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Gene-expression-based Biomarker Predicts Long-term Risk of Breast Cancer Recurrence

A comparison of three methods of predicting the risk of recurrence in women treated for estrogen-receptor (ER)-positive breast cancer finds that only the breast cancer index (BCI) – a biomarker based on the expression levels of seven tumor-specific genes – accurately identifies patients who continue to be at risk after five years of treatment with either tamoxifen or the aromatase inhibitor anastrozole. The study comparing the BCI with two other prognostic tests has been published online in Lancet Oncology.

Study Published Showing Advantages of the PAM50 Gene Signature, the Basis for Prosigna, in Helping to Estimate Risk of Late Distant Recurrence in Postmenopausal Estrogen Receptor Positive Breast Cancer Patients

NanoString Technologies, Inc., (NASDAQ: NSTG) a provider of life science tools for translational research and molecular diagnostic products, recently announced that a study published online in the Journal of the National Cancer Institute demonstrated that the PAM50 gene signature, which is the basis for the Prosigna™ Breast Cancer Prognostic Gene Signature Assay, provides important information to help estimate the risk of late distant recurrence in postmenopausal women with estrogen receptor positive (ER+) early-stage breast cancer. After comparing the PAM50 gene signature, the Oncotype DX® Breast Cancer Assay and the IHC4 score, the authors concluded that the PAM50 gene signature provided the strongest prognostic information regarding risk of distant recurrence five to 10 years following diagnosis in postmenopausal ER+ early-stage breast cancer patients treated with five years of endocrine therapy.

Biomarker May Predict Prostate Cancers Requiring Treatment

Not all early-stage prostate cancer diagnoses are alike. While some patients have aggressive tumors, others have slow-growing, low Gleason score tumors that may not require treatment, but instead can be monitored with regular clinical evaluations. But distinguishing between prostate cancers that require treatment and those that do not is still a major challenge.

Researchers at Columbia University in New York City have now identified a 3-gene signature that could indicate whether a particular early-stage prostate cancer is indolent. The test relies on a tissue sample, and along with a prostate-specific antigen (PSA) test and a histology assessment, could help clinicians make an accurate diagnosis. The early results, including a blinded retrospective analysis of 43 patients, show that the signature can accurately predict which patients with low-risk disease would develop metastatic prostate cancer and which patients would not progress. The study is published in Science Translational Medicine.

“These types of markers will, for the first time, give us the opportunity to measure biological features of cancer in the same patient, with multiple biopsies spread out over many years,” said Eric Klein, MD, chairman, Glickman Urological and Kidney Institute at the Cleveland Clinic in Ohio.
Cory Abate-Shen, PhD, professor of urological oncology at Columbia University; Andrea Califano, PhD, professor of systems biology at Columbia University; and colleagues used a computational approach that identified three genes—FGFR1, PMP22, and CDKN1A—all associated with aging, that could accurately predict outcomes of low-risk, low Gleason score prostate tumors. Protein and mRNA levels of all three genes were high in those patients who had non-aggressive, indolent disease and low in those who had aggressive tumors.

Clinicians still rely on the Gleason score, a histology and pathology evaluation that does not incorporate any molecular assessment. Those patients with a Gleason score of 8 or higher are candidates for immediate treatment, but whether men with a score of 6 or 7 require treatment is difficult to assess—no test exists to identify the small percentage of patients who have early-stage prostate cancer that is more likely to metastasize.

The 3-gene signature was validated using an independent prostate cancer cohort. According to the study authors, the signature was prognostic and improved prognosis compared with the use of PSA and clinical assessment.

“We would predict that the test would be beneficial for patients with low Gleason score prostate tumors,” said Abate-Shen. “These patients are now typically monitored on active surveillance protocols, and the patients get a biopsy periodically. The test would be conducted on the biopsy.”

Rather than focusing on the entire genome, the researchers focused on 377 genes involved in aging, predicting that genes involved in aging and senescence are critical for tumor suppression. Cellular senescence is known to play a role in tumor suppression and is associated with benign prostate tumors both in the clinic and in mouse models, according to the researchers. Using a computational analysis called gene set enrichment analysis (GSEA), they narrowed the long gene list to 19 genes, and then to a set of 3 genes that could identify indolent tumors.

