Three-dimensional single-cell imaging for the analysis of RNA and protein expression in intact tumour biopsies
Three-dimensional single-cell imaging for the analysis of RNA and protein expression in intact tumour biopsies
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DOI：
10.1038/s41551-020-0576-z
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发表时间：
2020-06
影响因子：
28.1
通讯作者：
N. Tanaka;Shigeaki Kanatani;D. Kaczyńska;K. Fukumoto;L. Louhivuori;Tomohiro Mizutani;O. Kopper;Pauliina Kronqvist;S. Robertson;C. Lindh;L. Kis;R. Pronk;N. Niwa;K. Matsumoto;M. Oya;A. Miyakawa;Anna Falk;J. Hartman;C. Sahlgren;H. Clevers;P. Uhlén
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文献类型：
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作者：
N. Tanaka;Shigeaki Kanatani;D. Kaczyńska;K. Fukumoto;L. Louhivuori;Tomohiro Mizutani;O. Kopper;Pauliina Kronqvist;S. Robertson;C. Lindh;L. Kis;R. Pronk;N. Niwa;K. Matsumoto;M. Oya;A. Miyakawa;Anna Falk;J. Hartman;C. Sahlgren;H. Clevers;P. Uhlén
肿瘤样本的显微镜分析通常在固定的、薄切片的和蛋白质标记的组织上进行。然而，这些检查不能揭示肿瘤复杂的三维结构，也不能检测异常转录本。在这里，我们报告了一种方法，我们命名为DIIFCO（用于诊断原位免疫荧光标记的清除癌样本），用于完整肿瘤体积和类器官中rna和蛋白质的多模态体积成像。我们使用DIIFCO在单细胞分辨率上对多种癌症组织中不同编码rna和非编码rna的表达进行了空间分析。定量单细胞分析发现了肿瘤干细胞样细胞的空间壁龛，并表明这种壁龛在三阴性乳腺癌组织中以更高的密度存在。改进的分子表型和癌症的组织病理学诊断可能导致新的见解到肿瘤患者的生物学。
Microscopy analysis of tumour samples is commonly performed on fixed, thinly sectioned and protein-labelled tissues. However, these examinations do not reveal the intricate three-dimensional structures of tumours, nor enable the detection of aberrant transcripts. Here, we report a method, which we name DIIFCO (for diagnosing in situ immunofluorescence-labelled cleared oncosamples), for the multimodal volumetric imaging of RNAs and proteins in intact tumour volumes and organoids. We used DIIFCO to spatially profile the expression of diverse coding RNAs and non-coding RNAs at the single-cell resolution in a variety of cancer tissues. Quantitative single-cell analysis revealed spatial niches of cancer stem-like cells, and showed that the niches were present at a higher density in triple-negative breast cancer tissue. The improved molecular phenotyping and histopathological diagnosis of cancers may lead to new insights into the biology of tumours of patients.