Functional annotation of proteins identified in human brain during the HUPO Brain Proteome Project pilot study

Deciphering the Interregional and Interhemisphere Proteome of the Human Brain in the Context of the Human Proteome Project

This study, which performs an extensive mass spectrometry-based analysis of 19 brain regions from both left and right hemispheres, presents the first draft of the human brain interhemispheric proteome. This high-resolution proteomics data provides comprehensive coverage of 3300 experimentally measured (nonhypothetical) proteins across multiple regions, allowing the characterization of protein-centric interhemispheric differences and synapse biology, and portrays the regional mapping of specific regions for brain disorder biomarkers. In the context of the Human Proteome Project (HPP), the interhemispheric proteome data reveal specific markers like chimerin 2 (CHN2) in the cerebellar vermis, olfactory marker protein (OMP) in the olfactory bulb, and ankyrin repeat domain 63 (ANKRD63) in basal ganglia, in line with regional brain transcriptomes mapped in the Human Protein Atlas (HPA). In addition, an in silico analysis pipeline was used to predict the structure and function of the uncharacterized uPE1 protein ANKRD63, and parallel reaction monitoring (PRM) was applied to validate its region-specific expression. Finally, we have built the Interhemispheric Brain Proteome Map (IBPM) Portal (www.brainprot.org) to stimulate the scientific community's interest in the brain molecular landscape and accelerate and support research in neuroproteomics. Data are available via ProteomeXchange with identifier PXD019936.

The Human Brain Proteome Project: Biological and Technological Challenges

Brain proteomics has become a method of choice that allows zooming-in where neuropathophysiological alterations are taking place, detecting protein mediators that might eventually be measured in cerebrospinal fluid (CSF) as potential neuropathologically derived biomarkers. Following this hypothesis, mass spectrometry-based neuroproteomics has emerged as a powerful approach to profile neural proteomes derived from brain structures and CSF in order to map the extensive protein catalog of the human brain. This chapter provides a historical perspective on the Human Brain Proteome Project (HBPP), some recommendation to the experimental design in neuroproteomic projects, and a brief description of relevant technological and computational innovations that are emerging in the neurobiology field thanks to the proteomics community. Importantly, this chapter highlights recent discoveries from the biology- and disease-oriented branch of the HBPP (B/D-HBPP) focused on spatiotemporal proteomic characterizations of mouse models of neurodegenerative diseases, elucidation of proteostatic networks in different types of dementia, the characterization of unresolved clinical phenotypes, and the discovery of novel biomarker candidates in CSF.

New insights into the human brain proteome: Protein expression profiling of deep brain stimulation target areas

Deep brain stimulation (DBS) is a neurosurgical procedure that provides therapeutic benefits for movement and affective disorders. The nucleus basalis of Meynert (NBM) and substantia nigra (SN) are considered target areas to apply DBS. Even though the degeneration of NBM and SN underlies the cognitive decline observed in neurological diseases, the protein knowledge derived from both areas is scarce. We have characterized the proteome present in both subcortical brain areas using the Triple TOF 5600 mass spectrometer, identifying 2775 and 3469 proteoforms in NBM and SN respectively. Data mining of MS-generated proteomic data have revealed that: i) 675 proteins tend to localize to synaptic ending, ii) 61% of the global dataset is also present in human CSF and/or plasma, and iii) 894 proteins have not been previously identified in healthy brain by MS. The correlation of NBM and SN proteomic expression profiles with human brain transcriptome data available at Allen Brain Atlas has revealed protein evidence for 250 genes considered with brain-wide expression and 112 genes with region-specific expression in human brain. In addition, protein datasets have been classified according to their chromosomal origin, increasing the current proteome coverage in healthy human brain.

BIOLOGICAL SIGNIFICANCE

The nucleus basalis of Meynert and substantia nigra are brain areas of clinical interest to apply the deep brain stimulation (DBS) technology in neurosurgery. Our proteomic characterization has revealed 675 proteins involved in the regulation of synaptic transmission, electrical machinery, and neurotransmitter release in both DBS target areas. Moreover, 2599 identified proteins present capacity to be secreted to the CSF and plasma. Our data contribute to a further step towards the characterization of the anatomical atlas of the human brain proteome, detecting 652 proteins that are common between different basal ganglia structures. This article is part of a Special Issue entitled: HUPO 2014.