“To focus on senescence genes is intellectually interesting,” said Klein. “There is already a body of work supporting the role of these genes in prostate cancer, but to my knowledge no one has looked at them in early-stage disease before.”

Forty-three patients, who had been under active surveillance for 10 years at Columbia University Medical School, were used for the blinded retrospective analysis to assess the predictive value of the gene signature. Each patient had been diagnosed with low-risk prostate cancer, with a Gleason score of 6 or less. The test was correctly able to identify all 14 patients who eventually developed advanced prostate cancer.

CDKN1A has been shown to be linked to senescence and to regulate the cell cycle. Previous studies have shown that downregulation of the gene is linked to cancer progression. The correlation of FGFR1 (fibroblast growth factor receptor 1) with indolent tumors was surprising, as fibroblast growth factors have been shown to play a role in prostate cancer development. But, as the authors highlight in their discussion, FGFR1 signaling in prostate cancer is likely complex. The third gene in the signature, PMP22, encodes a glycoprotein expressed in neurons and has not been previously associated with prostate cancer.

This 3-gene signature is different from previously identified biomarkers, which have largely focused on advanced tumors. The potential biomarker test could complement other approaches in development, such as urine or blood tests, according to the authors.

A trial to validate the genetic signature is underway at Columbia University, and a national trial is being planned.

“It is really important to find novel ways to help to define early-stage tumors that may or may not progress to aggressive disease,” said Abate-Shen. “This will ultimately really help to minimize overtreatment, while capitalizing on the benefits of cancer screening.”

Other genomic approaches to distinguish indolent and aggressive disease are also underway. The first-generation expression-based tests, including Oncotype DX prostate and Prolaris, can facilitate clinical decisions based on the molecular characteristics of a prostate tumor. Both the available tests and the new ones “promise to reduce overtreatment and help men make the right decisions based on biology rather than uncertainty,” said Klein. 

Study: A Molecular Signature Predictive of Indolent Prostate Cancer [Science Translational Medicine]

Source: CancerNetwork

NanoString Technologies Receives FDA 510(k) Clearance for Prosigna Breast Cancer Prognostic Gene Signature Assay

NanoString Technologies, Inc., (NASDAQ: NSTG) a provider of life science tools for translational research and molecular diagnostic products, recently announced that it has received 510(k) clearance from the U.S. Food and Drug Administration (FDA) for its Prosigna™ Breast Cancer Prognostic Gene Signature Assay. Based on the PAM50 gene signature, Prosigna is the company’s first FDA-cleared in vitro diagnostic assay and uses the gene expression profile of cells found in breast cancer tissue to assess a patient’s risk of distant recurrence of disease. The Prosigna Assay is performed using the nCounter® Dx Analysis System, which can be placed in qualified laboratories throughout the United States, empowering oncologists and pathologists to quickly and easily meet the testing needs of their breast cancer patients.

“Receipt of FDA 510(k) clearance for Prosigna marks a key milestone for NanoString and is an important step forward in the treatment of breast cancer. This achievement is a testament to the ongoing dedication and professionalism of our team, and the commitment of our collaborators,” said Brad Gray, President and Chief Executive Officer of NanoString Technologies. “Prosigna illustrates our approach of using nCounter technology to translate genomic discoveries into powerful in vitro diagnostic products, and it represents a significant growth opportunity beyond our robust life sciences research business.”

The Prosigna Assay is intended for use as a prognostic indicator for distant recurrence-free survival at 10 years, and is indicated for postmenopausal women with Stage I/II lymph node-negative or Stage II lymph node-positive (one to three positive nodes) hormone receptor-positive breast cancer who have undergone surgery in conjunction with locoregional treatment consistent with standard of care. For each patient, the Prosigna Assay reports the Prosigna Score (referred to as Risk of Recurrence Score, or ROR Score, in the scientific literature, including the TransATAC study recently published in the Journal of Clinical Oncology ) and a risk category based on both the Prosigna Score and nodal status. Node-negative patients are classified as low, intermediate or high risk, while node-positive patients are classified as low or high risk.

Other key features of the Prosigna Breast Cancer Prognostic Gene Signature Assay include:

  • All-in-one assay consumables, including RNA extraction kits, allowing laboratories to test as little as a single section of formalin-fixed paraffin embedded (FFPE) tumor tissue
  • High-throughput workflow allowing each nCounter Dx Analysis System to process up to 30 patient samples per eight hour work day
  • Automated generation of personalized full-color patient reports that can be quickly and easily shared electronically with ordering oncologists

Bruce Seeley, Senior Vice President & General Manager of Diagnostics of NanoString Technologies commented: “We believe that the compelling clinical data, clear patient reporting, and unique delivery model position Prosigna for success in the U.S. market. By integrating the Prosigna Assay into existing laboratory workflows, we are offering physicians and patients seamless and timely access to clinical insights and a powerful tool that can aid in making more informed treatment decisions.”

Prosigna-enabled nCounter Dx Analysis Systems are expected to be available for placement in high-complexity Clinical Laboratory Improvement Amendments (CLIA) certified laboratories late in the fourth quarter of 2013. Prosigna testing services are expected to be available through qualified U.S. clinical laboratories beginning in the first quarter of 2014.

Source: NanoString Technologies

Study Published in The Journal of Clinical Oncology Demonstrates Advantages of NanoString’s Prosigna Breast Cancer Assay

NanoString Technologies, Inc. (NASDAQ: NSTG), a provider of life science tools for translational research and molecular diagnostic products, recently announced that the TransATAC clinical validation study for its Prosigna Breast Cancer Prognostic Gene Signature Assay, which is based on the PAM50 gene signature, was published in the Journal of Clinical Oncology (JCO). This study, portions of which were initially presented at the 2011 CTRC-AACR San Antonio Breast Cancer Symposium, evaluated the ability of three breast cancer tests to predict risk of distant recurrence after endocrine therapy in postmenopausal women with hormone receptor-positive (HR+) early-stage breast cancer. The authors of the study concluded that the PAM50-based assay provides more prognostic information in endocrine treated patients with HR+ node negative disease than Oncotype DX®, with better differentiation of intermediate and high-risk groups.

The study included 1,017 samples from the landmark ATAC (Arimidex, Tamoxifen, Alone or in Combination) trial of postmenopausal women with HR+ early-stage breast cancer treated with five years of endocrine therapy. The study was performed on RNA extracted from tumor samples by Genomic Health, Inc. for validation of the Oncotype DX® Breast Cancer Assay. The goals of the TransATAC study were to determine if the PAM50 gene signature added prognostic information to clinical-pathological variables and to compare the performance of the PAM50 risk of recurrence (ROR) score, the Oncotype DX recurrence score (RS), and the IHC4 score, derived from immunohistochemical assessment of ER, PR, HER2 and Ki67 genes, in indicating risk of distant recurrence after endocrine therapy. All primary and secondary endpoints of the study were met.

Authors of the study reported that the PAM50 ROR score added prognostic information about the risk of 10-year distant recurrence in addition to that provided by standard clinical-pathological variables in the analysis of all patients studied (p < 0.001). Similar results were achieved in all three prospectively defined clinically important subsets of patients: node-negative (p < 0.001), node-positive (p = 0.002), and HER2-negative (p < 0.001). In addition, the study reported that patients with Luminal A subtype had a lower risk of recurrence than those with the Luminal B subtype further supporting the biological differences between these groups. The authors also concluded that the PAM50 ROR score provided more prognostic information than the widely used Oncotype DX RS. Compared to Oncotype DX RS, PAM50 ROR score categorized fewer patients as intermediate-risk and more as high-risk when using prospectively defined risk cutoffs for low, intermediate and high risk of <10%, 10% to 20% and >20% estimated risk of recurrence, respectively. Moreover, the authors concluded that the PAM50 ROR score provided at least as much information as the IHC4 and may provide more information than IHC4 in the node negative/HER2 negative patient group.

“The publication of the TransATAC study is an important milestone in our ongoing effort to enable genomic testing for breast cancer in local laboratories worldwide,” said Brad Gray, President and Chief Executive Officer of NanoString Technologies. “We look forward to discussing the results and conclusions of this study with oncologists, pathologists, and payers in the European Union and other countries that recognize the CE Mark, as we continue with our commercial launch in those regions.”

Study: Comparison of PAM50 Risk of Recurrence Score With Oncotype DX and IHC4 for Predicting Risk of Distant Recurrence After Endocrine Therapy

Source: Business Wire