Methods of using PVT1 exon 9 to diagnose and treat prostate cancer

#This application refers to a “Sequence Listing” listed below, which is provided as an electronic document entitled “Sequence.txt” (8 kb created on Nov. 5, 2016) which is incorporated herein by reference in its entirety.

#Prostate cancer (PCa) is the most common non-cutaneous cancer and the second leading cause of cancer-related death for men in the U.S. It is estimated that, in 2015, approximately 220,800 new cases of PCa will be diagnosed and 27,540 deaths will result from PCa. African Americans have the highest incidence of PCa in the world, with an annual average of 229 per 100,000 men for the period of 2006-2010, which represents about two-fold more than Caucasian Americans. PCa is also the leading cancer in terms of incidence and mortality in men from Africa and the Caribbean. Consequently, African ancestry is a very important risk factor.

#PCa is a heterogeneous disease, with multiple risks factors. The specific reasons for poor outcomes from PCa in males of African ancestry (MoAA) when compared to Caucasian males (CM) are not understood. However, it is widely believed that the causes of PCa disparities are complex and multifaceted. Two potential reasons are frequently proposed to explain this profound disparity in PCa: (1) MoAA present more often than CM with advanced incurable PCa due to more limited access to health care; (2) PCa is biologically more aggressive in MoAA than CM, and can be attributed to environmental and/or genetic risk factors.

#So that the manner in which the features of the invention can be understood, a detailed description of the invention may be had by reference to certain embodiments, some of which are illustrated in the accompanying drawings. It is to be noted, however, that the drawings illustrate only certain embodiments of this invention and are therefore not to be considered limiting of its scope, for the scope of the invention encompasses other equally effective embodiments. The drawings are not necessarily to scale, emphasis generally being placed upon illustrating the features of certain embodiments of the invention. In the drawings, like numerals are used to indicate like parts throughout the various views. Thus, for further understanding of the invention, reference can be made to the following detailed description, read in connection with the drawings in which:

#FIG. 1 is schematic depiction of the PCa susceptibility locus;

#FIG. 2A, FIG. 2B and FIG. 2C are graphs depicting expression of PVT1 exons 1a; 1b and 1c in non-tumorigenic and tumorigenic prostate epithelial cell lines;

#Prostate cancer has been shown to be associated with single nucleotide polymorphisms around regions 2 and 3 of the 8q24 human chromosomal region. The non-protein coding gene locus Plasmacytoma Variant Translocation 1 (PVT1) is located at 8q24 and is overexpressed in PCa and, therefore, is also a candidate biomarker to explain the well-known disparity among males of African ancestry. PVT1 has at least twelve exons that make separate transcripts which may have different functions, all of which are, at present unknown, in PCa. The disclosed study determined if any PVT1 transcripts play a role in aggressiveness and racial disparity in PCa. A panel of seven PCa cell lines was used, including three derived from males of African ancestry. Ribonucleic acid extraction, complementary deoxyribonucleic acid synthesis, and quantitative polymerase chain reaction (qPCR) were performed to evaluate expression of all twelve PVT1 exons. Each qPCR was performed in quadruplicates. At least four separate qPCR experiments were performed. Expression of PVT1 exons was inconsistent except for exon 9. There was no significant difference in exon 9 expression between cell lines derived from Caucasian males (CM), and an indolent cell line derived from males of African ancestry. However, exon 9 expression in the aggressive MDA PCa 2b and E006AA-hT cell lines derived from males of African ancestry was significantly higher than in other cell lines. Consequently, differential expression of exon 9 of PVT1 was observed in a manner that suggests that PVT1 exon 9 may be associated with aggressive PCa in males of African ancestry.

#FIG. 1 depicts the PCa susceptibility locus. The PVT1 gene locus expresses several alternatively spliced non-protein coding transcripts and it also encodes a cluster of microRNAs. However, no specific functional role for any of these transcripts has been identified. PVT1 is located downstream of MYC. It has a size of over 300 kb and, since its discovery in the mid-80s, it has been proven to play an important role in cancer. The upregulation of PVT1 has been found to be involved in poor prognosis in colorectal cancer and gastric cancer. In non-small cell lung cancer, it promotes tumorigenesis. In PCa, PVT1 has been found to have an increased expression in comparison to normal prostate tissue with the presence of a newly identified functional PCa specific genetic variant, rs378854. PVT1 encodes for several transcripts, approximately twelve exons, and their differential expression has not previously been investigated. Consequently, in the present disclosure data on the relative expression of the twelve different exons of PVT1 in models representative of a wide variety of clinical PCa. Observations indicate that exon 9 of PVT1 is significantly overexpressed in PCa derived from aggressive PCa in MoAA, thus suggesting the potential for clinical utility in this population group least served by current management strategies.

#Cell Lines