Harnessing computational spatial omics to explore the spatial biology intricacies

IF 12.1 1区医学 Q1 ONCOLOGY

Seminars in cancer biology Pub Date : 2023-10-01 DOI:10.1016/j.semcancer.2023.06.006

Zhiyuan Yuan , Jianhua Yao

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引用次数: 2

Abstract

Spatially resolved transcriptomics (SRT) has unlocked new dimensions in our understanding of intricate tissue architectures. However, this rapidly expanding field produces a wealth of diverse and voluminous data, necessitating the evolution of sophisticated computational strategies to unravel inherent patterns. Two distinct methodologies, gene spatial pattern recognition (GSPR) and tissue spatial pattern recognition (TSPR), have emerged as vital tools in this process. GSPR methodologies are designed to identify and classify genes exhibiting noteworthy spatial patterns, while TSPR strategies aim to understand intercellular interactions and recognize tissue domains with molecular and spatial coherence. In this review, we provide a comprehensive exploration of SRT, highlighting crucial data modalities and resources that are instrumental for the development of methods and biological insights. We address the complexities and challenges posed by the use of heterogeneous data in developing GSPR and TSPR methodologies and propose an optimal workflow for both. We delve into the latest advancements in GSPR and TSPR, examining their interrelationships. Lastly, we peer into the future, envisaging the potential directions and perspectives in this dynamic field.

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利用计算空间组学探索空间生物学的复杂性

空间分辨转录组学（SRT）为我们理解复杂的组织结构开辟了新的维度。然而，这个快速扩展的领域产生了丰富多样的海量数据，这就需要进化复杂的计算策略来解开固有的模式。基因空间模式识别和组织空间模式识别是这一过程中的重要工具。GSPR方法旨在识别和分类表现出显著空间模式的基因，而TSPR策略旨在了解细胞间相互作用并识别具有分子和空间一致性的组织结构域。在这篇综述中，我们对SRT进行了全面的探索，强调了有助于开发方法和生物学见解的关键数据模式和资源。我们解决了在开发GSPR和TSPR方法时使用异构数据带来的复杂性和挑战，并提出了两者的最佳工作流程。我们深入研究了GSPR和TSPR的最新进展，研究了它们的相互关系。最后，我们展望未来，展望这一动态领域的潜在方向和前景。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Seminars in cancer biology 医学-肿瘤学

CiteScore

26.80

自引率

4.10%

发文量

347

审稿时长

15.1 weeks

期刊介绍： Seminars in Cancer Biology (YSCBI) is a specialized review journal that focuses on the field of molecular oncology. Its primary objective is to keep scientists up-to-date with the latest developments in this field. The journal adopts a thematic approach, dedicating each issue to an important topic of interest to cancer biologists. These topics cover a range of research areas, including the underlying genetic and molecular causes of cellular transformation and cancer, as well as the molecular basis of potential therapies. To ensure the highest quality and expertise, every issue is supervised by a guest editor or editors who are internationally recognized experts in the respective field. Each issue features approximately eight to twelve authoritative invited reviews that cover various aspects of the chosen subject area. The ultimate goal of each issue of YSCBI is to offer a cohesive, easily comprehensible, and engaging overview of the selected topic. The journal strives to provide scientists with a coordinated and lively examination of the latest developments in the field of molecular oncology.