Featured Research

from universities, journals, and other organizations

Potential of protein-measurement technique to standardize quantification of entire human proteome

Date:
December 8, 2013
Source:
Fred Hutchinson Cancer Research Center
Summary:
A new study affirms the use of large-scale protein measurements to validate disease biomarkers and drug targets.

An international team of scientists led by Fred Hutchinson Cancer Research Center cancer proteomics expert Amanda Paulovich, M.D., has demonstrated the feasibility of large-scale, standardized protein measurements, which are necessary for validation of disease biomarkers and drug targets.

The study, to be published Dec. 8 online in the journal Nature Methods, shows that the scientists' targeted protein-detection approach has the potential to systematically and reliably measure the entire human repertoire of proteins, known as the proteome.

The technique, developed by Paulovich, a member of Fred Hutch's Clinical Research Division, and her colleagues, can simultaneously and precisely detect the abundance of hundreds of proteins in many different samples. Researchers from three different groups in Seattle, Boston and South Korea were able to reproduce measurements of 319 proteins from human breast cancer cells, showing that the method can be standardized across laboratory and international boundaries.

"This method has the potential to completely revolutionize how we measure human proteins," Paulovich said. "Having a global resource for standardized quantification of all human proteins would set new standards that would undoubtedly increase the reproducibility of preclinical research, which would have a dramatic impact on the translation of novel therapeutics and diagnostics."

Proteins, the molecular workhorses of all biological functions, hold the key to signaling early disease and disease progression. Cancer biomarkers are especially sought after -- the protein fingerprints in cells could lead to tests to detect the disease earlier, to identify a person's specific risk of cancer long before it develops, and to better guide patients' treatments. But validating newly discovered biomarker candidates has proven impossible without standardized and reproducible methods to measure their levels, Paulovich said.

Each promising biomarker must be further studied in clinical trials, which requires researchers to measure the abundance of each candidate biomarker in hundreds to thousands of patient samples. Because the odds are extraordinarily low that any one candidate will translate to clinical use, large numbers of proteins must be tested to identify a clinically useful biomarker.

"Right now, you can't make robust measurements of most human proteins," Paulovich said. "More than 10 years after the human genome has been sequenced and we have the full catalog of molecules as important as proteins, we still can't study the human proteome with any kind of throughput in a standardized, quantitative manner."

To address this problem, Paulovich and her colleagues used a sensitive and targeted protein-measurement technology called multiple reaction monitoring mass spectrometry, or MRM-MS. This type of mass spectrometry is not new -- it has been used for years in clinical laboratories worldwide to measure drug metabolites and small molecules associated with inborn errors of metabolism. More recently, Paulovich and others have begun using it to measure human proteins.

The researchers' method enables highly specific, precise, multiplex (meaning the technique measures several different proteins in a single experimental assay) quantification of a minimum of 170 proteins in 20 clinical samples per instrument per day; no other existing technology has this power.

Because the mass spectrometry technique is targeted, meaning the researchers can tune the instruments to look for a specific subset of proteins in cancer cells or other sample types, it can detect the presence of proteins of interest at much lower levels in tiny blood samples or biopsies than a non-targeted tactic.

"The goal is to position this technology to displace some very old technologies that are currently being used," said Jacob Kennedy, an analytical chemist in Paulovich's group and lead author of the study.

Currently, researchers usually use either Western blotting, ELISA (enzyme-linked immunosorbent assay), or immunohistochemistry (IHC) techniques to measure levels of proteins in clinical samples. These methods are often not reproducible from laboratory to laboratory, rendering validation of candidate biomarkers for clinical use very difficult, and they cannot be used for large numbers of proteins and samples at once.

Paulovich and her colleagues assayed more than 300 proteins known to be produced by breast cancer cells to validate their technique; their results showed that MRM-MS could recapitulate and extend observations made in previous studies of breast cancer using other technologies.

The study, which included collaborating research groups from the Broad Institute in Cambridge, Mass., and the Seoul National University and Korea Institute of Science and Technology, South Korea, demonstrated MRM-MS's capacity to measure many proteins at once in a standardized way, laying the foundation for an international, organized effort to quantitate every protein in the human proteome. Their study -- the largest to demonstrate the technique's reproducibility across laboratories and the only international study to do so -- has pushed the capacity of the technology the farthest, measuring hundreds of protein pieces where others have measured dozens.

"We really showed what could happen if governments cooperated to build a community resource," she said. "It's doable, it's scalable, and the resource is useful."

Paulovich's team hopes the technique catches on in research communities around the world. To facilitate this, her group is spearheading the development of an open-source website to create a centralized resource of highly validated assays for the research community.


Story Source:

The above story is based on materials provided by Fred Hutchinson Cancer Research Center. Note: Materials may be edited for content and length.


Journal Reference:

  1. Amanda Paulovich, M.D. et al. Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins. Nature Methods, December 2013

Cite This Page:

Fred Hutchinson Cancer Research Center. "Potential of protein-measurement technique to standardize quantification of entire human proteome." ScienceDaily. ScienceDaily, 8 December 2013. <www.sciencedaily.com/releases/2013/12/131208133358.htm>.
Fred Hutchinson Cancer Research Center. (2013, December 8). Potential of protein-measurement technique to standardize quantification of entire human proteome. ScienceDaily. Retrieved October 22, 2014 from www.sciencedaily.com/releases/2013/12/131208133358.htm
Fred Hutchinson Cancer Research Center. "Potential of protein-measurement technique to standardize quantification of entire human proteome." ScienceDaily. www.sciencedaily.com/releases/2013/12/131208133358.htm (accessed October 22, 2014).

Share This



More Plants & Animals News

Wednesday, October 22, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Working Mother DIY: Pumpkin Pom-Pom

Working Mother DIY: Pumpkin Pom-Pom

Working Mother (Oct. 22, 2014) How to make a pumpkin pom-pom. Video provided by Working Mother
Powered by NewsLook.com
Cadaver Dogs Aid Search for More Victims of Suspected Indiana Serial Killer

Cadaver Dogs Aid Search for More Victims of Suspected Indiana Serial Killer

Reuters - US Online Video (Oct. 21, 2014) Police in Gary, Indiana are using cadaver dogs to search for more victims after a suspected serial killer confessed to killing at least seven women. Linda So reports. Video provided by Reuters
Powered by NewsLook.com
Trick-or-Treating Banned Because of Polar Bears

Trick-or-Treating Banned Because of Polar Bears

Buzz60 (Oct. 21, 2014) Mother Nature is pulling a trick on the kids of Arviat, Canada. As Mara Montalbano (@maramontalbano) tells us, the effects of global warming caused the town to ban trick-or-treating this Halloween. Video provided by Buzz60
Powered by NewsLook.com
White Lion Cubs Unveiled to the Public

White Lion Cubs Unveiled to the Public

Reuters - Light News Video Online (Oct. 21, 2014) Visitors to Belgrade zoo meet a pair of three-week-old lion cubs for the first time. Tara Cleary reports. Video provided by Reuters
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:

Breaking News:

Strange & Offbeat Stories


Plants & Animals

Earth & Climate

Fossils & Ruins

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:

Free Subscriptions


Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile: iPhone Android Web
Follow: Facebook Twitter Google+
Subscribe: RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins