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

Michal Slyper; Caroline B.M. Porter; Orr Ashenberg; Julia Waldman; Eugene Drokhlyansky; Isaac Wakiro; Christopher Smillie; Gabriela Smith-Rosario; Jingyi Wu; Danielle Dionne; Sébastien Vigneau; Judit Jané-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. Suvà; 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

doi:10.1038/s41591-020-0844-1

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

Michal Slyper, Caroline B.M. Porter, Orr Ashenberg, Julia Waldman, Eugene Drokhlyansky, Isaac Wakiro, Christopher Smillie, Gabriela Smith-Rosario, Jingyi Wu, Danielle Dionne, Sébastien Vigneau, Judit Jané-Valbuena, Timothy L. Tickle, Sara Napolitano, Mei Ju Su, Anand G. Patel, Asa Karlstrom, Simon Gritsch, Masashi Nomura, Avinash WaghraySatyen 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. Suvà, 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

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

357 Scopus citations

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.

Original language	English
Pages (from-to)	792-802
Number of pages	11
Journal	Nature Medicine
Volume	26
Issue number	5
DOIs	https://doi.org/10.1038/s41591-020-0844-1
State	Published - 1 May 2020
Externally published	Yes

Bibliographical note

Publisher Copyright:
© 2020, The Author(s).

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This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1038/s41591-020-0844-1

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Slyper, M., Porter, C. B. M., Ashenberg, O., Waldman, J., Drokhlyansky, E., Wakiro, I., Smillie, C., Smith-Rosario, G., Wu, J., Dionne, D., Vigneau, S., Jané-Valbuena, J., Tickle, T. L., Napolitano, S., Su, M. J., Patel, A. G., Karlstrom, A., Gritsch, S., Nomura, M., ... Regev, A. (2020). A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors. Nature Medicine, 26(5), 792-802. https://doi.org/10.1038/s41591-020-0844-1

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title = "A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors",

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.",

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

note = "Publisher Copyright: {\textcopyright} 2020, The Author(s).",

year = "2020",

month = may,

day = "1",

doi = "10.1038/s41591-020-0844-1",

language = "אנגלית",

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Slyper, M, Porter, CBM, Ashenberg, O, Waldman, J, Drokhlyansky, E, Wakiro, I, Smillie, C, Smith-Rosario, G, Wu, J, Dionne, D, Vigneau, S, Jané-Valbuena, J, Tickle, TL, Napolitano, S, Su, MJ, Patel, AG, Karlstrom, A, Gritsch, S, Nomura, M, Waghray, A, Gohil, SH, Tsankov, AM, Jerby-Arnon, L, Cohen, O, Klughammer, J, Rosen, Y, Gould, J, Nguyen, L, Hofree, M, Tramontozzi, PJ, Li, B, Wu, CJ, Izar, B, Haq, R, Hodi, FS, Yoon, CH, Hata, AN, Baker, SJ, Suvà, ML, Bueno, R, Stover, EH, Clay, MR, Dyer, MA, Collins, NB, Matulonis, UA, Wagle, N, Johnson, BE, Rotem, A, Rozenblatt-Rosen, O & Regev, A 2020, 'A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors', Nature Medicine, vol. 26, no. 5, pp. 792-802. https://doi.org/10.1038/s41591-020-0844-1

TY - JOUR

T1 - A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

AU - Slyper, Michal

AU - Porter, Caroline B.M.

AU - Ashenberg, Orr

AU - Waldman, Julia

AU - Drokhlyansky, Eugene

AU - Wakiro, Isaac

AU - Smillie, Christopher

AU - Smith-Rosario, Gabriela

AU - Wu, Jingyi

AU - Dionne, Danielle

AU - Vigneau, Sébastien

AU - Jané-Valbuena, Judit

AU - Tickle, Timothy L.

AU - Napolitano, Sara

AU - Su, Mei Ju

AU - Patel, Anand G.

AU - Karlstrom, Asa

AU - Gritsch, Simon

AU - Nomura, Masashi

AU - Waghray, Avinash

AU - Gohil, Satyen H.

AU - Tsankov, Alexander M.

AU - Jerby-Arnon, Livnat

AU - Cohen, Ofir

AU - Klughammer, Johanna

AU - Rosen, Yanay

AU - Gould, Joshua

AU - Nguyen, Lan

AU - Hofree, Matan

AU - Tramontozzi, Peter J.

AU - Li, Bo

AU - Wu, Catherine J.

AU - Izar, Benjamin

AU - Haq, Rizwan

AU - Hodi, F. Stephen

AU - Yoon, Charles H.

AU - Hata, Aaron N.

AU - Baker, Suzanne J.

AU - Suvà, Mario L.

AU - Bueno, Raphael

AU - Stover, Elizabeth H.

AU - Clay, Michael R.

AU - Dyer, Michael A.

AU - Collins, Natalie B.

AU - Matulonis, Ursula A.

AU - Wagle, Nikhil

AU - Johnson, Bruce E.

AU - Rotem, Asaf

AU - Rozenblatt-Rosen, Orit

AU - Regev, Aviv

PY - 2020/5/1

Y1 - 2020/5/1

N2 - 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.

AB - 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.

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

Abstract

Bibliographical note

UN SDGs

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