Scientists publish seminal paper and announce project to develop biomarkers of aging

November 21, 2016, Biogerontology Research Foundation

Today the Biogerontology Research Foundation announced the international collaboration on signaling pathway perturbation-based transcriptomic biomarkers of aging. On November 16th scientists at the Biogerontology Research Foundation alongside collaborators from Insilico Medicine, Inc, the Johns Hopkins University, Albert Einstein College of Medicine, Boston University, Novartis, Nestle and BioTime Inc. announced the publication of their proof of concept experiment demonstrating the utility of a novel approach for analyzing transcriptomic, metabolomic and signalomic data sets, titled iPANDA, in Nature Communications.

"Given the high volume of data being generated in the life sciences, there is a huge need for tools that make sense of that data. As such, this new method will have widespread applications in unraveling the molecular basis of age-related diseases and in revealing biomarkers that can be used in research and in clinical settings. In addition, tools that help reduce the complexity of biology and identify important players in disease processes are vital not only to better understand the underlying mechanisms of age-related disease but also to facilitate a personalized medicine approach. The future of medicine is in targeting diseases in a more specific and personalized fashion to improve clinical outcomes, and tools like iPANDA are essential for this emerging paradigm," said Joao Pedro de Megalhaes, PhD, a trustee of the Biogerontology Research Foundation.

The algorithm, iPANDA, applies to complex gene expression data sets and signal pathway activation data for the purposes of analysis and integration, and their proof of concept article demonstrates that the system is capable of significantly reducing noise and dimensionality of transcriptomic data sets and of identifying patient-specific pathway signatures associated with that characterize their response to Toxicol-based neoadjuvant therapy.

The system represents a substantially new approach to the analysis of microarray data sets, especially as it pertains to data obtained from multiple sources, and appears to be more scalable and robust than other current approaches to the analysis of transcriptomic, metabolomic and signalomic data obtained from different sources. The system also has applications in rapid biomarker development and , discrimination between distinct biological and clinical conditions, and the identification of functional pathways relevant to disease diagnosis and treatment, and ultimately in the development of personalized treatments for .

"iPANDA represents a significant contribution to the emerging application of algorithms to transcriptomic and signalomic data analysis, and is a substantial extension of the approach the team put forward previously through their OncoFinder algorithm. The capacity of iPANDA to reduce the dimensionality of transcriptomic and signalomic makes it a very useful tool in rapid biomarker development and accelerated drug discovery, in formulating personalized treatments to promote improved clinical outcomes, in bringing the results of in silico analyses closer to their experimental counterparts, and in the analysis of transcriptomic and signalomic data originating from multiple sources. While the team predicted and compared the response of breast cancer patients to Taxol-based neoadjuvant therapy as their proof of concept, the application of this approach to patient-specific responses to biomedical gerontological interventions (e.g. to geroprotectors, which is a clear focus of the team's past efforts), to the development of both generalized and personalized biomarkers of ageging, and to the characterization and analysis of minute differences in ageging over time, between individuals, and between different organisms would represent a promising and exciting future application" said Franco Cortese, Deputy Director of the Biogerontology Research Foundation.

"This latest achievement on the part of Alex Zhavoronkov and his team is yet another step toward greater heights and bolder frontiers in the application of deep learning to personalized medicine, biomarker characterization and accelerated drug discovery. The publication of this proof-of-concept experiment in Nature Communications is a testament to the importance of their latest accomplishment, to the substantial progress that the team has made over the past 2 years, and to the great heights and ground-breaking achievements that they are sure to reach in the years to come. It represents yet another successful validation of the usefulness of their entire approach - namely, the application of deep learning to biomedicine, geroscience and P3 (personalized, precision and preventative) medicine." said Dmitry Kaminskiy, Managing Trustee of the Biogerontology Research Foundation.

Explore further: Personalized medicine leads to better outcomes for patients with cancer

More information: Ivan V. Ozerov et al, In silico Pathway Activation Network Decomposition Analysis (iPANDA) as a method for biomarker development, Nature Communications (2016). DOI: 10.1038/NCOMMS13427

Related Stories

Personalized medicine leads to better outcomes for patients with cancer

June 6, 2016
In a meta-analysis of hundreds of clinical trials involving thousands of patients, researchers at University of California San Diego School of Medicine report that therapeutic approaches using precision medicine, which emphasizes ...

BGRF announces OncoFinder algorithm for reducing errors in transcriptome analysis

August 18, 2014
Scientists from the Biogerontology Research Foundation (BGRF), a UK-based charity founded to support ageing research and address the challenges of a rapidly ageing population, propose a new concept for signalome-wide analysis ...

A vision for medicine precision with new disease data link-up

March 23, 2016
Vast amounts of data generated by screening patients for diseases like cancer and arthritis at The University of Manchester will now be used to improve treatment and drug safety in partnership with the University of Dundee.

Precision medicine can widen cancer care options: studies (Update)

June 4, 2016
Using a patient's individual tumor biomarkers to determine the best treatment can improve success rates, studies showed Saturday.

Researchers report clinical utility of personalized medicine program for cancer patients

June 1, 2016
Scientists from the Icahn School of Medicine at Mount Sinai developed and tested a personalized cancer therapy program using an integrated genomic approach that led to therapeutic recommendations for 91 percent of patients. ...

Recommended for you

Bioprinting bone substitute materials with cell-laden bioinks

August 21, 2018
Bone tissue engineering (BTE) is a developing field in materials science and bioengineering, in which researchers aim to engineer an ideal, bioinspired material to promote assisted bone repair. Since experimental strategies ...

I hear what you say! Or do I?

August 21, 2018
Even with an acute sense of hearing adults don't always pick up exactly what someone has said. That's because from childhood to adulthood we rely on vision to understand speech and this can influence our perception of sound.

How do muscles know what time it is?

August 21, 2018
How do muscle cells prepare for the particular metabolic challenges of the day? Scientists at Helmholtz Zentrum München and Ludwig-Maximilians-Universität München (LMU), members of the German Center for Diabetes Research ...

High-speed atomic force microscopy reveals clock protein interactions

August 21, 2018
For the first time, researchers have seen how proteins involved in the daily biological clock interact with each other, helping them to further understand a process tied to numerous metabolic and eating disorders, problems ...

Could vitamin B3 treat acute kidney injury?

August 20, 2018
Acute kidney injury, an often fatal condition without a specific treatment, affects up to 10 percent of all hospitalized adults in the United States and 30-40 percent in low-income countries. The condition causes a build-up ...

New assay to detect genetic abnormalities in sarcomas outperforms conventional techniques

August 20, 2018
Sarcomas are rare tumors that are often misdiagnosed. Specific recurrent chromosomal rearrangements, known as translocations, can serve as essential diagnostic markers and are found in about 20 percent of sarcomas. Identification ...

0 comments

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.