Tracking Changes in Protein Isoforms
Gary Nelsestuen, Ph.D., professor at the University of Minnesota in Minneapolis, maintains that a growing body of evidence points to the absence of a single new clinical test that has resulted from proteomics studies.
“Most ‘bottom-up’ methods are expensive and suffer from inconsistent protein detection. Perhaps, instead of striving to identify as many proteins as possible, we should focus on approaches that analyze just a few proteins but with excellent predictive value,” he says.
Dr. Nelsestuen’s work focuses on MALDI-TOF analysis of intact protein isoforms. While seemingly low-tech, this approach allows the screening of a large number of samples in a reproducible and cost-efficient manner.
Profiling of a 5,000 blood/urine sample set representing a wide variety of disease states revealed important information about biological variations in normal populations.
“We found that isoform ratios are consistent for each individual,” continues Dr. Nelsestuen. “At the same time, even if the individual ratio falls within the ‘normal’ range, a person may be still very ill. This necessitates comparison of each individual to his/her own baseline to improve the ability to detect change in health status.”
Change of isoform ratio related to health outcomes is illustrated by the analysis of glyco-isoforms of intact apolipoprotein C3 (ApoC3). A 1.8-fold change in the glyco-isoform ratios correlated with obesity, specifically among subjects eligible for bariatric surgery.
Bariatric surgery resulted in the rapid change of isoform distribution to that of non-obese individuals, after which the distribution was stable in each individual. Similarly, glyco-isoform ratios were indicative of chronic hepatitis C, liver cirrhosis, and sepsis.
The information provided by glyco-isoform ratio changes may provide important, novel information for diagnostic, prognostic, and therapy response to metabolic conditions. However, it requires monitoring of each patient over time.
“Our method was sufficient to provide clinically important information for monitoring kidney transplants,” says Dr. Nelsestuen. “The health of transplanted kidneys is often monitored by frequent biopsies. A non-invasive urine analysis for anomalous protein biomarkers would provide significant advantage over current clinical practice.”
Remarkably, two ubiquitous isoforms of saposin B, thought to be an activator of lipid degradation, were low or absent in patients with advanced kidney disease, while a number of other components appeared. The team is combining this data with metabolomics profiling to identify early diagnostic biomarkers.