Transrenal DNA testing: Progress and perspectives

Expert Review of Molecular Diagnostics

Volumn 6, Issue 2, 2006, Pages 153-163

  Umansky, Samuil R ^a   Tomei, L David ^b  

^a Xenomics Inc   (United States)

^b NATIONAL INSTITUTE FOR INFECTIOUS DISEASES L SPALLANZANI   (Italy)

Author keywords

Diagnostic; Infection; Prenatal testing; Tr DNA; Transplantation; Transrenal DNA; Tumor; Urine

Indexed keywords

BACTERIAL DNA; DNA; VIRUS DNA;

ACQUIRED IMMUNE DEFICIENCY SYNDROME; AMPLICON; BLOOD FLOW; CELL DEATH; COLON TUMOR; DIAGNOSTIC PROCEDURE; DNA ISOLATION; DNA SEQUENCE; GENETIC PROCEDURES; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; MASS SCREENING; PANCREAS TUMOR; PATIENT MONITORING; PREGNANT WOMAN; PRENATAL DIAGNOSIS; PUBLIC HEALTH; REVIEW; TUMOR DIAGNOSIS; ANIMAL; APOPTOSIS; GENETICS; METHODOLOGY; MOLECULAR WEIGHT; SENSITIVITY AND SPECIFICITY; URINE;

ANIMALS; APOPTOSIS; DNA; DNA, VIRAL; HIV; HUMANS; MOLECULAR DIAGNOSTIC TECHNIQUES; MOLECULAR WEIGHT; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA;

EID: 33745489779     PISSN: 14737159     EISSN: 17448352     Source Type: Journal    
DOI: 10.1586/14737159.6.2.153     Document Type: Review

References (91)

