Prostate Cancer Biomarkers: Improvement in Predicting Clinically Significant Disease

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Richard J. Boxer, MD, FACS

The doctor needs to balance the results of the markers with the common sense and clinical judgment of treating only those whose life will be impacted more by the disease than by the treatment.

—Richard J. Boxer, MD, FACS

Prostate cancer will be diagnosed in 233,000 American men in 2014. It is one of the leading causes of death by a cancer (killing ~29,500 men annually).1 Hundreds of thousands of men undergo prostate biopsies each year, most for either benign disease or for a cancer that will never lead to their death. Basic and clinical scientists have been focused on discovering or refining tumor markers that can differentiate between benign and malignant prostate disease and between prostate cancer that will cause death and that which will never have a serious impact on the patient’s life. American men have a 16% chance of being diagnosed, but only a 3% chance of dying from prostate cancer.

Search for Tumor Markers

Each year, nearly 30 million Americans have a prostate-specific antigen (PSA) blood test. It has been hailed and reviled by PSA researcher Richard J. Ablin, PhD, DSc (Hon), Professor of Pathology at the University of Arizona, Tucson.2 “In approving the procedure, the Food and Drug Administration [FDA] relied heavily on a study that showed testing could detect 3.8 percent of prostate cancers, which was a better rate than the standard method, a digital rectal exam,” he wrote.

The race for discovery of more accurate tumor markers (ie, resulting in fewer false-positives and false-negatives, or greater accuracy for clinically significant disease) has produced many new markers or combinations of markers that will lead to better predictive value.

Prostate Health Index

The Prostate Health Index (phi), approved by the FDA in 2012, combines the measurements of protein-free and protein-attached PSA along with a subcategory of free PSA, known as pro-PSA. “The phi can play a valuable role in determining whether an elevated PSA is likely due to prostate cancer or benign changes,” said Brant Thrasher, MD, Chair of Urology, University of Kansas Medical Center, Kansas City. “This option may prevent patients from potentially undergoing unnecessary biopsies.”

PCA3 Test

The test for prostate cancer antigen 3 (PCA3) gene (formerly known as DD3) has not been approved by the FDA, but some research and reference laboratories are offering it. The PCA3 urine test measures a non–protein-coding messenger RNA that is highly overexpressed in prostate cancer tissue as compared to benign prostate tissue. The proposed utilization for the PCA3 test is to help decide whether to biopsy or rebiopsy and whether a positive biopsy should lead to curative therapy (surgery or radiation).

Recent reports describe the use of PCA3 testing to identify patients with aggressive vs indolent prostate cancer. Results of studies have been mixed. If the PCA3 test is found to correlate with disease prognosis, it could be a valuable tool in identifying patients who are better treated with expectant management (eg, aggressive follow-up of the tumor without radical treatment intervention) vs those better treated with curative therapy (eg, surgery or radiation therapy).

Speaking at the recent International Prostate Cancer Symposium in Vail, Colorado, Alan W. Partin, MD, PhD, Chairman of the James Buchanan Brady Urological Institute and David Hall McConnell Professor, Director, and Urologist-in-Chief at Johns Hopkins Medicine, Baltimore, said this about the PCA3 test: “If the score was greater than 60, the positive predictive value of having prostate cancer—meaning you should get a biopsy—was 80%, and that is pretty good for a biomarker. And those of us who have been using PCA3 for years now realize there are 10% to 15% of the people coming in the door with values that are above 60.”


The 4Kscore is a blood test developed by OPKO Diagnostics that measures the serum levels of four different prostate-derived kallikrein proteins: total PSA, free PSA, intact PSA, and hK2.3 Levels of these biomarkers are combined with a patient’s age and digital rectal exam status using a proprietary algorithm to calculate the probability of finding aggressive prostate cancer.

The 4Kscore test is based on over a decade of research of the four-kallikrein panel of biomarkers conducted by scientists at Memorial Sloan Kettering Cancer Center and leading research centers in Europe on over 10,000 patients. The information provided by the 4Kscore test has been reported to facilitate the shared decision-making process between urologist and patient in determining the advisability of a prostate biopsy.

Stephen M. Zappala, MD, FACS, of Andover Urology, Andover, Massachusetts, recently stated, “The 4Kscore test offers new information on the probability of having a Gleason score ≥ 7 cancer prior to undergoing a prostate biopsy. This is important, because we know that besides the potential side effects of biopsy such as bleeding and infection, up to 80% of prostate biopsies will either be negative for prostate cancer or will indicate a low-grade disease that may be better monitored than treated. The 4Kscore test will offer both the urologist and patient new information for the shared decision-making discussion about whether or not to have a prostate biopsy.”

TMPRSS2-ERG Fusion Transcript

The test for the TMPRSS2-ERG gene fusion measures an androgen-regulated transcription factor found in the urine. Through a rearrangement on chromosome 21, TMPRSS2 can get fused to ERG, which is a member of the ETS oncogene family. This is found to be an early event in prostatic intraepithelial neoplasia and atypia, as well as prostate cancer.

Dr. Partin, quoting data from Jack Groskopf, PhD, Senior Director, Research and Development at Hologic Gen-Probe,4 said that by coupling these two assays—PCA3 score and TMPRSS2-ERG score—“you come up with a level between 1 and 5 to determine what your probabilities [of having prostate cancer] are. So if you are at level 5 for both of those assays, you are up at around a 75% to 80% chance of having cancer, a 75% to 80% chance of significant cancer, and over a 40% chance that it’s higher than grade 6.”

