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Tregub P, Motin Y, Kulikov V, Kovzelev P, Chaykovskaya A, Ibrahimli I. Ultrastructural Changes in Hippocampal Region CA1 Neurons After Exposure to Permissive Hypercapnia and/or Normobaric Hypoxia. Cell Mol Neurobiol 2023; 43:4209-4217. [PMID: 37716927 DOI: 10.1007/s10571-023-01407-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 08/31/2023] [Indexed: 09/18/2023]
Abstract
Isolated exposure to intermittent hypoxia and permissive hypercapnia activates signaling mechanisms that induce ultrastructural changes in mitochondria and endoplasmic reticulum, accompanied by the development of maximal ischemic tolerance in neurons under the combined influence of these factors. However, there are a lack of data on the combined impact of these factors on the ultrastructure of neuronal organelles. The present study aims to comparatively assess the ultrastructural changes in neurons following isolated and combined exposure to hypoxia and hypercapnia, as well as to correlate these changes with the neuroprotective potential previously observed for these factors. Following a 15-session course of 30-min exposures to permissive hypercapnia (PCO2 ≈ 50 mmHg) and/or normobaric hypoxia (PO2 ≈ 150 mmHg), morphometric assessment was conducted to evaluate the extent of ultrastructural changes in hippocampal neurons (mitochondria, perinuclear space, and granular endoplasmic reticulum). It was found that in hippocampal neurons from the CA1 region, permissive hypercapnia resulted in increased mitochondrial size, expansion of membranous compartments of the granular endoplasmic reticulum, and perinuclear space. Normobaric hypoxia affected only mitochondrial size, while hypercapnic hypoxia specifically widened the perinuclear space. These ultrastructural changes objectively reflect varying degrees of the influence of hypoxia and hypercapnia on organelles responsible for energy metabolism, anti-apoptotic, and synthetic functions of neurons. This confirms the effect of potentiation of their neuroprotective effects under combined exposure and highlights the dominant role of the hypercapnic component in this mechanism.
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Affiliation(s)
- Pavel Tregub
- Department of Pathophysiology, I.M. Sechenov First Moscow State Medical University, Trubetskaya Str., 8, P. 2, Moscow, Russian Federation, 119991.
- Peoples Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya St., Moscow, Russian Federation, 117198.
- Research Center of Neurology, Moscow, Russian Federation, 125367.
| | - Yuri Motin
- Altai State Medical University, 40 Lenin Prospekt, Barnaul, Russian Federation, 656038
| | - Vladimir Kulikov
- Altai State Medical University, 40 Lenin Prospekt, Barnaul, Russian Federation, 656038
| | - Pavel Kovzelev
- V.A. Almazov National Medical Research Center, Akkuratov Str., P. 2, St. Petersburg, Russian Federation, 197341
| | - Aleksandra Chaykovskaya
- V.A. Almazov National Medical Research Center, Akkuratov Str., P. 2, St. Petersburg, Russian Federation, 197341
| | - Irada Ibrahimli
- Department of Pathophysiology, I.M. Sechenov First Moscow State Medical University, Trubetskaya Str., 8, P. 2, Moscow, Russian Federation, 119991
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Chen Z, Zhang SL. Endoplasmic Reticulum Stress: A Key Regulator of Cardiovascular Disease. DNA Cell Biol 2023. [PMID: 37140435 DOI: 10.1089/dna.2022.0532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023] Open
Abstract
The problems associated with economic development and social progress have led to an increase in the occurrence of cardiovascular diseases (CVDs), which affect the health of an increasing number of people and are a leading cause of disease and population mortality worldwide. Endoplasmic reticulum stress (ERS), a hot topic of interest for scholars in recent years, has been confirmed in numerous studies to be an important pathogenetic basis for many metabolic diseases and play an important role in maintaining physiological processes. The endoplasmic reticulum (ER) is a major organelle that is involved in protein folding and modification synthesis, and ERS occurs when several physiological and pathological factors allow excessive amounts of unfolded/misfolded proteins to accumulate. ERS often leads to initiation of the unfolded protein response (UPR) in a bid to re-establish tissue homeostasis; however, UPR has been documented to induce vascular remodeling and cardiomyocyte damage under various pathological conditions, leading to or accelerating the development of CVDs such as hypertension, atherosclerosis, and heart failure. In this review, we summarize the latest knowledge gained concerning ERS in terms of cardiovascular system pathophysiology, and discuss the feasibility of targeting ERS as a novel therapeutic target for the treatment of CVDs. Investigation of ERS has immense potential as a new direction for future research involving lifestyle intervention, the use of existing drugs, and the development of novel drugs that target and inhibit ERS.
