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Berg and Medical University of South Carolina Announce First of Its Kind Collaboration to Discover Lupus Biomarker

Berg and the Medical University of South Carolina recently announced a strategic partnership, designed to identify new therapeutic pathways and potential biomarkers to treat Lupus, the autoimmune disease affecting one in every 2,000 people and one in every 250 young African American women.

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

Study Expands Use of Biomarker for Early Diagnosis of Acute Kidney Injury

A biomarker test developed initially to identify early acute kidney injury (AKI) after surgery has been shown to successfully detect AKI in emergency room patients with a variety of urgent health issues.

In a study published online Sept. 5 in the Clinical Journal of the American Society of Nephrology, the findings expand the overall utility and potential medical settings for using the test, according to researchers.

The test measures the protein neutrophil gelatinase-associated lipocalin (NGAL) as a biomarker of early AKI. It was invented by researchers at Cincinnati Children’s Hospital Medical Center to detect AKI earlier than existing methods, and to more promptly begin treatment.

“The majority of our studies on NGAL have been performed in well controlled settings of hospital-acquired AKI, such as cardiac surgery, contrast administration or other critically ill patients,” said Prasad Devarajan, MD, senior author and director of Nephrology and Hypertension at Cincinnati Children’s. “The purpose of this study was to determine the biomarker’s accuracy in a diverse group of patients admitted from the emergency department, where patients with early signs of AKI are often misdiagnosed.”

The study involved patients admitted through the emergency room of Fernando Fonseca Hospital in Portugal, which also closely collaborated on the study. The findings demonstrate the NGAL test, which uses a single drop of blood and provides results within 15 minutes, was able to accurately distinguish AKI from reversible transient kidney dysfunction.

Of 616 patients who participated in the study, individuals who were subsequently diagnosed with true AKI had the highest levels of NGAL detected at the time of hospital admission. The study also identified a cutoff point in NGAL levels above which the risk of acute kidney injury increases tenfold.

Results of a study previously published in 2008 by Devarajan showed that the NGAL test predicted AKI in pediatric heart surgery patients within hours instead of days, allowing treatment that prevented serious damage to kidneys. Prior to the NGAL test, serum creatinine was the only reliable method for detecting kidney damage; however, the long wait for results often resulted in permanent kidney damage.

With a growing number of patients coming to emergency rooms with community-acquired AKI, Devarajan says having a rapid, reliable method of detecting kidney injury is increasingly important.

“This latest study showed that this simple laboratory test provides an accurate prediction of acute kidney injury and its severity in a diverse clinical setting,” said Devarajan. “The identification of biomarkers that differentiate intrinsic AKI from transient reversible forms of renal dysfunction and predict outcomes is a high priority.”

Study: Plasma NGAL for the Diagnosis of AKI in Patients Admitted from the Emergency Department Setting [Clinical Journal of the American Society of Nephrology]

Source: EurekAlert!

Exosome Diagnostics Enters Collaboration Agreement with Lilly for Exosome Blood-Based Biomarker Discovery

Exosome Diagnostics recently announced it has entered into a collaboration agreement with Eli Lilly and Company (NYSE: LLY) for biomarker discovery and validation using Exosome Diagnostics proprietary EXO50 nucleic acid extraction kit. Under the agreement, Lilly will gain early access to Exosome Diagnostics technology to help identify key gene mutations and expression levels in blood that may be correlated with drug response and disease recurrence. Financial terms were not disclosed.

“Exosome Diagnostics technology may provide a unique opportunity to gain insight into the biology of complex conditions such as cancer and immune disorders,” said Andrew Schade, senior medical director, diagnostic and experimental pathology at Lilly. “Exosome technology enables biofluid molecular sampling and the ability to monitor disease progression in real time. As Lilly explores new ways to pursue patient tailoring, we’ll continue to work with partners to expand our capabilities.”

“Accessing high quality messenger and microRNA directly from frozen patient fluid samples offers a rapid, cost-effective route to identify and validate biomarkers, which may be correlated with drug response and disease recurrence,” said James McCullough, chief executive officer of Exosome Diagnostics. “Lilly has accumulated an extensive and well annotated clinical blood sample biobank that provides a unique opportunity to track target biomarkers through the clinical trial process and help overcome the limitations of stored biopsy tissue.”

