Proteomic comparison between human young and old brains by two-dimensional gel electrophoresis and identification of proteins

A cytoskeleton symphony: Actin and microtubules in microglia dynamics and aging

Microglia dynamically reorganize their cytoskeleton to perform essential functions such as phagocytosis of toxic protein aggregates, surveillance of the brain parenchyma, and regulation of synaptic plasticity during neuronal activity bursts. Recent studies have shed light on the critical role of the microtubule cytoskeleton in microglial reactivity and function, revealing key regulators like cyclin-dependent kinase 1 and centrosomal nucleation in the remodeling of microtubules in activated microglia. Concurrently, the role of the actin cytoskeleton is also pivotal, particularly in the context of small GTPases like RhoA, Rac1, and Cdc42 and actin-binding molecules such as profilin-1 and cofilin. This article delves into the intricate molecular landscape of actin and microtubules, exploring their synergistic roles in driving microglial cytoskeletal dynamics. We propose a more integrated view of actin and microtubule cooperation, which is fundamental to understanding the functional coherence of the microglial cytoskeleton and its pivotal role in propelling brain homeostasis. Furthermore, we discuss how alterations in microglial cytoskeleton dynamics during aging and in disease states could have far-reaching implications for brain function. By unraveling the complexities of microglia cytoskeletal dynamics, we can deepen our understanding of microglial functional states and their implications in health and disease, offering insights into potential therapeutic interventions for neurologic disorders.

Resilient protein co-expression network in male orbitofrontal cortex layer 2/3 during human aging

The orbitofrontal cortex (OFC) is vulnerable to normal and pathologic aging. Currently, layer resolution large-scale proteomic studies describing "normal" age-related alterations at OFC are not available. Here, we performed a large-scale exploratory high-throughput mass spectrometry-based protein analysis on OFC layer 2/3 from 15 "young" (15-43 years) and 18 "old" (62-88 years) human male subjects. We detected 4193 proteins and identified 127 differentially expressed (DE) proteins (p-value ≤0.05; effect size >20%), including 65 up- and 62 downregulated proteins (e.g., GFAP, CALB1). Using a previously described categorization of biological aging based on somatic tissues, that is, peripheral "hallmarks of aging," and considering overlap in protein function, we show the highest representation of altered cell-cell communication (54%), deregulated nutrient sensing (39%), and loss of proteostasis (35%) in the set of OFC layer 2/3 DE proteins. DE proteins also showed a significant association with several neurologic disorders; for example, Alzheimer's disease and schizophrenia. Notably, despite age-related changes in individual protein levels, protein co-expression modules were remarkably conserved across age groups, suggesting robust functional homeostasis. Collectively, these results provide biological insight into aging and associated homeostatic mechanisms that maintain normal brain function with advancing age.

Quantitative protein profiling of hippocampus during human aging

The hippocampus appears commonly affected by aging and various neurologic disorders in humans, whereas little is known about age-related change in overall protein expression in this brain structure. Using the 4-plex tandem mass tag labeling, we carried out a quantitative proteomic study of the hippocampus during normal aging using postmortem brains from Chinese subjects. Hippocampal samples from 16 subjects died of non-neurological/psychiatric diseases were divided into 4 age groups: 22-49, 50-69, 70-89, and >90. Among 4582 proteins analyzed, 35 proteins were significantly elevated, whereas 25 proteins were downregulated, along with increasing age. Several upregulated proteins, including transgelin, vimentin, myosin regulatory light polypeptide 9, and calcyphosin, were further verified by quantitative Western blot analysis of hippocampal tissues from additional normal subjects. Bioinformatic analysis showed that the upregulated and downregulated proteins were largely involved in several important protein-protein interaction networks. Proteins in the electron transport chain and synaptic vesicle fusion pathway were consistently downregulated with aging, whereas proteins associated with Alzheimer's disease showed little change. Our study demonstrates substantial protein profile changes in the human hippocampus during aging, which could be of relevance to age-related loss of hippocampal functions.

Proteomics approach to analyze protein profiling related with ADME/Tox in rat treated with Scutellariae radix and Coptidis rhizoma as well as their compatibility

ETHNOPHARMACOLOGICAL RELEVANCE

Scutellariae radix (Scutellaria baicalensis Georgi) and Coptidis rhizoma (Coptis chinensis Franch), known as traditional Chinese medicine (TCM), have been widely used with the effects of suppressing fever, dispelling dampness, purging fire and removing toxicosis. Owing to their unimaginable complexity, it is difficult to understand their pharmacokinetic properties in detail. The aim of this study was to develop an optimal proteomics approach to analyze the protein profiling related with ADME/Tox in rat liver treated with S. radix and C. rhizoma as well as their compatibility.

MATERIALS AND METHODS

Male rats were respectively administered the extracts of S. radix, C. rhizoma and their mixture for 7 days, and their liver tissue samples were prepared for the comparative proteomic analysis. The significantly differentially expressed proteins between the experimental groups and the control group were found and identified by 2-DE and MALDI-TOF-MS analyses. To validate the proteomic analysis results, glutathion peroxidase, catalase and betaine homocysteine methyl transferase were selected and confirmed by western blotting.

RESULTS

Seventy eight significantly differentially expressed proteins between the experimental groups and the control group were found and identified. By querying the relational databases, the identified differentially expressed proteins were summarized and classified into three groups, phase I drug metabolic enzymes, phase II drug metabolic enzymes and the rest proteins which mainly involve in energy metabolism, signal transduction and cytoskeleton. These proteins involved in ADME/Tox may be the targets for metabolic studies or markers for toxicity.

CONCLUSIONS

Our findings indicated S. radix and C. rhizoma as well as their compatibility can assuredly influence the expression of the proteins in rat liver. After administration, the majority of these expressions presented a downward trend, which may be closely related to the pharmacological properties of the medicine. The method in this study may open up a new road for the complementary tests for ADME/Tox properties of S. radix and C. rhizoma as well as their compatibility.

