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Kobeissy F, Goli M, Yadikar H, Shakkour Z, Kurup M, Haidar MA, Alroumi S, Mondello S, Wang KK, Mechref Y. Advances in neuroproteomics for neurotrauma: unraveling insights for personalized medicine and future prospects. Front Neurol 2023; 14:1288740. [PMID: 38073638 PMCID: PMC10703396 DOI: 10.3389/fneur.2023.1288740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/01/2023] [Indexed: 02/12/2024] Open
Abstract
Neuroproteomics, an emerging field at the intersection of neuroscience and proteomics, has garnered significant attention in the context of neurotrauma research. Neuroproteomics involves the quantitative and qualitative analysis of nervous system components, essential for understanding the dynamic events involved in the vast areas of neuroscience, including, but not limited to, neuropsychiatric disorders, neurodegenerative disorders, mental illness, traumatic brain injury, chronic traumatic encephalopathy, and other neurodegenerative diseases. With advancements in mass spectrometry coupled with bioinformatics and systems biology, neuroproteomics has led to the development of innovative techniques such as microproteomics, single-cell proteomics, and imaging mass spectrometry, which have significantly impacted neuronal biomarker research. By analyzing the complex protein interactions and alterations that occur in the injured brain, neuroproteomics provides valuable insights into the pathophysiological mechanisms underlying neurotrauma. This review explores how such insights can be harnessed to advance personalized medicine (PM) approaches, tailoring treatments based on individual patient profiles. Additionally, we highlight the potential future prospects of neuroproteomics, such as identifying novel biomarkers and developing targeted therapies by employing artificial intelligence (AI) and machine learning (ML). By shedding light on neurotrauma's current state and future directions, this review aims to stimulate further research and collaboration in this promising and transformative field.
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Affiliation(s)
- Firas Kobeissy
- Department of Neurobiology, School of Medicine, Neuroscience Institute, Atlanta, GA, United States
| | - Mona Goli
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
| | - Hamad Yadikar
- Department of Biological Sciences Faculty of Science, Kuwait University, Safat, Kuwait
| | - Zaynab Shakkour
- Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, MO, United States
| | - Milin Kurup
- Alabama College of Osteopathic Medicine, Dothan, AL, United States
| | | | - Shahad Alroumi
- Department of Biological Sciences Faculty of Science, Kuwait University, Safat, Kuwait
| | - Stefania Mondello
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy
| | - Kevin K. Wang
- Department of Neurobiology, School of Medicine, Neuroscience Institute, Atlanta, GA, United States
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
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Chaubey K, Alam SI, Waghmare CK, Bhattacharya BK. Differential phosphoproteome analysis of rat brain regions after organophosphorus compound sarin intoxication. Toxicol Res (Camb) 2023; 12:253-263. [PMID: 37125338 PMCID: PMC10141768 DOI: 10.1093/toxres/tfad013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/11/2023] [Accepted: 02/15/2023] [Indexed: 03/12/2023] Open
Abstract
Introduction Sarin is a highly toxic organophosphorus nerve agent that irreversibly inhibits neuronal enzyme acetylcholinesterase. In the prevailing scenario, it is of paramount importance to develop early diagnosis and medical countermeasures for sarin exposure. A deeper understanding of the molecular mechanism of sarin intoxication and perturbations in the associated cellular processes is likely to provide valuable clues for the elucidation of diagnostic markers and therapeutic targets for sarin exposure. Methods Present study, uncovered the changes in phosphorylation patterns of multiple proteins in different rat brain regions after sarin intoxication using 2-DE/MS approach. It provided a holistic view of the phosphorylation-mediated changes in the cellular proteome and highlighted various signaling and response pathways affected at an early time point of sarin intoxication. Results We found total 22 proteins in the cortex, 25 proteins in the corpus striatum, and 17 proteins in the hippocampus, showed ≥1.5 fold changes (hyper- or hypo- phosphorylated) with respect to control, either at 2.5 h or 1 d after sarin exposure. These results indicated the differential expression of phosphoproteins involved in protein folding in the endoplasmic reticulum, carbon metabolism, metabolic function, and energy metabolism. Conclusion Four candidates (protein disulfide-isomerase A3, heat shock cognate 71 kDa protein, alpha-enolase, and creatine kinase B-type), hyperphosphorylated in all three brain regions, can be further studied to understand the molecular mechanism behind neurodegenerative changes mediated by sarin exposure. The study sheds light on major pathogenic processes initiated during sarin intoxication and provides putative diagnostic markers/therapeutic targets for further validation.
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Affiliation(s)
- Kalyani Chaubey
- Department of Biochemistry, Defence Research & Development Establishment (DRDE), Jhansi Road, Gwalior 474002, India
- Department of Psychiatry, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106, USA
| | - Syed Imteyaz Alam
- Department of Biochemistry, Defence Research & Development Establishment (DRDE), Jhansi Road, Gwalior 474002, India
| | - Chandra Kant Waghmare
- Department of Biochemistry, Defence Research & Development Establishment (DRDE), Jhansi Road, Gwalior 474002, India
| | - Bijoy K Bhattacharya
- Department of Biochemistry, Defence Research & Development Establishment (DRDE), Jhansi Road, Gwalior 474002, India
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Millet A, Jendzjowsky N. Pathogen recognition by sensory neurons: hypotheses on the specificity of sensory neuron signaling. Front Immunol 2023; 14:1184000. [PMID: 37207232 PMCID: PMC10189129 DOI: 10.3389/fimmu.2023.1184000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 04/19/2023] [Indexed: 05/21/2023] Open
Abstract
Sensory neurons cooperate with barrier tissues and resident immune cells to form a significant aspect of defensive strategies in concert with the immune system. This assembly of neuroimmune cellular units is exemplified across evolution from early metazoans to mammalian life. As such, sensory neurons possess the capability to detect pathogenic infiltrates at barrier surfaces. This capacity relies on mechanisms that unleash specific cell signaling, trafficking and defensive reflexes. These pathways exploit mechanisms to amplify and enhance the alerting response should pathogenic infiltration seep into other tissue compartments and/or systemic circulation. Here we explore two hypotheses: 1) that sensory neurons' potential cellular signaling pathways require the interaction of pathogen recognition receptors and ion channels specific to sensory neurons and; 2) mechanisms which amplify these sensing pathways require activation of multiple sensory neuron sites. Where possible, we provide references to other apt reviews which provide the reader more detail on specific aspects of the perspectives provided here.
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Affiliation(s)
- Antoine Millet
- Respiratory & Exercise Physiology, The Lundquist Institute for Biomedical Innovation at Harbor University of California Los Angeles (UCLA) Medical Center, Torrance, CA, United States
| | - Nicholas Jendzjowsky
- Respiratory & Exercise Physiology, The Lundquist Institute for Biomedical Innovation at Harbor University of California Los Angeles (UCLA) Medical Center, Torrance, CA, United States
- Division of Respiratory and Critical Care Medicine and Physiology, David Geffen School of Medicine, University of California Los Angeles (UCLA), Los Angeles, CA, United States
- *Correspondence: Nicholas Jendzjowsky,
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Panchamia B, Raimalani V, Prashar V, Kumar M, Ratna Prabha C. Structural and Functional Characterisation of the Domains of Ubiquitin-Activating Enzyme (E1) of Saccharomyces cerevisiae. Cell Biochem Biophys 2020; 78:309-319. [PMID: 32583128 DOI: 10.1007/s12013-020-00924-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 06/05/2020] [Indexed: 10/23/2022]
Abstract
Ubiquitin-activating enzyme (E1) is the first enzyme of the ubiquitination pathway and is required to activate ubiquitin. E1 of Saccharomyces cerevisiae is a large multidomain monomeric protein. There are no studies available on the domains of yeast E1 as independent entities. Four domains of E1 namely, first catalytic cysteine half-domain (FCCH), four-helix bundle (4HB), second catalytic cysteine half-domain (SCCH) and ubiquitin fold domain (UFD) were characterised to understand their structural and functional independence vis-a-vis full length E1. Spectroscopic characterisation using circular dichroism and fluorescence suggested that these domains can act as independent folding units and attain native-like secondary structure. The structural features obtained with the peptides SCCH and FCCH of S. cerevisiae bear a high degree of structural similarity to the corresponding fragments of mouse from literature. Nearly 50% of the residues of the 4HB domain of the S. cerevisiae sample showed helical conformation. They displayed a high degree of conservation when compared with 4HB of mouse with respect to their identity and arrangement. The fragment UFD of yeast formed an α/β domain as in the whole protein and exhibited 45% homology with that of mouse, showing a similar arrangement of α and β elements in its secondary structure. Overexpression of the domains in vivo indicated that the SCCH domain and to some extent UFD apparently interfere with cellular functions such as survival under various stresses.
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Affiliation(s)
- Brinda Panchamia
- Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, 390002, India
| | - Varsha Raimalani
- Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, 390002, India
| | - Vishal Prashar
- Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 450085, India
| | - Mukesh Kumar
- Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 450085, India
| | - C Ratna Prabha
- Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, 390002, India.