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Affiliation(s)
- Zhao Chen
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Shi-Liang Zhang
- Section 4, Department of Cardiology, The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
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Sazonova MA, Sinyov VV, Ryzhkova AI, Sazonova MD, Kirichenko TV, Khotina VA, Khasanova ZB, Doroschuk NA, Karagodin VP, Orekhov AN, Sobenin IA. Some Molecular and Cellular Stress Mechanisms Associated with Neurodegenerative Diseases and Atherosclerosis. Int J Mol Sci 2021; 22:E699. [PMID: 33445687 PMCID: PMC7828120 DOI: 10.3390/ijms22020699] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/29/2020] [Accepted: 01/04/2021] [Indexed: 12/14/2022] Open
Abstract
Chronic stress is a combination of nonspecific adaptive reactions of the body to the influence of various adverse stress factors which disrupt its homeostasis, and it is also a corresponding state of the organism's nervous system (or the body in general). We hypothesized that chronic stress may be one of the causes occurence of several molecular and cellular types of stress. We analyzed literary sources and considered most of these types of stress in our review article. We examined genes and mutations of nuclear and mitochondrial genomes and also molecular variants which lead to various types of stress. The end result of chronic stress can be metabolic disturbance in humans and animals, leading to accumulation of reactive oxygen species (ROS), oxidative stress, energy deficiency in cells (due to a decrease in ATP synthesis) and mitochondrial dysfunction. These changes can last for the lifetime and lead to severe pathologies, including neurodegenerative diseases and atherosclerosis. The analysis of literature allowed us to conclude that under the influence of chronic stress, metabolism in the human body can be disrupted, mutations of the mitochondrial and nuclear genome and dysfunction of cells and their compartments can occur. As a result of these processes, oxidative, genotoxic, and cellular stress can occur. Therefore, chronic stress can be one of the causes forthe occurrence and development of neurodegenerative diseases and atherosclerosis. In particular, chronic stress can play a large role in the occurrence and development of oxidative, genotoxic, and cellular types of stress.
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Affiliation(s)
- Margarita A. Sazonova
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, Russian Academy of Medical Sciences, 125315 Moscow, Russia; (V.V.S.); (A.I.R.); (M.D.S.); (T.V.K.); (V.A.K.); (V.P.K.); (A.N.O.); (I.A.S.)
- Laboratory of Medical Genetics, National Medical Research Center of Cardiology, 121552 Moscow, Russia; (Z.B.K.); (N.A.D.)
| | - Vasily V. Sinyov
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, Russian Academy of Medical Sciences, 125315 Moscow, Russia; (V.V.S.); (A.I.R.); (M.D.S.); (T.V.K.); (V.A.K.); (V.P.K.); (A.N.O.); (I.A.S.)
- Laboratory of Medical Genetics, National Medical Research Center of Cardiology, 121552 Moscow, Russia; (Z.B.K.); (N.A.D.)
| | - Anastasia I. Ryzhkova
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, Russian Academy of Medical Sciences, 125315 Moscow, Russia; (V.V.S.); (A.I.R.); (M.D.S.); (T.V.K.); (V.A.K.); (V.P.K.); (A.N.O.); (I.A.S.)
| | - Marina D. Sazonova
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, Russian Academy of Medical Sciences, 125315 Moscow, Russia; (V.V.S.); (A.I.R.); (M.D.S.); (T.V.K.); (V.A.K.); (V.P.K.); (A.N.O.); (I.A.S.)
| | - Tatiana V. Kirichenko
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, Russian Academy of Medical Sciences, 125315 Moscow, Russia; (V.V.S.); (A.I.R.); (M.D.S.); (T.V.K.); (V.A.K.); (V.P.K.); (A.N.O.); (I.A.S.)
- Laboratory of Medical Genetics, National Medical Research Center of Cardiology, 121552 Moscow, Russia; (Z.B.K.); (N.A.D.)
