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 languageEnglish (US)
Article number202
JournalNature communications
Volume9
Issue number1
DOIs
StatePublished - Dec 1 2018

Fingerprint

gene expression
Gene expression
Tissue
Gene Expression
ribonucleic acids
Amplification
RNA-Directed DNA Polymerase
chips
Messenger RNA
nucleic acids
Fluorescence In Situ Hybridization
Heterografts
purification
reaction time
Nucleic Acids
preserving
Purification
Prostatic Neoplasms
spatial resolution
cancer

ASJC Scopus subject areas

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)

Cite this

Ganguli, A., Ornob, A., Spegazzini, N., Liu, Y., Damhorst, G., Ghonge, T., ... Bashir, R. (2018). Pixelated spatial gene expression analysis from tissue. Nature communications, 9(1), [202]. https://doi.org/10.1038/s41467-017-02623-9

Pixelated spatial gene expression analysis from tissue. / Ganguli, A.; Ornob, A.; Spegazzini, N.; Liu, Y.; Damhorst, G.; Ghonge, T.; Thornton, B.; Konopka, C. J.; Dobrucki, Wawrzyniec; Clare, S. E.; Bhargava, Rohit; Smith, Andrew M; Kosari, F.; Bashir, Rashid.

In: Nature communications, Vol. 9, No. 1, 202, 01.12.2018.

Research output: Contribution to journalArticle

Ganguli, A, Ornob, A, Spegazzini, N, Liu, Y, Damhorst, G, Ghonge, T, Thornton, B, Konopka, CJ, Dobrucki, W, Clare, SE, Bhargava, R, Smith, AM, Kosari, F & Bashir, R 2018, 'Pixelated spatial gene expression analysis from tissue', Nature communications, vol. 9, no. 1, 202. https://doi.org/10.1038/s41467-017-02623-9
Ganguli A, Ornob A, Spegazzini N, Liu Y, Damhorst G, Ghonge T et al. Pixelated spatial gene expression analysis from tissue. Nature communications. 2018 Dec 1;9(1). 202. https://doi.org/10.1038/s41467-017-02623-9
Ganguli, A. ; Ornob, A. ; Spegazzini, N. ; Liu, Y. ; Damhorst, G. ; Ghonge, T. ; Thornton, B. ; Konopka, C. J. ; Dobrucki, Wawrzyniec ; Clare, S. E. ; Bhargava, Rohit ; Smith, Andrew M ; Kosari, F. ; Bashir, Rashid. / Pixelated spatial gene expression analysis from tissue. In: Nature communications. 2018 ; Vol. 9, No. 1.
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