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Kim YG, Woo J, Park J, Kim S, Lee YS, Kim Y, Kim SJ. Quantitative Proteomics Reveals Distinct Molecular Signatures of Different Cerebellum-Dependent Learning Paradigms. J Proteome Res 2020; 19:2011-2025. [PMID: 32181667 DOI: 10.1021/acs.jproteome.9b00826] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The cerebellum improves motor performance by adjusting motor gain appropriately. As de novo protein synthesis is essential for the formation and retention of memories, we hypothesized that motor learning in the opposite direction would induce a distinct pattern of protein expression in the cerebellum. We conducted quantitative proteomic profiling to compare the level of protein expression in the cerebellum at 1 and 24 h after training from mice that underwent different paradigms of cerebellum-dependent oculomotor learning from specific directional changes in motor gain. We quantified a total of 43 proteins that were significantly regulated in each of the three learning paradigms in the cerebellum at 1 and 24 h after learning. In addition, functional enrichment analysis identified protein groups that were differentially enriched or depleted in the cerebellum at 24 h after the three oculomotor learnings, suggesting that distinct biological pathways may be engaged in the formation of three oculomotor memories. Weighted correlation network analysis discovered groups of proteins significantly correlated with oculomotor memory. Finally, four proteins (Snca, Sncb, Cttn, and Stmn1) from the protein group correlated with the learning amount after oculomotor training were validated by Western blot. This study provides a comprehensive and unbiased list of proteins related to three cerebellum-dependent motor learning paradigms, suggesting the distinct nature of protein expression in the cerebellum for each learning paradigm. The proteomics data have been deposited to the ProteomeXchange Consortium with identifiers <PXD008433>.
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Affiliation(s)
- Yong Gyu Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea.,Department of Physiology, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Jongmin Woo
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea.,Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Joonho Park
- Interdisciplinary Program in Bioengineering, College of Engineering, Seoul National University, 1 Gwanak-ro, Seoul 151-742, Korea
| | - Sooyong Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea.,Department of Physiology, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Yong-Seok Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea.,Department of Physiology, Seoul National University College of Medicine, Seoul 03080, Korea.,Neuroscience Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Youngsoo Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea.,Interdisciplinary Program in Bioengineering, College of Engineering, Seoul National University, 1 Gwanak-ro, Seoul 151-742, Korea
| | - Sang Jeong Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea.,Department of Physiology, Seoul National University College of Medicine, Seoul 03080, Korea.,Neuroscience Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea
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Hu K, Wu W, Li Y, Lin L, Chen D, Yan H, Xiao X, Chen H, Chen Z, Zhang Y, Xu S, Guo Y, Koeffler HP, Song E, Yin D. Poly(ADP-ribosyl)ation of BRD7 by PARP1 confers resistance to DNA-damaging chemotherapeutic agents. EMBO Rep 2019; 20:embr.201846166. [PMID: 30940648 DOI: 10.15252/embr.201846166] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 01/25/2019] [Accepted: 03/01/2019] [Indexed: 01/05/2023] Open
Abstract
The bromodomain-containing protein 7 (BRD7) is a tumour suppressor protein with critical roles in cell cycle transition and transcriptional regulation. Whether BRD7 is regulated by post-translational modifications remains poorly understood. Here, we find that chemotherapy-induced DNA damage leads to the rapid degradation of BRD7 in various cancer cell lines. PARP-1 binds and poly(ADP)ribosylates BRD7, which enhances its ubiquitination and degradation through the PAR-binding E3 ubiquitin ligase RNF146. Moreover, the PARP1 inhibitor Olaparib significantly enhances the sensitivity of BRD7-positive cancer cells to chemotherapeutic drugs, while it has little effect on cells with low BRD7 expression. Taken together, our findings show that PARP1 induces the degradation of BRD7 resulting in cancer cell resistance to DNA-damaging agents. BRD7 might thus serve as potential biomarker in clinical trial for the prediction of synergistic effects between chemotherapeutic drugs and PARP inhibitors.
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Affiliation(s)
- Kaishun Hu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Wenjing Wu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Department of Breast Oncology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yu Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Lehang Lin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Dong Chen
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Department of Interventional Radiology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Haiyan Yan
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Xing Xiao
- Department of Dermatology and Venerology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Hengxing Chen
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Zhen Chen
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yin Zhang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Shuangbing Xu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yabin Guo
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - H Phillip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore, Singapore City, Singapore.,Division of Hematology/Oncology, Cedars-Sinai Medical Center, University of California Los Angeles School of Medicine, Los Angeles, CA, USA
| | - Erwei Song
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China .,Department of Breast Oncology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Dong Yin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
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Ramadan N, Ghazale H, El-Sayyad M, El-Haress M, Kobeissy FH. Neuroproteomics Studies: Challenges and Updates. Methods Mol Biol 2017; 1598:3-19. [PMID: 28508355 DOI: 10.1007/978-1-4939-6952-4_1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The Human Genome Project in 2003 has resulted in the complete sequence of ~99% of the human genome paving the road for the Human Proteome Project (HPP) assessing the full characterization of the translated protein map of the 20,300 protein-coding genes. Consequently, the emerging of the proteomics field has successfully been adopted as the method of choice for the proteome characterization. Proteomics is a term that is used to encompass multidisciplinary approaches combining different technologies that aim to study the entire spectrum of protein changes at a specific physiological condition. Proteomics research has shown excellent outcomes in different fields, among which is neuroscience; however, the complexity of the nervous systems necessitated the genesis of a new subdiscipline of proteomics termed as "neuroproteomics." Neuroproteomics studies involve assessing the quantitative and qualitative aspects of nervous system components encompassing global dynamic events underlying various brain-related disorders ranging from neuropsychiatric disorders, degenerative disorders, mental illness, and most importantly brain-specific neurotrauma-related injuries. In this introductory chapter, we will provide a brief historical perspective on the field of neuroproteomics. In doing so, we will highlight on the recent applications of neuroproteomics in the areas of neurotrauma, an area that has benefitted from neuroproteomics in terms of biomarker research, spatiotemporal injury mechanism, and its use to translate its findings from experimental settings to human translational applications. Importantly, this chapter will include some recommendation to the general studies in the area of neuroproteomics and the need to move from this field from being a descriptive, hypothesis-free approach to being an independent mature scientific discipline.
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Affiliation(s)
- Naify Ramadan
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Hussein Ghazale
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | | | - Mohamad El-Haress
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Faculty of Medicine, Beirut Arab University, Beirut, Lebanon
| | - Firas H Kobeissy
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon.
- Department of Psychiatry, Center for Neuroproteomics and Biomarkers Research, University of Florida, Gainesville, FL, USA.
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Marquez J, Lee SR, Kim N, Han J. Post-Translational Modifications of Cardiac Mitochondrial Proteins in Cardiovascular Disease: Not Lost in Translation. Korean Circ J 2016; 46:1-12. [PMID: 26798379 PMCID: PMC4720839 DOI: 10.4070/kcj.2016.46.1.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 10/26/2015] [Accepted: 10/27/2015] [Indexed: 01/08/2023] Open
Abstract
Protein post-translational modifications (PTMs) are crucial in regulating cellular biology by playing key roles in processes such as the rapid on and off switching of signaling network and the regulation of enzymatic activities without affecting gene expressions. PTMs lead to conformational changes in the tertiary structure of protein and resultant regulation of protein function such as activation, inhibition, or signaling roles. PTMs such as phosphorylation, acetylation, and S-nitrosylation of specific sites in proteins have key roles in regulation of mitochondrial functions, thereby contributing to the progression to heart failure. Despite the extensive study of PTMs in mitochondrial proteins much remains unclear. Further research is yet to be undertaken to elucidate how changes in the proteins may lead to cardiovascular and metabolic disease progression in particular. We aimed to summarize the various types of PTMs that occur in mitochondrial proteins, which might be associated with heart failure. This study will increase the understanding of cardiovascular diseases through PTM.
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Affiliation(s)
- Jubert Marquez
- Department of Health Sciences and Technology, Graduate School of Inje University, Busan, Korea
| | - Sung Ryul Lee
- Department of Health Sciences and Technology, Graduate School of Inje University, Busan, Korea.; National Research Laboratory for Mitochondrial Signaling, Department of Physiology, College of Medicine, Cardiovascular and Metabolic Disease Center, Inje University, Busan, Korea
| | - Nari Kim
- Department of Health Sciences and Technology, Graduate School of Inje University, Busan, Korea.; National Research Laboratory for Mitochondrial Signaling, Department of Physiology, College of Medicine, Cardiovascular and Metabolic Disease Center, Inje University, Busan, Korea
| | - Jin Han
- Department of Health Sciences and Technology, Graduate School of Inje University, Busan, Korea.; National Research Laboratory for Mitochondrial Signaling, Department of Physiology, College of Medicine, Cardiovascular and Metabolic Disease Center, Inje University, Busan, Korea
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Kinetic modulation of a disordered protein domain by phosphorylation. Nat Commun 2014; 5:5272. [PMID: 25348080 DOI: 10.1038/ncomms6272] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 09/15/2014] [Indexed: 12/19/2022] Open
Abstract
Phosphorylation is a major post-translational mechanism of regulation that frequently targets disordered protein domains, but it remains unclear how phosphorylation modulates disordered states of proteins. Here we determine the kinetics and energetics of a disordered protein domain the kinase-inducible domain (KID) of the transcription factor CREB and that of its phosphorylated form pKID, using high-throughput molecular dynamic simulations. We identify the presence of a metastable, partially ordered state with a 60-fold slowdown in conformational kinetics that arises due to phosphorylation, kinetically stabilizing residues known to participate in an early binding intermediate. We show that this effect is only partially reconstituted by mutation to glutamate, indicating that the phosphate is uniquely required for the long-lived state to arise. This mechanism of kinetic modulation could be important for regulation beyond conformational equilibrium shifts.
