in some groups with no obvious equivalent in others. For instance, homologues of vertebrate immune cells (e.g. B cells or T cells) are difficult to identify in non-vertebrate types. How did this diversity of cell types emerge across evolution? Do all animals have the same cell types? Alternatively, do new cell types arise frequently in evolution? Do cell types vary only across phyla, or also within the same phylum?Several models of cell type evolution have been proposed. For instance, cell types could arise due to duplication of an original cell type. Then, one of the duplicated types specialises in a different function, while the other keeps the original function. A described example of this are a type of electroreceptor cells in fish that has diversified from hair cells. Other authors propose that novel expression of a new group of genes can lead to the creation of novel cell types. For instance, cells could express some genes under stress to enable new functions, but then if this expression becomes independent of stress it gives rise to a new cell type. Ultimately, the mechanisms by which cell types evolve and new cell types emerge are largely unknown. This is primarily due to a lack of techniques to profile them. Cell types are typically identified by markers (protein or RNA), but these are unknown in many species. Thus, cell type comparisons have been extremely challenging. In recent years, however, a novel technique called single cell transcriptomics (scRNA-seq) has allowed us to study the gene expression profiles of cells, enabling their classification in cell types by unbiased mathematical approaches. Using scRNA-seq we can sequence individual mRNAs, for thousands of individual cells. This allows us to classify them in types, since they express different mRNAs. Single-cell transcriptomics has already been applied to a broad range of animals and will therefore revolutionise our understanding of cell type evolution.Even harnessing single-cell transcriptomics methods, comparing highly divergent species (i.e. from different animal groups) is challenging, due to the sheer phylogenetic distance that hinders the identification of genes that are equivalent across species. To begin to address the mystery of cell type evolution, I propose to compare closely related species. This is a promising way to first develop the computational comparison of cell types to then understand differences from species to species. We expect that they will share a large set of cell types, and this will allow us to fine tune the mathematical algorithms used for comparison. Planarians are an exceptional model to perform this research since they can constantly generate all adult cell types. Thus, here I propose to study by scRNA-seq a collection of planarian species, to then identify their shared cell types, as well as any lineage specific cell type, and analyse their differences by functional studies. We will then study the similarities and dissect the differences by inhibiting the genes that underlie them. This will light the way of studying cell type evolution in other animal groups and lead to an understanding of cell types, the building blocks of all multicellular organisms.