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Nat Commun. 2017 Aug 9;8(1):228. doi: 10.1038/s41467-017-00244-w.

Nanogrid single-nucleus RNA sequencing reveals phenotypic diversity in breast cancer.

Author information

1
Department of Genetics, UT MD Anderson Cancer Center, Houston, TX, 77030, USA.
2
Graduate School of Biological Sciences, UT MD Anderson Cancer Center, Houston, TX, 77030, USA.
3
Department of Oncology-Pathology, Karolinska Institutet, 171 76, Stockholm, Sweden.
4
Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77, Stockholm, Sweden.
5
Wafergen Biosystems, Inc, 34700 Campus Drive, Fremont, CA, 94555, USA.
6
Department of Pathology, UT MD Anderson Cancer Center, Houston, TX, 77030, USA.
7
Department of Investigational Cancer Therapeutics, UT MD Anderson Cancer Center, Houston, TX, 77030, USA.
8
Department of Genetics, UT MD Anderson Cancer Center, Houston, TX, 77030, USA. nnavin@mdanderson.org.
9
Graduate School of Biological Sciences, UT MD Anderson Cancer Center, Houston, TX, 77030, USA. nnavin@mdanderson.org.

Abstract

Single cell RNA sequencing has emerged as a powerful tool for resolving transcriptional diversity in tumors, but is limited by throughput, cost and the ability to process archival frozen tissue samples. Here we develop a high-throughput 3' single-nucleus RNA sequencing approach that combines nanogrid technology, automated imaging, and cell selection to sequence up to ~1800 single nuclei in parallel. We compare the transcriptomes of 485 single nuclei to 424 single cells in a breast cancer cell line, which shows a high concordance (93.34%) in gene levels and abundance. We also analyze 416 nuclei from a frozen breast tumor sample and 380 nuclei from normal breast tissue. These data reveal heterogeneity in cancer cell phenotypes, including angiogenesis, proliferation, and stemness, and a minor subpopulation (19%) with many overexpressed cancer genes. Our studies demonstrate the utility of nanogrid single-nucleus RNA sequencing for studying the transcriptional programs of tumor nuclei in frozen archival tissue samples.Single cell RNA sequencing is a powerful tool for understanding cellular diversity but is limited by cost, throughput and sample preparation. Here the authors use nanogrid technology with integrated imaging to sequence thousands of cancer nuclei in parallel from fresh or frozen tissue.

PMID:
28794488
PMCID:
PMC5550415
DOI:
10.1038/s41467-017-00244-w
[Indexed for MEDLINE]
Free PMC Article

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