Carstens Julienne L, Krishnan Santhoshi N, Rao Arvind, Sorace Anna G, Seeley Erin H, Ferri-Borgogno Sammy, Burks Jared K
Department of Medicine, Division of Hematology & Oncology, University of Alabama at Birmingham, Birmingham, AL, 35233, USA.
O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, 35233, USA.
Nat Rev Methods Primers. 2024;4(1). doi: 10.1038/s43586-024-00330-6. Epub 2024 Aug 1.
Much like solving a game of Clue, understanding physiological mysteries involves answering who, what, when, and where. Multi-omics approaches delve into cellular and molecular identities (the who and what), while longitudinal data collection addresses the when. Spatial dimensions address the where. This Primer discusses current technologies enabling quantification across biological scales, emphasizing the importance of retaining the spatial dimension of that data. We outline experimental design considerations, including targeted versus untargeted approaches, sample types, biological scale, and four main classes of molecule detection. Spatial analytics are explored, covering questioning approaches, analytical platforms, image segmentation and sampling. Example applications, reproducibility considerations, limitations and our outlook for the future are provided. Our goal is to unite spatial platforms and biological scales that not commonly brought together to encourage collaboration and innovation between diverse biological fields, offering a conceptional framework and an apples-to-apples comparison for understanding major technologies to foster cross-disciplinary dialogue.
就像解开一场《妙探寻凶》游戏一样，理解生理奥秘涉及回答谁、什么、何时以及何地的问题。多组学方法深入探究细胞和分子身份（即谁和什么），而纵向数据收集解决何时的问题。空间维度解决何地的问题。本入门指南讨论了当前能够跨生物尺度进行量化的技术，强调了保留数据空间维度的重要性。我们概述了实验设计考量，包括靶向与非靶向方法、样本类型、生物尺度以及四类主要的分子检测。探讨了空间分析，涵盖提问方法、分析平台、图像分割和采样。提供了示例应用、可重复性考量、局限性以及我们对未来的展望。我们的目标是将通常未结合在一起的空间平台和生物尺度统一起来，以鼓励不同生物领域之间的合作与创新，提供一个概念框架以及一个同类比较，以理解主要技术，促进跨学科对话。