The Proteome Profiles of the Cerebellum of Juvenile, Adult and Aged Rats--An Ontogenetic Study

In this study, we searched for proteins that change their expression in the cerebellum (Ce) of rats during ontogenesis. This study focuses on the question of whether specific proteins exist which are differentially expressed with regard to postnatal stages of development. A better characterization of the microenvironment and its development may result from these study findings. A differential two-dimensional polyacrylamide gel electrophoresis (2DE) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) analysis of the samples revealed that the number of proteins of the functional classes differed depending on the developmental stages. Especially members of the functional classes of biosynthesis, regulatory proteins, chaperones and structural proteins show the highest differential expression within the analyzed stages of development. Therefore, members of these functional protein groups seem to be involved in the development and differentiation of the Ce within the analyzed development stages. In this study, changes in the expression of proteins in the Ce at different postnatal developmental stages (postnatal days (P) 7, 90, and 637) could be observed. At the same time, an identification of proteins which are involved in cell migration and differentiation was possible. Especially proteins involved in processes of the biosynthesis and regulation, the dynamic organization of the cytoskeleton as well as chaperones showed a high amount of differentially expressed proteins between the analyzed dates.

Life-time expression of the proteins peroxiredoxin, beta-synuclein, PARK7/DJ-1, and stathmin in the primary visual and primary somatosensory cortices in rats

Four distinct proteins are regulated in the aging neuroretina and may be regulated in the cerebral cortex, too: peroxiredoxin, beta-synuclein, PARK[Parkinson disease(autosomal recessive, early onset)]7/DJ-1, and Stathmin. Thus, we performed a comparative analysis of these proteins in the the primary somatosensory cortex (S1) and primary visual cortex (V1) in rats, in order to detect putative common development-, maturation- and age-related changes. The expressions of peroxiredoxin, beta-synuclein, PARK[Parkinson disease (autosomal recessive, early onset)]7/DJ-1, and Stathmin were compared in the newborn, juvenile, adult, and aged S1 and V1. Western blot (WB), quantitative reverse-transcription polymerase chain reaction (qRT-PCR), and immunohistochemistry (IHC) analyses were employed to determine whether the changes identified by proteomics were verifiable at the cellular and molecular levels. All of the proteins were detected in both of the investigated cortical areas. Changes in the expressions of the four proteins were found throughout the life-time of the rats. Peroxiredoxin expression remained unchanged over life-time. Beta-Synuclein expression was massively increased up to the adult stage of life in both the S1 and V1. PARK[Parkinson disease (autosomal recessive, early onset)]7/DJ-1 exhibited a massive up-regulation in both the S1 and V1 at all ages. Stathmin expression was massively down regulated after the neonatal period in both the S1 and V1. The detected protein alterations were analogous to their retinal profiles. This study is the first to provide evidence that peroxiredoxin, beta-synuclein, PARK[Parkinson disease (autosomal recessive, early onset)]7/DJ-1, and Stathmin are associated with postnatal maturation and aging in both the S1 and V1 of rats. These changes may indicate their involvement in key functional pathways and may account for the onset or progression of age-related pathologies.

The neuroprotective effect of Klotho is mediated via regulation of members of the redox system

Generation of reactive oxygen species (ROS), leading to oxidative damage and neuronal cell death, plays an important role in the pathogenesis of neurodegenerative disorders, including Alzheimer disease. The present study aimed to examine the mechanism by which the anti-aging protein Klotho exerts neuroprotective effects against neuronal damage associated with neurodegeneration and oxidative stress. Pretreatment of rat primary hippocampal neurons and mouse hippocampal neuronal cell line HT22 with recombinant Klotho protected these cells from glutamate and oligomeric amyloid β (oAβ)-induced cytotoxicity. In addition, primary hippocampal neurons obtained from Klotho-overexpressing mouse embryos were more resistant to both cytotoxic insults, glutamate and oAβ, compared with neurons from wild-type littermates. An antioxidative stress array analysis of neurons treated with Klotho revealed that Klotho significantly enhances the expression of the thioredoxin/peroxiredoxin (Trx/Prx) system with the greatest effect on the induction of Prx-2, an antioxidant enzyme, whose increase was confirmed at the mRNA and protein levels. Klotho-induced phosphorylation of the PI3K/Akt pathway, a pathway important in apoptosis and longevity, was associated with sustained inhibitory phosphorylation of the transcription factor forkhead box O3a (FoxO3a) and was essential for the induction of Prx-2. Down-regulation of Prx-2 expression using a lentivirus harboring shRNA almost completely abolished the ability of Klotho to rescue neurons from glutamate-induced death and significantly, but not completely, inhibited cell death mediated by oAβ, suggesting that Prx-2 is a key modulator of neuroprotection. Thus, our results demonstrate, for the first time, the neuroprotective role of Klotho and reveal a novel mechanism underlying this effect.

Proteomic approach to aging research

The scope of the current paper is to review existing and potential applications of proteomic analysis to aging research. The focus will lie on the unique opportunities of high-throughput studies for uncovering specific alterations in protein expression, protein complexes or protein modifications caused by biological aging. The result of such studies will outline aging phenotypes and potentially indicate pathways involved in the pathogenesis of age-associated disfunctions. Specific attention is paid to the illustrations of successful applications of proteomic technologies and potential applications of new proteomic concepts to biogerontological studies.

Characterization and expression of Rubisco activase genes in Ipomoea batatas

Two-dimensional electrophoresis, coupled with MALDI-TOF-MS, was used to identify differentially expressed proteins between young and mature leaves of sweet potato [Ipomoea batatas (L.) Lam]. The results showed that there were 25 differential proteins between young and mature leaves. The Rubisco activase (RCA) that catalyzes the activation of Rubisco in vivo and plays a crucial role in photosynthesis was among these 25 proteins. So far, little was known about the molecular biology of RCA in sweet potato. Here, this research reports the cloning and characterization of two genes encoding the short isoform and the long isoform of sweet potato RCAs. Analysis of DNA sequences of RCA suggested that the corresponding mRNAs were transcribed from two different genes. To study the roles of these two RCA isoforms in photosynthesis, we investigated the expression patterns of these RCA genes at the mRNA and protein levels every 2 h in a photoperiod and under different temperatures conditions. The results indicated that these two RCA isoforms may play different roles in regulating photosynthesis and they may be regulated by light, heat or both. In addition, there were interactions between Rubisco large subunit (RBCl) and short isoform RCA (RCAs) as well as RCAs and long isoform RCA (RCAl), but no interaction between RBCl and RCAl, implying they might form a sandwich-like structure (RBCl–RCAs–RCAl), at least in yeast cells. These results provided new information on the modulation of RCA genes in sweet potato, which could be useful in improving photosynthesis and plant growth in sweet potato.

