proteomics: the branch of genetics that studies the full set of proteins encoded by a genome
ge·nome: The total genetic content contained in a haploid set of chromosomes in eukaryotes, in a single chromosome in bacteria, or in the DNA or RNA of viruses; an organism’s genetic material
One of the most valuable pieces of advice we are given in life is to share: if people share what they have – be it time, space, resources or talent – chances are they will reap the rewards. That is exactly what the U.S. Army Edgewood Chemical Biological Center (ECBC) and the U.S. Army Medical Research Institute of Chemical Defense (USAMRICD) are doing with a groundbreaking new facility, the Proteomics Core Facility. This is an unprecedented shared resource designed to support basic and applied research projects that will apply a broad but integrated biological approach to a wide variety of chemical, biological, radiological, nuclear and high-yield explosives (CBRNE) issues.
“Both ECBC and MRICD saw this as a need,” says Jennifer Sekowski, Ph.D., DABT, molecular toxicologist and ECBC lead for standing up the Proteomics Core Facility. “We already had some individual proteomics and genomics tools at hand, but knew we both needed to expand our toolset,” she says. “Rather than duplicate the capabilities, why not build our capabilities in one joint facility? Having a combined Genomics and Proteomics Core now allows us to more easily share our resources, provide new training opportunities and expand the amount and type of research we both can do.”
The Proteomics Core Facility is in proximity to ECBC’s state-of-the-art Genomics Laboratory at Aberdeen Proving Ground, which USAMRICD can utilize. Additionally, USAMRICD has an exceptional transcriptomics core facility, which can be utilized by ECBC scientists. Together, the organizations can support the Defense Threat Reduction Agency (DTRA) Joint Science and Technology Office (JSTO), the National Institutes of Health and other sponsored research in the areas of whole genomic sequencing and finishing, whole transcriptome analysis (RNA-Seq), array-based mRNA and microRNA analysis. With the newly added equipment, ECBC and USAMRICD can extend their research utilizing mass spectrometry-based proteomics, high content image analysis of cells and tissues, and gel-based imaging.
“This revolutionary joint capability is a wonderful illustration of the cooperation and collaboration across the Aberdeen Proving Ground Edgewood campus,” says Joseph Wienand, ECBC’s technical director. “In this time of fiscal awareness, it is a great example of our nation’s leading scientists working together to share resources and save funding while working toward the common goal of the protection of our soldiers and our nation.”
Colonel Bruce Schoneboom, USAMRICD Commander, is excited to see this unique facility officially launch. “The fact that two organizations came together to build a joint capability is a wonderful testament to the true spirit of collaboration in support of common scientific research, and I hope that this serves as a great example for other installations,” says Col. Schoneboom. “I am very excited to see the great strides the talented MRICD and ECBC staff will take in proteomics and genomics research.”
The initial infrastructure funds to create the Proteomics Core Facility originated from the Office of the Assistant Secretary of Defense for Chemical and Biological (CB) Defense, and was augmented by both ECBC and USAMRICD investments. One key goal is the support of the DTRA-JSTO FY13 Systems Biology of emerging threats project, a multi-year, multi-institutional project aimed at biomarker and toxicological target discovery. The Proteomics Core Facility will be used to support the DTRA-JSTO CB Defense Program, and USAMRICD and ECBC missions to protect the Warfighter from the harmful effects of chemical and biological agents.
ECBC scientists will focus their research efforts on the detection and understanding of exposures to toxins, and traditional and emerging chemical and biological threat agents. This knowledge is translated into the development of more capable masks and uniforms for the Warfighter as well as more effective decontamination materials.
USAMRICD scientists will focus their research efforts toward a thorough, foundational knowledge and understanding of the toxicology of chemical agents, toxic industrial chemicals, and toxins for the development of therapeutics and prophylactic treatments to protect Warfighters and civilians. Through this work, researchers will develop and test countermeasures to protect against the acute and long-term effects of exposure to such agents.
“We are so excited to see all of our efforts come to fruition with the launch of this facility. We have already initiated several projects and look forward to the development of a broader medical and non-medical understanding of and response to chemical and biological threats,” says Sekowski.
ECBC and USAMRICD scientists currently work on independent projects in the Core, but the Systems Biology of emerging threats project will be a new collaborative systems biology project that is just getting started.
ECBC and USAMRICD scientists have been joining forces for more than a year to build the Proteomics Core Facility. Instrumental in the development of the facility were Peter Emanuel, Ph.D., chief of the R&T BioSciences Division; James Dillman, Ph.D., Chief, USAMRICD Research Programs Office; Mary Wade, Ph.D., chief of the R&T Point Detection Branch; Heidi Hoard-Fruchey, Ph.D., USAMRICD Molecular Toxicology Team Lead; Rabih Jabbour, Ph.D., ECBC Research Chemist Point Detection Branch; James Wright, M.S., ECBC Chemist and Proteomics Core Facility Manager; and Jennifer Sekowski, Ph.D., ECBC molecular toxicologist and lead for standing up the Proteomics Core. Non-agent research operations began in August, with the official launch of the facility in October.
Looking Ahead: Why the Work in the Proteomics Facility Matters
Imagine this scenario: A chemical attack hits a major city. From the heart of the attack to the perimeter, thousands of people could have been exposed to a chemical agent. All those who are able rush to nearby hospitals with a rapid heartbeat, trouble breathing, excessive sweating and tearing. These could be signs of a panic attack, or could be physiological symptoms of exposure to the agent. The medical staff is overwhelmed and supplies are running short. Those who were near the attack site can’t make it to the hospital, so medical staff must go to them. Best-case scenario? All are able to be treated quickly and accurately, reducing potentially immense casualties. The reality? Supplies run short because people who were not actually exposed received treatment, or the correct course of treatment for those exposed was not given.
