Copy number-based quantification assay for non-invasive detection of PVT1-derived transcripts

Autoři: Gargi Pal aff001;  Olorunseun O. Ogunwobi aff001
Působiště autorů: Department of Biological Sciences, Hunter College of The City University of New York, New York, NY, United States of America aff001;  Hunter College Center for Cancer Health Disparities Research, New York, NY, United States of America aff002;  Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, United States of America aff003
Vyšlo v časopise: PLoS ONE 14(12)
Kategorie: Research Article
doi: 10.1371/journal.pone.0226620



One of the most important susceptibility loci for cancer is the 8q24 human chromosomal region. The non-protein coding gene locus plasmacytoma variant translocation 1 (PVT1) is located at 8q24 and is dysregulated in prostate cancer. PVT1 gives rise to multiple transcripts which may have different functions. Here, we describe a real-time quantitative polymerase chain reaction (qPCR)-based assay for copy number-based quantitation of PVT1 exons 4A, 4B, and 9 to enable accurate, reproducible, and quantifiable detection.


PVT1 exons 4A, 4B, and 9 were cloned into a plasmid vector to create standards for subsequent creation of linear standard curves representing a broad range of concentrations. PCR was carried out using SYBR-Green signal detection to quantify PVT1 exons 4A, 4B, and 9. The efficacy of this assay was evaluated by using it to detect these transcripts in prostate epithelial and prostate cancer cell lines, normal and cancerous human prostate tissues, human serum, mouse plasma, and urine samples.


The results indicate that the assay can be used to quantify both low and high copy numbers of PVT1-derived transcripts. This is the first report of a copy number-based quantification assay for non-invasive detection of PVT1 derived transcripts.


This novel assay holds promise for routine non-invasive testing in diseases where PVT1 is dysregulated.

Klíčová slova:

Biomarkers – Blood plasma – Long non-coding RNAs – Plasmid vectors – Polymerase chain reaction – Prostate cancer – Prostate gland – Urine


1. Yang Z, Li X, Yang Y, He Z, Qu X, Zhang Y. Long noncoding RNAs in the progression, metastasis, and prognosis of osteosarcoma. Cell Death Dis. 2016;7: e2389. doi: 10.1038/cddis.2016.272 27685633

2. Fang Y, Fullwood MJ. Roles, Functions, and Mechanisms of Long Non-coding RNAs in Cancer. Genomics Proteomics Bioinformatics. 2016;14: 42–54. doi: 10.1016/j.gpb.2015.09.006 26883671

3. Ghoussaini M, Song H, Koessler T, Al Olama AA, Kote-Jarai Z, Driver KE, et al. Multiple loci with different cancer specificities within the 8q24 gene desert. J Natl Cancer Inst. 2008;100: 962–966. doi: 10.1093/jnci/djn190 18577746

4. Wang F, Ni H, Sun F, Li M, Chen L. Overexpression of lncRNA AFAP1-AS1 correlates with poor prognosis and promotes tumorigenesis in colorectal cancer. Biomed Pharmacother. 2016;81: 152–159. doi: 10.1016/j.biopha.2016.04.009 27261589

5. Siegel RL, Miller KD, Jemal A. Cancer statistics, 2018. CA Cancer J Clin. 2018;68: 7–30. doi: 10.3322/caac.21442 29313949

6. Global Burden of Disease Cancer Collaboration, Fitzmaurice C, Allen C, Barber RM, Barregard L, Bhutta ZA, et al. Global, Regional, and National Cancer Incidence, Mortality, Years of Life Lost, Years Lived With Disability, and Disability-Adjusted Life-years for 32 Cancer Groups, 1990 to 2015: A Systematic Analysis for the Global Burden of Disease Study. JAMA Oncol. 2017;3: 524–548. doi: 10.1001/jamaoncol.2016.5688 27918777

7. Shenoy D, Packianathan S, Chen AM, Vijayakumar S. Do African-American men need separate prostate cancer screening guidelines? BMC Urol. 2016;16: 19. doi: 10.1186/s12894-016-0137-7 27165293

8. Meyer KB, Maia A-T, O’Reilly M, Ghoussaini M, Prathalingam R, Porter-Gill P, et al. A Functional Variant at a Prostate Cancer Predisposition Locus at 8q24 Is Associated with PVT1 Expression. PLoS Genet. 2011;7: e1002165. doi: 10.1371/journal.pgen.1002165 21814516

9. Datta D, Aftabuddin M, Gupta DK, Raha S, Sen P. Human Prostate Cancer Hallmarks Map. Sci Rep. 2016;6: 30691. doi: 10.1038/srep30691 27476486

10. Xu J, Sun J, Zheng SL. Prostate cancer risk-associated genetic markers and their potential clinical utility. Asian J Androl. 2013;15: 314–322. doi: 10.1038/aja.2013.42 23564047

11. Evans S, Metcalfe C, Ibrahim F, Persad R, Ben-Shlomo Y. Investigating Black-White differences in prostate cancer prognosis: A systematic review and meta-analysis. Int J Cancer. 2008;123: 430–435. doi: 10.1002/ijc.23500 18452170

12. Evans S, Metcalfe C, Patel B, Ibrahim F, Anson K, Chinegwundoh F, et al. Clinical presentation and initial management of black men and white men with prostate cancer in the United Kingdom: the PROCESS cohort study. Br J Cancer. 2010;102: 249–254. doi: 10.1038/sj.bjc.6605461 19935788

13. Cuzick J, Thorat MA, Andriole G, Brawley OW, Brown PH, Culig Z, et al. Prevention and early detection of prostate cancer. Lancet Oncol. 2014;15: e484–92. doi: 10.1016/S1470-2045(14)70211-6 25281467

14. Hessels D, Schalken JA. The use of PCA3 in the diagnosis of prostate cancer. Nat Rev Urol. 2009;6: 255–261. doi: 10.1038/nrurol.2009.40 19424173

15. Saini S. PSA and beyond: alternative prostate cancer biomarkers. Cell Oncol. 2016;39: 97–106.

16. Loeb S, Partin AW. Review of the literature: PCA3 for prostate cancer risk assessment and prognostication. Rev Urol. 2011;13: e191–5. 22232568

17. Garitano-Trojaola A, Agirre X, Prósper F, Fortes P. Long non-coding RNAs in haematological malignancies. Int J Mol Sci. 2013;14: 15386–15422. doi: 10.3390/ijms140815386 23887658

18. Yang J, Li C, Mudd A, Gu X. LncRNA PVT1 predicts prognosis and regulates tumor growth in prostate cancer. Biosci Biotechnol Biochem. 2017;81: 2301–2306. doi: 10.1080/09168451.2017.1387048 29050519

19. Wan B, Wu H-Y, Lv D-J, Zhou X-M, Zhong L-R, Lei B, et al. Downregulation of lncRNA PVT1 expression inhibits proliferation and migration by regulating p38 expression in prostate cancer. Oncol Lett. 2018;16: 5160–5166. doi: 10.3892/ol.2018.9305 30250582

20. Mendy ME, Kaye S, van der Sande M, Rayco-Solon P, Waight PA, Shipton D, et al. Application of real-time PCR to quantify hepatitis B virus DNA in chronic carriers in The Gambia. Virol J. 2006;3: 23. doi: 10.1186/1743-422X-3-23 16594999

21. Welzel TM, Miley WJ, Parks TL, Goedert JJ, Whitby D, Ortiz-Conde BA. Real-Time PCR Assay for Detection and Quantification of Hepatitis B Virus Genotypes A to G. J Clin Microbiol. 2006;44: 3325–3333. doi: 10.1128/JCM.00024-06 16954268

22. Potter NT, Hurban P, White MN, Whitlock KD, Lofton-Day CE, Tetzner R, et al. Validation of a real-time PCR-based qualitative assay for the detection of methylated SEPT9 DNA in human plasma. Clin Chem. 2014;60: 1183–1191. doi: 10.1373/clinchem.2013.221044 24938752

23. Hymas WC, Aldous WK, Taggart EW, Stevenson JB, Hillyard DR. Description and validation of a novel real-time RT-PCR enterovirus assay. Clin Chem. 2008;54: 406–413. doi: 10.1373/clinchem.2007.095414 18039718

24. Shen MM, Abate-Shen C. Molecular genetics of prostate cancer: new prospects for old challenges. Genes Dev. 2010;24: 1967–2000. doi: 10.1101/gad.1965810 20844012

25. Shtivelman E, Henglein B, Groitl P, Lipp M, Bishop JM. Identification of a human transcription unit affected by the variant chromosomal translocations 2;8 and 8;22 of Burkitt lymphoma. Proc Natl Acad Sci U S A. 1989;86: 3257–3260. doi: 10.1073/pnas.86.9.3257 2470097

26. Huppi K, Siwarski D, Skurla R, Klinman D, Mushinski JF. Pvt-1 transcripts are found in normal tissues and are altered by reciprocal(6;15) translocations in mouse plasmacytomas. Proceedings of the National Academy of Sciences. 1990;87: 6964–6968.

