Optimization of RNA yield, purity and mRNA copy number by treatment of urine cell pellets with RNAlater

M. Medeiros, V. K. Sharma, R. Ding, K. Yamaji, B. Li, T. Muthukumar, S. Valderde-Rosas, A. M. Hernandez, R. Muñoz, Manikkam Suthanthiran

Research output: Contribution to journalArticle

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Abstract

Background: We have shown that measurement of mRNA for cytotoxic attack proteins perforin and granzyme B in urinary cells is a noninvasive means of diagnosing acute rejection of human renal allografts. Urinary cell mRNA studies have yielded useful information in other patient populations such as patients with cancer. The isolation of sufficient and high quality ribonucleic acid (RNA) from urinary cells however is problematic. RNAlater, an RNA stabilization solution, has been reported to optimize RNA isolation from tumor tissues stored at room temperature and from pigment-rich ocular tissues. Methods: We explored whether the addition of RNAlater to urine cell pellets improves RNA yield, enhances purity and facilitates measurement of low abundance mRNAs. We measured, with the use of real-time quantitative polymerase chain reaction (PCR) assay, levels of expression of a constitutively expressed gene 18S rRNA and mRNA for granzyme B and transforming growth factor-β1 (TGF-β 1) in urine specimens and renal biopsies obtained from renal allograft recipients. Results: RNA yield (P < 0.01, Wilcoxon signed rank test) and the A260/A280 ratio (P < 0.01) were both higher with urine cell pellets treated with RNAlater prior to snap freezing compared to cell pellets that were not treated with RNAlater prior to snap freezing. Levels (copy number per 1 μg of total RNA) of 18S rRNA (P < 0.02), granzyme B mRNA (P = 0.002) and TGF-β1 (P = 0.02) were all higher with treated urine cell pellets compared to untreated cell pellets. Kruskall-Wallis one way analysis of variance and pair-wise comparisons with Student-Newman-Keuls test showed that the levels of mRNA for granzyme B (P < 0.05) and TGF-β1 (P < 0.05) are significantly different between renal allograft biopsies and untreated urine cell pellets but not between the biopsy specimens and RNAlater-treated urine cell pellets. Conclusions: The addition of RNAlater to urine cell pellets improves RNA isolation from urinary cells and facilitates measurement of low abundance mRNAs.

Original languageEnglish
Pages (from-to)135-142
Number of pages8
JournalJournal of Immunological Methods
Volume279
Issue number1-2
DOIs
Publication statusPublished - 1 Jan 2003
Externally publishedYes

Fingerprint

Urine
RNA
Messenger RNA
Granzymes
Therapeutics
Allografts
Kidney
Biopsy
Freezing
Cell Separation
Transforming Growth Factors
Nonparametric Statistics
rRNA Genes
Real-Time Polymerase Chain Reaction
Neoplasms
Analysis of Variance
Students
Temperature
Population

Keywords

  • Real time quantitative PCR
  • RNAlater
  • Transplantation
  • Urine PCR

ASJC Scopus subject areas

  • Immunology and Allergy
  • Immunology

Cite this

Optimization of RNA yield, purity and mRNA copy number by treatment of urine cell pellets with RNAlater. / Medeiros, M.; Sharma, V. K.; Ding, R.; Yamaji, K.; Li, B.; Muthukumar, T.; Valderde-Rosas, S.; Hernandez, A. M.; Muñoz, R.; Suthanthiran, Manikkam.

In: Journal of Immunological Methods, Vol. 279, No. 1-2, 01.01.2003, p. 135-142.

