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

被引：462

作者：

Slyper, Michal ^{[1
]}

Porter, Caroline B. M. ^{[1
]}

Ashenberg, Orr ^{[1
]}

Waldman, Julia ^{[1
]}

Drokhlyansky, Eugene ^{[1
]}

Wakiro, Isaac ^{[2
,3
,4
]}

Smillie, Christopher ^{[1
]}

Smith-Rosario, Gabriela ^{[1
]}

Wu, Jingyi ^{[2
,3
,4
]}

Dionne, Danielle ^{[1
]}

Vigneau, Sebastien ^{[2
,3
,4
]}

Jane-Valbuena, Judit ^{[1
]}

Tickle, Timothy L. ^{[1
]}

Napolitano, Sara ^{[2
,3
,4
]}

Su, Mei-Ju ^{[2
,3
,4
]}

Patel, Anand G. ^{[5
,6
]}

Karlstrom, Asa ^{[5
]}

Gritsch, Simon ^{[7
,8
,9
]}

Nomura, Masashi ^{[7
,8
,9
]}

Waghray, Avinash ^{[10
]}

Gohil, Satyen H. ^{[2
,3
]}

Tsankov, Alexander M. ^{[1
,25
]}

Jerby-Arnon, Livnat ^{[1
]}

Cohen, Ofir ^{[2
,3
,4
]}

Klughammer, Johanna ^{[1
]}

Rosen, Yanay ^{[1
]}

Gould, Joshua ^{[1
]}

Lan Nguyen ^{[1
]}

Hofree, Matan ^{[1
]}

Tramontozzi, Peter J. ^{[11
]}

Li, Bo ^{[2
,8
,12
]}

Wu, Catherine J. ^{[2
,3
,8
,13
]}

Izar, Benjamin ^{[2
,3
,4
,8
,14
,15
,16
,17
,26
,27
]}

Haq, Rizwan ^{[2
,3
]}

Hodi, F. Stephen ^{[3
,17
]}

Yoon, Charles H. ^{[3
,18
]}

Hata, Aaron N. ^{[8
,13
,18
,19
]}

Baker, Suzanne J. ^{[5
]}

Suva, Mario L. ^{[2
,7
,8
,9
]}

Bueno, Raphael ^{[11
]}

Stover, Elizabeth H. ^{[2
,3
]}

Clay, Michael R. ^{[20
]}

Dyer, Michael A. ^{[5
,21
]}

Collins, Natalie B. ^{[2
,22
,23
]}

Matulonis, Ursula A. ^{[3
]}

Wagle, Nikhil ^{[2
,3
,4
,8
,13
]}

Johnson, Bruce E. ^{[3
,4
]}

Rotem, Asaf ^{[2
,3
,4
]}

Rozenblatt-Rosen, Orit ^{[1
]}

Regev, Aviv ^{[1
,21
,24
]}

机构：

[1] Broad Inst MIT & Harvard, Klarman Cell Observ, Cambridge, MA 02142 USA

[2] Broad Inst MIT & Harvard, Cambridge, MA 02142 USA

[3] Dana Farber Canc Inst, Dept Med Oncol, Boston, MA 02115 USA

[4] Dana Farber Canc Inst, Ctr Canc Precis Med, Boston, MA 02115 USA

[5] St Jude Childrens Res Hosp, Dept Dev Neurobiol, 332 N Lauderdale St, Memphis, TN 38105 USA

[6] St Jude Childrens Res Hosp, Dept Oncol, 332 N Lauderdale St, Memphis, TN 38105 USA

[7] Massachusetts Gen Hosp, Dept Pathol, Boston, MA 02114 USA

[8] Harvard Med Sch, Boston, MA 02115 USA

[9] Massachusetts Gen Hosp, Canc Res Ctr, Boston, MA 02114 USA

[10] Massachusetts Gen Hosp, Ctr Regenerat Med, Boston, MA 02114 USA

[11] Brigham & Womens Hosp, Div Thorac Surg, 75 Francis St, Boston, MA 02115 USA

[12] Massachusetts Gen Hosp, Div Rheumatol Allergy & Immunol, Ctr Immunol & Inflammatory Dis, Boston, MA 02114 USA

[13] Brigham & Womens Hosp, Dept Internal Med, 75 Francis St, Boston, MA 02115 USA

[14] Harvard Med Sch, Lab Syst Pharmacol, Boston, MA 02115 USA

[15] Dana Farber Canc Inst, Ctr Immunol & Virol, Boston, MA 02115 USA

[16] Ludwig Ctr Canc Res Harvard, Boston, MA USA

[17] Dana Farber Canc Inst, Melanoma Dis Ctr, Boston, MA 02115 USA

[18] Brigham & Womens Hosp, Dept Surg Oncol, 75 Francis St, Boston, MA 02115 USA

[19] Massachusetts Gen Hosp, Dept Med, Boston, MA 02114 USA

[20] St Jude Childrens Res Hosp, Dept Pathol, 332 N Lauderdale St, Memphis, TN 38105 USA