Toward defining the anatomo-proteomic puzzle of the human brain: An integrative analysis

The human brain is exceedingly complex, constituted by billions of neurons and trillions of synaptic connections that, in turn, define ∼900 neuroanatomical subdivisions in the adult brain (Hawrylycz et al. An anatomically comprehensive atlas of the human brain transcriptome. Nature 2012, 489, 391-399). The human brain transcriptome has revealed specific regional transcriptional signatures that are regulated in a spatiotemporal manner, increasing the complexity of the structural and molecular organization of this organ (Kang et al. Spatio-temporal transcriptome of the human brain. Nature 2011, 478, 483-489). During the last decade, neuroproteomics has emerged as a powerful approach to profile neural proteomes using shotgun-based MS, providing complementary information about protein content and function at a global level. Here, we revise recent proteome profiling studies performed in human brain, with special emphasis on proteome mapping of anatomical macrostructures, specific subcellular compartments, and cerebrospinal fluid. Moreover, we have performed an integrative functional analysis of the protein compilation derived from these large-scale human brain proteomic studies in order to obtain a comprehensive view of human brain biology. Finally, we also discuss the potential contribution of our meta-analysis to the Chromosome-centric Human Proteome Project initiative.

Applying mass spectrometry-based qualitative proteomics to human amygdaloid complex

The amygdaloid complex is a key brain structure involved in the expression of behaviors and emotions such as learning, fear, and anxiety. Brain diseases including depression, epilepsy, autism, schizophrenia, and Alzheimer's disease, have been associated with amygdala dysfunction. For several decades, neuroanatomical, neurophysiological, volumetric, and cognitive approaches have been the gold standard techniques employed to characterize the amygdala functionality. However, little attention has been focused specifically on the molecular composition of the human amygdala from the perspective of proteomics. We have performed a global proteome analysis employing protein and peptide fractionation methods followed by nano-liquid chromatography tandem mass spectrometry (nanoLC-MS/MS), detecting expression of at least 1820 protein species in human amygdala, corresponding to 1814 proteins which represent a nine-fold increase in proteome coverage with respect to previous proteomic profiling of the rat amygdala. Gene ontology analysis were used to determine biological process represented in human amygdala highlighting molecule transport, nucleotide binding, and oxidoreductase and GTPase activities. Bioinformatic analyses have revealed that nearly 4% of identified proteins have been previously associated to neurodegenerative syndromes, and 26% of amygdaloid proteins were also found to be present in cerebrospinal fluid (CSF). In particular, a subset of amygdaloid proteins was mainly involved in axon guidance, synaptic vesicle release, L1CAM interactome, and signaling pathways transduced by NGF and NCAM1. Taken together, our data contributes to the repertoire of the human brain proteome, serving as a reference library to provide basic information for understanding the neurobiology of the human amygdala.

Mining protein lists from proteomics studies: applications for drug discovery

IMPORTANCE OF THE FIELD

In recent years, proteomics has become a common technique applied to a wide spectrum of scientific problems, including the identification of diagnostic biomarkers, monitoring the effects of drug treatments or identification of chemical properties of a protein or a drug. Although being significantly different in scientific essence, the ultimate result of the majority of proteomics studies is a protein list. Thousands of independent proteomics studies have reported protein lists in various functional contexts.

AREAS COVERED IN THIS REVIEW

We review here the spectrum of scientific problems where proteomics technology was applied recently to deliver protein lists. The available bioinformatics methods commonly used to understand the properties of the protein lists are compared.

WHAT THE READER WILL GAIN

The types and common functional properties of the reported protein lists are discussed. The range of scientific problems where this knowledge could be potentially helpful with a focus on drug discovery issues is explored.

TAKE HOME MESSAGE

Reported protein lists represent a valuable resource which can be used for a variety of goals, ranging from biomarkers discovery to identification of novel therapeutic implications of known drugs.