Phenotypic profiles and functional genomics in Alzheimer's disease and in dementia with a vascular component

Alzheimer's disease (AD) and dementia with vascular component (DVC) are the most prevalent forms of dementia. Both clinical entities share many similarities, but they differ in major phenotypic and genotypic profiles as revealed by structural and functional genomics studies. Comparative phenotypic studies have identified significant differences in 25% of more than 100 parametric variables, including anthropometry, cardiovascular function, aortic atherosclerosis, brain atrophy, blood pressure, blood biochemistry, hematology, thyroid function, folate and vitamin B12 levels, brain hemodynamics and lymphocyte markers. The phenotypic profile of patients with DVC differs from that of AD patients in the following: anthropometric values (weight, height); cardiovascular function (ECG, heart rate); blood pressure; lipid metabolism (HDL-CHO, TGs); uric acid metabolism; peripheral calcium homeostasis; liver function (GOT, GPT, GGT); alkaline phosphatase; lactate dehydrogenase; red and white blood cells; regional brain atrophy (left temporal region, inter-hippocampal distance); and left anterior blood flow velocity. Functional genomics studies incorporating APOE-related changes in biological markers extended the difference between AD and DVC up to 57%. Brain perfusion studies show a severe brain hypoperfusion in dementia associated with enlarged age-dependent arterial perfusion times. Structural genomics studies with AD-related genes, including APP, MAPT, APOE, PS1, PS2, A2M, ACE, AGT, cFOS and PRNP genes, demonstrate different genetic profiles in AD and DVC, with an absolute genetic variation rate ranging from 30% to 80%, depending upon genes and genetic clusters. Single gene analysis identifies relative genetic variations ranging from 0% to 5%. The relative polymorphic variation in genetic clusters integrated by two, three or four genes associated with AD ranges from 1% to 3%. The main phenotypic differences between AD and DVC are genotype-dependent, especially in AD, probably indicating that different genomic factors are determinant for the expression of dementia symptoms which might be accelerated or induced by environmental and/or cerebrovascular factors.

Relationship among expression of β-tubulin Ⅲ, Stathmin and P-gp proteins, response to paclitaxel chemotherapy, and prognosis in ESCC

AIM: To investigate the relationship among the expression of β-tubulin Ⅲ, Stathmin and P-gp proteins, and response to paclitaxel chemotherapy, and prognosis in esophageal squamous cell carcinoma (ESCC).

METHODS: Seventy-six ESCC patients were enrolled in this study and their tumor samples were collected for analysis. The expression of β-tubulin Ⅲ, Stathmin, and P-gp proteins in these ESCC samples and 40 normal esophageal mucosal samples was detected by immunohistochemistry. The correlation among the expression of these proteins, response to paclitaxel chemotherapy, and prognosis was then analyzed.

RESULTS: The positive rates of β-tubulin Ⅲ, Stathmin, and P-gp in ESCC were significantly higher than those in normal esophageal mucosal tissue (63.2% vs 10.0%, 54% vs 10%, 64.5% vs 20.0%, all P < 0.05). Increased expression of β-tubulin Ⅲ, Stathmin, and P-gp was significantly correlated with poor tumor differentiation, lymph node metastasis, and advanced tumor stage (all P < 0.05). In 64 cases treated by paclitaxel chemotherapy, the response rate was significantly lower in patients who had positive expression of β-tubulin Ⅲ, Stathmin, and P-gp than in those who had negative expression (P = 0.024, 0.024, 0.012).

CONCLUSION: The expression of β-tubulin Ⅲ, Stathmin, P-gp is increased in ESCC. Increased expression of β-tubulin Ⅲ, Stathmin, and P-gp is associated with high malignancy and poor prognosis.

Stathmin: a protein with many tasks. New biomarker and potential target in cancer

INTRODUCTION

Stathmin is a microtubule-destabilizing phosphoprotein, firstly identified as the downstream target of many signal transduction pathways. Several studies then indicated that stathmin is overexpressed in many types of human malignancies, thus deserving the name of Oncoprotein 18 (Op18). At molecular level, stathmin depolymerizes microtubules by either sequestering free tubulin dimers or directly inducing microtubule-catastrophe. A crucial role for stathmin in the control of mitosis has been proposed, since both its overexpression and its downregulation induce failure in the correct completion of cell division. Accordingly, stathmin is an important target of the main regulator of M phase, cyclin-dependent kinase 1.

AREAS COVERED

Recent evidences support a role for stathmin in the regulation of cell growth and motility, both in vitro and in vivo, and indicate its involvement in advanced, invasive and metastatic cancer more than in primary tumors.

EXPERT OPINION

Many studies suggest that high stathmin expression levels in cancer negatively influence the response to microtubule-targeting drugs. These notions together with the fact that stathmin is expressed at very low levels in most adult tissues strongly support the use of stathmin as marker of prognosis and as target for novel anti-tumoral and anti-metastatic therapies.

The hippocampal neuroproteome with aging and cognitive decline: past progress and future directions

Although steady progress on understanding brain aging has been made over recent decades through standard anatomical, immunohistochemical, and biochemical techniques, the biological basis of non-neurodegenerative cognitive decline with aging remains to be determined. This is due in part to technical limitations of traditional approaches, in which only a small fraction of neurobiologically relevant proteins, mRNAs or metabolites can be assessed at a time. With the development and refinement of proteomic technologies that enable simultaneous quantitative assessment of hundreds to thousands of proteins, neuroproteomic studies of brain aging and cognitive decline are becoming more widespread. This review focuses on the contributions of neuroproteomic investigations to advances in our understanding of age-related deficits of hippocampus-dependent spatial learning and memory. Accumulating neuroproteomic data demonstrate that hippocampal aging involves common themes of dysregulated metabolism, increased oxidative stress, altered protein processing, and decreased synaptic function. Additionally, growing evidence suggests that cognitive decline does not represent a "more aged" phenotype, but rather is associated with specific neuroproteomic changes that occur in addition to age-related alterations. Understanding if and how age-related changes in the hippocampal neuroproteome contribute to cognitive decline and elucidating the pathways and processes that lead to cognitive decline are critical objectives that remain to be achieved. Progress in the field and challenges that remain to be addressed with regard to animal models, behavioral testing, and proteomic reporting are also discussed.

