The immune system comprises diverse specialized cell types that cooperate to defend the host against a wide range of pathogenic threats. Recent advancements in single-cell and spatial multi-omics technologies provide rich information about the molecular state of immune cells. Here, we review how the integration of single-cell and spatial multi-omics data with prior knowledge—gathered from decades of detailed biochemical studies—allows us to obtain functional insights, focusing on gene regulatory processes and cell–cell interactions. We present diverse applications in immunology and critically assess underlying assumptions and limitations. Finally, we offer a perspective on the ongoing technological and algorithmic developments that promise to get us closer to a systemic mechanistic understanding of the immune system.

免疫系统由多种特殊细胞类型组成，它们合作保护宿主免受多种病原体威胁。单细胞和空间多组学技术的最新进展提供了有关免疫细胞分子状态的丰富信息。在这里，我们回顾了如何将单细胞和空间多组学数据与从数十年的详细生化研究中收集到的先验知识相结合，使我们能够获得功能性见解，重点关注基因调控过程和细胞与细胞的相互作用。我们提出了免疫学中的多种应用，并严格评估了潜在的假设和局限性。最后，我们提供了对正在进行的技术和算法发展的看法，这些发展有望使我们更接近对免疫系统的系统机制的理解。