1. Bret L, Lule J, Pourrat JP, Fournie GJ. Extracellular DNA in blood and urine as a potential marker for cytotoxicity and nephrotoxicity in the mouse. Ren. Fail. 12(3), 133-139 (1990).
2. Virtanen M, Syvanen AC, Oram J, Soderlund H, Ranki M. Cytomegalovirus in urine: detection of viral DNA by sandwich hybridization. Clin. Microbiol. 20(6), 1083-1088 (1984).
3. Melchers WJ, Schift R, Stolz E, Lindeman J, Quint WG. Human papillomavirus detection in urine samples from male patients by the polymerase chain reaction. J. Clin. Microbiol. 27(8), 1711-1714 (1989).
4. Malloy DC, Nauman RK, Paxton HJ. Detection of Borrelia burgdorferi using the polymerase chain reaction. Clin. Microbiol. 28(6), 1089-1093 (1990).
5. Prinz M, Grellner W, Schmitt C. DNA typing of urine samples following several years of storage. Int. J. Legal. Med. 106(2), 75-79 (1993).
6. Yokota M, Tatsumi N, Tsuda I, Takubo T, Hiyoshi M. DNA extraction from human urinary sediment. J. Clin. Lab. Anal. 12(2), 88-91 (1998).
7. Bret L, Hasim M, Lefebvre H, Fournie GJ, Braun JP. Kidney tubule enzymes and extracellular DNA in urine as markers for nephrotoxicity in the guinea-pig. Enzyme Protein 47(1), 27-36 (1993).
8. Le Lann AD, Bret LC, Delverdier ME, Amardeilh MF, Alary C, Fournie GJ. Urinary DNA as an indicator of nephrotoxicity caused by endotoxin and gentamicin in mice. Toxicology 92(1-3), 1-10 (1994).
9. Fitzgerald JM, Ramchurren N, Rieger K et al. Identification of H-ras mutations in urine sediments complements cytology in the detection of bladder tumors. J. Natl Cancer Inst. 87(2), 129-133 (1995).
10. Mao L, Schoenberg MP, Scicchitano M et al. Molecular detection of primary bladder cancer by microsatellite analysis. Science 271(5249), 659-662 (1996).
11. Yamada H, Kakehi Y, Okuno H, Yoshida O. Detection of tumor-derived DNA in exfoliated cells of urine sediments with a novel quantitative PCR method based on allele-specific PCR. Cancer Lett. 126(1), 111-118 (1998).
12. Cairns P, Esteller M, Herman JG et al. Molecular detection of prostate cancer in urine by GSTP1 hypermethylation. Clin. Cancer Res. 7(9), 2727-2730 (2001).
13. Goessl C, Muller M, Heicappell R et al. DNA-based detection of prostate cancer in urine after prostatic massage. Urology 58(3), 335-338 (2001).
14. Chan MW, Chan LW, Tang NL et al. Frequent hypermethylation of promoter region of RASSF1A in tumor tissues and voided urine of urinary bladder cancer patients. Int. J. Cancer. 104(5), 611-616 (2003).
15. Cairns P. Detection of promoter hypermethylation of tumor suppressor genes in urine from kidney cancer patients. Ann. NY Acad. Sci. 1022, 40-43 (2004).
16. Hoque MO, Begum S, Topaloglu O et al. Quantitative detection of promoter hypermethylation of multiple genes in the tumor, urine, and serum DNA of patients with renal cancer. Cancer Res. 64(15), 5511-5517 (2004).
17. Chernesky MA, Lee H, Schachter J et al. Diagnosis of Chlamydia trachomatis urethral infection in symptomatic and asymptomatic men by testing first-void urine in a ligase chain reaction assay. J. Infect. Dis. 170(5), 1308-1311 (1994).
18. Smith KR, Ching S, Lee H et al. Evaluation of ligase chain reaction for use with urine for identification of Neisseria gonorrhoeae in females attending a sexually transmitted disease clinic. Clin. Microbiol. 33(2), 455-457 (1995).
19. Murdoch DR, Walford EJ, Jennings LC et al. Use of the polymerase chain reaction to detect Legionella DNA in urine and serum samples from patients with pneumonia. Clin. Infect. Dis. 23(3), 475-480 (1996).
20. Kafwabulula M, Ahmed K, Nagatake T et al. Evaluation of PCR-based methods for the diagnosis of tuberculosis by identification of mycobacterial DNA in urine samples. Int. J. Tuberc. Lung Dis. 6(8), 732-737 (2002).
21. Hinata N, Shirakawa T, Okada H, Shigemura K, Kamidono S, Gotoh A. Quantitative detection of Escherichia coli from urine of patients with bacteriuria by real-time PCR. Mol. Diagn. 8(3), 179-184 (2004).
22. Yasuda T, Iida R, Takeshita H et al. A simple method of DNA extraction and STR typing from urine samples using a commercially available DNA/RNA extraction kit. J. Forensic Sci. 48(1), 108-110 (2003).