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Agrawal S, Singh A, Tripathi P, Mishra M, Singh PK, Singh MP. Cypermethrin-Induced Nigrostriatal Dopaminergic Neurodegeneration Alters the Mitochondrial Function:A Proteomics Study. Mol Neurobiol 2014; 51:448-65. [DOI: 10.1007/s12035-014-8696-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 03/24/2014] [Indexed: 12/29/2022]
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Kobeissy FH, Gulbakan B, Alawieh A, Karam P, Zhang Z, Guingab-Cagmat JD, Mondello S, Tan W, Anagli J, Wang K. Post-genomics nanotechnology is gaining momentum: nanoproteomics and applications in life sciences. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2014; 18:111-31. [PMID: 24410486 DOI: 10.1089/omi.2013.0074] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The post-genomics era has brought about new Omics biotechnologies, such as proteomics and metabolomics, as well as their novel applications to personal genomics and the quantified self. These advances are now also catalyzing other and newer post-genomics innovations, leading to convergences between Omics and nanotechnology. In this work, we systematically contextualize and exemplify an emerging strand of post-genomics life sciences, namely, nanoproteomics and its applications in health and integrative biological systems. Nanotechnology has been utilized as a complementary component to revolutionize proteomics through different kinds of nanotechnology applications, including nanoporous structures, functionalized nanoparticles, quantum dots, and polymeric nanostructures. Those applications, though still in their infancy, have led to several highly sensitive diagnostics and new methods of drug delivery and targeted therapy for clinical use. The present article differs from previous analyses of nanoproteomics in that it offers an in-depth and comparative evaluation of the attendant biotechnology portfolio and their applications as seen through the lens of post-genomics life sciences and biomedicine. These include: (1) immunosensors for inflammatory, pathogenic, and autoimmune markers for infectious and autoimmune diseases, (2) amplified immunoassays for detection of cancer biomarkers, and (3) methods for targeted therapy and automatically adjusted drug delivery such as in experimental stroke and brain injury studies. As nanoproteomics becomes available both to the clinician at the bedside and the citizens who are increasingly interested in access to novel post-genomics diagnostics through initiatives such as the quantified self, we anticipate further breakthroughs in personalized and targeted medicine.
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Affiliation(s)
- Firas H Kobeissy
- 1 Center for Neuroproteomics and Biomarkers Research, Department of Psychiatry, McKnight Brain Institute, University of Florida , Gainesville, Florida
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Fan X, Li D, Zhang Y, Green TA. Differential phosphoproteome regulation of nucleus accumbens in environmentally enriched and isolated rats in response to acute stress. PLoS One 2013; 8:e79893. [PMID: 24278208 PMCID: PMC3838351 DOI: 10.1371/journal.pone.0079893] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 10/07/2013] [Indexed: 11/18/2022] Open
Abstract
Increasing evidence shows that stress contributes to the pathogenesis of major depressive disorder which is a severe neuropsychiatric disorder and influences over 10% of the world's population. Our previous studies revealed that rats reared in an enriched environment display less depression-related behavior compared to rats raised in an isolated environment, which implies that environmental enrichment produces an antidepressant-like behavioral phenotype. However, the molecular mechanisms are not fully understood. Protein phosphorylation rapidly changes signaling pathway function and alters the function of proteins associated with the stress-induced depressive disorder. Thus, in this study, a phosphoproteomic approach was used to uncover differential phosphoprotein regulation in rat nucleus accumbens between isolated (IC) and enriched environmental conditions (EC) under basal conditions, and in response to acute stress. We found 23 phosphoproteins were regulated in EC vs. IC rats under basal conditions; 10 phosphoproteins regulated by stress in IC rats; and 15 regulated by stress in EC rats. Among all significantly regulated phosphoproteins, 11 of them were represented in at least two conditions. The regulated phosphoproteins represent signaling pathway proteins (including ERK2), enzymes, transcriptional regulators, protein translation regulators, transporters, chaperones and cytoskeletal proteins. These findings provide a global view for further understanding the contribution of protein phosphorylation in depression pathogenesis and antidepressant action.
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Affiliation(s)
- Xiuzhen Fan
- Center for Addiction Research, Department of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Dingge Li
- Center for Addiction Research, Department of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Yafang Zhang
- Center for Addiction Research, Department of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Thomas A. Green
- Center for Addiction Research, Department of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, Texas, United States of America
- * E-mail:
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Nguyen M, Yang E, Neelkantan N, Mikhaylova A, Arnold R, Poudel MK, Stewart AM, Kalueff AV. Developing 'integrative' zebrafish models of behavioral and metabolic disorders. Behav Brain Res 2013; 256:172-87. [PMID: 23948218 DOI: 10.1016/j.bbr.2013.08.012] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 07/31/2013] [Accepted: 08/03/2013] [Indexed: 02/09/2023]
Abstract
Recently, the pathophysiological overlap between metabolic and mental disorders has received increased recognition. Zebrafish (Danio rerio) are rapidly becoming a popular model organism for translational biomedical research due to their genetic tractability, low cost, quick reproductive cycle, and ease of behavioral, pharmacological or genetic manipulation. High homology to mammalian physiology and the availability of well-developed assays also make the zebrafish an attractive organism for studying human disorders. Zebrafish neurobehavioral and endocrine phenotypes show promise for the use of zebrafish in studies of stress, obesity and related behavioral and metabolic disorders. Here, we discuss the parallels between zebrafish and other model species in stress and obesity physiology, as well as outline the available zebrafish models of weight gain, metabolic deficits, feeding, stress, anxiety and related behavioral disorders. Overall, zebrafish demonstrate a strong potential for modeling human behavioral and metabolic disorders, and their comorbidity.
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Affiliation(s)
- Michael Nguyen
- Department of Biomedical Engineering, University of Virginia, 415 Lane Road, Charlottesville, VA 22908, USA; Thomas Jefferson High School for Science and Technology, 6560 Braddock Road, Alexandria, VA 22312, USA
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14
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D'hondt C, Iyyathurai J, Vinken M, Rogiers V, Leybaert L, Himpens B, Bultynck G. Regulation of connexin- and pannexin-based channels by post-translational modifications. Biol Cell 2013; 105:373-98. [PMID: 23718186 DOI: 10.1111/boc.201200096] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 05/24/2013] [Indexed: 12/28/2022]
Abstract
Connexin (Cx) and pannexin (Panx) proteins form large conductance channels, which function as regulators of communication between neighbouring cells via gap junctions and/or hemichannels. Intercellular communication is essential to coordinate cellular responses in tissues and organs, thereby fulfilling an essential role in the spreading of signalling, survival and death processes. The functional properties of gap junctions and hemichannels are modulated by different physiological and pathophysiological stimuli. At the molecular level, Cxs and Panxs function as multi-protein channel complexes, regulating their channel localisation and activity. In addition to this, gap junctional channels and hemichannels are modulated by different post-translational modifications (PTMs), including phosphorylation, glycosylation, proteolysis, N-acetylation, S-nitrosylation, ubiquitination, lipidation, hydroxylation, methylation and deamidation. These PTMs influence almost all aspects of communicating junctional channels in normal cell biology and pathophysiology. In this review, we will provide a systematic overview of PTMs of communicating junction proteins and discuss their effects on Cx and Panx-channel activity and localisation.
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Affiliation(s)
- Catheleyne D'hondt
- Laboratory of Molecular and Cellular Signalling, Department Cellular and Molecular Medicine, KU Leuven, Campus Gasthuisberg O/N 1, BE-3000, Leuven, Belgium.
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15
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Meléndez LM, Colon K, Rivera L, Rodriguez-Franco E, Toro-Nieves D. Proteomic analysis of HIV-infected macrophages. J Neuroimmune Pharmacol 2011; 6:89-106. [PMID: 21153888 PMCID: PMC3028070 DOI: 10.1007/s11481-010-9253-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Accepted: 11/23/2010] [Indexed: 12/21/2022]
Abstract
Mononuclear phagocytes (monocytes, macrophages, and microglia) play an important role in innate immunity against pathogens including HIV. These cells are also important viral reservoirs in the central nervous system and secrete inflammatory mediators and toxins that affect the tissue environment and function of surrounding cells. In the era of antiretroviral therapy, there are fewer of these inflammatory mediators. Proteomic approaches including surface enhancement laser desorption ionization, one- and two-dimensional difference in gel electrophoresis, and liquid chromatography tandem mass spectrometry have been used to uncover the proteins produced by in vitro HIV-infected monocytes, macrophages, and microglia. These approaches have advanced the understanding of novel mechanisms for HIV replication and neuronal damage. They have also been used in tissue macrophages that restrict HIV replication to understand the mechanisms of restriction for future therapies. In this review, we summarize the proteomic studies on HIV-infected mononuclear phagocytes and discuss other recent proteomic approaches that are starting to be applied to this field. As proteomic instruments and methods evolve to become more sensitive and quantitative, future studies are likely to identify more proteins that can be targeted for diagnosis or therapy and to uncover novel disease mechanisms.
