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Yuditskaya S, Suffredini AF, J Kato G. The proteome of sickle cell disease: insights from exploratory proteomic profiling. Expert Rev Proteomics 2010; 7:833-48. [PMID: 21142886 PMCID: PMC3068560 DOI: 10.1586/epr.10.88] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The expanding realm of exploratory proteomics has added a unique dimension to the study of the complex pathophysiology involved in sickle cell disease. A review of proteomic studies published on sickle cell erythrocytes and plasma shows trends of upregulation of antioxidant proteins, an increase in cytoskeletal defects, an increase in protein repair and turnover components, a decrease in lipid raft proteins and apolipoprotein dysregulation. Many of these findings are consistent with the pathophysiology of sickle cell disease, including high oxidant burden, resulting in damage to cytoskeletal and other proteins, and erythrocyte rigidity. More unexpected findings, such as a decrease in lipid raft components and apolipoprotein dysregulation, offer previously unexplored targets for future investigation and potential therapeutic intervention. Exploratory proteomic profiling is a valuable source of hypothesis generation for the cellular and molecular pathophysiology of sickle cell disease.
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Affiliation(s)
| | | | - Gregory J Kato
- Critical Care Medicine Department, Clinical Center, MD, USA
- Sickle Cell Vascular Disease Section, Cardiovascular and Pulmonary Branch, National Heart, Lung and Blood Institute, NIH, 9000 Rockville Pike, MSC 1476, Building 10-CRC, Room 5-5140, Bethesda, MD 20892-1476, USA
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Pasini EM, Mann M, Thomas AW. Red blood cell proteomics. Transfus Clin Biol 2010; 17:151-64. [PMID: 20655788 DOI: 10.1016/j.tracli.2010.05.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Accepted: 05/21/2010] [Indexed: 12/23/2022]
Abstract
Since its discovery in the 17th century, the red blood cell, recognized in time as the critical cell component for survival, has been the focus of much attention. Its unique role in gas exchange (oxygen/CO(2) transport) and its distinct characteristics (absence of nucleus; biconcave cell shape) together with an - in essence - unlimited supply lead to extensive targeted biochemical, molecular and structural studies. A quick PubMed query with the word "erythrocyte" results in 198 013 scientific articles of which 162 are red blood cell proteomics studies, indicating that this new technique has been only recently applied to the red blood cell and related fields. Standard and comparative proteomics have been widely used to study different blood components. A growing body of proteomics literature has since developed, which deals with the characterization of red blood cells in health and disease. The possibility offered by proteomics to obtain a global snapshot of the whole red blood cell protein make-up, has provided unique insights to many fields including transfusion medicine, anaemia studies, intra-red blood cell parasite biology and translational research. While the contribution of proteomics is beyond doubt, a full red blood cell understanding will ultimately require, in addition to proteomics, lipidomics, glycomics, interactomics and study of post-translational modifications. In this review we will briefly discuss the methodology and limitations of proteomics, the contribution it made to the understanding of the erythrocyte and the advances in red blood cell-related fields brought about by comparative proteomics.
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Affiliation(s)
- E M Pasini
- Biomedical Primate Research Centre, Lange Kleiweg 139, 2288 GJ Rijswijk, The Netherlands
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Barlow CA, Laishram RS, Anderson RA. Nuclear phosphoinositides: a signaling enigma wrapped in a compartmental conundrum. Trends Cell Biol 2009; 20:25-35. [PMID: 19846310 DOI: 10.1016/j.tcb.2009.09.009] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Revised: 09/27/2009] [Accepted: 09/28/2009] [Indexed: 01/09/2023]
Abstract
While the presence of phosphoinositides in the nuclei of eukaryotes and the identity of the enzymes responsible for their metabolism have been known for some time, their functions in the nucleus are only now emerging. This is illustrated by the recent identification of effectors for nuclear phosphoinositides. Like the cytosolic phosphoinositide signaling pathway, nuclear phosphatidylinositol 4,5-bisphosphate (PI4,5P(2)) is at the center of the pathway and acts both as a messenger and as a precursor for many additional messengers. Here, recent advances in the understanding of nuclear phosphoinositide signaling and its functions are reviewed with an emphasis on PI4,5P(2) and its role in gene expression. The compartmentalization of nuclear phosphoinositide phosphates (PIP(n)) remains a mystery, but emerging evidence suggests that phosphoinositides occupy several functionally distinct compartments.
