Tags

Type your tag names separated by a space and hit enter

A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors.
Nat Med. 2020 05; 26(5):792-802.NMed

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.

Links

PMC Free PDF

Authors+Show Affiliations

Slyper M
Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
Porter CBM
Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
Ashenberg O
Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
Waldman J
Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
Drokhlyansky E
Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
Wakiro I
Broad Institute of Harvard and MIT, Cambridge, MA, USA. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA.
Smillie C
Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
Smith-Rosario G
Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
Wu J
Broad Institute of Harvard and MIT, Cambridge, MA, USA. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA.
Dionne D
Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
Vigneau S
Broad Institute of Harvard and MIT, Cambridge, MA, USA. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA.
Jané-Valbuena J
Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
Tickle TL
Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
Napolitano S
Broad Institute of Harvard and MIT, Cambridge, MA, USA. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA.
Su MJ
Broad Institute of Harvard and MIT, Cambridge, MA, USA. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA.
Patel AG
Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA. Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA.
Karlstrom A
Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA.
Gritsch S
Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
Nomura M
Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
Waghray A
Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA.
Gohil SH
Broad Institute of Harvard and MIT, Cambridge, MA, USA. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
Tsankov AM
Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA. Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Jerby-Arnon L
Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
Cohen O
Broad Institute of Harvard and MIT, Cambridge, MA, USA. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA.
Klughammer J
Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
Rosen Y
Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
Gould J
Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
Nguyen L
Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
Hofree M
Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
Tramontozzi PJ
Division of Thoracic Surgery, Brigham and Women's Hospital, Boston, MA, USA.
Li B
Broad Institute of Harvard and MIT, Cambridge, MA, USA. Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
Wu CJ
Broad Institute of Harvard and MIT, Cambridge, MA, USA. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. Department of Internal Medicine, Brigham and Women's Hospital, Boston, MA, USA. Harvard Medical School, Boston, MA, USA.
Izar B
Broad Institute of Harvard and MIT, Cambridge, MA, USA. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA. Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, USA. Center for Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA. Ludwig Center for Cancer Research at Harvard, Boston, MA, USA. Melanoma Disease Center, Dana-Farber Cancer Institute, Boston, MA, USA. Columbia Center for Translational Immunology and Division of Hematology and Oncology, Columbia University Medical Center, New York, NY, USA.
Haq R
Broad Institute of Harvard and MIT, Cambridge, MA, USA. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
Hodi FS
Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. Melanoma Disease Center, Dana-Farber Cancer Institute, Boston, MA, USA.
Yoon CH
Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. Department of Surgical Oncology, Brigham and Women's Hospital, Boston, MA, USA.
Hata AN
Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
Baker SJ
Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA.
Suvà ML
Broad Institute of Harvard and MIT, Cambridge, MA, USA. Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
Bueno R
Division of Thoracic Surgery, Brigham and Women's Hospital, Boston, MA, USA.
Stover EH
Broad Institute of Harvard and MIT, Cambridge, MA, USA. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
Clay MR
Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA.
Dyer MA
Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA. Howard Hughes Medical Institute, Chevy Chase, MD, USA.
Collins NB
Broad Institute of Harvard and MIT, Cambridge, MA, USA. Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. Division of Pediatric Hematology and Oncology, Boston Children's Hospital, Boston, MA, USA.
Matulonis UA
Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
Wagle N
Broad Institute of Harvard and MIT, Cambridge, MA, USA. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA. Department of Internal Medicine, Brigham and Women's Hospital, Boston, MA, USA. Harvard Medical School, Boston, MA, USA.
Johnson BE
Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA.
Rotem A
Broad Institute of Harvard and MIT, Cambridge, MA, USA. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA.
Rozenblatt-Rosen O
Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA. orit@broadinstitute.org.
Regev A
Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA. aregev@broadinstitute.org. Howard Hughes Medical Institute, Chevy Chase, MD, USA. aregev@broadinstitute.org. Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. aregev@broadinstitute.org.

MeSH

AdultAlgorithmsAnimalsCell NucleusChildComputational BiologyFemaleFreezingGene Expression ProfilingGene Expression Regulation, NeoplasticGenomicsHumansMiceMice, KnockoutMice, NudeNeoplasmsRNA-SeqSequence Analysis, RNASingle-Cell AnalysisTumor Cells, CulturedExome Sequencing

Pub Type(s)

Evaluation Study
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

32405060

Citation

Slyper, Michal, et al. "A Single-cell and Single-nucleus RNA-Seq Toolbox for Fresh and Frozen Human Tumors." Nature Medicine, vol. 26, no. 5, 2020, pp. 792-802.
Slyper M, Porter CBM, Ashenberg O, et al. A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors. Nat Med. 2020;26(5):792-802.
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
Slyper M, et al. A Single-cell and Single-nucleus RNA-Seq Toolbox for Fresh and Frozen Human Tumors. Nat Med. 2020;26(5):792-802. PubMed PMID: 32405060.
* Article titles in AMA citation format should be in sentence-case
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, Y1 - 2020/05/11/ PY - 2019/08/13/received PY - 2020/03/20/accepted PY - 2020/5/15/entrez PY - 2020/5/15/pubmed PY - 2020/8/25/medline SP - 792 EP - 802 JF - Nature medicine JO - Nat Med VL - 26 IS - 5 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. SN - 1546-170X UR - https://www.unboundmedicine.com/medline/citation/32405060/A_single_cell_and_single_nucleus_RNA_Seq_toolbox_for_fresh_and_frozen_human_tumors_ DB - PRIME DP - Unbound Medicine ER -