Molecular identification of DNA present in human colorectal adenocarcinomas by 16S rDNA PCR amplification and pyrosequencing analysis Free

Abstract

Seroepidemiological studies have indicated that infection might be a possible risk factor for colorectal adenocarcinoma (CRC) development. However, limited information is available as to whether or not species are present in CRC tissues. In this study the presence of DNA in 77 CRC biopsies was investigated by means of a species-specific 16S rDNA PCR assay and real-time DNA pyrosequencing of the 16S rDNA variable V3 region. Pyrosequencing revealed the presence of DNA sequences in 21 of 77 biopsy specimens (27 %). 16S rDNA sequences corresponding to 26695 and J99 were most commonly found. Intriguingly, one sequence belonged to , previously identified in ferrets. No significant correlations were found in the prevalence of DNA between colon and rectum tumour biopsies ( = 0.815), nor between Dukes’ classes A/B and C/D ( = 0.262). 16S rDNA PCR amplification combined with pyrosequencing analysis of 16S rDNA variable V3 regions provides a powerful molecular tool to identify species in human biopsy specimens.

Loading

Article metrics loading...

/content/journal/jmm/10.1099/jmm.0.46122-0
2005-11-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/jmm/54/11/JM541105.html?itemId=/content/journal/jmm/10.1099/jmm.0.46122-0&mimeType=html&fmt=ahah