Thioredoxin and glutaredoxin system proteins-immunolocalization in the rat central nervous system

BACKGROUND

The oxidoreductases of the thioredoxin (Trx) family of proteins play a major role in the cellular response to oxidative stress. Redox imbalance is a major feature of brain damage. For instance, neuronal damage and glial reaction induced by a hypoxic-ischemic episode is highly related to glutamate excitotoxicity, oxidative stress and mitochondrial dysfunction. Most animal models of hypoxia-ischemia in the central nervous system (CNS) use rats to study the mechanisms involved in neuronal cell death, however, no comprehensive study on the localization of the redox proteins in the rat CNS was available.

METHODS

The aim of this work was to study the distribution of the following proteins of the thioredoxin and glutathione/glutaredoxin (Grx) systems in the rat CNS by immunohistochemistry: Trx1, Trx2, TrxR1, TrxR2, Txnip, Grx1, Grx2, Grx3, Grx5, and γ-GCS, peroxiredoxin 1 (Prx1), Prx2, Prx3, Prx4, Prx5, and Prx6. We have focused on areas most sensitive to a hypoxia-ischemic insult: Cerebellum, striatum, hippocampus, spinal cord, substantia nigra, cortex and retina.

RESULTS AND CONCLUSIONS

Previous studies implied that these redox proteins may be distributed in most cell types and regions of the CNS. Here, we have observed several remarkable differences in both abundance and regional distribution that point to a complex interplay and crosstalk between the proteins of this family.

GENERAL SIGNIFICANCE

We think that these data might be helpful to reveal new insights into the role of thiol redox pathways in the pathogenesis of hypoxia-ischemia insults and other disorders of the CNS. This article is part of a Special Issue entitled Human and Murine Redox Protein Atlases.

Cyanophage Pf-WMP4, a T7-like phage infecting the freshwater cyanobacterium Phormidium foveolarum: complete genome sequence and DNA translocation

We report the complete 40,938-bp genome sequence of a cyanophage, Pf-WMP4, which infects the freshwater cyanobacterium Phormidium foveolarum Gom. Nine of the forty-five potential open reading frames in the Pf-WMP4 genome share similarities with the genes found in T7-like phages. Using in vitro transcription, we found that seven promoters at the leftmost end of the genome can be recognized by the host RNA polymerase. By blocking transcriptional and translational inhibitors, we found that Pf-WMP4 DNA translocation, with an average translocation rate of 19.8+/-2.7 bp s(-1) at 28 degrees C, requires both host transcription and protein synthesis of an unknown factor. Therefore the mechanism of cyanophage Pf-WMP4 DNA injection may be driven both by a T7-like internalization mechanism as well as an additional unknown mechanism requiring de novo protein synthesis. Our analysis of the Pf-WMP4 genome sheds new light on the translocation strategies and evolutionary traces of phages belonging to the T7 supergroup.

Peroxiredoxins in the central nervous system

Oxidative stress is considered one of the causative pathomechanisms of nervous system diseases such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, stroke and excitotoxicity. The basal expression of six different peroxiredoxin (Prx) isozymes show distinct distribution profiles in different brain regions and different cell types. PrxI and VI are expressed in glial cells but not in neurons; while PrxII, III, IV and V are expressed in neurons. Various diseases or models show altered expression levels of these isozymes, such as by upregulation of PrxI, II and VI and downregulation of PrxIII. Thioredoxin (Trx)I mRNA is distributed widely in the rat brain. This distribution pattern may reflect the specific functions of these isozymes. Recently, the neuroprotective roles of Prx III and V against ibotenate-induced-excitotoxicity were reported by two independent groups. Adenovirus transduction of PrxIII eliminated protein nitration and prevented gliosis caused by direct infusion of ibotenate. Systemic administration of recombinant PrxV diminished brain lesions in animals treated with ibotenate. In this chapter, we review the causative mechanisms of oxidative stress in neurodegenerative diseases, as well as describe the basal and disease-induced changes in Prxs/Trxs/Trx reductases expression levels and neuroprotective roles of Trxs and Prxs as demonstrated in overexpression models.

Proteomics of cerebral injury in a neonatal model of cardiopulmonary bypass with deep hypothermic circulatory arrest

OBJECTIVE

Concern over neurologic injury limits safe duration of deep hypothermic circulatory arrest (DHCA) in surgery for congenital cardiac disease. Proteomics is a novel and powerful technique to study global protein changes in a given protein system. Using a neonatal model of cardiopulmonary bypass with DHCA, we sought to characterize the protein changes associated with DHCA brain injury.

METHODS

Ten neonatal piglets were randomized to cardiopulmonary bypass with DHCA or sham operation. DHCA animals underwent induction of bypass (100 mL x kg(-1) x min(-1)), cooling to 18 degrees C, then DHCA for 60 minutes. Animals were rewarmed to normothermia, weaned from bypass, and harvested after 30 minutes off bypass. Sham animals underwent sternotomy without further instrumentation. Plasma samples were taken before bypass and before harvest. Proteins differentially expressed in the cerebral neocortex between the 2 groups were determined by 2-dimensional differential gel electrophoresis using fluorescent cyanine dyes and mass spectrometry. A second group of 4 piglets were similarly randomized and, after the experiment, tissues underwent perfusion-fixation for histologic examination.

RESULTS

Cardiopulmonary bypass with DHCA caused extensive histologic and ultrastructural cerebral injury. Proteomic analysis of cerebral cortex found 10 protein spots to be differentially expressed; 9 were identified by mass spectrometry to represent 6 proteins, including apolipoprotein A-1, neurofilament-M protein, and enolase. Decreased expression of plasma apolipoprotein A-1 was found in DHCA.

CONCLUSIONS

The acute protein changes associated with cerebral injury in a neonatal model of cardiopulmonary bypass with DHCA have been characterized. These may direct further research aimed at attenuating injury seen from cardiopulmonary bypass with DHCA.

