Multidimensional advancement of neuroproteomics

Abstract

Tim Veenstra is the Director of the Laboratory of Proteomics and Analytical Technologies at the National Cancer Institute at Frederick, MD, USA. Veenstra acquired his PhD in biochemistry from the University of Windsor, Canada, in 1994 under the guidance of Lana Lee. He then moved to the laboratory of Rajiv Kumar at the Mayo Clinic in Rochester, MN, USA, where he completed a postdoctoral fellowship in molecular biology. He has been at his current position for 7 years. The focus of his research deals primarily with the discovery of novel biomarkers for diseases such as cancer. To accomplish this goal, his laboratory has developed methods to analyze the proteomes and metabolomes of thin sections obtained from both fresh-frozen and formalin-fixed paraffin-embedded tissues. His laboratory is also interested in developing and applying methods to more effectively characterize the proteomes and metabolomes of various biofluids for the discovery of both diagnostic and therapeutic biomarkers.

Katrin Marcus studied Biochemistry at the Ruhr-University Bochum, Germany. After finishing her diploma thesis, she elaborated her PhD at the Proteinstrukturlabor of Professor HE Meyer in Bochum, Germany, analyzing the phosphoproteome of human thrombin-stimulated platelets. Since August 2002, she has been group leader at the Medizinisches Proteom-Center, supervising several projects such as the ‘Human Brain Proteome Project’ and ‘Clinical Neuroproteomics of Neurodegenerative Diseases’. In August 2003, she was appointed as an Assistant Professor for proteomics at the Medical Faculty of the Ruhr-University. In December 2007, she became full Professor and now leads the Department of Functional Proteomics. Her scientific work is focused on the discovery of biomarkers for Alzheimer’s and Parkinson’s disease, and the analysis of integral membrane proteins of human hepatocytes that play a pivotal role in all phases of xenobiotics metabolism.

The nervous system is the most complex system within the human body. In a gross sense, the nervous system can be broken down into the brain, spinal cord, and the central and peripheral nervous systems. While much is known regarding the physical structure of the nervous system, how it functions is still shrouded in mystery, unlike any other system or organ. The brain is the most complex and fascinating organ in the human body, and many technologies have been developed over the past few decades to study how it functions. However, scientific study has still been unable to adequately describe the processes by which the brain turns mental thoughts into physical processes and vice versa. This understanding is critical for patients suffering from dementia or schizophrenia, where ‘abnormal’ thought processes can have life-threatening consequences.

Medical advances, as well as lifestyle changes, have progressively increased the population’s life expectancy. Unfortunately, longer life spans have also led to an increase in the number of individuals who will be afflicted by some neurodegenerative diseases. For example, the prevalence of dementia is estimated to range from 1% for those between 65 and 69 years of age, to 39% in the 90–95 years old population [1]. A large percentage of the population has been or will be affected by Alzheimer’s disease (AD) at some point in their life, either directly or through an afflicted family member. Neurological disorders, including AD, Parkinson’s disease (PD), Lewy body dementia, frontotemporal dementia, amyotrophic lateral sclerosis, Creutzfeldt–Jakob disease, Huntington’s disease (HD), schizophrenia and stroke often have debilitating effects on the patient and the family members who care for them. Unfortunately, absolute cures for many of these neurological disorders are lacking.

While there are no absolute cures, there are a number of treatments being developed that will slow or delay the progression of a number of neurological disorders. These treatments can have a major impact on the patient’s lifestyle if it is possible to delay or minimize the onset of disorders such as AD, PD and HD by 20–40 years until the patient dies from natural causes. The great unknown in this equation is when to begin treatment. For example, the symptoms in early-stage AD may be subtle and resemble signs that people mistakenly attribute to natural aging. The medical community would face an epidemic of people on unnecessary medication if every time someone misplaced items or repeated a statement they were prescribed a drug to delay the onset of AD, PD or HD-related dementia. In the case of HD, doctors often use simple, vague coordination tests (e.g., standing on one foot and touching your finger to your nose from an outstretched arm) to assess early-stage manifestation of this disorder in patient’s that are known to carry the genetic defect responsible for this disease. The discovery of an early-stage protein biomarker that indicates the onset of such conditions would be a huge benefit to physicians in knowing when to begin treating such patients. The same biomarkers, or possibly others, for monitoring the effect of such drugs would also be extremely beneficial.

