寄生虫如何发展和生存，以及他们如何刺激或调节宿主免疫反应，对于理解疾病病理学和设计新的控制策略至关重要。微阵列分析和大规模RNA测序为基因表达提供了丰富的数据，揭示了寄生虫在不同的生命周期阶段中发育的基因表达和宿主细胞对感染的响应。这些技术使得整个生物体或宿主组织的基因表达得以详细研究，但并未考虑不同类型或发育阶段细胞之间的异质性，也未考虑这些细胞的空间组织结构。单细胞RNA测序为在个体细胞层面上聚焦研究寄生虫生物学和宿主免疫提供了新的维度。在这里，我们回顾了单细胞RNA测序在建立多细胞螺旋体基因表达细胞图谱以及探索涉及寄生虫免疫和组织修复的个别宿主细胞类型的扩张和分子表达方面的应用。在体内研究宿主寄生虫互动具有挑战性，最后我们简要讨论了器官样本（干细胞衍生的小组织）的应用，以在局部层面上研究宿主寄生虫互动，并作为研究体外寄生虫发育的潜在系统。器官样本技术及其应用已经迅速发展，目前所进行的精细研究支持使用器官样本作为研究螺旋体寄生虫的体外替代系统。 版权所有 © 2023 作者。由Elsevier Ltd.出版。 保留所有权利。

How parasites develop and survive, and how they stimulate or modulate host immune responses are important in understanding disease pathology and for the design of new control strategies. Microarray analysis and bulk RNA sequencing have provided a wealth of data on gene expression as parasites develop through different life-cycle stages and on host cell responses to infection. These techniques have enabled gene expression in the whole organism or host tissue to be detailed, but do not take account of the heterogeneity between cells of different types or developmental stages, nor the spatial organisation of these cells. Single-cell RNA-seq (scRNA-seq) adds a new dimension to studying parasite biology and host immunity by enabling gene profiling at the individual cell level. Here we review the application of scRNA-seq to establish gene expression cell atlases for multicellular helminths and to explore the expansion and molecular profile of individual host cell types involved in parasite immunity and tissue repair. Studying host-parasite interactions in vivo is challenging and we conclude this review by briefly discussing the applications of organoids (stem-cell derived mini-tissues) to examine host-parasite interactions at the local level, and as a potential system to study parasite development in vitro. Organoid technology and its applications have developed rapidly, and the elegant studies performed to date support the use of organoids as an alternative in vitro system for research on helminth parasites.Copyright © 2023 The Author(s). Published by Elsevier Ltd.. All rights reserved.