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Affiliation(s)
- Loyda M Meléndez
- Department of Microbiology and Medical Zoology, School of Medicine, University of Puerto Rico, San Juan 00935, Puerto Rico.
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16
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Shevchenko G, Sjödin MOD, Malmström D, Wetterhall M, Bergquist J. Cloud-Point Extraction and Delipidation of Porcine Brain Proteins in Combination with Bottom-Up Mass Spectrometry Approaches for Proteome Analysis. J Proteome Res 2010; 9:3903-11. [DOI: 10.1021/pr100116k] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ganna Shevchenko
- Department of Physical and Analytical Chemistry, Analytical Chemistry, Uppsala University, Uppsala, Sweden
| | - Marcus O. D. Sjödin
- Department of Physical and Analytical Chemistry, Analytical Chemistry, Uppsala University, Uppsala, Sweden
| | - David Malmström
- Department of Physical and Analytical Chemistry, Analytical Chemistry, Uppsala University, Uppsala, Sweden
| | - Magnus Wetterhall
- Department of Physical and Analytical Chemistry, Analytical Chemistry, Uppsala University, Uppsala, Sweden
| | - Jonas Bergquist
- Department of Physical and Analytical Chemistry, Analytical Chemistry, Uppsala University, Uppsala, Sweden
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17
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Liu X, Wen F, Yang J, Chen L, Wei YQ. A review of current applications of mass spectrometry for neuroproteomics in epilepsy. MASS SPECTROMETRY REVIEWS 2010; 29:197-246. [PMID: 19598206 DOI: 10.1002/mas.20243] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The brain is unquestionably the most fascinating organ, and the hippocampus is crucial in memory storage and retrieval and plays an important role in stress response. In temporal lobe epilepsy (TLE), the seizure origin typically involves the hippocampal formation. Despite tremendous progress, current knowledge falls short of being able to explain its function. An emerging approach toward an improved understanding of the complex molecular mechanisms that underlie functions of the brain and hippocampus is neuroproteomics. Mass spectrometry has been widely used to analyze biological samples, and has evolved into an indispensable tool for proteomics research. In this review, we present a general overview of the application of mass spectrometry in proteomics, summarize neuroproteomics and systems biology-based discovery of protein biomarkers for epilepsy, discuss the methodology needed to explore the epileptic hippocampus proteome, and also focus on applications of ingenuity pathway analysis (IPA) in disease research. This neuroproteomics survey presents a framework for large-scale protein research in epilepsy that can be applied for immediate epileptic biomarker discovery and the far-reaching systems biology understanding of the protein regulatory networks. Ultimately, knowledge attained through neuroproteomics could lead to clinical diagnostics and therapeutics to lessen the burden of epilepsy on society.
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Affiliation(s)
- Xinyu Liu
- National Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
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18
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Liu Y, Wu J, Yan G, Hou R, Zhuang D, Chen L, Pang Q, Zhu J. Proteomic analysis of prolactinoma cells by immuno-laser capture microdissection combined with online two-dimensional nano-scale liquid chromatography/mass spectrometry. Proteome Sci 2010; 8:2. [PMID: 20205839 PMCID: PMC2825229 DOI: 10.1186/1477-5956-8-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2009] [Accepted: 01/29/2010] [Indexed: 02/08/2023] Open
Abstract
Background Pituitary adenomas, the third most common intracranial tumor, comprise nearly 16.7% of intracranial neoplasm and 25%-44% of pituitary adenomas are prolactinomas. Prolactinoma represents a complex heterogeneous mixture of cells including prolactin (PRL), endothelial cells, fibroblasts, and other stromal cells, making it difficult to dissect the molecular and cellular mechanisms of prolactin cells in pituitary tumorigenesis through high-throughout-omics analysis. Our newly developed immuno-laser capture microdissection (LCM) method would permit rapid and reliable procurement of prolactin cells from this heterogeneous tissue. Thus, prolactin cell specific molecular events involved in pituitary tumorigenesis and cell signaling can be approached by proteomic analysis. Results Proteins from immuno-LCM captured prolactin cells were digested; resulting peptides were separated by two dimensional-nanoscale liquid chromatography (2D-nanoLC/MS) and characterized by tandem mass spectrometry. All MS/MS spectrums were analyzed by SEQUEST against the human International Protein Index database and a specific prolactinoma proteome consisting of 2243 proteins was identified. This collection of identified proteins by far represents the largest and the most comprehensive database of proteome for prolactinoma. Category analysis of the proteome revealed a widely unbiased access to various proteins with diverse functional characteristics. Conclusions This manuscript described a more comprehensive proteomic profile of prolactinomas compared to other previous published reports. Thanks to the application of immuno-LCM combined with online two-dimensional nano-scale liquid chromatography here permitted identification of more proteins and, to our best knowledge, generated the largest prolactinoma proteome. This enlarged proteome would contribute significantly to further understanding of prolactinoma tumorigenesis which is crucial to the management of prolactinomas.
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Affiliation(s)
- Yingchao Liu
- Department of Neurosurgery, Shandong Provincial hospital affiliated to Shandong University, Jinan, 250021, China.,Shanghai Neurosurgical Center, Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Jinsong Wu
- Shanghai Neurosurgical Center, Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Guoquan Yan
- Department of Chemistry, Fudan University, Institutes for Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Ruiping Hou
- Department of Gastroenterology, Shandong Provincial Qianfoshan Hospital affiliated to Shandong University, Jinan, 250014, China
| | - Dongxiao Zhuang
- Shanghai Neurosurgical Center, Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Luping Chen
- Shanghai Neurosurgical Center, Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Qi Pang
- Department of Neurosurgery, Shandong Provincial hospital affiliated to Shandong University, Jinan, 250021, China
| | - Jianhong Zhu
- Shanghai Neurosurgical Center, Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China.,National Key Lab for Medical Neurobiology, Institutes of Brain Sciences, Fudan University, Shanghai, 200032, China
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19
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Identification of differentially displayed proteins in cerebrospinal fluid of Parkinson's disease patients: A proteomic approach. Clin Chim Acta 2009; 400:14-20. [DOI: 10.1016/j.cca.2008.09.026] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2008] [Revised: 08/20/2008] [Accepted: 09/24/2008] [Indexed: 11/17/2022]
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20
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Tsai MC, Shen LF, Kuo HS, Cheng H, Chak KF. Involvement of acidic fibroblast growth factor in spinal cord injury repair processes revealed by a proteomics approach. Mol Cell Proteomics 2008; 7:1668-87. [PMID: 18482974 PMCID: PMC2556019 DOI: 10.1074/mcp.m800076-mcp200] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2008] [Revised: 05/14/2008] [Indexed: 12/30/2022] Open
Abstract
Acidic fibroblast growth factor (aFGF; also known as FGF-1) is a potent neurotrophic factor that affects neuronal survival in the injured spinal cord. However, the pathological changes that occur with spinal cord injury (SCI) and the attribution to aFGF of a neuroprotective effect during SCI are still elusive. In this study, we demonstrated that rat SCI, when treated with aFGF, showed significant functional recovery as indicated by the Basso, Beattie, and Bresnahan locomotor rating scale and the combined behavior score (p < 0.01-0.001). Furthermore proteomics and bioinformatics approaches were adapted to investigate changes in the global protein profile of the damaged spinal cord tissue when experimental rats were treated either with or without aFGF at 24 h after injury. We found that 51 protein spots, resolvable by two-dimensional PAGE, had significant differential expression. Using hierarchical clustering analysis, these proteins were categorized into five major expression patterns. Noticeably proteins involved in the process of secondary injury, such as astrocyte activation (glial fibrillary acidic protein), inflammation (S100B), and scar formation (keratan sulfate proteoglycan lumican), which lead to the blocking of injured spinal cord regeneration, were down-regulated in the contusive spinal cord after treatment with aFGF. We propose that aFGF might initiate a series of biological processes to prevent or attenuate secondary injury and that this, in turn, leads to an improvement in functional recovery. Moreover the quantitative expression level of these proteins was verified by quantitative real time PCR. Furthermore we identified various potential neuroprotective protein factors that are induced by aFGF and may be involved in the spinal cord repair processes of SCI rats. Thus, our results could have a remarkable impact on clinical developments in the area of spinal cord injury therapy.