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Affiliation(s)
- Christy A Barlow
- University of Wisconsin-Madison, Department of Pharmacology, 1300 University Ave. University of Wisconsin Medical School, Madison, WI 53706, USA
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Postle AD, Hunt AN. Dynamic lipidomics with stable isotope labelling. J Chromatogr B Analyt Technol Biomed Life Sci 2009; 877:2716-21. [DOI: 10.1016/j.jchromb.2009.03.046] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Revised: 03/29/2009] [Accepted: 03/30/2009] [Indexed: 01/22/2023]
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Pasini EM, Lutz HU, Mann M, Thomas AW. Red blood cell (RBC) membrane proteomics--Part I: Proteomics and RBC physiology. J Proteomics 2009; 73:403-20. [PMID: 19540949 DOI: 10.1016/j.jprot.2009.06.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Revised: 05/29/2009] [Accepted: 06/04/2009] [Indexed: 10/20/2022]
Abstract
Membrane proteomics is concerned with accurately and sensitively identifying molecules involved in cell compartmentalisation, including those controlling the interface between the cell and the outside world. The high lipid content of the environment in which these proteins are found often causes a particular set of problems that must be overcome when isolating the required material before effective HPLC-MS approaches can be performed. The membrane is an unusually dynamic cellular structure since it interacts with an ever changing environment. A full understanding of this critical cell component will ultimately require, in addition to proteomics, lipidomics, glycomics, interactomics and study of post-translational modifications. Devoid of nucleus and organelles in mammalian species other than camelids, and constantly in motion in the blood stream, red blood cells (RBCs) are the sole mammalian oxygen transporter. The fact that mature mammalian RBCs have no internal membrane-bound organelles, somewhat simplifies proteomics analysis of the plasma membrane and the fact that it has no nucleus disqualifies microarray based methods. Proteomics has the potential to provide a better understanding of this critical interface, and thereby assist in identifying new approaches to diseases.
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Affiliation(s)
- Erica M Pasini
- Biomedical Primate Research Centre, Lange Kleiweg 139, 2288 GJ Rijswijk, The Netherlands
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Hunt AN, Postle AD. Mass spectrometry determination of endonuclear phospholipid composition and dynamics. Methods 2006; 39:104-11. [PMID: 16831558 DOI: 10.1016/j.ymeth.2006.05.005] [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] [Received: 01/06/2006] [Accepted: 05/01/2006] [Indexed: 11/19/2022] Open
Abstract
Mammalian cell lipid analyses using tandem electrospray ionization mass spectrometry, in conjunction with stable isotope labeling, permit unparalleled access to membrane phospholipid molecular species compositions and turnover. Lipidomic data from isolable compartments of lipid second messenger generation, such as membrane-free nuclei, can provide dynamic insights into the topology of phospholipid turnover. For example, ESI-MS/MS precursor scans of characteristic phosphocholine m/z 184(+) fragments reveal a highly saturated endonuclear phosphatidylcholine pool with homeostatic maintenance properties. A spatially distinct CDPcholine pathway yields, within minutes of choline-d(9) labeling, unsaturated endonuclear phosphatidylcholines progressively remodeled to more saturated species evidenced by tracking the deuteriated headgroup through precursor scans of phosphocholine-d(9) (m/z 193(+) fragment). Among the other endonuclear phospholipids, diacyl phosphatidylethanolamines (neutral loss of m/z 141(+)) are also highly saturated compared with those of whole cell whereas, phophatidylinositols (precursor scans of m/z 241(-) fragment) are essentially identical in nuclei and whole cells. Moreover, the pattern of myo-inositol-d(6) acquisition into endonuclear phosphatidylinositol (precursor scans of m/z 247(-) fragment) is inconsistent with compartment-specific synthesis. Endonuclear sphingomyelins (seen in precursor scans of m/z 184(+) and confirmed from precursor scans of m/z 168(-) fragments) are enriched but similar in composition to whole cell species whereas endonuclear phosphatidylserines (neutral loss of m/z 87(-)) are more saturated than their whole cell counterparts. The focus of described methodologies emphasize their value in probing the compositions and dynamics of endonuclear phospholipids, but in principle may be extended to exploration of other isolable compartments including ER or plasma membranes.
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Affiliation(s)
- Alan N Hunt
- Allergy and Inflammation Research, Division of Infection, Inflammation and Repair, School of Medicine, University of Southampton, Southampton SO16 6YD, UK.