Profiling human brain proteome by multi-dimensional separations coupled with MS

In our initial attempt to analyze the human brain proteome, we applied multi-dimensional protein separation and identification techniques using a combination of sample fractionation, 1-D SDS-PAGE, and MS analysis. The complexity of human brain proteome requires multiple fractionation strategies to extend the range and total number of proteins identified. According to the method of Klose (Methods Mol. Biol. 1999, 112, 67), proteins of the temporal lobe of human brain were fractionated into (i) cytoplasmic and nucleoplasmic, (ii) membrane and other structural, and (iii) DNA-binding proteins. Each fraction was then separated by SDS-PAGE, and the resulting gel line was cut into approximately 50 bands. After trypsin digestion, the resulting peptides from each band were analyzed by RP-LC/ESI-MS/MS using an LTQ spectrometer. The SEQUEST search program, which searched against the IPI database, was used for peptide sequence identification, and peptide sequences were validated by reversed sequence database search and filtered by the Protein Hit Score. Ultimately, 1533 proteins could be detected from the human brain. We classified the identified proteins according to their distribution on cellular components. Among these proteins, 24% were membrane proteins. Our results show that the multiple separation strategy is effective for high-throughput characterization of proteins from complex proteomic mixtures.

2-D DIGE as a quantitative tool for investigating the HUPO Brain Proteome Project mouse series

Brain development and aging is a complex process involving proliferation, differentiation and apoptosis. Elucidating proteome changes in these processes can help to understand the mechanisms of brain development and maintenance as well as neurodegenerative diseases. The research reported here is a contribution to the HUPO Brain Proteome Project mouse pilot study. Whole, frozen C57BL/6J mouse brain comprising three different developmental stages (embryonic day 16, postnatal day 7, and postnatal days 54-58) were processed by using 2-D DIGE. A total of 1999 spots were matched between all gels. Of these, 206 spots were differentially expressed between the different stages: 122 spots were highest in intensity in embryonic stage E16, 26 highest in the juvenile group P7 and 58 spots highest in P56, the adult stage. The results show a pattern of temporal expression. Based on the expression patterns we tentatively suggest that proteins involved in the establishment of primary structures in the brain are expressed highest in the embryonic mouse. Proteins involved in the development of the brain are expressed highest in the juvenile phase and proteins that make utilization of the brain possible by delivering energy are expressed highest in the adult mice.

Age-related proteome analysis of the mouse brain: a 2-DE study

2-DE remains the most popular and versatile protein separation method among a rapidly growing array of various proteomics technologies. However, variability in sample processing, experimental design and data analyses results in a limited cross-validation between studies performed in different laboratories. One of the goals of the Human Proteome Organization (HUPO) is to establish standards and guidelines for proteomics studies. We contributed to the HUPO Brain Proteome Project by analyzing brains from neonatal and adult mice using 2-DE. Here we propose a standard workflow to analyze 2-DE images and extract statistically significant differences. After differential analysis and identification by MALDI-TOF/TOF, dihydropyrimidinase-related proteins, brain FABP, stathmin, isocitrate dehydrogenase, gamma enolase, annexin V, glutamine synthetase, creatine kinase B chain, triosephosphate dehydrogenase, and malate dehydrogenase were found differentially expressed between the two groups. The functions and potential mechanisms underlying the variation observed for these proteins are discussed.

Expression of the Op18 gene is maintained by the CCAAT-binding transcription factor NF-Y

Op18 (Oncoprotein 18, Stathmin) is a mitotic regulator that is highly expressed in many cancers. We have characterized four functional CCAAT boxes in the Op18 gene located at positions: -980, -745, -599 and -65, relative to the transcriptional start site. NF-Y is a ubiquitously expressed CCAAT-binding transcription factor that regulates a number of cell cycle controlled genes. We have used promoter-reporter assays and mobility shift assays to functionally examine these CCAAT boxes. All sites contribute to the basal expression of Op18, with the sites at -980 and -599 being repressive and the sites at -745 and -65 being stimulatory. Mobility shift assays indicate that all CCAAT box sites bind factors in nuclear extracts from Hek293. However, only the repressive site at -599 and the stimulatory site at -65 are competent to bind NF-Y, suggesting that NF-Y may play a role in promoting both activation and repression of Op18 expression. The NF-Y site at -65 accounts for greater than 60% of the Op18 gene expression. EMSA competition studies indicate that NF-Y binds with a much higher affinity to the -65 site than to the -599 site, suggesting that in asynchronously growing cells NF-Y functions only to stimulate expression through the -65 binding site. These data suggest that NF-Y is a major transcription factor promoting expression of Op18.

Mass spectrometry identification of circulating alpha-1-B glycoprotein, increased in aged female C57BL/6 mice

In this study, we surveyed the profiles of mouse circulating proteins by 2-dimensional SDS-PAGE in different strains, sexes and ages. Among visible protein spots on 2-D gels with silver-staining, we identified a unique set of 7 seemingly-related proteins whose levels were consistently elevated in older C57BL/6 female mice. This set of 7 proteins was absent in C57BL/6 males or in BALB/c mice of either sex of any age. When C57BL/6 female mice were crossed with BALB/c males, the age-related increase of these proteins became sporadic and not linear in the F1 offspring. All 7 spots of this protein group were picked and subjected to identification by mass spectrometric analysis after tryptic digestion. The results showed that all 7 spots were different isoforms of alpha(1)B-glycoprotein with different degrees of post-translational modifications, such as phosphorylation. These results suggest that alpha(1)B-glycoprotein changes in mice in a sex and age dependent manner.

Protein expression dynamics during replicative senescence of endothelial cells studied by 2-D difference in-gel electrophoresis

Endothelial senescence contributes to endothelium dysfunctionality and is thereby linked to vascular aging. A dynamic proteomic study on human umbilical vein endothelial cells, isolated from three umbilical cords, was performed. The cells were cultured towards replicative senescence and whole cell lysates were subjected to 2-D difference gel electrophoresis (DIGE). Despite the biological variability of the three independent isolations, a set of proteins was found that showed senescence-dependent expression patterns in all isolations. We focused on those proteins that showed significant changes, with a paired analysis of variance (RM-ANOVA) p-value of < or =0.05. Thirty-five proteins were identified with LC-Fourier transform MS, and functional annotation revealed that endothelial replicative senescence is accompanied by increased cellular stress, protein biosynthesis and reduction in DNA repair and maintenance. Nuclear integrity becomes affected and cytoskeletal structure is also changed. Such important changes in the cell infrastructure might accelerate endothelium dysfunctionality. This study provides biological information that will initiate studies to further unravel endothelial senescence and gain more knowledge about the consequences of this process in the in vivo situation.