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Affiliation(s)
- Ming-Chu Tsai
- Institute of Biochemistry and Molecular Biology, School of Life Sciences, National Yang-Ming University, Taipei 11221, Taiwan
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21
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Metzger J, Schanstra JP, Mischak H. Capillary electrophoresis–mass spectrometry in urinary proteome analysis: current applications and future developments. Anal Bioanal Chem 2008; 393:1431-42. [DOI: 10.1007/s00216-008-2309-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2008] [Revised: 06/11/2008] [Accepted: 07/18/2008] [Indexed: 11/30/2022]
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22
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Kobeissy FH, Sadasivan S, Liu J, Gold MS, Wang KKW. Psychiatric research: psychoproteomics, degradomics and systems biology. Expert Rev Proteomics 2008; 5:293-314. [PMID: 18466058 DOI: 10.1586/14789450.5.2.293] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
While proteomics has excelled in several disciplines in biology (cancer, injury and aging), neuroscience and psychiatryproteomic studies are still in their infancy. Several proteomic studies have been conducted in different areas of psychiatric disorders, including drug abuse (morphine, alcohol and methamphetamine) and other psychiatric disorders (depression, schizophrenia and psychosis). However, the exact cellular and molecular mechanisms underlying these conditions have not been fully investigated. Thus, one of the primary objectives of this review is to discuss psychoproteomic application in the area of psychiatric disorders, with special focus on substance- and drug-abuse research. In addition, we illustrate the potential role of degradomic utility in the area of psychiatric research and its application in establishing and identifying biomarkers relevant to neurotoxicity as a consequence of drug abuse. Finally, we will discuss the emerging role of systems biology and its current use in the field of neuroscience and its integral role in establishing a comprehensive understanding of specific brain disorders and brain function in general.
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Affiliation(s)
- Firas H Kobeissy
- McKnight Brain Institute, Department of Psychiatry, University of Florida College of Medicine, Gainesville, FL 32611, USA.
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23
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Schiffer E, Mischak H, Vanholder RC. Biomarkers for Renal Disease and Uremic Toxins. Clin Proteomics 2008. [DOI: 10.1002/9783527622153.ch25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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24
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Schiffer E, Mischak H, Theodorescu D, Vlahou A. Challenges of using mass spectrometry as a bladder cancer biomarker discovery platform. World J Urol 2008; 26:67-74. [PMID: 18175124 DOI: 10.1007/s00345-007-0234-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2007] [Accepted: 12/11/2007] [Indexed: 12/28/2022] Open
Abstract
INTRODUCTION Bladder cancer (BCa) is one of the most prevalent malignancies worldwide, mostly due to its high recurrence rates. In consequence, the necessity of repeated screening for reappearance demonstrates the urgent need for novel biomarkers as alternatives to invasive standard procedures. METHODS Proteomic technologies have emerged as powerful platforms for unbiased biomarker discovery and revolutionized the classical "target-driven" analysis of single marker candidates. Although proteome profiling is still far from demonstrating its full potential in clinical diagnosis, first studies clearly denote its significant potential. CONCLUSIONS This review provides a discussion of the challenges related to clinical proteomics using mass spectrometry, emphasizing bladder cancer biomarker discovery. An outline of the technological prerequisites for reliable proteome profiling, data mining and interpretation, as well as, reflections on future trends in the field are provided.
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Affiliation(s)
- Eric Schiffer
- Mosaiques Diagnostics and Therapeutics AG, Hannover, Germany
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25
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Beyer S, Mix E, Hoffrogge R, Lünser K, Völker U, Rolfs A. Neuroproteomics in stem cell differentiation. Proteomics Clin Appl 2007; 1:1513-23. [PMID: 21136647 DOI: 10.1002/prca.200700324] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2007] [Indexed: 12/31/2022]
Abstract
The term "proteome" is used to describe the entire complement of proteins in a given organism or in a system at a given time. Proteome analysis in neuroscience, also called "neuroproteomics" or "neuromics" is in its initial stage, and shows a deficit of studies in the context of brain development. It is the main objective of this review to illustrate the potential of neuroproteomics as a tool to unravel the differentiation of neural stem or progenitor cells to terminally differentiated neurons. Experimental results regarding the rat striatal progenitor model cell line ST14A are presented to illustrate the large rearrangements of the proteome during the differentiation process of neural progenitor cells and their modification by neurotrophic factors like the glial cell line-derived neurotrophic factor (GDNF). Thereby native stem cells and cells transfected with GDNF gene were investigated at the proliferative state and at seven time points up to 72 h after induction of differentiation. In addition, the immortalized human fetal midbrain stem cell line ReNcell VM was analyzed in order to detect stem cell differentiation associated changes of the protein profile. This review gives also an outlook on technical improvements and perspectives of application of neural stem cell proteomics.
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Affiliation(s)
- Susanne Beyer
- Neurobiological Laboratory, Department of Neurology, Medical Faculty, University of Rostock, Rostock, Germany
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26
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Li MD, Wang J. Neuroproteomics and its applications in research on nicotine and other drugs of abuse. Proteomics Clin Appl 2007; 1:1406-27. [PMID: 21136639 DOI: 10.1002/prca.200700321] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2007] [Indexed: 12/24/2022]
Abstract
The rapidly growing field of neuroproteomics is able to track changes in protein expression and protein modifications underlying various physiological conditions, including the neural diseases related to drug addiction. Thus, it presents great promise in characterizing protein function, biochemical pathways, and networks to understand the mechanisms underlying drug dependence. In this article, we first provide an overview of proteomics technologies and bioinformatics tools available to analyze proteomics data. Then we summarize the recent applications of proteomics to profile the protein expression pattern in animal or human brain tissues after the administration of nicotine, alcohol, amphetamine, butorphanol, cocaine, and morphine. By comparing the protein expression profiles in response to chronic nicotine exposure with those appearing in response to treatment with other drugs of abuse, we identified three biological processes that appears to be regulated by multiple drugs of abuse: energy metabolism, oxidative stress response, and protein degradation and modification. Such similarity indicates that despite the obvious differences among their chemical properties and the receptors with which they interact, different substances of abuse may cause some similar changes in cellular activities and biological processes in neurons.
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Affiliation(s)
- Ming D Li
- Department of Psychiatry and Neurobehavioral Sciences, University of Virginia, Charlottesville, VA, USA.
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27
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Theodorescu D, Mischak H. Mass spectrometry based proteomics in urine biomarker discovery. World J Urol 2007; 25:435-43. [PMID: 17703310 DOI: 10.1007/s00345-007-0206-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2007] [Accepted: 07/13/2007] [Indexed: 11/28/2022] Open
Abstract
All organisms contain 1,000s of proteins and peptides in their body fluids, which undergo disease-specific changes. Advances in the understanding of the functional relevance of these polypeptides under different (patho)physiological conditions and the identification of indicative changes with disease would greatly enhance diagnosis and therapy. The low-molecular-weight proteome, also termed peptidome, provides a rich source of information. Due to its lower molecular weight, the peptidome can be assessed without the need for sample manipulation like tryptic digests. This advantage facilitates comparative analysis but it also raises technical challenges differing from those in proteomics. The first part of this manuscript, is focused on the low-molecular-weight urinary proteome and reviews methodological aspects of sample collection, preparation, analysis, and data evaluation. The second part summarizes the recent progress in the definition and identification of clinically relevant polypeptide markers.
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Affiliation(s)
- Dan Theodorescu
- Department of Molecular Physiology, University of Virginia, Charlottesville, USA
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28
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Nogoy N. Neuroproteomics: the hunt for biomarkers of neurotrauma. Andrew Ottens talks to Nicole Nogoy. Expert Rev Proteomics 2007; 4:343-5. [PMID: 17552916 DOI: 10.1586/14789450.4.3.343] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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29
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Mischak H, Julian BA, Novak J. High-resolution proteome/peptidome analysis of peptides and low-molecular-weight proteins in urine. Proteomics Clin Appl 2007; 1:792. [PMID: 20107618 PMCID: PMC2811330 DOI: 10.1002/prca.200700043] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2007] [Indexed: 11/09/2022]
Abstract
All organisms contain thousands of proteins and peptides in their body fluids. A deeper insight into the functional relevance of these polypeptides under different physiological and pathophysiological conditions and the discovery of specific peptide biomarkers would greatly enhance diagnosis and therapy of specific diseases. The low-molecular-weight proteome, also termed peptidome, provides a rich source of information. Due to its unique features, the technical challenges differ somewhat from those in "common" proteomics. In this manuscript, we focus on the low-molecular-weight urinary proteome. We review the methodological aspects of sample collection, preparation, analysis, and subsequent data evaluation. In the second part of this review, we summarize the recent progress in the definition and identification of clinically relevant polypeptide markers.