27. Derderian C, Orunmuyi AT, Olapade-Olaopa EO, Ogunwobi OO. PVT1 Signaling Is a Mediator of Cancer Progression. Front Oncol. 2019;9: 502. doi: 10.3389/fonc.2019.00502 31249809

28. Ogunwobi OO, Kumar A. Chemoresistance Mediated by ceRNA Networks Associated With the PVT1 Locus. Front Oncol. 2019. doi: 10.3389/fonc.2019.00834 31508377

29. Ogunwobi OO, Ilboudo A. Abstract A77: PVT1 exon 9 overexpression as a potential biomarker of prostate cancer in black men. Cancer Epidemiol Biomarkers Prev. 2015;24: A77–A77.

30. Ilboudo A, Chouhan J, McNeil BK, Osborne JR, Ogunwobi OO. PVT1 Exon 9: A Potential Biomarker of Aggressive Prostate Cancer? Int J Environ Res Public Health. 2015;13: ijerph13010012.

31. Das DK, Ogunwobi OO. Abstract 1473: miR-1207-3p regulates c-Myc in aggressive prostate cancer. Cancer Res. 2017;77: 1473–1473.

32. Orunmuyi AT, Ilboudo A, Ogun OG, Bach C, Adebayo SA, Salako AA, et al. Abstract 3507: PVT1 exons 4A, 4B, and 9 are overexpressed in aggressive prostate cancer, and PVT1 exon 4B may distinguish between indolent and aggressive prostate cancer. Cancer Res. 2017;77: 3507–3507.

33. Guo K, Yao J, Yu Q, Li Z, Huang H, Cheng J, Wang Z, Zhu Y.The expression pattern of long non-coding RNA PVT1 in tumor tissues and in extracellular vesicles of colorectal cancer correlates with cancer progression. Tumor biology; 2017: 1–12.

34. Ling H, Vincent K, Pichler M, Fodde R, Berindan-Neagoe I, Slack FJ, et al. Junk DNA and the long non-coding RNA twist in cancer genetics. Oncogene. 2015;34: 5003–5011. doi: 10.1038/onc.2014.456 25619839

35. Ding J, Li D, Gong M, Wang J, Huang X, Wu T, et al. Expression and clinical significance of the long non-coding RNA PVT1 in human gastric cancer. Onco Targets Ther. 2014; 1625.

36. Yang Y-R, Zang S-Z, Zhong C-L, Li Y-X, Zhao S-S, Feng X-J. Increased expression of the lncRNA PVT1 promotes tumorigenesis in non-small cell lung cancer. Int J Clin Exp Pathol. 2014;7: 6929–6935. 25400777

37. Huang C, Yu W, Wang Q, Cui H, Wang Y, Zhang L, et al. Increased expression of the lncRNA PVT1 is associated with poor prognosis in pancreatic cancer patients. Minerva Med. 2015;106: 143–149. 25668599

38. Bronson PG, Chang D, Bhangale T, Seldin MF, Ortmann W, Ferreira RC, et al. Common variants at PVT1, ATG13-AMBRA1, AHI1 and CLEC16A are associated with selective IgA deficiency. Nat Genet. 2016;48: 1425–1429. doi: 10.1038/ng.3675 27723758

39. Liu H-T, Fang L, Cheng Y-X, Sun Q. LncRNA PVT1 regulates prostate cancer cell growth by inducing the methylation of miR-146a. Cancer Med. 2016;5: 3512–3519. doi: 10.1002/cam4.900 27794184

40. Madu CO, Lu Y. Novel diagnostic biomarkers for prostate cancer. J Cancer. 2010; 150–177. doi: 10.7150/jca.1.150 20975847

41. Zauli DAG, de Menezes CLP, de Oliveira CL, Mateo ECC, de Souza Ferreira AC. In-house quantitative real-time PCR for the diagnosis of hepatitis B virus and hepatitis C virus infections. Braz J Microbiol. 2016;47: 987–992. doi: 10.1016/j.bjm.2016.07.008 27637170

42. Ren X, Cao D, Yang L, Li X, Zhang W, Xiao Y, Xi Y, Li F,4, Li D, Pan Z. High Expression of long non-coding RNA PVT1 predicts metastasis in Han and Uygur Patients with Gastric Cancer in Xinjiang, China. Sci. Rep. 2019: 9:548. doi: 10.1038/s41598-018-36985-x 30679629

43. Ballester M, Castelló A, Ibáñez E, Sánchez A, Folch JM. Real-time quantitative PCR-based system for determining transgene copy number in transgenic animals. BioTechniques 37:610–613. doi: 10.2144/04374ST06 15517974

44. Joshi MU, Pittman HK, Haisch CE, Verbanac KM, Real-time PCR to determine transgene copy number and to quantitate the biolocalization of adoptively transferred cells from EGFP-transgenic mice. BioTechniques 45:247–258. doi: 10.2144/000112913 18778249

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2019 Číslo 12