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

Ruli Gao; Charissa Kim; Emi Sei; Theodoros Foukakis; Nicola Crosetto; Leong Keat Chan; Maithreyan Srinivasan; Hong Zhang; Funda Meric-Bernstam; Nicholas Navin

doi:10.1038/s41467-017-00244-w

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

Ruli Gao, Charissa Kim, Emi Sei, Theodoros Foukakis, Nicola Crosetto, Leong Keat Chan, Maithreyan Srinivasan, Hong Zhang, Funda Meric-Bernstam, Nicholas Navin^*

^*Corresponding author for this work

Biochemistry and Molecular Genetics

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

91 Scopus citations

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.

Original language	English (US)
Article number	228
Journal	Nature communications
Volume	8
Issue number	1
DOIs	https://doi.org/10.1038/s41467-017-00244-w
State	Published - Dec 1 2017

Funding

This work was supported by grants to N.N. from the Lefkofsky Family Foundation, NCI (1RO1CA169244-01), and from the American Cancer Society (129098-RSG-16-092-01- TBG). N.N. is a T.C. Hsu Endowed Scholar, AAAS Wachtel Scholar, and Andrew Sabin Family Fellow. The study was supported by grants from the Breast Cancer Research Foundation and the Swedish Cancer Society to T.F. and the Soderberg Fellowship to N.C. The work was also supported by a Sister Institution Network Grant (SINF) through the Global Access Program (GAP) at MD Anderson). The study also supported by a TL1 fellowship (TL1TR000369 and UL1TR000371) and American Legion Auxiliary fellowship to C.K., and a Susan Komen Postdoctoral Fellowship (PDF17487910) and AACR-John and Elizabeth Leonard Family Foundation Basic Cancer Research Fellowship (17-40-42-GAO) to R.G. We also thank support from the UT MD Anderson Cancer Center Sequencing Core grant (CA016672 SMF). We are also grateful to the employees of Wafergen Inc. for their support and collaboration and Adriana Paulucci for assistance with microscopy. We thank Aislyn Schalck for preparing illustrations that were used in the figures.

ASJC Scopus subject areas

General Chemistry
General Biochemistry, Genetics and Molecular Biology
General Physics and Astronomy

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10.1038/s41467-017-00244-w

Cite this

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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.",

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AU - Chan, Leong Keat

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

Abstract

Funding

ASJC Scopus subject areas

UN SDGs

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