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Affiliation(s)
| | | | - Jan Novak
- University of Alabama at Birmingham, Birmingham, AL, USA
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30
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Julian BA, Wittke S, Haubitz M, Zürbig P, Schiffer E, McGuire BM, Wyatt RJ, Novak J. Urinary biomarkers of IgA nephropathy and other IgA-associated renal diseases. World J Urol 2007; 25:467-76. [PMID: 17619884 DOI: 10.1007/s00345-007-0192-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2007] [Accepted: 06/05/2007] [Indexed: 01/12/2023] Open
Abstract
IgA nephropathy is the most common primary glomerulonephritis and is a frequent cause for chronic kidney disease in children and young adults. Glomerular deposition of IgA also characterizes other renal disorders, including Henoch-Schoenlein purpura nephritis and immune-complex glomerulonephritis afflicting patients with liver disease due to chronic infection with the hepatitis C virus. Several treatment options are often considered, with the goal to prevent end-stage renal failure. Unfortunately, the diagnosis currently requires an invasive procedure, a renal biopsy. Because of the inherent risks, repetitive renal biopsy is frequently foregone as a means to monitor the clinical course or response to treatment. Recent advances in the analysis of the urinary proteome suggest that the excreted polypeptides include disease-specific patterns. We review recent studies of the various techniques for the identification and validation of such urinary biomarkers of IgA-associated glomerulonephritides. Currently, capillary electrophoresis coupled with mass spectrometry (MS) offers the greatest promise. To date, it seems more likely that disease-specific urinary polypeptide biomarkers are comprised of a panel of several distinct and well-defined peptides rather than a single molecule. Even most patients in clinical remission with normal clinical testing (dipstick urinalysis and quantitative proteinuria) were correctly classified by the pattern of polypeptides identified by capillary electrophoresis coupled with MS. With confirmation and refinement, such urinary testing may provide a tool for the diagnosis and monitoring of patients with IgA-associated renal diseases that is more sensitive than current standard clinical testing and far less risky than renal biopsy.
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Affiliation(s)
- Bruce A Julian
- Department of Medicine, University of Alabama at Birmingham, 1530 Third Avenue South, Birmingham, AL 35294, USA.
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31
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Drabik A, Bierczynska-Krzysik A, Bodzon-Kulakowska A, Suder P, Kotlinska J, Silberring J. Proteomics in neurosciences. MASS SPECTROMETRY REVIEWS 2007; 26:432-50. [PMID: 17405153 DOI: 10.1002/mas.20131] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
This review provides an outline of the most important proteomic applications in the study of neurodegenerative disorders including Alzheimer's (AD), Parkinson's (PD), Huntington's (HD), and prion diseases, and also discusses advances in cancer and addiction. One of the scopes is to illustrate the potential of proteomics in the biomarkers discovery of these diseases. Finally, this article comments the advantages and drawbacks of the most commonly used techniques and methods for samples preparation.
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Affiliation(s)
- Anna Drabik
- Faculty of Chemistry and Regional Laboratory, Jagiellonian University, Krakow, Poland
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32
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Sinha A, Patel S, Singh MP, Shukla R. Blood proteome profiling in case controls and Parkinson's disease patients in Indian population. Clin Chim Acta 2007; 380:232-4. [PMID: 17367770 DOI: 10.1016/j.cca.2007.02.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2006] [Revised: 01/29/2007] [Accepted: 02/07/2007] [Indexed: 11/23/2022]
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33
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Cheng JC, Horwitz EM, Karsten SL, Shoemaker L, Kornblum HI, Malik P, Sakamoto KM. Report on the Workshop “New Technologies in Stem Cell Research,” Society for Pediatric Research, San Francisco, California, April 29, 2006. Stem Cells 2007; 25:1070-88. [PMID: 17255523 DOI: 10.1634/stemcells.2006-0397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Jerry C Cheng
- Division of Hematology/Oncology, Department of Pediatrics, Gwynne Hazen Cherry Memorial Laboratories and Mattel Children's Hospital, Jonsson Comprehensive Cancer Center, Los Angeles, California, USA
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Ottens AK, Kobeissy FH, Fuller BF, Liu MC, Oli MW, Hayes RL, Wang KKW. Novel neuroproteomic approaches to studying traumatic brain injury. PROGRESS IN BRAIN RESEARCH 2007; 161:401-18. [PMID: 17618994 DOI: 10.1016/s0079-6123(06)61029-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Neuroproteomics entails wide-scope study of the nervous system proteome in both its content and dynamics. The field employs high-end analytical mass spectrometry and novel high-throughput antibody approaches to characterize as many proteins as possible. The most common application has been differential analysis to identify a limited set of highly dynamic proteins associated with injury, disease, or other altered states of the nervous system. Traumatic brain injury (TBI) is an important neurological condition where neuroproteomics has revolutionized the characterization of protein dynamics, leading to a greater understanding of post-injury biochemistry. Further, proteins of altered abundance or post-translational modifications identified by neuroproteomic studies are candidate biochemical markers of TBI. This chapter explores the use of neuroproteomics in the study of TBI and the validation of identified putative biomarkers for subsequent clinical translation into novel injury diagnostics.
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Affiliation(s)
- Andrew K Ottens
- Department of Psychiatry, Center for Neuroproteomics and Biomarkers Research at the McKnight Brain Institute of the University of Florida, PO Box 100256, Gainesville, FL 32610, USA.
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Geng T, Seitz PK, Thomas ML, Xu B, Soman KV, Kurosky A, Luxon BA, Cunningham KA. Use of surface enhanced laser desorption/ionization-time of flight mass spectrometry (SELDI-TOF MS) to study protein expression in a rat model of cocaine withdrawal. J Neurosci Methods 2006; 158:1-12. [PMID: 16766040 DOI: 10.1016/j.jneumeth.2006.04.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2006] [Revised: 03/21/2006] [Accepted: 04/18/2006] [Indexed: 11/20/2022]
Abstract
Surface enhanced laser desorption/ionization-time of flight mass spectrometry (SELDI-TOF MS) is an analytical technology for proteomic analysis that combines chromatography and mass spectrometry. At present, this technology is most commonly being exploited for the simultaneous measurement of numerous proteins in serum, but has also been utilized in organ tissue, although rarely in the brain. We applied SELDI-TOF MS technology to study protein expression in the brain of rats withdrawn from repeated cocaine exposure. Our goals were to optimize sample preparation and ProteinChip Array protocols for brain tissue, to verify the reproducibility of SELDI-TOF mass spectra and to determine whether SELDI-TOF MS detects differentially expressed proteins in cocaine- versus saline-treated rats. Consequently, we have developed an optimal protocol and generated a reproducible spectral pattern with six dominant peaks in all test samples. We have detected two smaller peaks (m/z: 5179, 5030) that were significantly increased (p < 0.05) in cocaine-treated rats compared to saline-treated rats. In summary, the application of SELDI-TOF MS to the study of protein expression in a rat model of cocaine withdrawal is feasible and has the potential to generate new hypotheses.
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Affiliation(s)
- Tao Geng
- Center for Addiction Research, Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-1031, United States
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Abstract
Neuronal communication is tightly regulated in time and space. Following neuronal activation, an electrical signal triggers neurotransmitter (NT) release at the active zone. The process starts by the signal reaching the synapse followed by a fusion of the synaptic vesicle (SV) and diffusion of the released NT in the synaptic cleft. The NT then binds to the appropriate receptor and induces a membrane potential change at the target cell membrane. The entire process is controlled by a fairly small set of synaptic proteins, collectively called SYCONs. The biochemical features of SYCONs underlie the properties of NT release. SYCONs are characterized by their ability to detect and respond to changes in environmental signals. For example, consider synaptotagmin I (Syt1), a prototype of a protein family with over 20 gene and variants in mammals. Syt1 is a specific example of a multi-sensor device with a large repertoire of discrete states. Several of these states are stimulated by a local concentration of signaling molecules such as Ca2+. The ability of this protein to sense signaling molecules and to adopt multiple biochemical states is shared by other SYCONs such as the synapsins (Syns). Specific biochemical states of Syns determine the accessibility of SV for NT release. Each of these states is defined by a specific alternative spliced variant with a unique profile of phosphorylation modified sites. The plasticity of the synapse is a direct reflection of SYCON's multiple biochemical states. State transitions occurs in a wide range of time scales, and therefore these molecules need to cope with events that last milliseconds (i.e., exocytosis in fast responding synapses) and with events that can carry on for many minutes (i.e., organization of SV pools). We suggest that SYCONs are optimized throughout evolution as multi-sensor devices. A full repertoire of the switches leading to alternation of protein states and a detailed characterization of protein-protein network within the synapse is critical for the development of a dynamic model of synaptic transmission.
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Affiliation(s)
- Guy Brachya
- Dept of Biological Chemistry, The Hebrew University of Jerusalem, 91904, Israel
| | - Chava Yanay
- Dept of Biological Chemistry, The Hebrew University of Jerusalem, 91904, Israel
| | - Michal Linial
- Dept of Biological Chemistry, The Hebrew University of Jerusalem, 91904, Israel
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Schiffer E, Mischak H, Novak J. High resolution proteome/peptidome analysis of body fluids by capillary electrophoresis coupled with MS. Proteomics 2006; 6:5615-27. [PMID: 16991199 DOI: 10.1002/pmic.200600230] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
All organisms contain thousands of proteins and peptides in their body fluids. A deeper insight into the functional relevance of these polypeptides under different physiological and pathophysiological conditions and the discovery of specific peptide biomarkers would greatly enhance both diagnosis and therapy of specific diseases. Proteomic methods can provide means to accomplish this grand medical vision. In this review, we will focus on the potential use of proteome analysis for clinical applications, such as disease diagnosis and assessment of response to therapy. We focus on CE coupled with MS (CE-MS) and review in detail different aspects of CE-MS coupling and the results obtained using CE-MS analysis of clinically relevant samples. We also discuss clinical applications of the technology for the diagnosis of renal diseases, urogenital cancer, and arteriosclerosis as well as monitoring the responses to therapeutic interventions.
