1. A protocol for urine collection and storage prior to DNA methylation analysis
- Author
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Renske D.M. Steenbergen, Loes I. Segerink, Putri W. Novianti, S Bach, AP Van Splunter, Idris Bahce, Jakko A. Nieuwenhuijzen, Geert Kazemier, Irene V. Bijnsdorp, Judith Bosschieter, W.F. Rurup, R.J.A. Van Moorselaar, Urology, Surgery, CCA - Imaging and biomarkers, Pathology, Pulmonary medicine, AGEM - Re-generation and cancer of the digestive system, Amsterdam Neuroscience - Cellular & Molecular Mechanisms, CCA - Cancer Treatment and quality of life, Other Research, CCA - Evaluation of Cancer Care, and CCA - Imaging
- Subjects
0301 basic medicine ,Preservative ,Lung Neoplasms ,Urinary system ,Preservation, Biological ,Bisulfite sequencing ,lcsh:Medicine ,Pilot Projects ,Urine ,Polymerase Chain Reaction ,Specimen Handling ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Carcinoma, Non-Small-Cell Lung ,Biomarkers, Tumor ,Carcinoma ,medicine ,Humans ,lcsh:Science ,Edetic Acid ,Urine Specimen Collection ,Multidisciplinary ,Chemistry ,lcsh:R ,Liquid Biopsy ,DNA ,DNA, Neoplasm ,DNA Methylation ,medicine.disease ,Molecular biology ,Bisulfite ,030104 developmental biology ,Urinary Bladder Neoplasms ,030220 oncology & carcinogenesis ,DNA methylation ,lcsh:Q - Abstract
BACKGROUND: Urine poses an attractive non-invasive means for obtaining liquid biopsies for oncological diagnostics. Especially molecular analysis on urinary DNA is a rapid growing field. However, optimal and practical storage conditions that result in preservation of urinary DNA, and in particular hypermethylated DNA (hmDNA), are yet to be determined.AIM: To determine the most optimal and practical conditions for urine storage that result in adequate preservation of DNA for hmDNA analysis.METHODS: DNA yield for use in methylation analysis was determined by quantitative methylation specific PCR (qMSP) targeting the ACTB and RASSF1A genes on bisulfite modified DNA. First, DNA yield (ACTB qMSP) was determined in a pilot study on urine samples of healthy volunteers using two preservatives (Ethylenediaminetetraacetic acid (EDTA) and Urine Conditioning Buffer, Zymo Research) at four different temperatures (room temperature (RT), 4°C, -20°C, -80°C) for four time periods (1, 2, 7, 28 days). Next, hmDNA levels (RASSF1A qMSP) in stored urine samples of patients suffering from bladder cancer (n = 10) or non-small cell lung cancer (NSCLC; n = 10) were measured at day 0 and 7 upon storage with and without the addition of 40mM EDTA and/or 20 μl/ml Penicillin Streptomycin (PenStrep) at RT and 4°C.RESULTS: In the pilot study, DNA for methylation analysis was only maintained at RT upon addition of preserving agents. In urine stored at 4°C for a period of 7 days or more, the addition of either preserving agent yielded a slightly better preservation of DNA. When urine was stored at -20 °C or -80 °C for up to 28 days, DNA was retained irrespective of the addition of preserving agents. In bladder cancer and NSCLC samples stored at RT loss of DNA was significantly less if EDTA was added compared to no preserving agents (p0.99). Upon storage at 4°C, no difference in DNA preservation was found after the addition of preserving agents (p = 0.18). The preservation of methylated DNA (RASSF1A) was strongly correlated to that of unmethylated DNA (ACTB) in most cases, except when PCR values became inaccurate.CONCLUSIONS: Addition of EDTA offers an inexpensive preserving agent for urine storage at RT up to seven days allowing for reliable hmDNA analysis. To avoid bacterial overgrowth PenStrep can be added without negatively affecting DNA preservation.
- Published
- 2018
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