CASE STUDY: Researchers Discover Potential Diagnostic Tool for Alzheimer’s Disease with Help of Partek Software
Tuesday, September 8, 2015 - 14:04

As the world population ages, Alzheimer’s disease will become a significant socio-economic burden to the health care system. That’s why Dr. Lesley Cheng of La Trobe University, who recently moved from The University of Melbourne, set out to identify the disease specific exosomal microRNA (miRNA) biomarkers associated with Alzheimer’s disease (AD) in serum using deep-sequencing technology. 

“Current diagnostic tests for AD need to be greatly improved to allow early detection and preventative strategies to be implemented when they can do the most good. With numerous drug trials aiming to treat AD currently in development, a non-invasive and high throughput diagnostic test would be ideal to monitor benefits and side effects of therapeutic drugs.” according to Dr. Cheng.

Exosomes contain miRNAs and act as an intercellular delivery mechanism as they shuttle between neighboring and distant cells as a mode of cell-to-cell communication. The composition of miRNAs can therefore reflect the physiological state of an individual. By comparing exosomal miRNAs in individuals with and without Alzheimer’s disease, one can potentially discover useful biomarkers of the disease.

To find peripheral AD biomarkers, Dr. Cheng explained that she and her team isolated exosomal microRNA from the serum of 49 healthy controls and subjects with AD. They then sequenced the samples using the Ion Torrent™ Ion Personal Genome Machine® and analyzed the data using Partek® Genomics Suite®. This allowed them to identify a panel of 16-exosomal miRNAs that were differentially expressed in AD subjects compared to controls. After successfully validating the 16-exosomal miRNAs using qRT-PCR, they examined a second cohort of 60 subjects. AD prediction using the 16-exosomal miRNA panel resulted in a sensitivity of 87% and specificity of 77%. Furthermore, brain-imaging of healthy subjects incorrectly classified with AD suggested a progression towards the disease. This suggests that an exosomal miRNA signature may be a suitable peripheral screening tool for predicting early onset AD.

When asked how this study lessens the AD burden, Dr. Cheng replied, “This project represents a vital step towards developing a cost-effective, non-invasive and low risk diagnostic test to detect the AD onset and to monitor its various stages in order for physicians to provide optimal care for patients.”

One of the challenges Dr. Cheng faced with this study was that “There are almost no analyses pipelines that cater to small RNA analysis and handle normalization of small RNA data. Exosomes do not contain endogenous RNA so we had to explore different normalization methods.” She went on to say “Partek Genomics Suite provided us the ability to upload our own BED files for novel small RNA and to explore various types of normalization methods to suit exosomal samples. In addition, it provides an easy, user-friendly interface which allows all members of the lab to analyze data without having a strong bioinformatics background and provides publication quality images.”

Though Dr. Cheng’s team had an in-house analyse pipeline, it wasn’t sufficient. “Before using Partek Genomics Suite we had a simple in-house pipeline, however it could not handle more than ten run files. This was problematic as most of our studies involve large cohorts. Partek Genomics Suite has provided us a platform to analyze large amounts of samples relatively quickly without having to upload samples to a webserver or rely on a fast internet connection.” To read more about Dr. Cheng’s study, access the full paper. 

With the addition of Partek Genomics Suite to Dr. Cheng’s lab, her team has a tool that can take their research to new levels with much more ease than ever before. We look forward to following her team’s future research. 

If you would like to try Partek Genomics Suite for yourself, get a free two-week trial.

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Exosomes provide a protective and enriched source of miRNA for biomarker profiling compared to intracellular and cell-free blood
Lesley Cheng, Robyn A. Sharples, Benjamin J. Scicluna, and Andrew F. Hill
www.ncbi.nlm.nih.gov/pmc/articles/PMC3968297