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Affiliation(s)
- Eric Schiffer
- Mosaiques Diagnostics & Therapeutics AG, Hanover, Germany
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Kisby GE, Standley M, Park T, Olivas A, Fei S, Jacob T, Reddy A, Lu X, Pattee P, Nagalla SR. Proteomic Analysis of the Genotoxicant Methylazoxymethanol (MAM)-Induced Changes in the Developing Cerebellum. J Proteome Res 2006; 5:2656-65. [PMID: 17022636 DOI: 10.1021/pr060126g] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The genotoxicant methylazoxymethanol (MAM) is a widely used developmental neurotoxin, and its glucoside is an etiological factor for western Pacific amyotrophic lateral sclerosis-parkinsonism-dementia complex (ALS/PDC). Identification of global protein expression changes that occur in response to MAM in the developing cerebellum could provide valuable insight into the potential mechanisms involved in the neurodegeneration process. We have utilized fluorescence 2-dimensional differential gel electrophoresis (2D-DIGE), to determine the protein expression changes that occur during normal cerebellar development and in response to MAM. Three day-old postnatal C57BL/6 mice (PND3) received a single injection of MAM, and the cerebella of postnatal day 4 (PND4) and day 22 (PND22) were analyzed. Approximately, 1400 unique spots were matched and quantified in all samples. Comparison of PND4 and PND22 developing cerebellum showed that a significant fraction of the proteome (approximately 68%) changes at this stage. The immediate response of the developing cerebellum to MAM was minimal (approximately 10%). However, significant differences (27%) were noted 14 days after MAM exposure. In contrast, the transcriptome changes were more pronounced at 24 h compared to 14 days. MAM targeted several proteins networks including transport (e.g., alpha-synuclein), cytoskeletal (e.g., beta-tubulin, vimentin), and mitochondrial (e.g., Atp5b) proteins. Immunochemistry confirmed several of the changes in protein expression (alpha-synuclein). Comparison with gene expression changes revealed that the temporal changes observed in the transcriptome and proteome are not correlative. These studies demonstrate for the first time the potential networks involved during neuronal development and neurodegenerative processes that are perturbed by MAM.
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Affiliation(s)
- G E Kisby
- Center for Research on Occupational and Environmental Toxicology (CROET) and Center for Biomarker Discovery, Department of Pediatrics, Oregon Health & Science University, Portland, Oregon 97239, USA
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Ekegren T, Hanrieder J, Aquilonius SM, Bergquist J. Focused Proteomics in Post-Mortem Human Spinal Cord. J Proteome Res 2006; 5:2364-71. [PMID: 16944948 DOI: 10.1021/pr060237f] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
With a highly sensitive electrospray ionization-Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR MS) system, proteins were identified in minimal amounts of spinal cord from patients with the neurodegenerative disease amyotrophic lateral sclerosis (ALS) and compared to proteins in spinal cord from control subjects. The results show 18 versus 16 significantly identified (p < 0.05) proteins, respectively, all known to be found in the central nervous system. The most abundant protein in both groups was the glial fibrillary acidic protein, GFAP. Other proteins were, for example, hemoglobin alpha- and beta chain, myelin basic protein, thioredoxin, alpha enolase, and choline acetyltransferase. This study also includes the technique of laser microdissection in combination with pressure catapulting (LMPC) for the dissection of samples and specific neurons. Furthermore, complementary experiments with nanoLC-matrix assisted laser desorption ionization time-of-flight tandem mass spectrometry (MALDI-TOF-TOF MS) confirmed the results of the ESI-FTICR MS screening and provided additional results of further identified proteins.
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Affiliation(s)
- Titti Ekegren
- Department of Physical and Analytical Chemistry, Analytical Chemistry, Uppsala University, Uppsala, Sweden
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Ottens AK, Kobeissy FH, Golden EC, Zhang Z, Haskins WE, Chen SS, Hayes RL, Wang KKW, Denslow ND. Neuroproteomics in neurotrauma. MASS SPECTROMETRY REVIEWS 2006; 25:380-408. [PMID: 16498609 DOI: 10.1002/mas.20073] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
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.
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Affiliation(s)
- Andrew K Ottens
- Center of Neuroproteomics and Biomarkers Research, McKnight Brain Institute, University of Florida, Gainesville, FL, USA.
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Suk K. Proteomics-based discovery of biomarkers and therapeutic targets in neurodegenerative diseases: perspective of microglia and neuroinflammation. Expert Opin Ther Pat 2006. [DOI: 10.1517/13543776.16.3.237] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Ottens AK, Kobeissy FH, Wolper RA, Haskins WE, Hayes RL, Denslow ND, Wang KKW. A Multidimensional Differential Proteomic Platform Using Dual-Phase Ion-Exchange Chromatography−Polyacrylamide Gel Electrophoresis/Reversed-Phase Liquid Chromatography Tandem Mass Spectrometry. Anal Chem 2005; 77:4836-45. [PMID: 16053296 DOI: 10.1021/ac050478r] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Differential proteomic analysis has arisen as a large-scale means to discern proteome-wide changes upon treatment, injury, or disease. Tandem protein separation methods are required for large-scale differential proteomic analysis. Here, a novel multidimensional platform for resolving and differentially analyzing complex biological samples is presented. The platform, collectively termed CAX-PAGE/RPLC-MSMS, combines biphasic ion-exchange chromatography with polyacrylamide gel electrophoresis for protein separation, quantification, and differential band targeting, followed by capillary reversed-phase liquid chromatography and data-dependent tandem mass spectrometry for quantitative and qualitative peptide analysis. CAX-PAGE provides high protein resolving power with a theoretical peak capacity of 3570, extendable to 7600, a wide protein mass range verified from 16 to 273 kDa, and reproducible differential sample comparison without the added expense of fluorescent dyes and imaging equipment. Demonstrated using a neuroproteomic model, CAX-PAGE revealed an increased number of differential proteins, 137, compared with 82 found by 2D difference gel electrophoresis. When combined with RPLC-MSMS for protein identification, an additional quantification step is performed for internal validation, confirming a 2-fold or greater change in 89% of identified differential targets.
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Affiliation(s)
- Andrew K Ottens
- Center for Neuroproteomics and Biomarker Research, University of Florida, Gainesville, Florida 32610, USA.
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Gerrits RJ, Lunney JK, Johnson LA, Pursel VG, Kraeling RR, Rohrer GA, Dobrinsky JR. Perspectives for artificial insemination and genomics to improve global swine populations. Theriogenology 2005; 63:283-99. [PMID: 15626400 DOI: 10.1016/j.theriogenology.2004.09.013] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Civilizations throughout the world continue to depend on pig meat as an important food source. Approximately 40% of the red meat consumed annually worldwide (94 million metric tons) is pig meat. Pig numbers (940 million) and consumption have increased consistent with the increasing world population (FAO 2002). In the past 50 years, research guided genetic selection and nutrition programs have had a major impact on improving carcass composition and efficiency of production in swine. The use of artificial insemination (AI) in Europe has also had a major impact on pig improvement in the past 35 years and more recently in the USA. Several scientific advances in gamete physiology and/or manipulation have been successfully utilized while others are just beginning to be applied at the production level. Semen extenders that permit the use of fresh semen for more than 5 days post-collection are largely responsible for the success of AI in pigs worldwide. Transfer of the best genetics has been enabled by use of AI with fresh semen, and to some extent, by use of AI with frozen semen over the past 25 years. Sexed semen, now a reality, has the potential for increasing the rate of genetic progress in AI programs when used in conjunction with newly developed low sperm number insemination technology. Embryo cryopreservation provides opportunities for international transport of maternal germplasm worldwide; non-surgical transfer of viable embryos in practice is nearing reality. While production of transgenic animals has been successful, the low level of efficiency in producing these animals and lack of information on multigene interactions limit the use of the technology in applied production systems. Technologies based on research in functional genomics, proteomics and cloning have significant potential, but considerable research effort will be required before they can be utilized for AI in pig production. In the past 15 years, there has been a coordinated worldwide scientific effort to develop the genetic linkage map of the pig with the goal of identifying pigs with genetic alleles that result in improved growth rate, carcass quality, and reproductive performance. Molecular genetic tests have been developed to select pigs with improved traits such as removal of the porcine stress (RYR1) syndrome, and selection for specific estrogen receptor (ESR) alleles. Less progress has been made in developing routine tests related to diseases. Major research in genomics is being pursued to improve the efficiency of selection for healthier pigs with disease resistance properties. The sequencing of the genome of the pig to identify new genes and unique regulatory elements holds great promise to provide new information that can be used in pig production. AI, in vitro embryo production and embryo transfer will be the preferred means of implementing these new technologies to enhance efficiency of pig production in the future.