[21] Howard Hughes Med Inst, Chevy Chase, MD 20815 USA

[22] Dana Farber Canc Inst, Dept Pediat Oncol, Boston, MA 02115 USA

[23] Boston Childrens Hosp, Div Pediat Hematol & Oncol, Boston, MA USA

[24] MIT, Dept Biol, Koch Inst Integrat Canc Res, Cambridge, MA 02139 USA

[25] Icahn Sch Med Mt Sinai, New York, NY 10029 USA

[26] Columbia Univ, Med Ctr, Columbia Ctr Translat Immunol, New York, NY USA

[27] Columbia Univ, Med Ctr, Div Hematol & Oncol, New York, NY USA

来源：

NATURE MEDICINE | 2020年 / 26卷 / 05期

基金：

美国国家卫生研究院;

关键词：

CANCER; DISSOCIATION; EXPRESSION;

D O I：

10.1038/s41591-020-0844-1

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

070307 [化学生物学]; 071010 [生物化学与分子生物学];

摘要：

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.

引用

页码：792 / +

页数：28

共 45 条

[1]

Prospective identification of tumorigenic breast cancer cells [J].

Al-Hajj, M ;

Wicha, MS ;

Benito-Hernandez, A ;

Morrison, SJ ;

Clarke, MF .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2003, 100 (07) :3983-3988

[2]

[Anonymous], 2019, InferCNV of the trinity CTAT project. 1.14.2

[3]

Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage [J].

Aran, Dvir ;

Looney, Agnieszka P. ;

Liu, Leqian ;

Wu, Esther ;

Fong, Valerie ;

Hsu, Austin ;

Chak, Suzanna ;

Naikawadi, Ram P. ;

Wolters, Paul J. ;

Abate, Adam R. ;

Butte, Atul J. ;

Bhattacharya, Mallar .

NATURE IMMUNOLOGY, 2019, 20 (02) :163-+

[4]

Single-nucleus and single-cell transcriptomes compared in matched cortical cell types [J].

Bakken, Trygve E. ;

Hodge, Rebecca D. ;

Miller, Jeremy A. ;

Yao, Zizhen ;

Thuc Nghi Nguyen ;

Aevermann, Brian ;

Barkan, Eliza ;

Bertagnolli, Darren ;

Casper, Tamara ;

Dee, Nick ;

Garren, Emma ;

Goldy, Jeff ;

Graybuck, Lucas T. ;

Kroll, Matthew ;

Lasken, Roger S. ;

Lathia, Kanan ;

Parry, Sheana ;

Rimorin, Christine ;

Scheuermann, Richard H. ;

Schork, Nicholas J. ;

Shehata, Soraya I. ;

Tieu, Michael ;

Phillips, John W. ;

Bernard, Amy ;

Smith, Kimberly A. ;

Zeng, Hongkui ;

Lein, Ed S. ;

Tasic, Bosiljka .

PLOS ONE, 2018, 13 (12)

[5]

Unravelling biology and shifting paradigms in cancer with single-cell sequencing [J].

Baslan, Timour ;

Hicks, James .

NATURE REVIEWS CANCER, 2017, 17 (09) :557-569

[6]

CONTROLLING THE FALSE DISCOVERY RATE - A PRACTICAL AND POWERFUL APPROACH TO MULTIPLE TESTING [J].

BENJAMINI, Y ;

HOCHBERG, Y .

JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY, 1995, 57 (01) :289-300

[7]

Integrating single-cell transcriptomic data across different conditions, technologies, and species [J].

Butler, Andrew ;

Hoffman, Paul ;

Smibert, Peter ;

Papalexi, Efthymia ;

Satija, Rahul .

NATURE BIOTECHNOLOGY, 2018, 36 (05) :411-+

[8]

An Immune Atlas of Clear Cell Renal Cell Carcinoma [J].

Chevrier, Stephane ;

Levine, Jacob Harrison ;

Zanotelli, Vito Riccardo Tomaso ;

Silina, Karina ;

Schulz, Daniel ;

Bacac, Marina ;

Ries, Carola Hermine ;

Ailles, Laurie ;

Jewett, Michael Alexander Spencer ;

Moch, Holger ;

van den Broek, Maries ;

Beisel, Christian ;

Stadler, Michael Beda ;

Gedye, Craig ;

Reis, Bernhard ;

Pe'er, Dana ;

Bodenmiller, Bernd .

CELL, 2017, 169 (04) :736-749

[9]

Cancer transcriptome profiling at the juncture of clinical translation [J].

Cieslik, Marcin ;

Chinnaiyan, Arul M. .

NATURE REVIEWS GENETICS, 2018, 19 (02) :93-109

[10]

Drokhlyansky E., 2019, biorxiv, P746743, DOI [DOI 10.1101/746743V4, 10.1101/746743v4]

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