Single Nucleotide Polymorphisms

As described by the National Institutes of Health (NIH),5 “single nucleotide polymorphisms, frequently called SNPs (pronounced ‘snips’), are the most common type of genetic variation among people. Each SNP represents a difference in a single DNA building block, called a nucleotide. For example, a SNP may replace the nucleotide cytosine (C) with the nucleotide thymine (T) in a certain stretch of DNA.”

The NIH reference continues:

SNPs occur normally throughout a person’s DNA. They occur once in every 300 nucleotides on average, which means there are roughly 10 million SNPs in the human genome. Most commonly, these variations are found in the DNA between genes. They can act as biologic markers, helping scientists locate genes that are associated with disease. When SNPs occur within a gene or in a regulatory region near a gene, they may play a more direct role in disease by affecting the gene’s function.

Most SNPs have no effect on health or development. Some of these genetic differences, however, have proven to be very important in the study of human health. Researchers have found SNPs that may help predict an individual’s response to certain drugs, susceptibility to environmental factors such as toxins, and risk of developing particular diseases. SNPs can also be used to track the inheritance of disease genes within families.

SNPs have been investigated as a marker for prostate cancer. William ­Isaacs, PhD, Professor of Urology at Johns Hopkins Medical School and researchers at the Karolinska Institute in Sweden as well as researchers at deCODE Genetics in Reykjavik, Iceland, have studied SNPs as a marker for prostate cancer.6

Dr. Isaacs found five SNPs—three on chromosome 8 and two on chromosome 17—that relate to prostate cancer. If a patient had all five of those SNPs, the odds ratio for developing prostate cancer was ninefold higher.

The Karolinska group looked at 5,000 men using this SNP technology and found that they could avoid prostate biopsy in 22% of the patients, about the same as when using the PCA3 and TMPRSS2-ERG tests. However, using SNPs did not miss the aggressive cancers.

The researchers at deCODE Genetics, looking at 300,000 SNPs in 23,000 Icelanders, could predict prostate cancer. This was repeated in the United States in 15,000 men in seven different cohorts, and the predictive results were confirmed.

According to Dr. Partin, “[The results of evaluating the appropriate area of the genome for SNPs has demonstrated that] if you have none of the SNPs, there is a 5% risk of prostate cancer, … and if you have all eight of them, there is an 80% risk you are going to develop prostate cancer.”


Exosomes are one of many different subpopulations of microvesicles that can be isolated from biofluids such as blood, urine, and cerebrospinal fluid, and from which high-quality RNA and DNA can be extracted and purified for analysis. Exosomes are shed by cells under both normal and pathologic

In an article published online in Frontiers in Genetics,7 exosomal microRNAs (miRNAs) were identified as possible markers with great specificity for prostate cancer. The authors explained:

miRNAs are small non-coding RNAs that finely regulate gene expression in cells. Alterations in miRNA expression have been associated with development of cancer, and miRNAs are now being investigated as biomarkers for cancer as well as other diseases. Extracellular miRNAs exist in different forms—associated with Ago2 proteins, loaded into extracellular vesicles (exosomes, microvesicles, or apoptotic bodies) or into high density lipoprotein particles. These extracellular miRNAs are probably products of distinct cellular processes, and might therefore play different roles. However, their functions in vivo are currently unknown. In spite of this, they are considered as promising, non-invasive diagnostic, and prognostic tools.

Science and Common Sense

Cancer biomarkers are extraordinarily important to initial diagnosis and follow-up care. They are measured for accuracy by their specificity and sensitivity. Sensitivity measures the proportion of actual positives that are correctly identified as such, whereas specificity measures the proportion of negatives that are correctly identified as such. A perfect predictor would be 100% sensitive (ie, predicting all people from the sick group as sick) and 100% specific (ie, not predicting anyone from the healthy group as sick).

Prostate cancer markers have evolved from acid phosphatase decades ago that commonly indicated metastatic disease, to PSA that has led to too many biopsies and curative treatments and does not distinguish clinically significant disease, to the more sophisticated markers described in this commentary. What the patient needs is a marker that will determine whether clinically significant disease is present. The doctor needs to balance the results of the markers with the common sense and clinical judgment of treating only those whose life will be impacted more by the disease than by the treatment. The biomarkers described above are pushing back the lack of specificity and sensitivity to give both the patient and the doctor what they need. ■

Dr. Boxer is Visiting Professor of Urology and Scholar in Residence (Business of Science Center) at the David Geffen School of Medicine at UCLA.  He is also a Professor of Clinical Urology at the University of Wisconsin–Madison.

Disclosure: Dr. Boxer reported no potential conflicts of interest.


1. American Cancer Society: Cancer Facts & Figures 2014. Atlanta, American Cancer Society, 2014. Available at

2. Ablin RJ: The great prostate mistake. New York Times. March 9, 2010. Available at

3. OPKO Health, Inc, website. Available at

4. Hologic Gen-Probe website. Available at

5. National Institutes of Health: What are single nucleotide polymorphisms (SNPs)? Available at

6. deCODE genetics website. Available at

7. Hessvik NP, Sandvig K, Llorente A: Exosomal miRNAs as biomarkers for prostate cancer. Front Genet. March 21, 2013 (early release online).

Disclaimer: This commentary represents the views of the author and may not necessarily reflect the views of ASCO.