This scenario would require a biomarker that could be used as a test given at a routine physical when a patient reaches a certain age. In other neurological conditions, such as traumatic brain injury or stroke, the physician must make quick decisions on the most effective treatment to minimize short- and long-term disability to the patient. In these cases, biomarkers are needed that indicate the level of immediate care that is required in order to save the patient’s life. In addition, biomarkers that indicate the probability and severity of any long-term injury effects would also be beneficial in determining future medical needs and planning that may be required.

There are presently very few biomarkers available to diagnose and monitor nervous system-related disorders; however, the recent past has seen tremendous advances in technologies with the capabilities to find such proteins. As can be seen from a quick scan of the table of contents to this Special Focus issue, these technologies are being applied to a wide range of different conditions ranging from AD to depression. Researchers in AD are probably further ahead in the discovery of diagnostic biomarkers than those involved in other areas of neuroproteomics. From the many articles within this special edition, it becomes clear that neuroproteomics can have a tremendous impact on our understanding of the underlying pathological mechanisms that occur during neural disease progression, as well as the discovery of novel biomarkers that facilitate early and/or differential diagnosis and target molecules for future drug treatments.

Proteomics offers the potential for both hypothesis-driven proteomic studies that focus on only a single or limited number of species with the aim to specifically analyze and comprehensively characterize these proteins, as well as discovery-driven efforts aimed at globally characterizing proteomes with the aim of finding specific differences between healthy and disease-affected patients. From hypothesis-driven studies, specific information regarding cellular pathways involved in the disease, the importance of post-translational modifications and the role specific protein interactions play in modulating protein function can be determined. In their comprehensive review of proteomics in tau and phosphorylated tau characterization and its involvement in AD, Luc Buée and his coauthors summarize the future hope of these studies as: “proteomics analysis of Tau at the isoform, post-translational modifications and molecular partners levels will help in basic understanding of Tau functions”.

In addition, discovery-driven differential proteome analyses comparing samples obtained from patients suffering from the disease state against respective controls can generate extensive lists of proteins that demonstrate altered expression. The scientific community has already found, and will continue to find, novel protein candidates that appear to be affected in a specific neurological disease. The review by Mauro Fasano and Leonardo Lopiano details several proteomics studies using both animal and cellular models, as well as on human tissue, that investigate single factors, such as α-synuclein, which contribute to the pathogenesis of familial PD. Fortunately, the future looks positive in finding biomarkers for other neurological disorders, as illustrated in the articles by Portelius et al. and Sergeant et al. These articles both highlight research showing that amyloid-β42 (Aβ-42) and both total tau and phosphorylated tau protein have high diagnostic potential in the early diagnosis and progression of AD.

At present, the neuroproteomics field has two major questions it must answer:

•	How can we access high-quality tissue or body fluids?
•	How specific are the discovered biomarkers for a specific neurological disorder?

The first question is closely connected to how accurately model systems reflect the in vivo situation in human. Many researchers study model systems instead of human material out of necessity, as they show less variability and are more accessible. These studies are conducted with model systems with the understanding that candidate biomarkers will require further validation in human tissue or body fluids. This need implies the availability of an adequate number and quality of human samples. Post-mortem brain tissue is hard to obtain and exhibits substantial protein degradation, leaving the sample suboptimal for further studies [2]. Cerebrospinal fluid is not easy to handle and differs in consistency during the day and varies depending on the collection process. Thus, for future studies it will be critical to establish standard operation procedures to ensure consistent sample quality. The establishment of such standard operation procedures, as well as standards, is one major focus of joint efforts such as the German Competence Net Dementias, BrainNet Europe [2,3] or the Brain Proteome Project under the patronage of the Human Proteome Organization reviewed by Michael Hamacher [101]. The collective knowledge gained from these programs will be invaluable as the field of neuroproteomics continues to progress.

The second question is partly addressed in the paper by Claus Zabel and coworkers. They found extensive overlap after comparison of identified protein candidates from four different neurodegenerative disorders. The lesson that they convey is that in order to define proteins specifically altered in a certain disease, it is necessary to fully understand normal changes that occur during development, and specific changes that are observed in related as well as unrelated diseases. This knowledge is an essential prerequisite for both the identification of candidate proteins involved in the pathomechanisms of a disease, as well as the establishment of specific, diagnostic and therapeutic biomarkers.

As the guest editors of this special edition of Expert Reviews in Proteomics, we would like to thank all of the authors and coauthors for sharing their time, knowledge and experience to make this special focus issue possible. It is our hope that the reader will take advantage of the comprehensive and competent overview in the ever growing field of neuroproteomics and that it will aid in their research as well as stimulate novel ideas.

Financial & competing interests disclosure

The authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.

No writing assistance was utilized in the production of this manuscript.