References

  1. Alm R. A., Ling L. S., Moir D. T. & 20 other authors; 1999; Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori . Nature 397:176–180 [CrossRef]
    [Google Scholar]
  2. Altschul S. F., Gish W., Miller W., Lipman D. J. 1990; Basic local alignment search tool. J Mol Biol 215:403–410 [CrossRef]
    [Google Scholar]
  3. Benson D. A., Karsch-Mizrachi I., Lipman D. J., Ostell J., Rapp B. A., Wheeler D. L. 2000; GenBank. Nucleic Acids Res 28:15–18 [CrossRef]
    [Google Scholar]
  4. Blom K., Svennerholm A.-M., Böhlin I. 2002; The expression of the Helicobacter pylori genes ureA and nap is higher in vivo than in vitro measured by quantitative competitive reverse transcriptase-PCR. FEMS Immunol Med Microbiol 32:219–226 [CrossRef]
    [Google Scholar]
  5. Cohen A. M., Minsky B. D., Schilsky R. L. 1993 Colon Cancer. In Cancer: Principles and Practice of Oncology , 4th edn. Edited by DeVita V. T. Jr, Hellman S., Rosenberg S. A. Philadelphia: J. B. Lippincott;
    [Google Scholar]
  6. Cover T. L., Blaser M. J. 1992; Helicobacter pylori and gastroduodenal disease. Annu Rev Med 43:135–145 [CrossRef]
    [Google Scholar]
  7. Dukes C. E. 1932; The classification of cancer of the rectum. J Pathol 35:323–332 [CrossRef]
    [Google Scholar]
  8. Fox J. G., Correa P., Taylor N. S., Lee A., Otto G., Murphy J. C., Rose R. 1990; Helicobacter mustelae -associated gastritis in ferrets: an animal model of Helicobacter pylori gastritis in humans. Gastroenterology 99:352–361
    [Google Scholar]
  9. Fox J. G., Dangler C. A., Sager W., Borkowski R., Gliatto J. M. 1997; Helicobacter mustelae associated adenocarcinoma in ferrets ( Mustelae putorius furo ). Vet Pathol 34:225–229 [CrossRef]
    [Google Scholar]
  10. Fransén K., Klintenäs M., Österström A., Dimberg J., Monstein H.-J., Söderkvist P. 2004; Mutation analysis of the BRAF , ARAF , and RAF-1 genes in human colorectal adenocarcinomas. Carcinogenesis 25:527–533
    [Google Scholar]
  11. Grahn N., Olofsson M., Ellnebo-Svedlund K., Monstein H.-J., Jonasson J. 2003; Identification of mixed bacterial DNA contamination in broad-range PCR amplification of 16S rDNA V1 and V3 variable regions by pyrosequencing of cloned amplicons. FEMS Microbiol Lett 219:87–91 [CrossRef]
    [Google Scholar]
  12. Gray M., Sankoff D., Cedergren R. J. 1984; On the evolutionary descent of organisms and organelles: a global phylogeny based on a highly conserved structural core in small subunit ribosomal RNA. Nucleic Acids Res 12:5837–5852 [CrossRef]
    [Google Scholar]
  13. Jonasson J., Olofsson M., Monstein H.-J. 2002; Classification, identification and subtyping of bacteria based on pyrosequencing and signature matching of 16S rDNA fragments. APMIS 110:263–272 [CrossRef]
    [Google Scholar]
  14. Konturek P. C., Kania J., Konturek J. W., Nikiforuk A., Konturek S. J., Hahn E. G. 2003; H.pylori infection, atrophic gastritis, cytokines, gastrin, COX-2, PPAR and impaired apoptosis in gastric carcinogenesis. Med Sci Monit 9:SR65–SR78
    [Google Scholar]
  15. Logan R. P. 1994; Helicobacter pylori and gastric cancer. Lancet 344:1078–1079
    [Google Scholar]
  16. Marshall B. J., Warren J. R. 1983; Unidentified curved bacillus on gastric epithelium in active chronic gastritis. Lancet i:1273–1275
    [Google Scholar]
  17. Meucci G., Tatarelle M., Vecchi M., Ranzi M. L., Biguzzi E., Clerici E., de Franchis R. 1997; High prevalence of Helicobacter pylori infection in patients with colonic adenomas and carcinomas. J Clin Gastroenterol 25:605–607 [CrossRef]
    [Google Scholar]
  18. Monstein H.-J., Nikpour-Badr S., Jonasson J. 2001; Rapid molecular identification and subtyping of H.pylori by pyrosequencing of the 16S rDNA variable V1 and V3 regions. FEMS Microbiol Lett 199:103–107 [CrossRef]
    [Google Scholar]
  19. Monstein H.-J., Fransén K., Dimberg J., Söderkvist P. 2004; K- ras and B- raf mutations are not associated with gastrin and CCK2-receptor mRNA expression in human colorectal tumour tissues. Eur J Clin Invest 34:100–106 [CrossRef]
    [Google Scholar]
  20. Moss S. F., Neugut A. I., Garbowski G. C., Wang S., Treat M. R., Forde K. A. 1995; Seroprevalence and colorectal neoplasia: evidence against an association. J Natl Cancer Inst 87:762–763 [CrossRef]
    [Google Scholar]
  21. Parsonnet J., Friedman G. D., Vandersteen D. P., Chang Y., Vogelman J. H., Orentreich N., Sibley R. K. 1991; Helicobacter pylori infection and the risk of gastric adenocarcinoma. N Engl J Med 325:1127–1131 [CrossRef]
    [Google Scholar]
  22. Parsonnet J., Friedman G. D., Orentreich N., Vogelman H. 1997; Risk of gastric cancer in people with CagA positive or CagA negative Helicobacter pylori infection. Gut 40:297–301 [CrossRef]
    [Google Scholar]
  23. Semino-Mora C., Doi S. Q., Marty A., Simko V., Carlstedt I., Dubois A. 2003; Intracellular and interstitial expression of Helicobacter pylori virulence genes in gastric precancerous intestinal metaplasia and adenocarcinoma. J Infect Dis 187:1165–1177 [CrossRef]
    [Google Scholar]
  24. Shmuely H., Passaro D., Figer A., Niv Y., Pitlik S., Samara Z., Korean R., Yahav J. 2001; Relationship between Helicobacter pylori CagA status and colorectal cancer. Am J Gastroenterol 96:3406–3410 [CrossRef]
    [Google Scholar]
  25. Siddheshwar R. K., Muhammad K. B., Gray J. C., Kelly S. B. 2001; Seroprevalence of Helicobacter pylori in patients with colorectal polyps and colorectal carcinoma. Am J Gastroenterol 96:84–88 [CrossRef]
    [Google Scholar]
  26. Thompson J. D., Higgins D. G., Gibson T. J. 1994; clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680 [CrossRef]
    [Google Scholar]
  27. Thoreson A.-C. E., Borre M. B., Andersen P. & 6 other authors; 1995; Development of a PCR-based technique for detection of Helicobacter pylori . FEMS Immunol Med Microbiol 10:325–334 [CrossRef]
    [Google Scholar]
  28. Tiveljung A., Backström J., Forsum U., Monstein H.-J. 1995; Broad-range amplification and DNA sequence analysis reveals variable motifs in 16S rRNA genes of Mobiluncus species. APMIS 103:755–763 [CrossRef]
    [Google Scholar]
  29. Tomb J.-F., White O., Kerlavage A. R. & 39 other authors; 1997; The complete genome sequence of the gastric pathogen Helicobacter pylori . Nature 388:539–547 [CrossRef]
    [Google Scholar]
  30. Xiang Z., Censini S., Bayeli P. F., Telford J. L., Figura N., Covacci A. 1995; Analysis of expression CagA and VacA virulence factors in 43 strains of Helicobacter pylori reveals that clinical isolates can be divided into two major types and that CagA is not necessary for expression of the vacuolating cytotoxin. Infect Immun 63:94–98
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jmm/10.1099/jmm.0.46122-0
Loading
/content/journal/jmm/10.1099/jmm.0.46122-0
Loading

Data & Media loading...

Most cited Most Cited RSS feed