Pixelated spatial gene expression analysis from tissue

A. Ganguli; A. Ornob; N. Spegazzini; Y. Liu; G. Damhorst; T. Ghonge; B. Thornton; C. J. Konopka; W. Dobrucki; S. E. Clare; R. Bhargava; A. M. Smith; F. Kosari; R. Bashir

doi:10.1038/s41467-017-02623-9

Pixelated spatial gene expression analysis from tissue

A. Ganguli, A. Ornob, N. Spegazzini, Y. Liu, G. Damhorst, T. Ghonge, B. Thornton, C. J. Konopka, W. Dobrucki, S. E. Clare, R. Bhargava, A. M. Smith, F. Kosari^*, R. Bashir

^*Corresponding author for this work

Surgery, Breast Surgery Division

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

18 Scopus citations

Abstract

Here, we present a technique that performs on-chip picoliter real-time reverse transcriptase loop mediated isothermal amplification (RT-LAMP) reactions on a histological tissue section without any analyte purification while preserving the native spatial location of the nucleic acid molecules. We demonstrate this method by amplifying TOP2A messenger RNA (mRNA) in a prostate cancer xenograft with 100 μm spatial resolution and by visualizing the variation in threshold time of amplification across the tissue. The on-chip reaction was validated by mRNA fluorescence in situ hybridization (mFISH) from cells in the tissue section. The entire process, from tissue loading on microchip to results from RT-LAMP can be carried out in less than 2 h. We anticipate that this technique, with its ease of use, fast turnaround, and quantitative molecular outputs, would become an invaluable tissue analysis tool for researchers and clinicians in the biomedical arena.

Original language	English (US)
Article number	202
Journal	Nature communications
Volume	9
Issue number	1
DOIs	https://doi.org/10.1038/s41467-017-02623-9
State	Published - Dec 1 2018

ASJC Scopus subject areas

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

UN SDGs

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

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10.1038/s41467-017-02623-9

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title = "Pixelated spatial gene expression analysis from tissue",

abstract = "Here, we present a technique that performs on-chip picoliter real-time reverse transcriptase loop mediated isothermal amplification (RT-LAMP) reactions on a histological tissue section without any analyte purification while preserving the native spatial location of the nucleic acid molecules. We demonstrate this method by amplifying TOP2A messenger RNA (mRNA) in a prostate cancer xenograft with 100 μm spatial resolution and by visualizing the variation in threshold time of amplification across the tissue. The on-chip reaction was validated by mRNA fluorescence in situ hybridization (mFISH) from cells in the tissue section. The entire process, from tissue loading on microchip to results from RT-LAMP can be carried out in less than 2 h. We anticipate that this technique, with its ease of use, fast turnaround, and quantitative molecular outputs, would become an invaluable tissue analysis tool for researchers and clinicians in the biomedical arena.",

author = "A. Ganguli and A. Ornob and N. Spegazzini and Y. Liu and G. Damhorst and T. Ghonge and B. Thornton and Konopka, {C. J.} and W. Dobrucki and Clare, {S. E.} and R. Bhargava and Smith, {A. M.} and F. Kosari and R. Bashir",

note = "Funding Information: We thank the staff at the Micro and Nanotechnology Laboratory at UIUC for facilitating the chip fabrication. R.B. acknowledges the funding from Qualcomm, grant number 2016-01141-00-00, and CIMIT: NIH SUB MGH grant number 226421 to support A.G. and T.G., and the NSF to support A.O. under grant number 1534126. L.W.D. acknowledges the support of UIC Cancer Pilot Grant to support C.J.K and providing the tissue samples. R. Bhargava acknowledges the NIH grant R01CA197516 to support N.S. A.M.S. acknowledges the NIH grant number R33CA196458. Publisher Copyright: {\textcopyright} 2018 The Author(s).",

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doi = "10.1038/s41467-017-02623-9",

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AU - Ganguli, A.

AU - Ornob, A.

AU - Spegazzini, N.

AU - Liu, Y.

AU - Damhorst, G.

AU - Ghonge, T.

AU - Thornton, B.

AU - Konopka, C. J.

AU - Dobrucki, W.

AU - Clare, S. E.

AU - Bhargava, R.

AU - Smith, A. M.

AU - Kosari, F.

AU - Bashir, R.

N1 - Funding Information: We thank the staff at the Micro and Nanotechnology Laboratory at UIUC for facilitating the chip fabrication. R.B. acknowledges the funding from Qualcomm, grant number 2016-01141-00-00, and CIMIT: NIH SUB MGH grant number 226421 to support A.G. and T.G., and the NSF to support A.O. under grant number 1534126. L.W.D. acknowledges the support of UIC Cancer Pilot Grant to support C.J.K and providing the tissue samples. R. Bhargava acknowledges the NIH grant R01CA197516 to support N.S. A.M.S. acknowledges the NIH grant number R33CA196458. Publisher Copyright: © 2018 The Author(s).

PY - 2018/12/1

Y1 - 2018/12/1

N2 - Here, we present a technique that performs on-chip picoliter real-time reverse transcriptase loop mediated isothermal amplification (RT-LAMP) reactions on a histological tissue section without any analyte purification while preserving the native spatial location of the nucleic acid molecules. We demonstrate this method by amplifying TOP2A messenger RNA (mRNA) in a prostate cancer xenograft with 100 μm spatial resolution and by visualizing the variation in threshold time of amplification across the tissue. The on-chip reaction was validated by mRNA fluorescence in situ hybridization (mFISH) from cells in the tissue section. The entire process, from tissue loading on microchip to results from RT-LAMP can be carried out in less than 2 h. We anticipate that this technique, with its ease of use, fast turnaround, and quantitative molecular outputs, would become an invaluable tissue analysis tool for researchers and clinicians in the biomedical arena.

AB - Here, we present a technique that performs on-chip picoliter real-time reverse transcriptase loop mediated isothermal amplification (RT-LAMP) reactions on a histological tissue section without any analyte purification while preserving the native spatial location of the nucleic acid molecules. We demonstrate this method by amplifying TOP2A messenger RNA (mRNA) in a prostate cancer xenograft with 100 μm spatial resolution and by visualizing the variation in threshold time of amplification across the tissue. The on-chip reaction was validated by mRNA fluorescence in situ hybridization (mFISH) from cells in the tissue section. The entire process, from tissue loading on microchip to results from RT-LAMP can be carried out in less than 2 h. We anticipate that this technique, with its ease of use, fast turnaround, and quantitative molecular outputs, would become an invaluable tissue analysis tool for researchers and clinicians in the biomedical arena.

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Pixelated spatial gene expression analysis from tissue

Abstract

ASJC Scopus subject areas

UN SDGs

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