- Laboratory of Cellular and Molecular Pathology of Cardiovascular System, Research Institute of Human Morphology, 117418 Moscow, Russia
| | - Victoria A. Khotina
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, Russian Academy of Medical Sciences, 125315 Moscow, Russia; (V.V.S.); (A.I.R.); (M.D.S.); (T.V.K.); (V.A.K.); (V.P.K.); (A.N.O.); (I.A.S.)
- Laboratory of Cellular and Molecular Pathology of Cardiovascular System, Research Institute of Human Morphology, 117418 Moscow, Russia
| | - Zukhra B. Khasanova
- Laboratory of Medical Genetics, National Medical Research Center of Cardiology, 121552 Moscow, Russia; (Z.B.K.); (N.A.D.)
| | - Natalya A. Doroschuk
- Laboratory of Medical Genetics, National Medical Research Center of Cardiology, 121552 Moscow, Russia; (Z.B.K.); (N.A.D.)
| | - Vasily P. Karagodin
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, Russian Academy of Medical Sciences, 125315 Moscow, Russia; (V.V.S.); (A.I.R.); (M.D.S.); (T.V.K.); (V.A.K.); (V.P.K.); (A.N.O.); (I.A.S.)
- Department of Commodity Science and Expertise, Plekhanov Russian University of Economics, 125993 Moscow, Russia
| | - Alexander N. Orekhov
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, Russian Academy of Medical Sciences, 125315 Moscow, Russia; (V.V.S.); (A.I.R.); (M.D.S.); (T.V.K.); (V.A.K.); (V.P.K.); (A.N.O.); (I.A.S.)
- Laboratory of Cellular and Molecular Pathology of Cardiovascular System, Research Institute of Human Morphology, 117418 Moscow, Russia
- Institute for Atherosclerosis Research, Skolkovo Innovative Centre, 143024 Moscow, Russia
| | - Igor A. Sobenin
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, Russian Academy of Medical Sciences, 125315 Moscow, Russia; (V.V.S.); (A.I.R.); (M.D.S.); (T.V.K.); (V.A.K.); (V.P.K.); (A.N.O.); (I.A.S.)
- Laboratory of Medical Genetics, National Medical Research Center of Cardiology, 121552 Moscow, Russia; (Z.B.K.); (N.A.D.)
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Miao YY, Zhao W, Li GP, Gao Y, Du PF. Predicting Endoplasmic Reticulum Resident Proteins Using Auto-Cross Covariance Transformation With a U-Shaped Residue Weight-Transfer Function. Front Genet 2020; 10:1231. [PMID: 31921288 PMCID: PMC6932965 DOI: 10.3389/fgene.2019.01231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 11/06/2019] [Indexed: 11/13/2022] Open
Abstract
Background: The endoplasmic reticulum (ER) is an important organelle in eukaryotic cells. It is involved in many important biological processes, such as cell metabolism, protein synthesis, and post-translational modification. The proteins that reside within the ER are called ER-resident proteins. These proteins are closely related to the biological functions of the ER. The difference between the ER-resident proteins and other non-resident proteins should be carefully studied. Methods: We developed a support vector machine (SVM)-based method. We developed a U-shaped weight-transfer function and used it, along with the positional-specific physiochemical properties (PSPCP), to integrate together sequence order information, signaling peptides information, and evolutionary information. Result: Our method achieved over 86% accuracy in a jackknife test. We also achieved roughly 86% sensitivity and 67% specificity in an independent dataset test. Our method is capable of identifying ER-resident proteins.
