title: Improved amplification efficiency on stool samples by addition of spermidine and its use for non-invasive detection of colorectal cancer.
abstract: BACKGROUND
  Using quantitative methylation-specific PCR (QM-MSP) is a promising method for colorectal cancer (CRC) diagnosis from stool samples. Difficulty in eliminating PCR inhibitors of this body fluid has been extensively reported. Here, spermidine is presented as PCR facilitator for the detection of stool DNA methylation biomarkers using QM-MSP. We examined its effectiveness with NPY, PENK and WIF1, three biomarkers which we have previously shown to be of relevance to CRC.
  
  
  RESULTS
  We determined an optimal window for the amplification of the albumin (Alb) gene (100 ng of bisulfite-treated stool DNA added of 1 mM spermidine) at which we report that spermidine acts as a PCR facilitator (AE = 1680%) for SG RT-PCR. We show that the amplification of methylated PENK, NPY and WIF1 is considerably facilitated by QM-MSP as measured by an increase of CMI (Cumulative Methylation Index, i.e. the sum of the three methylation values) by a factor of 1.5 to 23 fold in individual samples, and of 10 fold in a pool of five samples.
  
  
  CONCLUSIONS
  We contend that spermidine greatly reduces the problems of PCR inhibition in stool samples. This observed feature, after validation on a larger sampling, could be used in the development of stool-based CRC diagnosis tests.
authors.affiliation: Profilome, Paris Biotech 24 rue du Faubourg St Jacques, Paris, 75014, France. roperch@oncodiag.fr.|OncoDiag, Agoranov 96 Bis, Boulevard Raspail, Paris, 75006, France. roperch@oncodiag.fr.
authors.forename: Jean-Pierre
authors.initials: JP
authors.lastname: Roperch
authors.affiliation: Centre d'Investigation Clinique (CIC), Henri Mondor Hospital, Créteil, France. karim.benzekri@hmn.aphp.fr.
authors.forename: Karim
authors.initials: K
authors.lastname: Benzekri
authors.affiliation: King Abdullah University of Science and Technology (KAUST), Bioscience Core Laboratory Research Department, Thuwal, 23955-6900, Saudi Arabia. hicham.mansour@kaust.edu.sa.
authors.forename: Hicham
authors.initials: H
authors.lastname: Mansour
authors.affiliation: King Abdullah University of Science and Technology (KAUST), Computational Biology Research Center, Thuwal, 23955-6900, Saudi Arabia. roberto.incitti@kaust.edu.sa.
authors.forename: Roberto
authors.initials: R
authors.lastname: Incitti
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics* / Q000302:isolation & purification; D015179:Colorectal Neoplasms / Q000175:diagnosis* / Q000235:genetics* / Q000473:pathology; D004247:DNA / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification; D019175:DNA Methylation; D005243:Feces; D006801:Humans; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods; D013095:Spermidine / Q000008:administration & dosage
chemical_list: D014408:Biomarkers, Tumor; D004247:DNA; D013095:Spermidine