Neuroproteomics in neurotrauma

Neurotrauma in the form of traumatic brain injury (TBI) afflicts more Americans annually than Alzheimer's and Parkinson's disease combined, yet few researchers have used neuroproteomics to investigate the underlying complex molecular events that exacerbate TBI. Discussed in this review is the methodology needed to explore the neurotrauma proteome-from the types of samples used to the mass spectrometry identification and quantification techniques available. This neuroproteomics survey presents a framework for large-scale protein research in neurotrauma, as applied for immediate TBI biomarker discovery and the far-reaching systems biology understanding of how the brain responds to trauma. Ultimately, knowledge attained through neuroproteomics could lead to clinical diagnostics and therapeutics to lessen the burden of neurotrauma on society.

Proteome analysis of chick embryonic cerebrospinal fluid

During early stages of embryo development, the brain cavity is filled with embryonic cerebrospinal fluid (E-CSF), a complex fluid containing different protein fractions that contributes to the regulation of the survival, proliferation and neurogenesis of the neuroectodermal stem cells. Using 2-DE, protein sequencing and database searches, we identified and analyzed the proteome of the E-CSF from chick embryos (Gallus gallus). We identified 26 different gene products, including proteins related to the extracellular matrix, proteins associated with the regulation of osmotic pressure and metal transport, proteins related to cell survival, MAP kinase activators, proteins involved in the transport of retinol and vitamin D, antioxidant and antimicrobial proteins, intracellular proteins and some unknown proteins. Most of these gene products are involved in the regulation of developmental processes during embryogenesis in systems other than E-CSF. Interestingly, 14 of them are also present in adult human CSF proteome, and it has been reported that they are altered in the CSF of patients suffering neurodegenerative diseases and/or neurological disorders. Understanding these molecules and the mechanisms they control during embryonic neurogenesis is a key contribution to the general understanding of CNS development, and may also contribute to greater knowledge of these human diseases.

Identification of serum proteins discriminating colorectal cancer patients and healthy controls using surface-enhanced laser desorption ionisation-time of flight mass spectrometry

AIM: To detect the new serum biomarkers for colorectal cancer (CRC) by serum protein profiling with surface-enhanced laser desorption ionisation - time of flight mass spectrometry (SELDI-TOF MS).

METHODS: Two independent serum sample sets were analysed separately with the ProteinChip technology (set A: 40 CRC + 49 healthy controls; set B: 37 CRC + 31 healthy controls), using chips with a weak cation exchange moiety and buffer pH 5. Discriminative power of differentially expressed proteins was assessed with a classification tree algorithm. Sensitivities and specificities of the generated classification trees were obtained by blindly applying data from set A to the generated trees from set B and vice versa. CRC serum protein profiles were also compared with those from breast, ovarian, prostate, and non-small cell lung cancer.

RESULTS: Mass-to-charge ratios (m/z) 3.1×10³, 3.3×10³, 4.5×10³, 6.6×10³ and 28×10³ were used as classifiers in the best-performing classification trees. Tree sensitivities and specificities were between 65% and 90%. Most of these discriminative m/z values were also different in the other tumour types investigated. M/z 3.3×10³, main classifier in most trees, was a doubly charged form of the 6.6×10³-Da protein. The latter was identified as apolipoprotein C-I. M/z 3.1×10³ was identified as an N-terminal fragment of albumin, and m/z 28×10³ as apolipoprotein A-I.

CONCLUSION: SELDI-TOF MS followed by classification tree pattern analysis is a suitable technique for finding new serum markers for CRC. Biomarkers can be identified and reproducibly detected in independent sample sets with high sensitivities and specificities. Although not specific for CRC, these biomarkers have a potential role in disease and treatment monitoring.

Oxidative modification of proteins in the frontal cortex of Alzheimer's disease brain

There is a large body of evidence highlighting the importance of oxidative stress in the pathogenesis of Alzheimer's disease (AD). We have previously standardised a method that can be applied to study oxidative changes in individual brain proteins by using two-dimensional oxyblots (Korolainen MA, Goldsteins G, Alafuzoff I, Koistinaho J, Pirttilä T. Proteomic analysis of protein oxidation in Alzheimer's disease brain. Electrophoresis 2002;23(19):3428-33). Here we have identified proteins that exhibited oxidative changes in AD when compared to age-matched controls and these protein changes have been further examined in relation to the neuropathological data. Indeed, several Tris-HCl soluble proteins tended to be less oxidised in AD when compared to controls. Two enzymes, mitochondrial glutamate dehydrogenase and cytosolic malate dehydrogenase, were increased in amount but showed significantly decreased degree of oxidation in AD brains when compared to controls. Furthermore, some changes related to the amounts or oxidation statuses of proteins were associated with the duration of the clinical impairment and also with the neuropathology. These results do not contradict the hypothesis of increased oxidative stress in AD but may represent co-existing compensatory changes in response to oxidative stress.

Methods for monitoring oxidative stress response in yeasts

Changes in the chemical or physical conditions of the cell that impose a negative effect on growth demand rapid cellular responses, which are essential for survival. Molecular mechanisms induced upon exposure of cells to such adverse conditions are commonly designated as stress responses. Herein, different methods which can be used to monitor oxidative stress response in yeasts are presented including monitoring of oxygen partial pressure during yeast cultivation, cell viability determination, measuring activity of enzymatic and level of nonenzymatic primary antioxidant defense systems, and examination of transcriptome and proteome changes. Additionally, some studies are given as examples of particular method's application for studying oxidative stress response in yeasts.

Molecular diversity of rat brain proteins as revealed by proteomic analysis

Multiple protein expression forms (MPEFs) presenting splicing forms or co- and posttranslation modifications, account for the vast diversity, the myriad of gene products and clearly indicate problems which proteomics research is facing. In the present study, we generated a rat brain map representing MPEFs by the use of an analytical method based on two-dimensional electrophoresis combined with mass spectrometry. Forty-nine individual proteins were selected that showed more than two spots, resulting altogether into a total number of 357 expression forms. Some proteins showed large MPEFs numbers as e.g. tubulin alpha-1 chain (24 spots), ATP synthase alpha-chain (28), beta chain (17) or septin 7 (13). The molecular diversity observed in this map clearly shows that immunochemical or even protein chemical results from expressional studies have to be interpreted with caution, in particular if one dimensional electrophoretic or western blot techniques are applied and MPEFs are poorly resolved.