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Affiliation(s)
- Yang-Yang Miao
- College of Intelligence and Computing, Tianjin University, Tianjin, China.,School of Chemical Engineering, Tianjin University, Tianjin, China
| | - Wei Zhao
- College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Guang-Ping Li
- College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Yang Gao
- School of Medicine, Nankai University, Tianjin, China
| | - Pu-Feng Du
- College of Intelligence and Computing, Tianjin University, Tianjin, China
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Varlamova EG, Goltyaev MV. The Effect of Sodium Selenite on the Expression of Genes of Endoplasmic Reticulum-Resident Selenoproteins in Human Fibrosarcoma Cells. Biophysics (Nagoya-shi) 2018. [DOI: 10.1134/s000635091805024x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Varlamova EG. Participation of selenoproteins localized in the ER in the processes occurring in this organelle and in the regulation of carcinogenesis-associated processes. J Trace Elem Med Biol 2018; 48:172-180. [PMID: 29773177 DOI: 10.1016/j.jtemb.2018.04.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 03/11/2018] [Accepted: 04/02/2018] [Indexed: 01/12/2023]
Abstract
The functions performed by the ER are diverse: synthesis of steroid hormones, synthesis of proteins for the plasma membrane, lysosomes, as well as proteins meant for exocytosis, protein folding, formation of disulfide bonds, N-linked glycosylation, etc. Selenoproteins localized in this organelle are definitely involved in the processes occurring in it, and the most common of them include participation in protein degradation, regulation of ER stress and redox metabolism. ER stress has been registered in many types of cancer cells. The ability to persist under prolonged ER stress increases their survival, resistance to drugs and immunity. Disturbances in the redox regulation of the cell cycle, which result in the accumulation of misfolded proteins in the ER, viral infection, disruption of Ca2+ regulation, are known to cause an evolutionarily conserved reaction - unfolded protein response (UPR) and, ultimately, lead to ER stress. Since selenoproteins, as oxidoreductases, possess antioxidant properties, and their role in the regulation of important processes, such as carcinogenesis and ER stress, has been actively studied in the recent decades, the subject of this review is highly relevant.
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Affiliation(s)
- Elena Gennadyevna Varlamova
- Federal State Institution of Science, Institute of Cell Biophysics, Russian Academy of Sciences, Institutskaya St. 3, Pushchino, Moscow Region, 142290, Russia.
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Kumar R, Kumari B, Kumar M. Prediction of endoplasmic reticulum resident proteins using fragmented amino acid composition and support vector machine. PeerJ 2017; 5:e3561. [PMID: 28890846 PMCID: PMC5588793 DOI: 10.7717/peerj.3561] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 06/20/2017] [Indexed: 12/15/2022] Open
Abstract
Background The endoplasmic reticulum plays an important role in many cellular processes, which includes protein synthesis, folding and post-translational processing of newly synthesized proteins. It is also the site for quality control of misfolded proteins and entry point of extracellular proteins to the secretory pathway. Hence at any given point of time, endoplasmic reticulum contains two different cohorts of proteins, (i) proteins involved in endoplasmic reticulum-specific function, which reside in the lumen of the endoplasmic reticulum, called as endoplasmic reticulum resident proteins and (ii) proteins which are in process of moving to the extracellular space. Thus, endoplasmic reticulum resident proteins must somehow be distinguished from newly synthesized secretory proteins, which pass through the endoplasmic reticulum on their way out of the cell. Approximately only 50% of the proteins used in this study as training data had endoplasmic reticulum retention signal, which shows that these signals are not essentially present in all endoplasmic reticulum resident proteins. This also strongly indicates the role of additional factors in retention of endoplasmic reticulum-specific proteins inside the endoplasmic reticulum. Methods This is a support vector machine based method, where we had used different forms of protein features as inputs for support vector machine to develop the prediction models. During training leave-one-out approach of cross-validation was used. Maximum performance was obtained with a combination of amino acid compositions of different part of proteins. Results In this study, we have reported a novel support vector machine based method for predicting endoplasmic reticulum resident proteins, named as ERPred. During training we achieved a maximum accuracy of 81.42% with leave-one-out approach of cross-validation. When evaluated on independent dataset, ERPred did prediction with sensitivity of 72.31% and specificity of 83.69%. We have also annotated six different proteomes to predict the candidate endoplasmic reticulum resident proteins in them. A webserver, ERPred, was developed to make the method available to the scientific community, which can be accessed at http://proteininformatics.org/mkumar/erpred/index.html. Discussion We found that out of 124 proteins of the training dataset, only 66 proteins had endoplasmic reticulum retention signals, which shows that these signals are not an absolute necessity for endoplasmic reticulum resident proteins to remain inside the endoplasmic reticulum. This observation also strongly indicates the role of additional factors in retention of proteins inside the endoplasmic reticulum. Our proposed predictor, ERPred, is a signal independent tool. It is tuned for the prediction of endoplasmic reticulum resident proteins, even if the query protein does not contain specific ER-retention signal.