Proteomic atlas of the human olfactory bulb

The olfactory bulb (OB) is the first site for the processing of olfactory information in the brain and its deregulation is associated with neurodegenerative disorders. Although different efforts have been made to characterize the human brain proteome in depth, the protein composition of the human OB remains largely unexplored. We have performed a comprehensive analysis of the human OB proteome employing protein and peptide fractionation methods followed by LC-MS/MS, identifying 1529 protein species, corresponding to 1466 unique proteins, which represents a 7-fold increase in proteome coverage with respect to previous OB proteome descriptions from translational models. Bioinformatic analyses revealed that protein components of the OB participated in a plethora of biological process highlighting hydrolase and phosphatase activities and nucleotide and RNA binding activities. Interestingly, 631 OB proteins identified were not previously described in protein datasets derived from large-scale Human Brain Proteome Project (HBPP) studies. In particular, a subset of these differential proteins was mainly involved in axon guidance, opioid signaling, neurotransmitter receptor binding, and synaptic plasticity. Taken together, these results increase our knowledge about the molecular composition of the human OB and may be useful to understand the molecular basis of the olfactory system and the etiology of its disorders.

Inter-lab proteomics: data mining in collaborative projects on the basis of the HUPO brain proteome project's pilot studies

Several projects were initiated by the Human Proteome Organisation (HUPO) focusing on the proteome analysis of distinct human organs. The initiative dedicated to the brain, its development and correlated diseases is the HUPO Brain Proteome Project (HUPO BPP). An objective data submission, storage, and reprocessing strategy have been established with the help of the results gained in a pilot study phase and within subsequent studies. The bioinformatic relevance of the data is drawn from the inter-laboratory comparisons as well as from the recalculation of all data sets submitted by the different groups. In the following, results of the single groups as well as the centralised reprocessing effort are summarised, demonstrating the added-value of this concerted work.

ms_lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics

MS-based proteomics produces large amounts of mass spectra that require processing, identification and possibly quantification before interpretation can be undertaken. High-throughput studies require automation of these various steps, and management of the data in association with the results obtained. We here present ms_lims (http://genesis.UGent.be/ms_lims), a freely available, open-source system based on a central database to automate data management and processing in MS-driven proteomics analyses.

Proteomic study of human glioblastoma multiforme tissue employing complementary two-dimensional liquid chromatography- and mass spectrometry-based approaches

An extensive data set comprising 2660 unique protein identifications was obtained for the proteome of a human brain tumor (glioblastoma multiforme) by combining the results of two complementary analytical strategies based on two-dimensional chromatography and mass spectrometry. A bottom-up method, performing peptide separation in both chromatographic dimensions was employed as well as a semi-top-down method, in which intact proteins were separated in the first and tryptic peptides in the second dimension. The identified proteins were assigned to their molecular functions and compared to previously identified proteins of glioblastoma multiforme (= astrocytoma WHO grade IV), lower WHO grade astrocytomas (grade II and III), and nontumor brain tissue. With the use of a subset of 104 identified membrane proteins, the properties of intact protein fractionation in the first dimension of the semi-top-down approach were elucidated in detail. The benefit of the semi-top-down approach was further demonstrated by the identification of a set of endogenous glioblastoma multiforme expressed proteins. These proteins correspond to recombinant antigens which were recently found to be reactive against autoantibodies in glioblastoma multiforme patients. The results indicate the usefulness of the semi-top-down approach for the investigation of immunogenic antigens in human tumor tissue samples.

Proteomics data collection (ProDaC): publishing and collecting proteomics data sets in public repositories using standard formats

In Proteomics, fast enhancements with regard to technology are responsible for the creation of huge data sets. Consequently, in 2006 the European Commission funded a Coordination Action named ProDaC (Proteomics Data Collection) within the 6th EU Framework Programme to foster a community-wide data collection and data sharing. The aims of ProDaC were the development of documentation and storage standards, setup of a standardized data submission pipeline and collection of data.To reach these goals, the necessary work was structured in six thematic fields (work packages): Standards for Proteomics Data Representation, Standards Implementation, Data Integration Tools, Proteomics Repository Adaptation, Data Flow Management, and Proteomics Data Exploitation. The methods building the basis of the respective fields and the achieved results are described in the following sections.

