Spatial transcriptomics and proteomics technologies for deconvoluting the tumor microenvironment,Biotechnology Journal

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Spatial transcriptomics and proteomics technologies for deconvoluting the tumor microenvironment
Biotechnology Journal ( IF 3.2 ) Pub Date : 2021-06-14 , DOI: 10.1002/biot.202100041
Nan Wang ₁ , Xia Li ₁ , Rongshui Wang ₁ , Zhiyong Ding ₁

Affiliation

The tumor microenvironment (TME) harbors heterogeneous contents and plays critical roles in tumorigenesis, metastasis, and drug resistance. Therefore, the deconvolution of the TME becomes increasingly essential to every aspect of cancer research and treatment. Novel spatially-resolved high-plex molecular profiling technologies have been emerging rapidly as powerful tools to obtain in-depth understanding from TME perspectives due to their capacity to allow high-plex protein and RNA profiling while keeping valuable spatial information. Based on our practical experience, we review a variety of available spatial proteogenomic technologies, including 10X Visium, GeoMx Digital Spatial Profiler (DSP), cyclic immunofluorescence-based CODEX and Multi-Omyx, mass spectrometry (MS)-based imaging mass spectrometry (IMS) and multiplex ion-beam imaging (MIBI). We also discuss FISSEQ, MERFISH, Slide-seq, and HDST, some of which may become commercially available in the near future. In particular, with our experience, we elaborate on DSP for spatial proteogenomic profiling and discuss its unique features designed for immuno-oncology and propose anticipation towards its future direction. The emerging spatially technologies are rapidly reshaping the magnitude of our understanding of the TME.

中文翻译：

用于解卷积肿瘤微环境的空间转录组学和蛋白质组学技术

肿瘤微环境（TME）含有异质成分，在肿瘤发生、转移和耐药性中起着关键作用。因此，TME 的去卷积对于癌症研究和治疗的各个方面变得越来越重要。新型空间分辨高密度分子分析技术已迅速成为从 TME 角度获得深入理解的强大工具，因为它们能够在保持有价值的空间信息的同时进行高密度蛋白质和 RNA 分析。根据我们的实践经验，我们回顾了各种可用的空间蛋白质基因组学技术，包括 10X Visium、GeoMx 数字空间分析器 (DSP)、基于循环免疫荧光的 CODEX 和 Multi-Omyx、基于质谱 (MS) 的成像质谱 (IMS) ) 和多重离子束成像 (MIBI)。我们还讨论了 FISSEQ、MERFISH、Slide-seq 和 HDST，其中一些可能在不久的将来上市。特别是，根据我们的经验，我们详细阐述了用于空间蛋白质基因组学分析的 DSP，并讨论了其为免疫肿瘤学设计的独特功能，并对其未来方向提出了展望。新兴的空间技术正在迅速重塑我们对 TME 的理解程度。

更新日期：2021-06-14

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