23. van der Hel OL, van der Luijt RB, Bueno de Mesquita HB et al. Quality and quantity of DNA isolated from frozen urine in population-based research. Anal. Biochem. 304(2), 206-211 (2002).
24. van Duijnhoven FJ, van der Hel OL, van der Luijt RB, Bueno de Mesquita HB, van Noord PA, Peeters PH. Quality of NAT2 genotyping with restriction fragment length polymorphism using DNA isolated from frozen urine. Cancer Epidemiol. Biomarkers Prev. 11(8), 771-776 (2002).
25. van Noord PA. Banking of urine sediments as DNA source in epidemiologic studies. Epidemiology 14(2), 254 (2003).
26. Rios M, Cash K, Strupp A, Uehlinger J, Reid M. DNA from urine sediment or buccal cells can be used for blood group molecular genotyping. Immunohematol 15(2), 61-65 (1999).
27. Botezatu I, Serdyuk O, Potapova G et al. Genetic analysis of DNA excreted in urine: a new approach for detecting specific genomic DNA sequences from cells dying in an organism. Clin. Chem. 46(8 Pt 1), 1078-1084 (2000). First demonstration of transrenal DNA (Tr-DNA) existence in animal and human models.
28. Lichtenstein AV, Melkonyan HS, Tomei LD, Umansky SR. Circulating nucleic acids and apoptosis. Ann. NY Acad. Sci. 945, 239-249 (2001).
29. Massry SG, Glassock RJ. Textbook of Nephrology (Volume 1). Williams & Wilkins, MD, USA, 102-103 (1995).
30. Lote C. Principles of Renal Physiology. Chapman & Hall, NY, USA, 39 (2000).
31. Al-Yatama MK, Mustafa AS, Ali S, Abraham S, Khan Z, Khaja N. Detection of Y chromosome-specific DNA in the plasma and urine of pregnant women using nested polymerase chain reaction. Prenat. Diagn. 21(5), 399-402 (2001).
32. Shi WJ, Sun YH, Cui LJ, Zhang Y, Li SR. Detection of cell-free fetal DNA in the urine of pregnant women by nested polymerase chain reaction. Zhonghua Yi Xue Za Zhi. 83(6), 482-484 (2003).
33. Koide K, Sekizawa A, Iwasaki M et al. Fragmentation of cell-free fetal DNA in plasma and urine of pregnant women. Prenat. Diagn. 25(7), 604-607 (2005).
34. Li Y, Zhong XY, Kang A, Troeger C, Holzgreve W, Hahn S. Inability to detect cell free fetal DNA in the urine of normal pregnant women nor in those affected by preeclampsia associated HELLP syndrome. J. Soc. Gynecol. Investig. 10(8), 503-508 (2003).
35. Zhang J, Tong KL, Li PK et al. Presence of donor- and recipient-derived DNA in cell-free urine samples of renal transplantation recipients: urinary DNA chimerism. Clin. Chem. 45(10), 1741-1746 (1999).
36. Zhang Z, Ohkohchi N, Sakurada M et al. Diagnosis of acute rejection by analysis of urinary DNA of donor origin in renal transplant recipients. Transplant. Proc. 33(1-2), 380-381 (2001).
37. Su YH, Wang M, Brenner DE et al. Human urine contains small, 150 to 250 nucleotide-sized, soluble DNA derived from the circulation and may be useful in the detection of colorectal cancer. J. Mol. Diagn. 6(2), 101-107 (2004). Detection of tumor markers in Tr-DNA of patients with early precancerous conditions.
38. Utting M, Werner W, Muller G, Schubert J, Junker K. A possible noninvasive method for the detection of bladder cancer in patients: microsatellite analysis of free DNA in urine and blood. Ann. NY Acad. Sci. 945, 31-35 (2001).
39. Zancan M, Franceschini R, Mimmo C et al. Free DNA in urine: a new marker for bladder cancer? Preliminary data. Int. J. Biol. Markers 20(2), 134-136 (2005).
40. Stroun M, Maurice P, Vasioukhin V et al. The origin and mechanism of circulating DNA. Ann. NY Acad. Sci. 906, 161-168 (2000). First authors to detect tumor-specific mutations in cell-free plasma DNA.
41. Bischoff FZ, Lewis DE, Simpson JL. Cell-free fetal DNA in maternal blood: kinetics, source and structure. Hum. Reprod. Update 11(1), 59-67 (2005).
42. Taback B, Hoon DS. Circulating nucleic acids in plasma and serum: past, present and future. Curr. Opin. Mol. Ther. 6(3), 273-278 (2004).
43. Wong BC, Lo YM. Cell-free DNA and RNA in plasma as new tools for molecular diagnostics. Expert Rev. Mol. Diagn. 3(6), 785-797 (2003).
44. Wyllie AH, Kerr JFR, Currie AR. The significance of apoptosis. Int. Rev. Cytol. 68, 251-306 (1980). First detailed description of morphology of two forms of cell death, apoptosis and necrosis.
