Understanding cell–cell interactions is critical in most, if not all, research fields in biology. Nevertheless, studying intercellular crosstalk in vivo remains a relevant challenge, due mainly to the difficulty in spatially locating the surroundings of particular cells in the tissue. Cherry-niche is a powerful new method that enables cells expressing a fluorescent protein to label their surrounding cells, facilitating their specific isolation from the whole tissue as live cells. We previously applied Cherry-niche in cancer research to study the tumor microenvironment (TME) in metastasis. Here we describe how to generate cancer cells with the ability to label their neighboring cells (within the tumor niche) by transferring a liposoluble fluorescent protein. Live niche cells can be isolated and compared with cells distant from the tumor bulk, using a variety of ex vivo approaches. As previously shown, this system has the potential to identify novel components in the TME and improve our understanding of their local interactions. Importantly, Cherry-niche can also be applied to study potential cell–cell interactions due to in vivo proximity in research fields beyond cancer. This protocol takes 2–3 weeks to generate the labeling cells and 1–2 weeks to test their labeling ability.

了解细胞与细胞之间的相互作用对于大多数（如果不是全部）生物学研究领域至关重要。然而，研究体内细胞间串扰仍然是一个相关的挑战，主要是由于在空间上定位组织中特定细胞周围环境的困难。 Cherry-niche 是一种强大的新方法，使表达荧光蛋白的细胞能够标记其周围的细胞，从而促进它们作为活细胞从整个组织中特异性分离。我们之前在癌症研究中应用了Cherry-niche来研究转移中的肿瘤微环境（TME）。在这里，我们描述了如何通过转移脂溶性荧光蛋白来产生能够标记其邻近细胞（在肿瘤微环境内）的癌细胞。可以使用各种离体方法分离活的微环境细胞并与远离肿瘤块的细胞进行比较。如前所述，该系统有潜力识别 TME 中的新成分，并提高我们对它们局部相互作用的理解。重要的是，Cherry-niche 还可以用于研究潜在的细胞间相互作用，因为在癌症以外的研究领域中体内接近。该方案需要 2-3 周来生成标记细胞，并需要 1-2 周来测试其标记能力。