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An unexpected finding arising from this study of the p53 tumor suppressor gene

Posted by miguelromero on 18 Oct 2015 at 12:18 GMT

In their paper studying the tumor suppressing activities of p53 Katharina Schlereth and colleagues used chromosomal material derived from cultures of two cell lines, Saos-2 and U2OS, both originating in patients with osteogenic sarcomas.  Given that their transcript was made with 18 runs (68.3 Gbp; 48.1Gb) it appears that they sequenced the total cellular DNA of their cell lines, which they generously made available at http://goo.gl/9qojw6.  BLASTN 1 analyses of these sequences rather surprisingly returned the presence of several sequences coding for the HIV-1 proteins 2.  Summary of these BLASTN results are at http://tiny.cc/muft4x and a PDF sample at https://goo.gl/1mDNQf.  Do the authors have an explanation for these unexpected findings?  Could it be that sometime between 1964 and 1973 (when the cell lines were developed) they have become  contaminated? 3  Or are HIV-1 sequences a marker for malignancy, as reported in the late 1990s by Rakowicz-Szulczynska in breast, ovarian and prostate cancers? 4,5,6.

""References:""


1. Agostino M. Introduction to the BLAST Suite and BLASTN. Practical Bioinformatics: Garland Science; 2012: 396.

2. Korber B, Foley B, Kuiken C, Pillai S, Sodroski J. HIV sequence database: Numbering Positions in HIV Relative to HXB2CG. 2008.
3. Romero Fernández-Bravo M. Contamination of genomic databases by HIV-1 and its possible consequences. A study in Bioinformatics. 2014. http://hdl.handle.net/106...
4. Rakowicz-Szulczynska EM. Viral markers RAK in early diagnosis and therapy of breast, ovarian, uterine, and prostate cancers. In: Diamandis E, Fritsche H, Lilja H, Chan D, Schwartz M, eds. Tumor markers: Physiology, Pathobiology, Technology, and Clinical Applications: American Association for Clinical Chemistry; 2002.

5. Rakowicz-Szulczynska EM, Jackson B, Szulczynska AM, Smith M. Human immunodeficiency virus type 1-like DNA sequences and immunoreactive viral particles with unique association with breast cancer. Clin Diagn Lab Immunol. Sep 1998;5:645-653.

6. Rakowicz-Szulczynska EM, Jackson B, Snyder W. Prostate, breast and gynecological cancer markers RAK with homology to HIV-1. Cancer Lett. Feb 27 1998;124:213-223.

No competing interests declared.