45. Umansky SR. The genetic program of cell death. Hypothesis and some applications: transformation, carcinogenesis, aging. J. Theor. Biol. 97, 591-602 (1982). Existence of the cell death program and its role in carcinogenesis was described for the first time.
46. Lockshin RA, Osborne B, Zakeri Z. Cell death in the third millennium. Cell Death Differ. 7(1), 2-7 (2000).
47. Umansky SR, Tomei LD. Apoptosis in the heart. Adv. Pharmacol. 41, 383-407 (1997).
48. Nawroz H, Koch W, Anker P, Stroun M, Sidransky D. Microsatellite alterations in serum DNA of head and neck cancer patients. Nature Med. 2(9), 1035-1037 (1996).
49. Jahr S, Hentze H, Englisch S et al. DNA fragments in the blood plasma of cancer patients: quantitations and evidence for their origin from apoptotic and necrotic cells. Cancer Res. 61(4), 1659-1665 (2001).
50. Castedo M, Perfettini JL, Roumier T, Andreau K, Medema R, Kroemer G. Cell death by mitotic catastrophe: a molecular definition. Oncogene 23(16), 2825-2837 (2004).
51. Roninson IB, Broude EV, Chang BD. If not apoptosis, then what? Treatment-induced senescence and mitotic catastrophe in tumor cells. Drug Resist. Update 4(5), 303-313 (2001).
52. Debrabant A, Lee N, Bertholet S, Duncan R, Nakhasi HL. Programmed cell death in trypanosomatids and other unicellular organisms. Int. J. Parasitol. 33, 257-267 (2003).
53. Lee N, Bertholet S, Debrabant A, Muller J, Duncan R, Nakhasi HL. Programmed cell death in the unicellular protozoan parasite Leishmania. Cell Death Differ. 9, 53-64 (2002).
54. Al-Olayan EM, Williams GT, Hurd H. Apoptosis in the malaria protozoan, Plasmodium berghei: a possible mechanism for limiting intensity of infection in the mosquito. Int. J. Parasitol. 32, 1133-1143 (2002).
55. Gal S, Fidler C, Turner S, Lo YM, Roberts DJ, Wainscoat JS. Detection of Plasmodium falciparum DNA in plasma. Ann. NY Acad. Sci. 945, 234-238 (2001).
56. Dery CV, Toth M, Brown M, Horvath J, Allaire S, Weber JM. The structure of adenovirus chromatin in infected cells. J. Gen. Virol. 66, 2671-2684 (1985).
57. Hsiao JR, Jin YT, Tsai ST. Detection of cell free Epstein-Barr virus DNA in sera from patients with nasopharyngeal carcinoma. Cancer 94, 723-729 (2002).
58. Chan KC, Lo YM. Circulating EBV DNA as a tumor marker for nasopharyngeal carcinoma. Semin. Cancer Biol. 12, 489-496 (2002).
59. Pornthanakasem W, Shotelersuk K, Termrungruanglert W, Voravud N, Niruthisard S, Mutirangura A. Human papillomavirus DNA in plasma of patients with cervical cancer. BMC Cancer 1, 2 (2001).
60. Chan KC, Zhang J, Chan AT et al. Molecular characterization of circulating EBV DNA in the plasma of nasopharyngeal carcinoma and lymphoma patients. Cancer Res. 63, 2028-2032 (2003).
61. Tenenbaum L, Lehtonen E, Monahan PE. Evaluation of risks related to the use of adeno-associated virus-based vectors. Curr. Gene Ther. 3, 545-565 (2003).
62. Navarre WW, Zychlinsky A. Pathogen-induced apoptosis of macrophages: a common end for different pathogenic strategies. Cell. Microbiol. 2, 265-273 (2000).
63. Bocchino M, Galati D, Sanduzzi A et al. Role of mycobacteria-induced monocyte/macrophage apoptosis in the pathogenesis of human tuberculosis. Int. J. Tuberc. Lung Dis. 9, 375-383 (2005).
64. Friedlander AM. DNA release as a direct measure of microbial killing by phagocytes. Infect. Immune. 22, 148-154 (1978).
65. Mancuso M, Filosto M, Stevens JC et al. Mitochondrial myopathy and complex III deficiency in a patient with a new stop-codon mutation (G339X) in the cytochrome b gene. J. Neurol. Sci. 209, 61-63 (2003).
66. Wang M, Block TM, Steel L, Brenner DE, Su YH. Preferential isolation of fragmented DNA enhances the detection of circulating mutated k-ras DNA. Clin. Chem. 50, 211-213 (2004).
67. Schmidt B, Weickmann S, Witt C, Fleischhacker M. Improved method for isolating cell-free DNA. Clin. Chem. 51(8), 1561-1563 (2005).
68. Murai K, Yamanaka M, Akagi K, Anai M. Purification and properties of deoxyribonuclease II from human urine. J. Biochem. (Tokyo) 87(4), 1097-1103 (1980).
69. Ito K, Minamiura N, Yamamoto T. Human urine DNase I: immunological identity with human pancreatic DNase I, and enzymic and proteochemical properties of the enzyme. J. Biochem. (Tokyo) 95(5), 1399-1406 (1984).
70. Duerksen JD, Connor KW. Periodicity and fragment size of DNA from mouse TLT hepatoma chromatin and chromatin fractions using endogenous and exogenous nucleases. Mol. Cell. Biochem. 19(2), 93-112 (1978).
