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RT-qPCR for Fecal Mature MicroRNA Quantification and Validation

  • Farid E. Ahmed
  • Nancy C. Ahmed
  • Mostafa M. Gouda
  • Paul W. Vos
  • Chris Bonnerup
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1765)

Abstract

By routinely and systematically being able to perform quantitative stem-loop reverse transcriptase (RT) followed by TaqMan® minor-groove binding (MGB) probe, real-time quantitative PCR analysis on exfoliated enriched colonocytes in stool, using human (Homo sapiens, hsa) micro(mi)RNAs to monitor changes of their expression at various stages of colorectal (CRC) progression, this method allows for the reliable and quantitative diagnostic screening of colon cancer (CC). Although the expression of some miRNA genes tested in tissue shows less variability in normal or cancerous patients than in stool, the noninvasive stool by itself is well suited for CC screening. An miRNA approach using stool promises to offer more sensitivity and specificity than currently used genomic, methylomic, or proteomic methods for CC screening.

To present an application of employing miRNAs as diagnostic markers for CC screening, we carried out global microarray expression studies on stool colonocytes isolated by paramagnetic beads, using Affymetrix GeneChip miRNA 3.0 Array, to select a panel of miRNAs for subsequent focused semiquantitative PCR analysis studies. We then conducted a stem-loop RT-TaqMan® MGB probes, followed by a modified real-time qPCR expression study on 20 selected miRNAs for subsequent validation of the extracted immunocaptured total small RNA isolated from stool colonocytes. Results showed 12 miRNAs (miR-7, miR-17, miR-20a, miR-21, miR-92a, miR-96, miR-106a, miR-134, miR-183, miR-196a, miR-199a-3p, and miR214) to have an increased expression in stool of CC patients, and that later TNM stages exhibited more increased expressions than adenomas, while 8 miRNAs (miR-9, miR-29b, miR-127-5p, miR-138, miR-143, miR-146a, miR-222, and miR-938) showed decreased expressions in stool of CC patients, which becomes more pronounced as the cancer progresses from early to late TNM stages (0–IV).

Key words

Adenocarcinoma Colon cancer Colonocyte Colorectal cancer TaqMan 

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Farid E. Ahmed
    • 1
  • Nancy C. Ahmed
    • 1
  • Mostafa M. Gouda
    • 2
  • Paul W. Vos
    • 3
  • Chris Bonnerup
    • 4
  1. 1.GEM Tox LabsInstitute for Research in BiotechnologyGreenvilleUSA
  2. 2.Department of Nutrition & Food ScienceNational Research CenterCairoEgypt
  3. 3.Department of BiostatisticsEast Carolina UniversityGreenvilleUSA
  4. 4.Department of PhysicsEast Carolina UniversityGreenvilleUSA

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