Extravasation of plasma proteins can confound interpretation of proteomic studies of brain: A lesson from apo A-I in mesial temporal lobe epilepsy

Apolipoprotein A-I (apo A-I), a major component of high density lipoproteins, has been shown to be involved in lipid metabolism, cholesterol homeostasis and degeneration/regeneration of brain tissues and was proposed as a useful marker for the extent and severity of CNS injury. We searched for aberrant protein expression in hippocampus from patients with mesial temporal lobe epilepsy (MTLE) by an analytical method based on two-dimensional gel electrophoresis coupled with mass spectrometry (MALDI-TOF/TOF) and unambiguously identified 2 spots as apolipoprotein A-I forms in brain of MTLE patients with 7.5-fold increased levels (controls: 0.046 +/- 0.046; MTLE patients: 0.343 +/- 0.154, mean +/- SD, P = 0.003). Western blot analysis confirmed increased apo A-I levels in MTLE. Immunohistochemistry detected staining for apo A-I extracellularly in perivasal brain parenchyma, neuropil and areas with increased glial fibrillary acidic protein (GFAP) expression as well as some pyramidal neurons and subpial astrocytes. These findings indicate that the increase of apo A-I in MTLE was possibly not reflecting a pathogenetic role but was rather due to extravasates, bleedings or increase of microvascular endothelial cells known to synthesize apo A-I. Care has to be taken when protein expressional findings are to be interpreted in the presence of plasma proteins, including apo A-I, thus clearly representing a confounding factor.

Proteomic identification of differentially expressed proteins in the aging murine olfactory system and transcriptional analysis of the associated genes

Decline in olfactory ability has been associated with aging as well as neurodegenerative disorders. The aim of this study was to gain fundamental insight into molecular events associated with the aging olfactory system. We report a comparative proteomic analysis of the olfactory epithelium (OE) and olfactory bulb (OB) of old (80-week old) and young (6-week old) mice with further analysis of age-related differences in differentially expressed proteins at the mRNA level using real-time RT-PCR. Nine proteins in the OE and 20 in the OB were differentially expressed in old and young mice; of these, aldolase 1, peptidyl prolyl isomerase A, mitochondrial aconitase 2, mitochondrial aldehyde dehydrogenase 2 and albumin 1 were identified in the OE; and ATP synthase isoform 1, enolase 1, ferritin heavy chain, malate dehydrogenase 1, tropomyosin alpha 3 chain and dynamin 1 were identified in the OB. At the transcriptional level, aconitase 2 in the OE and ferritin heavy chain 1 in the OB were differentially expressed with aging, in concordance with the proteomic data. Our results demonstrate an altered proteomic profile of the aged murine olfactory system. The identified proteins fall into three broadly defined functional categories: (i) metabolism, (ii) transport/motility and (iii) stress response. Our transcriptional analysis provides insight into possible mechanisms by which protein expression may be regulated in the OE and OB. The results are discussed in relation to the decrement in olfactory sensitivity with aging.

Proteome analysis in the clinical chemistry laboratory: Myth or reality?

BACKGROUND

We review here modern aspects of proteomic analysis, as displayed via orthogonal mass/charge analysis (isoelectric focusing in the first dimension, followed by sodium dodecyl sulphate electrophoresis in polyacrylamide gels, SDS-PAGE, at right angles, in the second dimension).

METHODS

This technique is capable of displaying a few thousand polypeptide chains, characterized by a single pI and M(r) value as coordinates, and recognized via elution, digestion and mass spectrometry analysis. Although, up to the present, this technique has been used mostly for advanced research, with no immediate applications in the clinical chemistry laboratory, there are hints that such applications will soon become a reality.

RESULTS AND CONCLUSIONS

In the field of cancer research, it is here shown that stathmin (Op18) becomes heavily phosphorylated in cancerous mantle cell lymphomas and that the progression of the disease can be followed by the progression of phosphorylation of Op18 and by the appearance of additional phosphorylated spots. Also chemoresistance of different tumors has been evaluated via 2D-PAGE through quantitative, differential proteomics: among up- and down-regulated proteins in a human cervix squamous cell carcinoma cell line (A431), rendered resistant to cisplatin, one particular protein was found to appear in large quantities by de novo synthesis: 14-3-3, a protein known to impart resistance to apoptosis to cells. In the field of brain disorders, we could set up an easy test for detecting pathological prions in sporadic Creutzfeldt-Jakob disease (sCJD), by simply searching for those pathological forms in the olfactory mucosa (up to this finding, diagnosis could only be confirmed post-mortem). We are currently working on a test for differentiating sCJD from all the other degenerative dementias. Upon 2D mapping of cerebrospinal fluid (CSF) and immunoblot analysis, we could identify a major spot (pI 4.8, M(r) 30 kDa) followed by some two-three minor spots (pIs 5.0-6.0, same M(r) value) of the same 14-3-3 anti-apoptotic protein involved in chemoresistance. By this test, sCJD could be differentiated from all the other degenerative dementias, which are 14-3-3 negative (in sCJD, the rapid and massive brain cell damage releases large quantities of 14-3-3 in the cerebrospinal fluid). Another protein that appears very promising as a marker for sCJD is cystatin C, that is strongly up-regulated in this pathology. Human sera should also be mined for discovery of many more markers for disease. Up to the present, no one could be found, but this was due to the presence of several major proteins, obscuring all rare ones. Via several immuno-subtraction steps, followed by ion exchange and size exclusion chromatography, one can now detect proteins and peptides present in sera at levels below 10 ng/mL, highlighting the road to discovery of novel markers of disease. Another technique that could revolutionize biomarker discovery in biological fluids consists in the use of combinatorial beads to reduce the dynamic range. They consist in a library of combinatorial ligands coupled to small beads. Such a library comprises hexameric ligands composed of amino acids, resulting in millions different structures. When these beads are impregnated with complex proteomes (e.g., human sera, CSF, urines) of widely differing protein compositions, they are able to significantly reduce the concentration differences, thus greatly enhancing the possibility of evidencing low-abundance species.

