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 () and R. Bashir ()
Additional contact information
A. Ganguli: University of Illinois at Urbana-Champaign
A. Ornob: University of Illinois at Urbana-Champaign
N. Spegazzini: University of Illinois at Urbana-Champaign
Y. Liu: University of Illinois at Urbana-Champaign
G. Damhorst: University of Illinois at Urbana-Champaign
T. Ghonge: University of Illinois at Urbana-Champaign
B. Thornton: Tuskegee University
C. J. Konopka: University of Illinois at Urbana-Champaign
W. Dobrucki: University of Illinois at Urbana-Champaign
S. E. Clare: Northwestern University
R. Bhargava: University of Illinois at Urbana-Champaign
A. M. Smith: University of Illinois at Urbana-Champaign
F. Kosari: Mayo Clinic Cancer Center Research
R. Bashir: University of Illinois at Urbana-Champaign

Nature Communications, 2018, vol. 9, issue 1, 1-9

Abstract: 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.

Date: 2018
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DOI: 10.1038/s41467-017-02623-9

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