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Bunce MW, Bergendahl K, Anderson RA. Nuclear PI(4,5)P(2): a new place for an old signal. Biochim Biophys Acta Mol Cell Biol Lipids 2006; 1761:560-9. [PMID: 16750654 DOI: 10.1016/j.bbalip.2006.03.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2005] [Revised: 03/03/2006] [Accepted: 03/03/2006] [Indexed: 10/24/2022]
Abstract
Over the last decades, evidence has accumulated suggesting that there is a distinct nuclear phosphatidylinositol pathway. One of the best examined nuclear lipid pathways is the hydrolysis of phosphatidylinositol 4,5-bisphosphate (PI4,5P(2)) by PLC resulting in activation of nuclear PKC and production of inositol polyphosphates. However, there is a growing number of data that phosphoinositides are not only precursor for soluble inositol phosphates and diacylglycerol, instead they can act as second messengers themselves. They have been implicated to play a role in different important nuclear signaling events such as cell cycle progression, apoptosis, chromatin remodeling, transcriptional regulation and mRNA processing. This review focuses on the role of specifically PI4,5P(2) in the nucleus as a second messenger as well as a precursor for PI3,4,5P3, inositol polyphosphates and diacylglycerol.
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Affiliation(s)
- Matthew W Bunce
- Department of Pharmacology, University of Wisconsin Medical School, 1300 University Ave., Madison, WI 53706, USA
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Hunt AN. Completing the cycles; the dynamics of endonuclear lipidomics. Biochim Biophys Acta Mol Cell Biol Lipids 2006; 1761:577-87. [PMID: 16581290 DOI: 10.1016/j.bbalip.2006.02.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2006] [Revised: 02/17/2006] [Accepted: 02/20/2006] [Indexed: 12/29/2022]
Abstract
Signal transductions via periodic generation and mobilisation of lipid second messengers within the nuclear matrix of eukaryotic cells have focused renewed attention on their precursor phospholipids' location, structure, form and function. The nuclear matrix contains and supports dynamic pools of phosphatidylcholine and phosphatidylinositol which serve as parent molecules of lipid second messengers but also of other phospholipids requiring cyclical replacement as cells proliferate. Applications of new, highly sensitive and specific analytical methodologies based on tandem electrospray ionisation mass spectrometry and the use of stable isotopes have allowed both static and dynamic lipidomic profiling of these endonuclear phospholipid pools. Together with more conventional enzymatic analyses and evaluation of the effect of specific "knock-out" of phospholipid transfer capacity, a number of important principles have been established. Specifically, a compartmental capacity to synthesise and remodel highly saturated phosphatidylcholine exists alongside transport mechanisms that facilitate the nuclear import of phosphatidylinositol and other phospholipids synthesised elsewhere within the cell. Subnuclear fractionation and the use of newly emerging techniques for sensitive lipidomic profiling of polyphosphoinositides, diacylglycerols and phosphatidate molecular species offer the potential for further significant advances in the near future.
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Affiliation(s)
- Alan N Hunt
- Allergy and Inflammation Research, Division of Infection, Inflammation and Repair, School of Medicine, University of Southampton, Southampton General Hospital, Tremona Road, Southampton SO16 6YD, UK.
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Abstract
Once nuclear envelope membranes have been removed from isolated nuclei, around 6% of mammalian cell phospholipid is retained within the nuclear matrix, which calculations suggest may occupy 10% of the volume of this subcellular compartment. It is now acknowledged that endonuclear phospholipid, largely ignored for the past 40 years, provides substrate for lipid-mediated signaling events. However, given its abundance, it likely also has other as yet incompletely defined roles. Endonuclear phosphatidylcholine is the predominant phospholipid comprising distinct and highly saturated molecular species compared with that of the whole cell. Moreover, this unusual composition is subject to tight homeostatic maintenance even under conditions of extreme dietary manipulation, presumably reflecting a functional requirement for highly saturated endonuclear phosphatidylcholine. Recent application of new lipidomic technologies exploiting tandem electrospray ionization mass spectrometry in conjunction with deuterium stable isotope labeling have permitted us to probe not just molecular species compositions but endonuclear phospholipid acquisition and turnover with unparalleled sensitivity and specificity. What emerges is a picture of a dynamic pool of endonuclear phospholipid subject to autonomous regulation with respect to bulk cellular phospholipid metabolism. Compartmental biosynthesis de novo of endonuclear phosphatidylcholine contrasts with import of phosphatidylinositol synthesized elsewhere. However, irrespective of the precise temporal-spatial-dynamic relationships underpinning phospholipid acquisition, derangement of endonuclear lipid-mediated signaling from these parental phospholipids halts cell growth and division indicating a pivotal control point. This in turn defines the manipulation of compartmentalized endonuclear phospholipid acquisition and metabolism as intriguing potential targets for the development of future antiproliferative strategies.
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Affiliation(s)
- Alan N Hunt
- Allergy and Inflammation Research, Division of Infection, Inflammation & Repair, School of Medicine, University of Southampton, Southampton SO16 6YD, United Kingdom.
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Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2005; 40:1110-21. [PMID: 16106339 DOI: 10.1002/jms.809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
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