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Affiliation(s)
- Ravindra Kumar
- Department of Biophysics, University of Delhi South Campus, New Delhi, India.,Current affiliation: Newe-Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Bandana Kumari
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
| | - Manish Kumar
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
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Xie W, Nielsen ME, Pedersen C, Thordal-Christensen H. A Split-GFP Gateway Cloning System for Topology Analyses of Membrane Proteins in Plants. PLoS One 2017; 12:e0170118. [PMID: 28085941 PMCID: PMC5234810 DOI: 10.1371/journal.pone.0170118] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 12/29/2016] [Indexed: 11/18/2022] Open
Abstract
To understand the function of membrane proteins, it is imperative to know their topology. For such studies, a split green fluorescent protein (GFP) method is useful. GFP is barrel-shaped, consisting of 11 β-sheets. When the first ten β-sheets (GFP1-10) and the 11th β-sheet (GFP11) are expressed from separate genes they will self-assembly and reconstitute a fluorescent GFP protein. However, this will only occur when the two domains co-localize in the same cellular compartment. We have developed an easy-to-use Gateway vector set for determining on which side of the membrane the N- and C-termini are located. Two vectors were designed for making N- and C-terminal fusions between the membrane proteins-of-interest and GFP11, while another three plasmids were designed to express GFP1-10 in either the cytosol, the endoplasmic reticulum (ER) lumen or the apoplast. We tested functionality of the system by applying the vector set for the transmembrane domain, CNXTM, of the ER membrane protein, calnexin, after transient expression in Nicotiana benthamiana leaves. We observed GFP signal from the ER when we reciprocally co-expressed GFP11-CNXTM with GFP1-10-HDEL and CNXTM-GFP with cytosolic GFP1-10. The opposite combinations did not result in GFP signal emission. This test using the calnexin ER-membrane domain demonstrated its C-terminus to be in the cytosol and its N-terminus in the ER lumen. This result confirmed the known topology of calnexin, and we therefore consider this split-GFP system highly useful for ER membrane topology studies. Furthermore, the vector set provided is useful for detecting the topology of proteins on other membranes in the cell, which we confirmed for a plasma membrane syntaxin. The set of five Ti-plasmids are easily and efficiently used for Gateway cloning and transient transformation of N. benthamiana leaves.
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Affiliation(s)
- Wenjun Xie
- Plant Defence Genetics, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Denmark
| | - Mads Eggert Nielsen
- Plant Defence Genetics, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Denmark
| | - Carsten Pedersen
- Plant Defence Genetics, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Denmark
| | - Hans Thordal-Christensen
- Plant Defence Genetics, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Denmark
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Chi X, Kale J, Leber B, Andrews DW. Regulating cell death at, on, and in membranes. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1843:2100-13. [PMID: 24927885 DOI: 10.1016/j.bbamcr.2014.06.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 05/29/2014] [Accepted: 06/03/2014] [Indexed: 11/17/2022]
Abstract
Bcl-2 family proteins are central regulators of apoptosis. Various family members are located in the cytoplasm, endoplasmic reticulum, and mitochondrial outer membrane in healthy cells. However during apoptosis most of the interactions between family members that determine the fate of the cell occur at the membranes of intracellular organelles. It has become evident that interactions with membranes play an active role in the regulation of Bcl-2 family protein interactions. Here we provide an overview of various models proposed to explain how the Bcl-2 family regulates apoptosis and discuss how membrane binding affects the structure and function of each of the three categories of Bcl-2 proteins (pro-apoptotic, pore-forming, and anti-apoptotic). We also examine how the Bcl-2 family regulates other aspects of mitochondrial and ER physiology relevant to cell death.