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Affiliation(s)
- Roger J Gerrits
- Biotechnology and Germplasm Laboratory, ANRI, BARC, ARS, USDA, Beltsville, MD, USA
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Basso M, Giraudo S, Corpillo D, Bergamasco B, Lopiano L, Fasano M. Proteome analysis of human substantia nigra in Parkinson's disease. Proteomics 2004; 4:3943-52. [PMID: 15526345 DOI: 10.1002/pmic.200400848] [Citation(s) in RCA: 206] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Protein expression has been compared in human substantia nigra specimens from Parkinson's disease (PD) patients and from controls, and 44 proteins expressed in this midbrain region were identified by peptide mass fingerprinting. Among them, nine showed changes in their abundance. L and M neurofilament chains are less abundant in PD specimens, whereas peroxiredoxin II, mitochondrial complex III, ATP synthase D chain, complexin I, profilin, L-type calcium channel delta-subunit, and fatty-acid binding protein are significantly more present in PD samples than in controls. Besides the consolidated view of oxidative stress involvement in PD pathogenesis, suggested by overexpression of mitochondrial and reactive oxygen species (ROS)-scavenging proteins, these results indicate a possible potentiation mechanism of afferent signals to substantia nigra following degeneration of dopaminergic neurons.
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Affiliation(s)
- Manuela Basso
- Department of Structural and Functional Biology, and Center of Neuroscience, University of Insubria, Busto Arsizio, Italy
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45
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Rai AJ, Chan DW. Cancer proteomics: Serum diagnostics for tumor marker discovery. Ann N Y Acad Sci 2004; 1022:286-94. [PMID: 15251974 DOI: 10.1196/annals.1318.044] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Cancer proteomics is an exciting field that is witnessing many new developments in recent years. It is hoped that these advances will result in decreased cancer death rates, which have not declined dramatically in the last several decades. Some of the problems with current tumor markers include the lack of sensitivity and specificity, factors that prevent their use in population-based screening of disease. Thus, there is an urgent need to identify novel biomarkers that can faithfully detect the disease state. As we are now in the post-genome era, many opportunities have been created. Genomic sequence data are available for human, as well as several other species. We are now poised to mine these data and to determine the functions of the encoded proteins constituting the human genome. Proteomics affords this opportunity by providing enhanced procedures and tools for discovery and also a framework for understanding these components in terms of pathogenesis. New technologies and improvements in existing methodologies will allow for the rapid growth in the identification and characterization of peptides and proteins that are unique to various clinical states. This technology can be successfully applied to clinical specimens for the identification of new tumor markers.
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Affiliation(s)
- Alex J Rai
- Department of Pathology, Division of Clinical Chemistry, and Center for Biomarker Discovery, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.
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46
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Matarazzo V, Ronnett GV. Temporal and regional differences in the olfactory proteome as a consequence of MeCP2 deficiency. Proc Natl Acad Sci U S A 2004; 101:7763-8. [PMID: 15128950 PMCID: PMC419680 DOI: 10.1073/pnas.0307083101] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rett syndrome (RTT) is a neurodevelopmental disorder caused by mutations in the gene encoding MeCP2. By binding to methylated CpG dinucleotide promoter regions, MeCP2 acts as a transcriptional repressor, predicting that its absence might result in widespread aberrant gene transcription, leading to the RTT phenotype. Considering this potentially broad action of MeCP2 on expression and the complexity of the brain, especially during development, we approached the consequences of MeCP2 deficiency in a mouse model by using a temporal and regional proteomic strategy. We used the olfactory system (olfactory epithelium and bulb) because its attributes make it an excellent developmental model system. We find evidence of temporal and regional proteomic pattern differences between WT and MeCP2-deficient mice. It was possible to segregate these changes in protein expression into five biological function groups: cytoskeleton arrangement, chromatin modeling, energy metabolism, cell signaling, and neuroprotection. By combining the proteomic results with the RNA levels of the identified proteins, we show that protein expression changes are the consequence of differences in mRNA level or posttranslational modifications. We conclude that brain regions and ages must be carefully considered when investigating MeCP2 deficiency, and that not only transcription should be taken into account as a source for these changes, but posttranslational protein modifications as well.
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Affiliation(s)
- Valéry Matarazzo
- Department of Neuroscience, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA
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Maurer MH, Berger C, Wolf M, Fütterer CD, Feldmann RE, Schwab S, Kuschinsky W. The proteome of human brain microdialysate. Proteome Sci 2003; 1:7. [PMID: 14675487 PMCID: PMC317363 DOI: 10.1186/1477-5956-1-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2003] [Accepted: 12/14/2003] [Indexed: 12/02/2022] Open
Abstract
Background Cerebral microdialysis has been established as a monitoring tool in neurocritically ill patients suffering from severe stroke. The technique allows to sample small molecules in the brain tissue for subsequent biochemical analysis. In this study, we investigated the proteomic profile of human cerebral microdialysate and if the identified proteins might be useful predictors for disease characteristics in stroke for tissue at risk in the contralateral hemisphere. We analysed cerebral protein expression in microdialysate from three stroke patients sampled from the hemisphere contralateral to the lesion. Using a proteomic approach based on two-dimensional gel electrophoresis and subsequent mass spectrometry, we created a protein map for the global protein expression pattern of human microdialyste. Results We found an average of 158 ± 24 (N = 18) protein spots in the human cerebral microdialysate and could identify 95 spots, representing 27 individual proteins. Most of these have been detected in human cerebrospinal fluid before, but 10 additional proteins mainly of cerebral intracellular origin were identified exclusively in the microdialysate. Conclusions The 10 proteins found exclusively in human cerebral microdialysate, but not in cerebrospinal fluid, indicate the possibility to monitor the progression of the disease towards deterioration. The correlation of protein composition in the human cerebral microdialysate with the patients' clinical condition and results of cerebral imaging may be a useful approach to future applications for neurological stroke diagnosis, prognosis, and treatment.
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Affiliation(s)
- Martin H Maurer
- Dept. of Physiology and Pathophysiology, University of Heidelberg, Im Neuenheimer Feld 326, 69120 Heidelberg, Germany
| | - Christian Berger
- Dept. of Neurology, University of Heidelberg, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany
| | - Margit Wolf
- Dept. of Neurology, University of Heidelberg, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany
| | - Carsten D Fütterer
- Dept. of Anesthesiology and Critical Care Medicine, University of Heidelberg, Faculty of Clinical Medicine Mannheim, Theodor-Kutzer-Ufer, 68167 Mannheim, Germany
| | - Robert E Feldmann
- Dept. of Physiology and Pathophysiology, University of Heidelberg, Im Neuenheimer Feld 326, 69120 Heidelberg, Germany
| | - Stefan Schwab
- Dept. of Neurology, University of Heidelberg, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany
| | - Wolfgang Kuschinsky
- Dept. of Physiology and Pathophysiology, University of Heidelberg, Im Neuenheimer Feld 326, 69120 Heidelberg, Germany
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Maurer MH, Feldmann RE, Fütterer CD, Kuschinsky W. The proteome of neural stem cells from adult rat hippocampus. Proteome Sci 2003; 1:4. [PMID: 12818002 PMCID: PMC165415 DOI: 10.1186/1477-5956-1-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2003] [Accepted: 06/12/2003] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND: Hippocampal neural stem cells (HNSC) play an important role in cerebral plasticity in the adult brain and may contribute to tissue repair in neurological disease. To describe their biological potential with regard to plasticity, proliferation, or differentiation, it is important to know the cellular composition of their proteins, subsumed by the term proteome. RESULTS: Here, we present for the first time a proteomic database for HNSC isolated from the brains of adult rats and cultured for 10 weeks. Cytosolic proteins were extracted and subjected to two-dimensional gel electrophoresis followed by protein identification through mass spectrometry, database search, and gel matching. We could map about 1141 PlusMinus; 209 (N = 5) protein spots for each gel, of which 266 could be identified. We could group the identified proteins into several functional categories including metabolism, protein folding, energy metabolism and cellular respiration, as well as cytoskeleton, Ca2+ signaling pathways, cell cycle regulation, proteasome and protein degradation. We also found proteins belonging to detoxification, neurotransmitter metabolism, intracellular signaling pathways, and regulation of DNA transcription and RNA processing. CONCLUSIONS: The HNSC proteome database is a useful inventory which will allow to specify changes in the cellular protein expression pattern due to specific activated or suppressed pathways during differentiation or proliferation of neural stem cells. Several proteins could be identified in the HNSC proteome which are related to differentiation and plasticity, indicating activated functional pathways. Moreover, we found a protein for which no expression has been described in brain cells before.
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Affiliation(s)
- Martin H Maurer
- Dept. of Physiology and Pathophysiology, University of Heidelberg, Im Neuenheimer Feld 326, 69120 Heidelberg, Germany
| | - Robert E Feldmann
- Dept. of Physiology and Pathophysiology, University of Heidelberg, Im Neuenheimer Feld 326, 69120 Heidelberg, Germany
| | - Carsten D Fütterer
- Dept. of Anesthesiology and Critical Care Medicine, University of Heidelberg, Faculty of Clinical Medicine Mannheim, Theodor-Kutzer-Ufer, 68167 Mannheim, Germany
| | - Wolfgang Kuschinsky
- Dept. of Physiology and Pathophysiology, University of Heidelberg, Im Neuenheimer Feld 326, 69120 Heidelberg, Germany
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