Bioinformatics and Proteomics Approaches for Aging Research

Aging is a natural phenomenon that affects the entire physiology of an organism. Elucidating the molecular mechanisms underlying this complex process remains a major challenge today. Humans make poor models for research into aging because of their long life span. Thus, most of the current knowledge is through studies conducted in lower organisms. Large differences in life spans make it difficult to extrapolate the results of experiments carried out in model organisms to humans. Recent advances in genomic and proteomic technologies now permit generation of data pertaining to aging on a large-scale. In addition, several web-based community resources and databases are available that provide easy access to the available data. Use of bioinformatics and systems biology type of approaches provide a framework to start dissecting this complex biological phenomenon. Here, we discuss various genomic, transcriptomic and proteomic approaches that have the potential to provide a comprehensive mechanistic insight into the aging process.

From proteomics to biomarker discovery in Alzheimer's disease

Alzheimer's disease (AD) is the most common form of dementia in the elderly. AD is an invariably fatal neurodegenerative disorder with no effective treatment or definitive antemortem diagnostic test. Little is known about the changes in the brain preceding or accompanying initiation of the disease. Understanding the biological processes, which occur during AD onset and/or progression, will improve the diagnosis and treatment of the disease. As we will discuss in this review article, using high-throughput cDNA microarray we identified candidate genes whose expression is altered in the brain of cases at risk for AD dementia. However, it is possible that the use of the cDNA microarray technology alone may underestimate post-transcriptional modifications and therefore provides only a partial view of the biological problem of interest. As such, the combination of cDNA and protein arrays may provide a more global picture of the biological processes being studied. Based on this hypothesis, we initiated a series of high-throughput proteomic studies and found that the expressions of proteins involved in synaptic plasticity are selectively altered in the brain of cases at high risk to develop AD dementia (mild cognitive impairment; MCI). This is consistent with our cDNA microarray evidence showing that the expression of a-type synapsins is selectively altered in the brain of MCI cases. Collectively, these studies support the feasibility and usefulness of high-throughput cDNA microarray and proteomics techniques to study the sequential changes of distinctive gene expression patterns in the brain as a function of the progression of AD dementia.

Proteomics analysis of rat brain protein modulations by grape seed extract

Dietary supplements such as grape seed extract (GSE) enriched in proanthocyanidins (PA) (oligomeric polyphenols) have been suggested to have multiple health benefits, due to antioxidant and other beneficial activities of the PA. However, a systematic analysis of the molecular basis of these benefits has not been demonstrated. Because the brain is vulnerable to age-related oxidative damage and other insults including inflammation, it was hypothesized that rats ingesting GSE would experience changes in expression or modifications of specific brain proteins that might protect against pathologic events. Normal adult female rats were fed diets supplemented with 5% GSE for 6 weeks. Proteomics analysis (2D electrophoresis and mass spectrometry) of brain homogenates from these animals identified 13 proteins that were altered in amount and/or charge. Because many of these changes were quantitatively in the opposite direction from previous findings for the same proteins in either Alzheimer disease or mouse models of neurodegeneration, the data suggest that these identified proteins may mediate the neuroprotective actions of GSE. This is the first identification and quantitation of specific proteins in mammalian tissues modulated by a dietary supplement, as well as the first to demonstrate links of such proteins with any disease.

Peripheral detection of S100β during cardiothoracic surgery: what are we really measuring?

BACKGROUND

S100beta has been used in cardiac surgery to identify patients with postoperative neurologic complications. However, extracranial proteins may falsely elevate measurements of serum S100beta;. Objectives of this study were (1) to quantify S100 beta levels in serum and pericardial cavity during coronary artery bypass grafting (CABG), and (2) to identify proteins recognized by standard immunodetection as S100beta.

METHODS

Systemic and pericardial cavity blood from 5 patients undergoing CABG were sampled before, during, and after cardiopulmonary bypass (CPB). A commercially available enzyme-linked immunosorbent assay (ELISA) kit was used to quantify S100beta. Two-dimensional gel electrophoresis, Western blot, and mass spectroscopy were also performed to identify S100a and other proteins.

RESULTS

Mean S100beta levels measured by ELISA, systemic and pericardial cavity blood were (in ng x mL(-1)) 1.0 +/- 0.46 and 111 +/- 71 before CPB, 0.6 +/- 0.11 and 113 +/- 54 during CPB, and 1.7 +/- 0.64 and 101 +/- 42 after CPB, respectively. However, gel electrophoresis and Western blot analysis revealed proteins other than S100beta to be present in the pericardial cavity giving a falsely elevated serum S100a levels measured by immunoassay. Mass spectroscopy of identified potential candidates revealed contaminants including haptoglobin I precursor, apolipoprotein A-1 precursor, complement factor B precursor, and complement C3 precursor.

CONCLUSIONS

S100beta immunoassays are not specific for S100a and give a falsely elevated reading due to contaminants from the surgical field that cross react with the assay's antibody. This does not appear to be an issue in nonsurgical patients. Caution must be exerted when evaluating immunodetection results for low-abundance proteins under conditions where contamination of the sample is likely.

Free radicals and brain aging

We reviewed here the formation of free radicals and its effect physiologically. Studies mentioned above have indicated that free radical/ROS/RNS involvement in brain aging is direct as well as correlative. Increasing evidence demonstrates that accumulation of oxidation of DNA, proteins, and lipids by free radicals are responsible for the functional decline in aged brains. Also, lipid peroxidation products, such as MDA, HNE, and acrolein, were reported to react with DNA and proteins to produce further damage in aged brains. Therefore, the impact of free radicals on brain aging is pronounced. It has been estimated that 10,000 oxidative interactions occur between DNA and endogenously generated free radicals per human cell per day, and at least one of every three proteins in the cell of older animals is dysfunctional as an enzyme or structural protein, due to oxidative modification. Although these estimated numbers reveal that free radical-mediated protein and DNA modification play significant roles in the deterioration of aging brain, they do not imply that free radical damages are the only cause of functional decline in aged brain. Nevertheless,although other factors may be involved in the cascade of damaging effects in the brain, the key role of free radicals in this process cannot be underestimated. This article has examined the role and formation of free radicals in brain aging. We propose that free radicals are critical to cell damage in aged brain and endogenous, and that exogenous antioxidants, therefore, may play effective roles in therapeutic strategies for age-related neurodegenerative disorders.