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Affiliation(s)
- Xiaoke Chi
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Justin Kale
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Brian Leber
- Department of Medicine, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - David W Andrews
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8N 3Z5, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada; Biological Sciences, Sunnybrook Research Institute, Toronto, Ontario M4N 3M5, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
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10
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Vannuvel K, Renard P, Raes M, Arnould T. Functional and morphological impact of ER stress on mitochondria. J Cell Physiol 2013; 228:1802-18. [PMID: 23629871 DOI: 10.1002/jcp.24360] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 03/04/2013] [Indexed: 12/15/2022]
Abstract
Over the past years, knowledge and evidence about the existence of crosstalks between cellular organelles and their potential effects on survival or cell death have been constantly growing. More recently, evidence accumulated showing an intimate relationship between endoplasmic reticulum (ER) and mitochondria. These close contacts not only establish extensive physical links allowing exchange of lipids and calcium but they can also coordinate pathways involved in cell life and death. It is now obvious that ER dysfunction/stress and unfolded protein response (UPR) as well as mitochondria play major roles in apoptosis. However, while the effects of major ER stress on cell death have been largely studied and reviewed, it becomes more and more evident that cells might regularly deal with sublethal ER stress, a condition that does not necessarily lead to cell death but might affect the function/activity of other organelles such as mitochondria. In this review, we will particularly focus on these new, interesting and intriguing metabolic and morphological events that occur during the early adaptative phase of the ER stress, before the onset of cell death, and that remain largely unknown. Relevance and implication of these mitochondrial changes in response to ER stress conditions for human diseases such as type II diabetes and Alzheimer's disease will also be considered.
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Affiliation(s)
- Kayleen Vannuvel
- Laboratory of Biochemistry and Cellular Biology, URBC-NARILIS, University of Namur, Namur, Belgium
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11
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Dedov II, Smirnova OM, Gorelyshev AS. Stress of endoplasmic reticulum: the cytological "scenario" of pathogenesis of human diseases. ACTA ACUST UNITED AC 2012. [DOI: 10.14341/probl201258557-65] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The phenomenon of stress of endoplasmic reticulum (ER) attracts an increasingly higher attention of the researchers. The available data suggest that ER dysfunction is a common component of many human pathologies including oncological diseases and neurodegenerative viral diseases. Stress of ER is of special significance in the cell populations actively secreting proteins because protein folding disturbances play an important role in its development. This fact opens up prospects for the better understanding of pathogenesis of diabetes mellitus and some other diseases. The present work summarizes the current concepts of biochemical mechanisms underlying stress of endoplasmic reticulum and elucidates the key signal pathways for its compensation and proapoptosis.
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12
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Van Summeren A, Renes J, van Delft JH, Kleinjans JC, Mariman EC. Proteomics in the search for mechanisms and biomarkers of drug-induced hepatotoxicity. Toxicol In Vitro 2012; 26:373-85. [DOI: 10.1016/j.tiv.2012.01.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 12/22/2011] [Accepted: 01/09/2012] [Indexed: 10/14/2022]
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Lynes EM, Simmen T. Urban planning of the endoplasmic reticulum (ER): how diverse mechanisms segregate the many functions of the ER. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2011; 1813:1893-905. [PMID: 21756943 PMCID: PMC7172674 DOI: 10.1016/j.bbamcr.2011.06.011] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 06/22/2011] [Accepted: 06/23/2011] [Indexed: 12/21/2022]
Abstract
The endoplasmic reticulum (ER) is the biggest organelle in most cell types, but its characterization as an organelle with a continuous membrane belies the fact that the ER is actually an assembly of several, distinct membrane domains that execute diverse functions. Almost 20 years ago, an essay by Sitia and Meldolesi first listed what was known at the time about domain formation within the ER. In the time that has passed since, additional ER domains have been discovered and characterized. These include the mitochondria-associated membrane (MAM), the ER quality control compartment (ERQC), where ER-associated degradation (ERAD) occurs, and the plasma membrane-associated membrane (PAM). Insight has been gained into the separation of nuclear envelope proteins from the remainder of the ER. Research has also shown that the biogenesis of peroxisomes and lipid droplets occurs on specialized membranes of the ER. Several studies have shown the existence of specific marker proteins found on all these domains and how they are targeted there. Moreover, a first set of cytosolic ER-associated sorting proteins, including phosphofurin acidic cluster sorting protein 2 (PACS-2) and Rab32 have been identified. Intra-ER targeting mechanisms appear to be superimposed onto ER retention mechanisms and rely on transmembrane and cytosolic sequences. The crucial roles of ER domain formation for cell physiology are highlighted with the specific targeting of the tumor metastasis regulator gp78 to ERAD-mediating membranes or of the promyelocytic leukemia protein to the MAM.
