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

By M. Slyper, C. Porter, Orr Ashenberg, Julia Waldman, Eugene Drokhlyansky, Isaac Wakiro, Chris S. Smillie, Gabriela Smith-Rosario, Jingyi Wu, Danielle Dionne and 40 more. Nature Medicine, 2019

607 citations recorded by the source corpus.

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. A set of ready-to-use tools for profiling fresh and frozen clinical tumor samples using scRNA-Seq and snRNA-Seq facilitates the implementation of single-cell technologies in clinical settings and the construction of single-cell tumor atlases.

Subfields: Cancer Research, Molecular Biology, Oncology

View Paper: https://www.semanticscholar.org/paper/7e304fed0bfed10b334c822994d896ca0ce45a15

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In Cancer Research

1. K. Polyak
2. Aviv Regev
3. Justin Guinney
4. Gad Getz
5. W.J. Greenleaf
6. S. Sen
7. J. Massagué
8. Lisa M. Coussens

In Molecular Biology

1. Aviv Regev
2. Garry P. Nolan
3. Dana Pe'er
4. K. Polyak
5. Anshul B Kundaje
6. Itsik Pe'er
7. F. Chen
8. R. Fulton

In Oncology

1. Lisa M. Coussens
2. J. Massagué
3. D. DeNardo
4. K. Polyak
5. Carlo C. Maley
6. K. Flaherty
7. Nikolaus Schultz
8. Garry P. Nolan

Citations in the corpus

• The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution (2020, positive): “HTAPP has developed a sc/snRNA-seq toolbox for systematic processing of various fresh and frozen tumor samples (Slyper et al., 2019) and a cloud analysis pipeline (Li et al.”