71. Umansky SR, Korol' BA, Nelipovich PA. In vivo DNA degradation in thymocytes of γ-irradiated or hydrocortisone-treated rats. Biochim. Biophys. Acta 655(1), 9-17 (1981).
72. Su YH, Wang M, Block TM et al. Transrenal DNA as a diagnostic tool: important technical notes. Ann. NY Acad. Sci. 1022, 81-89 (2004). Significance of amplicon size for Tr-DNA analysis is demonstrated.
73. Hashida S, Hashinaka K, Saitoh A et al. Diagnosis of HIV-1 infection by detection of antibody IgG to HIV-1 in urine with ultrasensitive enzyme immunoassay (immune complex transfer enzyme immunoassay) using recombinant proteins as antigens. J. Clin. Lab. Anal. 8(4), 237-246 (1994).
74. Lui YY, Chik KW, Chiu RW, Ho CY, Lam CW, Lo YM. Predominant hematopoietic origin of cell-free DNA in plasma and serum after sex-mismatched bone marrow transplantation. Clin. Chem. 48(3), 421-427 (2002).
75. Hanss B, Leal-Pinto E, Bruggeman LA, Copeland TD, Klotman PE. Identification and characterization of a cell membrane nucleic acid channel. Proc. Natl Acad. Sci. USA 95(4), 1921-1926 (1998).
76. Winters-Hilt S, Akeson M. Nanopore cheminformatics. DNA Cell Biol. 23(10), 675-683 (2004).
77. Lo YM, Corbetta N, Chamberlain PF et al. Presence of fetal DNA in maternal plasma and serum. Lancet 350(9076), 485-487 (1997). Fetal DNA sequences were detected in maternal plasma for the first time.
78. Lo YM, Tein MS, Lau TK et al. Quantitative analysis of fetal DNA in maternal plasma and serum: implications for noninvasive prenatal diagnosis. Am. J. Hum. Genet. 62(4), 768-775 (1998).
79. Angert RM, LeShane ES, Lo YM, Chan LY, Delli-Bovi LC, Bianchi DW. Fetal cell-free plasma DNA concentrations in maternal blood are stable 24 h after collection: analysis of first- and third-trimester samples. Clin. Chem. 49(1), 195-198 (2003).
80. Jin P, Warren ST. Understanding the molecular basis of fragile X syndrome. Hum. Mol. Genet. 9(6), 901-908 (2000).
81. Lo YM, Leung TN, Tein MS et al. Quantitative abnormalities of fetal DNA in maternal serum in preeclampsia. Clin. Chem. 45(2), 184-188 (1999).
82. Sekizawa A, Farina A, Koide K et al. β-globin DNA in maternal plasma as a molecular marker of pre-eclampsia. Prenat. Diagn. 24(9), 697-700 (2004).
83. Gazzaniga P, Nofroni I, Gandini O et al. Tenascin C and epidermal growth factor receptor as markers of circulating tumoral cells in bladder and colon cancer. Oncol. Rep. 14(5), 1199-1202 (2005).
84. Steiner G, Schoenberg MP, Linn JF, Mao L, Sidransky D. Detection of bladder cancer recurrence by microsatellite analysis of urine. Nature Med. 3(6), 621-624 (1997).
85. Sachs MD, Schlechte H, Lenk VS et al. Genetic analysis of Tp53 from urine sediment as a tool for diagnosing recurrence and residual of bladder carcinoma. Eur. Urol. 38(4), 426-433 (2000).
86. Lo YM, Chan LY, Chan AT et al. Quantitative and temporal correlation between circulating cell-free Epstein-Barr virus DNA and tumor recurrence in nasopharyngeal carcinoma. Cancer Res. 59(21), 5452-5455 (1999). Use of circulating plasma DNA analysis for tumor monitoring.
87. Tomei LD, Cannas A, Fimia G et al. Detection of cell-free proviral HIV DNA in urine of AIDS patients. Proc. XIX Internatl Congr. Clin. Chem. IFCC/AACC July 24-28 (2005).
88. Goletti D, Cannas A, Chiaccio T et al. Detection of Mycobacterium tuberculosis transrenal DNA from urine samples of patients with pulmonary TB. Proc. 36th Union World Conf. Lung Health & Centers for Disease Control October, Paris, France (2005).
89. Marini M, Giangregorio M, Kraskinski JC. Complying with the Occupational Safety and Health Administration's Bloodborne Pathogens Standard: implementing needleless systems and intravenous safety devices. Pediatr. Emerg. Care 20(3), 209-214 (2004).
90. Lee JM, Botteman MF, Xanthakos N, Nicklasson L. Needlestick injuries in the United States: Epidemiological, economic, and quality of life issues. AAOHN J. 53(3), 117-133 (2005).
91. Beekman SE, Vaughan TE, McCoy KD et al. Hospital bloodborne pathogens programs: program characteristics and blood and body fluid exposure rates. Infect. Control Hosp. Epidemiol. 22(2), 70-72 (2001).