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Affiliation(s)
- Emily M Lynes
- Department of Cell Biology, University of Alberta, Alberta, Canada
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14
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Lavoie C, Roy L, Lanoix J, Taheri M, Young R, Thibault G, Farah CA, Leclerc N, Paiement J. Taking organelles apart, putting them back together and creating new ones: lessons from the endoplasmic reticulum. ACTA ACUST UNITED AC 2011; 46:1-48. [PMID: 21536318 DOI: 10.1016/j.proghi.2011.04.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/02/2011] [Indexed: 12/11/2022]
Abstract
The endoplasmic reticulum (ER) is a highly dynamic organelle. It is composed of four subcompartments including nuclear envelope (NE), rough ER (rER), smooth ER (sER) and transitional ER (tER). The subcompartments are interconnected, can fragment and dissociate and are able to reassemble again. They coordinate with cell function by way of protein regulators in the surrounding cytosol. The activity of the many associated molecular machines of the ER as well as the fluid nature of the limiting membrane of the ER contribute extensively to the dynamics of the ER. This review examines the properties of the ER that permit its isolation and purification and the physiological conditions that permit reconstitution both in vitro and in vivo in normal and in disease conditions.
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Affiliation(s)
- Christine Lavoie
- Département de pharmacologie, Faculté de médecine, Université de Sherbrooke, Sherbrooke, QC, Canada
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Fujimoto M, Hayashi T. New Insights into the Role of Mitochondria-Associated Endoplasmic Reticulum Membrane. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2011; 292:73-117. [DOI: 10.1016/b978-0-12-386033-0.00002-5] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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16
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Chen X, Karnovsky A, Sans MD, Andrews PC, Williams JA. Molecular characterization of the endoplasmic reticulum: insights from proteomic studies. Proteomics 2010; 10:4040-52. [PMID: 21080494 DOI: 10.1002/pmic.201000234] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The endoplasmic reticulum (ER) is a multifunctional intracellular organelle responsible for the synthesis, processing and trafficking of a wide variety of proteins essential for cell growth and survival. Therefore, comprehensive characterization of the ER proteome is of great importance to the understanding of its functions and has been actively pursued in the past decade by scientists in the proteomics field. This review summarizes major proteomic studies published in the past decade that focused on the ER proteome. We evaluate the data sets obtained from two different organs, liver and pancreas each of which contains a primary cell type (hepatocyte and acinar cell) with specialized functions. We also discuss how the nature of the proteins uncovered is related to the methods of organelle purification, organelle purity and the techniques used for protein separation prior to MS. In addition, this review also puts emphasis on the biological insights gained from these studies regarding the molecular functions of the ER including protein synthesis and translocation, protein folding and quality control, ER-associated degradation and ER stress, ER export and membrane trafficking, calcium homeostasis and detoxification and drug metabolism.
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Affiliation(s)
- Xuequn Chen
- Department of Molecular and Integrative Physiology, The University of Michigan, Ann Arbor, MI, USA.
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17
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Abstract
The lumen of the endoplasmic reticulum constitutes a separate intracellular compartment with a special proteome and metabolome. The redox conditions of the organelle are also characteristically different from those of the other subcellular compartments. The luminal environment has been considered more oxidizing than the cytosol due to the presence of oxidative protein folding. However, recent observations suggest that redox systems in reduced and oxidized states are present simultaneously. The concerted action of membrane transporters and oxidoreductase enzymes maintains the oxidized state of the thiol-disulfide and the reduced state of the pyridine nucleotide redox systems, which are prerequisites for the normal redox reactions localized in the organelle. The powerful thiol-oxidizing machinery of oxidative protein folding continuously challenges the local antioxidant defense. Alterations of the luminal redox conditions, either in oxidizing or reducing direction, affect protein processing, are sensed by the accumulation of misfolded/unfolded proteins, and may induce endoplasmic reticulum stress and unfolded protein response. The activated signaling pathways attempt to restore the balance between protein loading and processing and induce programmed cell death if these attempts fail. Recent findings strongly support the involvement of redox-based endoplasmic reticulum stress in a plethora of human diseases, either as causative agents or as complications.