Altered proteome biology of cardiac mitochondria under stress conditions

Myocardial ischemia-reperfusion induces mitochondrial dysfunction and, depending upon the degree of injury, may lead to cardiac cell death. However, our ability to understand mitochondrial dysfunction has been hindered by an absence of molecular markers defining the various degrees of injury. To address this paucity of knowledge, we sought to characterize the impact of ischemic damage on mitochondrial proteome biology. We hypothesized that ischemic injury induces differential alterations in various mitochondrial subcompartments, that these proteomic changes are specific to the severity of injury, and that they are important to subsequent cellular adaptations to myocardial ischemic injury. Accordingly, an in vitro model of cardiac mitochondria injury in mice was established to examine two stress conditions: reversible injury (induced by mild calcium overload) and irreversible injury (induced by hypotonic stimuli). Both forms of injury had a drastic impact on the proteome biology of cardiac mitochondria. Altered mitochondrial function was concomitant with significant protein loss/shedding from the injured organelles. In the setting of mild calcium overload, mitochondria retained functionality despite the release of numerous proteins, and the majority of mitochondria remained intact. In contrast, hypotonic stimuli caused severe damage to mitochondrial structure and function, induced increased oxidative modification of mitochondrial proteins, and brought about detrimental changes to the subproteomes of the inner mitochondrial membrane and matrix. Using an established in vivo murine model of regional myocardial ischemic injury, we validated key observations made by the in vitro model. This preclinical investigation provides function and suborganelle location information on a repertoire of cardiac mitochondrial proteins sensitive to ischemia reperfusion stress and highlights protein clusters potentially involved in mitochondrial dysfunction in the setting of ischemic injury.

Systematic characterization of the murine mitochondrial proteome using functionally validated cardiac mitochondria

Mitochondria play essential roles in cardiac pathophysiology and the murine model has been extensively used to investigate cardiovascular diseases. In the present study, we characterized murine cardiac mitochondria using an LC/MS/MS approach. We extracted and purified cardiac mitochondria; validated their functionality to ensure the final preparation contains necessary components to sustain their normal function; and subjected these validated organelles to LC/MS/MS-based protein identification. A total of 940 distinct proteins were identified from murine cardiac mitochondria, among which, 480 proteins were not previously identified by major proteomic profiling studies. The 940 proteins consist of functional clusters known to support oxidative phosphorylation, metabolism, and biogenesis. In addition, there are several other clusters, including proteolysis, protein folding, and reduction/oxidation signaling, which ostensibly represent previously under-appreciated tasks of cardiac mitochondria. Moreover, many identified proteins were found to occupy other subcellular locations, including cytoplasm, ER, and golgi, in addition to their presence in the mitochondria. These results provide a comprehensive picture of the murine cardiac mitochondrial proteome and underscore tissue- and species-specification. Moreover, the use of functionally intact mitochondria insures that the proteomic observations in this organelle are relevant to its normal biology and facilitates decoding the interplay between mitochondria and other organelles.

Capillary liquid chromatography combined with tandem mass spectrometry for the study of neurosteroids and oxysterols in brain

Neurosteroids and neurosterols are found in brain at low levels (ng/g-microg/g) against a high background of cholesterol (mg/g). As such their analysis can be challenging. Traditionally, these molecules have been analysed by gas chromatography (GC)-mass spectrometry (MS), however, the absence of molecular ions in GC-MS spectra, even from derivatised molecules, can make the discovery and identification of novel neurosteroids/sterols difficult. To avoid this scenario, liquid chromatography (LC) combined with desorption ionisation methods are employed. In this review we discuss the application of LC-MS and LC-tandem mass spectrometry (MS/MS) for the identification of neurosteroids/sterols, paying particular attention to the use of low-flow-rate LC to maximise chromatographic and mass spectrometric performance.

Annotating the human proteome: Beyond establishing a parts list

The completion of the human genome has shifted the attention from deciphering the sequence to the identification and characterisation of the functional components, including genes. Improved gene prediction algorithms, together with the existing transcript and protein information, have enabled the identification of most exons in a genome. Availability of the 'parts list' has fostered the development of experimental approaches to systematically interrogate gene function on the genome, transcriptome and proteome level. Studying gene function at the protein level is vital to the understanding of how cells perform their functions as variations in protein isoforms and protein quantity which may underlie a change in phenotype can often not be deduced from sequence or transcript level genomics experiments alone. Recent advancements in proteomics have afforded technologies capable of measuring protein expression, post-translational modifications of these proteins, their subcellular localisation and assembly into complexes and pathways. Although an enormous amount of data already exists on the function of many human proteins, much of it is scattered over multiple resources. Public domain databases are therefore required to manage and collate this information and present it to the user community in both a human and machine readable manner. Of special importance here is the integration of heterogeneous data to facilitate the creation of resources that go beyond a mere parts list.