小柯机器人

切换到桌面版
新单细胞工具可用于新鲜和冷冻人类肿瘤分析
2020-05-14 12:37
来源：小柯机器人

美国麻省理工学院Aviv Regev、Orit Rozenblatt-Rosen等研究人员，合作开发了新单细胞工具可用于新鲜和冷冻人类肿瘤的分析。这一研究成果发表在2020年5月11日的《自然—医学》上。

研究人员开发了系统型工具，即分别使用单细胞RNA-Seq（scRNA-Seq）和单核RNA-Seq（snRNA-Seq）对新鲜和冷冻的临床肿瘤样品进行分析。研究人员分析了23个标本中40个样品的216,490个细胞和细胞核，这些标本涵盖了八种不同组织和样品特征的肿瘤类型。
 
研究人员通过细胞和细胞核质量、恢复率和细胞组成评估了方案。匹配样品中的scRNA-Seq和snRNA-Seq可得到相同的细胞类型，但比例不同。
 
这一工作为广泛的肿瘤研究提供了指导，包括从其他肿瘤工具中测试和选择方法的标准，从而为绘制肿瘤图谱铺平了道路。
 
据了解，单细胞基因组学对于绘制肿瘤生态系统至关重要。尽管单细胞RNA-Seq（scRNA-Seq）可以分析从新鲜肿瘤中分离的细胞中的RNA，但仍需要单核RNA-Seq（snRNA-Seq）来分析冷冻或难分离的肿瘤。每一种都需要针对不同的组织和肿瘤类型进行定制，这为采用提供了障碍。
 
附：英文原文

Title: A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

Author: Michal Slyper, Caroline B. M. Porter, Orr Ashenberg, Julia Waldman, Eugene Drokhlyansky, Isaac Wakiro, Christopher Smillie, Gabriela Smith-Rosario, Jingyi Wu, Danielle Dionne, Sbastien Vigneau, Judit Jan-Valbuena, Timothy L. Tickle, Sara Napolitano, Mei-Ju Su, Anand G. Patel, Asa Karlstrom, Simon Gritsch, Masashi Nomura, Avinash Waghray, Satyen H. Gohil, Alexander M. Tsankov, Livnat Jerby-Arnon, Ofir Cohen, Johanna Klughammer, Yanay Rosen, Joshua Gould, Lan Nguyen, Matan Hofree, Peter J. Tramontozzi, Bo Li, Catherine J. Wu, Benjamin Izar, Rizwan Haq, F. Stephen Hodi, Charles H. Yoon, Aaron N. Hata, Suzanne J. Baker, Mario L. Suv, Raphael Bueno, Elizabeth H. Stover, Michael R. Clay, Michael A. Dyer, Natalie B. Collins, Ursula A. Matulonis, Nikhil Wagle, Bruce E. Johnson, Asaf Rotem, Orit Rozenblatt-Rosen, Aviv Regev

Issue&Volume: 2020-05-11

Abstract: Single-cell genomics is essential to chart tumor ecosystems. Although single-cell RNA-Seq (scRNA-Seq) profiles RNA from cells dissociated from fresh tumors, single-nucleus RNA-Seq (snRNA-Seq) is needed to profile frozen or hard-to-dissociate tumors. Each requires customization to different tissue and tumor types, posing a barrier to adoption. Here, we have developed a systematic toolbox for profiling fresh and frozen clinical tumor samples using scRNA-Seq and snRNA-Seq, respectively. We analyzed 216,490 cells and nuclei from 40 samples across 23 specimens spanning eight tumor types of varying tissue and sample characteristics. We evaluated protocols by cell and nucleus quality, recovery rate and cellular composition. scRNA-Seq and snRNA-Seq from matched samples recovered the same cell types, but at different proportions. Our work provides guidance for studies in a broad range of tumors, including criteria for testing and selecting methods from the toolbox for other tumors, thus paving the way for charting tumor atlases.

DOI: 10.1038/s41591-020-0844-1

Source: https://www.nature.com/articles/s41591-020-0844-1

Nature Medicine：《自然—医学》，创刊于1995年。隶属于施普林格·自然出版集团，最新IF：87.241
官方网址：https://www.nature.com/nm/
投稿链接：https://mts-nmed.nature.com/cgi-bin/main.plex


本期文章：《自然—医学》：Online/在线发表

分享到:

0