Polymorphic L1 transposons as a Genetic Variable Distinguishing Aggressive from Indolent Prostate Cancer

The development and approval of new drugs (such as PARP inhibitors) marks a breakthrough in
prostate cancer treatment. Despite this progress, metastatic prostate cancer remains a lethal
disease highlighting a critical need for discovery of biomarkers and development of tests that can
timely identify prostate cancer patients who are at highly elevated risk for developing metastatic
disease before it appears. Having such a test would allow clinicians to treat these patients early
to stop disease progression to its aggressive form.
The proposed study identifies predictive biomarkers and describes useful clinical testing for their
presence in the human genome. Our preliminary analysis of Whole Genome Sequencing (WGS)
datasets and samples from our unique cohort of prostate cancer patients shows that specific
polymorphic L1 retrotransposons (pL1s) are enriched in the genomes of patients with metastatic
prostate cancer, meaning that this genetic variable is a potential new and powerful marker of
aggressive disease. Prior work has shown that pL1s can contribute to cancer by insertional
mutagenesis. Our findings show that in addition to previously reported insertional mutagenesis,
pL1s cause large genomic deletions, making the presence of more pL1s in some patients'
genomes highly relevant to prostate cancer progression. Furthermore, we have developed and
experimentally validated the utility of a novel, high throughput method for detection of pL1s in
human DNA. This method is more sensitive and cost effective than WGS, making performing a
case-control study of genomic pL1 content on hundreds or thousands of samples possible.
Capitalizing on these findings and methods, we hypothesize that a high number of specific pL1s
present in the genomes of prostate cancer patients is associated with an increased risk of
developing metastatic disease because these elements drive genomic instability and, thus,
disease progression. We propose two specific aims that use our unique cohort composed of
patients with either indolent or aggressive prostate cancers, available WGS datasets, and our
novel methodologies to test this hypothesis. Aim 1 will perform a case-control study to identify
pL1s present in genomes of prostate cancer patients in our cohort. Aim 2 will perform targeted
sequencing of genes frequently mutated in metastatic prostate cancer to identify pL1-associated
mutations and novel mechanisms by which pL1s may contribute to cancer progression.
By interrogating the genomes of ~400 prostate cancer patients for the presence of pL1s and for
mutations in genes relevant to prostate cancer, the proposed study will determine whether the
number and/or composition of pL1s in patient genomes (alone or in combination with identified
gene mutations) is positively associated with aggressive prostate cancer and to determine the
frequency of mutagenic events cause by pL1s in specific genes. The long-term outcome of the
success of this proposal will be clinically ready reliable genetic tests prospectively identifying men,
including Veterans, who are at high risk of developing aggressive prostate cancer. The test could
be performed using blood DNA at any time, including prior to prostate cancer diagnosis.

Grant Number: 5I01BX005633-03
NIH Institute/Center: VA
Principal Investigator: Victoria Belancio