Research output: Contribution to journalArticle

Medeiros, M, Sharma, VK, Ding, R, Yamaji, K, Li, B, Muthukumar, T, Valderde-Rosas, S, Hernandez, AM, Muñoz, R & Suthanthiran, M 2003, 'Optimization of RNA yield, purity and mRNA copy number by treatment of urine cell pellets with RNAlater', Journal of Immunological Methods, vol. 279, no. 1-2, pp. 135-142. https://doi.org/10.1016/S0022-1759(03)00237-0
Medeiros, M. ; Sharma, V. K. ; Ding, R. ; Yamaji, K. ; Li, B. ; Muthukumar, T. ; Valderde-Rosas, S. ; Hernandez, A. M. ; Muñoz, R. ; Suthanthiran, Manikkam. / Optimization of RNA yield, purity and mRNA copy number by treatment of urine cell pellets with RNAlater. In: Journal of Immunological Methods. 2003 ; Vol. 279, No. 1-2. pp. 135-142.
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abstract = "Background: We have shown that measurement of mRNA for cytotoxic attack proteins perforin and granzyme B in urinary cells is a noninvasive means of diagnosing acute rejection of human renal allografts. Urinary cell mRNA studies have yielded useful information in other patient populations such as patients with cancer. The isolation of sufficient and high quality ribonucleic acid (RNA) from urinary cells however is problematic. RNAlater, an RNA stabilization solution, has been reported to optimize RNA isolation from tumor tissues stored at room temperature and from pigment-rich ocular tissues. Methods: We explored whether the addition of RNAlater to urine cell pellets improves RNA yield, enhances purity and facilitates measurement of low abundance mRNAs. We measured, with the use of real-time quantitative polymerase chain reaction (PCR) assay, levels of expression of a constitutively expressed gene 18S rRNA and mRNA for granzyme B and transforming growth factor-β1 (TGF-β 1) in urine specimens and renal biopsies obtained from renal allograft recipients. Results: RNA yield (P < 0.01, Wilcoxon signed rank test) and the A260/A280 ratio (P < 0.01) were both higher with urine cell pellets treated with RNAlater prior to snap freezing compared to cell pellets that were not treated with RNAlater prior to snap freezing. Levels (copy number per 1 μg of total RNA) of 18S rRNA (P < 0.02), granzyme B mRNA (P = 0.002) and TGF-β1 (P = 0.02) were all higher with treated urine cell pellets compared to untreated cell pellets. Kruskall-Wallis one way analysis of variance and pair-wise comparisons with Student-Newman-Keuls test showed that the levels of mRNA for granzyme B (P < 0.05) and TGF-β1 (P < 0.05) are significantly different between renal allograft biopsies and untreated urine cell pellets but not between the biopsy specimens and RNAlater-treated urine cell pellets. Conclusions: The addition of RNAlater to urine cell pellets improves RNA isolation from urinary cells and facilitates measurement of low abundance mRNAs.",
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AU - Sharma, V. K.

AU - Ding, R.

AU - Yamaji, K.

AU - Li, B.

AU - Muthukumar, T.

AU - Valderde-Rosas, S.

AU - Hernandez, A. M.

AU - Muñoz, R.

AU - Suthanthiran, Manikkam

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N2 - Background: We have shown that measurement of mRNA for cytotoxic attack proteins perforin and granzyme B in urinary cells is a noninvasive means of diagnosing acute rejection of human renal allografts. Urinary cell mRNA studies have yielded useful information in other patient populations such as patients with cancer. The isolation of sufficient and high quality ribonucleic acid (RNA) from urinary cells however is problematic. RNAlater, an RNA stabilization solution, has been reported to optimize RNA isolation from tumor tissues stored at room temperature and from pigment-rich ocular tissues. Methods: We explored whether the addition of RNAlater to urine cell pellets improves RNA yield, enhances purity and facilitates measurement of low abundance mRNAs. We measured, with the use of real-time quantitative polymerase chain reaction (PCR) assay, levels of expression of a constitutively expressed gene 18S rRNA and mRNA for granzyme B and transforming growth factor-β1 (TGF-β 1) in urine specimens and renal biopsies obtained from renal allograft recipients. Results: RNA yield (P < 0.01, Wilcoxon signed rank test) and the A260/A280 ratio (P < 0.01) were both higher with urine cell pellets treated with RNAlater prior to snap freezing compared to cell pellets that were not treated with RNAlater prior to snap freezing. Levels (copy number per 1 μg of total RNA) of 18S rRNA (P < 0.02), granzyme B mRNA (P = 0.002) and TGF-β1 (P = 0.02) were all higher with treated urine cell pellets compared to untreated cell pellets. Kruskall-Wallis one way analysis of variance and pair-wise comparisons with Student-Newman-Keuls test showed that the levels of mRNA for granzyme B (P < 0.05) and TGF-β1 (P < 0.05) are significantly different between renal allograft biopsies and untreated urine cell pellets but not between the biopsy specimens and RNAlater-treated urine cell pellets. Conclusions: The addition of RNAlater to urine cell pellets improves RNA isolation from urinary cells and facilitates measurement of low abundance mRNAs.

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