This is a sensationalized example of a very real need: quick and accurate diagnosis of exposure to a toxicant to better triage patients, and the identification of the agent so proper treatment can be administered.
From Diagnostics to Detection, Treatment, Countermeasures
DTRA-JSTO is currently funding projects at ECBC to research and develop rapid diagnostic tools to determine if someone has been exposed to a chemical or biological agent; a comprehensive understanding of how the cells communicate with the overall system after it has been exposed to an agent; and countermeasures against such agents. This collaborative work is being conducted using the highly sophisticated instruments and technology in the core facility.
Scientists and researchers with ECBC’s Research & Technology Directorate are collaborating with USAMRICD, Johns Hopkins Medical Institution, Centers for Disease Control (CDC), the Netherlands Organization and the Johns Hopkins University Applied Physics Lab to look for biomarkers, which are detectable molecules in the body that can give an indication of exposure to a foreign toxicant or disease.
ECBC’s Toxicology Division, in collaboration with the CDC, is currently testing methods for extracting acetylcholinesterase (AChE) from red blood cells and breaking them down to identify the agent that has bound to the active site polypeptides. This differs from one of the current practices, which focuses on butyrylcholinesterase (BChE) active site polypeptides as an indication of agent exposure. Though BChE is easier to isolate, it is variable within a population and less specific than AChE. AChE is the main target of nerve agents which, when inhibited in the nervous system, can cause severe effects and possibly death.
|The Proteomics Core Facility currently includes:
1) Thermo Orbitrap Velos Elite LC-MS
2) Agilent 6520 Q-TOF LC-MS
3) Agilent 6490 Triple Quadrupole LC-MS
4) Thermo Cellomics ArrayScan VTI
5) GE Typhoon TRIO Plus Scanner
6) Sage-N Research Enterprise server
“AChE in the red blood cells, unlike BChE in the plasma, is identical for all practical purposes to AChE in the nervous system. Therefore, one significant advantage of this new method is that it will be more specific of agents that attack the nervous system. Second, since AChE in the blood is associated with red blood cells, we don’t have the issue of variance that we currently have with BChE,” says Mike Jakubowski, Ph.D., acting chief of the Operational Toxicology Branch. “With the advanced capabilities of the proteomics and genomics center at ECBC, we can use the instrumentation to develop this unique method to detect and identify agent exposure in an individual.”
This type of diagnostic capability allows the medical staff to detect what agent the patient has been exposed to – or if they have even been exposed – so they can more accurately treat the individual. Not all agents require the same level of treatment; it can be possible for particularly resistant agents to remain in the body and redistribute over time, leading to prolonged or repeat illness.
Sekowski is leading a team of researchers using a systems biology systems approach to address two main goals: discovery of exposure biomarkers and the discovery of new targets for countermeasure development. By using a systems biology approach, the interacting toxic pathways of a given toxicant can be measured at the organism, organ system, tissue, cellular and molecular level. Out of all this data, a more complete picture can be reconstructed for which molecules might work best as biomarkers to enable more rapid and accurate diagnosis, as well as for which molecules in the body serve as targets for prophylactic or therapeutic drugs that can be developed to block a toxicant’s effect.
Their biomarkers work has the same end goal of the work being done by the Toxicology Branch, but is approaching the research from another angle. Sekowski, along with USAMRICD and members of R&T’s, BioChemistry, BioDefense, BioSensors, Point Detection and Chemistry Branches, are looking at two different biomarkers in the blood: mRNA, the transcript that comes off of DNA when it is expressed, or “turned on,” and microRNAs, which are very stable in the blood and have a very high ability to relay valuable information about transcriptional regulation.
The team is also utilizing phosphoproteomics, a form of proteomics that catalogs certain protein modified by phosphate groups, as a tool to identify and understand signaling mechanisms that are affected by exposure to an agent. When a molecule interacts with a receptor on the surface of a cell, it causes a chemical cascade, called a signal transduction. The team is looking to take apart that signal transduction to understand what happens during that process, and how the communication process works. This area could lead to exciting discoveries regarding the specific toxic pathways of chemical agents.
“This is both basic and applied research. Once we understand some of the signaling cascades, or understand which proteins interact with the agent directly, we may find we already have a drug that could mitigate some or all of the effects of exposure to an agent,” says Sekowski. “Or, perhaps there’s a target receptor or a modification of a signaling cascade that we can target for development of a new drug. Overall, in this project, we‘re starting with multiple types of basic research data and beginning to build models that can better explain how toxicants exert their toxic effects so that we can learn how to better predict and counter those effects.”
In addition, ECBC Point Detection Branch has developed and patented an algorithm, Agents of Biological Organs Identification, ABOID©, for the detection and identification of microbes without prior knowledge of the sample. ABOID© can provide a bioforensic profile of the sample, including present pathogen and background microbes. It uses taxonomic classification that helps classify unsequenced or emerging biothreats with their closest near neighbor microbes. ABOID© has been validated with numerous blinded microbial samples originating from culture, food, blood, saliva, environmental and biological matrices. Point Detection Branch was the recipient of the 2009 DTRA Basic Research Award for their work in the area of proteomics-based mass spectrometry detection of biological agents to include development of ABOID©. This algorithm development and testing is a testament to the chemical and biological techniques using the proteomics facility.
Article contributed by ECBC, the Army’s principal research and development center for chemical and biological defense technology, engineering and field operations. ECBC has achieved major technological advances for the warfighter and for our national defense, with a long and distinguished history of providing the Armed Forces with quality systems and outstanding customer service. ECBC is a U.S. Army Research, Development and Engineering Command laboratory located at the Edgewood Area of Aberdeen Proving Ground.