Exosomes and other microvesicles are secreted by all cells into all biofluids, and provide a natural biological packaging and distribution mechanism for RNA and DNA. Exosome Diagnostics’ rapid exosome isolation and extraction technology produces high-quality RNA and DNA, including full length mRNA and microRNA, from small volumes of patient biofluids, such as blood (serum and plasma), urine and cerebrospinal fluid, for analysis by standard PCR, array and sequencing instruments. Analysis can be performed on fresh or frozen fluid samples, allowing for broad, flexible and convenient analyses of clinical trial samples, both in real-time and retrospectively, with no special preservation methods required. Exosomes and their protected nucleic acid contents are being investigated in a broad range of diseases including cancer, CNS disorders such as Alzheimer’s and Parkinson’s disease, cardiovascular disease, maternal/fetal medicine, and chronic kidney disease, among others. In July, QIAGEN and Exosome Diagnostics signed an agreement for the creation of High-Performance Biofluid Sample Preparation Kits for Personalized Healthcare Research which covers the exclusive supply of these products upon availability in 2014.

Source: Exosome Diagnostics

Researchers Develop Rapid, Cost-effective Early Detection Method for Organ Transplant Injury

A recently reported blood test for the early detection of organ transplant injury could enable more timely therapeutic intervention in transplant patients and thus help to avoid longer term damage. As described by scientists at the University Medical Center Göttingen and Chronix Biomedical, a molecular diagnostics company, the new method uses Bio-Rad Laboratories’ Droplet Digital PCR (ddPCR™) technology to overcome the obstacles of earlier tests, which were both time-consuming and costly. The method was presented at the American Association of Clinical Chemistry (AACC) 2013 annual meeting and has been accepted for publication in Clinical Chemistry.

Approximately 28,000 organ transplantations (known as grafts) are performed each year in the U.S., with another 100,000 patients on waiting lists. However, transplant patients are often subject to organ rejection: acute rejection of liver transplants within three years is nearly 22 percent, while heart and lung rejection is close to 50 percent. In addition, nearly half of all of kidney transplants fail within 10 years.

Graft-derived cell-free DNA (GcfDNA) in the circulation of transplant recipients is a potential rejection biomarker. But previous attempts to determine GcfDNA, which require parallel sequencing of donor and recipient DNA, are expensive and require a long turnaround and use of donor DNA. University Medical Center Göttingen and Chronix Biomedical researchers sought to develop a new method in an attempt to address these drawbacks.

Using ddPCR for Fast, Cost-Effective Test

The researchers applied Bio-Rad’s ddPCR technology to quantify graft-derived cfDNA in recent liver transplant patients and in stable patients who had undergone a transplant procedure more than six months earlier. ddPCR technology allowed them to develop a cost-effective and fast laboratory test that detects cfDNA being released into the blood stream by dying cells from the transplanted organ.

“GcfDNA from dying graft cells are the most direct and sensitive indicator of organ rejection and we needed an instrument that could measure it,” said Chronix Biomedical’s Chief Technology Officer and the study’s senior author, Ekkehard Schuetz, MD, PhD. “ddPCR added an additional level of reliability and precision to traditional PCR.”

Sequencing methods typically require batch sampling, but by using ddPCR, researchers are able to run single samples. Additionally, this method is reducing test time from three days or more to one day and costs by 90 percent. The study authors were able to address the need for donor DNA by preselecting SNPs that ensure enough heterogeneity between donor and recipient. The new blood test can also deliver results up to several days before the conventional aspartate aminotransferase (AST) and bilirubin tests for liver transplantation rejection, with the potential for an immediate positive impact on patient care.

“We will now be able to detect subclinical rejection and early intervention may allow us to avoid a full-blown rejection,” said Michael Oellerich, M.D., FACB, FRCPath and Lower Saxony Distinguished Professor of Clinical Chemistry at the University Medical Center Göttingen and study Principal Investigator. “This test may be useful to personalize immunosuppression and to improve long-term outcomes.”

“Detecting non-host cfDNA is the third example for the commercial potential of cfDNA diagnostics. Researchers will now be able to extend the applications from fetal cfDNA in maternal blood and personalized biomarkers for minimal residual disease in cancer to solid organ transplantation,” said Howard Urnovitz, PhD, Chronix Biomedical’s Chief Executive Officer.

“We are looking forward to the improvements in precision medicine we can offer with ddPCR and this example in transplantation highlights the diagnostic value for the technology,” said Paula Stonemetz, Director Diagnostic Business Development, Digital Biology Center, Bio-Rad Laboratories.

The researchers were awarded a National Academy of Clinical Biochemistry (NACB) Distinguished Abstract Award at the 2013 AACC annual conference. The results are part of a larger planned study to determine if cfDNA is the earliest indication of a transplant organ rejection.

Source: EurekAlert!