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Affiliation(s)
- Miklós Csala
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
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Roy L, Laboissière S, Abdou E, Thibault G, Hamel N, Taheri M, Boismenu D, Lanoix J, Kearney RE, Paiement J. Proteomic analysis of the transitional endoplasmic reticulum in hepatocellular carcinoma: an organelle perspective on cancer. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:1869-81. [PMID: 20576523 DOI: 10.1016/j.bbapap.2010.05.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Revised: 05/05/2010] [Accepted: 05/18/2010] [Indexed: 02/06/2023]
Abstract
The transitional endoplasmic reticulum (tER) is composed of both rough and smooth ER membranes and thus participates in functions attributed to both these two subcellular compartments. In this paper we have compared the protein composition of tER isolated from dissected liver tumor nodules of aflatoxin B1-treated rats with that of tER from control liver. Tandem mass spectrometry (MS), peptide counts and immunoblot validation were used to identify and determine the relative expression level of proteins. Inhibitors of apoptosis (i.e. PGRMC1, tripeptidyl peptidase II), proteins involved in ribosome biogenesis (i.e. nucleophosmin, nucleolin), proteins involved in translation (i.e. eEF-2, and subunits of eIF-3), proteins involved in ubiquitin metabolism (i.e. proteasome subunits, USP10) and proteins involved in membrane traffic (i.e. SEC13-like 1, SEC23B, dynactin 1) were found overexpressed in tumor tER. Transcription factors (i.e. Pur-beta, BTF3) and molecular targets for C-Myc and NF-kappa B were observed overexpressed in tER from tumor nodules. Down-regulated proteins included cytochrome P450 proteins and enzymes involved in fatty acid metabolism and in steroid metabolism. Unexpectedly expression of the protein folding machinery (i.e. calreticulin) and proteins of the MHC class I peptide-loading complex did not change. Proteins of unknown function were detected in association with the tER and the novel proteins showing differential expression are potential new tumor markers. In many cases differential expression of proteins in tumor tER was comparable to that of corresponding genes reported in the Oncomine human database. Thus the molecular profile of tumor tER is different and this may confer survival advantage to tumor cells in cancer.
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Affiliation(s)
- Line Roy
- McGill University and Genome Quebec Innovation Centre, Proteomics Services, Genome Quebec, Montreal, Quebec, Canada
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Simmen T, Lynes EM, Gesson K, Thomas G. Oxidative protein folding in the endoplasmic reticulum: tight links to the mitochondria-associated membrane (MAM). BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1798:1465-73. [PMID: 20430008 DOI: 10.1016/j.bbamem.2010.04.009] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Revised: 04/15/2010] [Accepted: 04/16/2010] [Indexed: 12/18/2022]
Abstract
The production of secretory proteins at the ER (endoplasmic reticulum) depends on a ready supply of energy and metabolites as well as the close monitoring of the chemical conditions that favor oxidative protein folding. ER oxidoreductases and chaperones fold nascent proteins into their export-competent three-dimensional structure. Interference with these protein folding enzymes leads to the accumulation of unfolded proteins within the ER lumen, causing an acute organellar stress that triggers the UPR (unfolded protein response). The UPR increases the transcription of ER chaperones commensurate with the load of newly synthesized proteins and can protect the cell from ER stress. Persistant stress, however, can force the UPR to commit cells to undergo apoptotic cell death, which requires the emptying of ER calcium stores. Conversely, a continuous ebb and flow of calcium occurs between the ER and mitochondria during resting conditions on a domain of the ER that forms close contacts with mitochondria, the MAM (mitochondria-associated membrane). On the MAM, ER folding chaperones such as calnexin and calreticulin and oxidoreductases such as ERp44, ERp57 and Ero1alpha regulate calcium flux from the ER through reversible, calcium and redox-dependent interactions with IP3Rs (inositol 1,4,5-trisphophate receptors) and with SERCAs (sarcoplasmic/endoplasmic reticulum calcium ATPases). During apoptosis progression and depending on the identity of the ER chaperone and oxidoreductase, these interactions increase or decrease, suggesting that the extent of MAM targeting of ER chaperones and oxidoreductases could shift the readout of ER-mitochondria calcium exchange from housekeeping to apoptotic. However, little is known about the cytosolic factors that mediate the on/off interactions between ER chaperones and oxidoreductases with ER calcium channels and pumps. One candidate regulator is the multi-functional molecule PACS-2 (phosphofurin acidic cluster sorting protein-2). Recent studies suggest that PACS-2 mediates localization of a mobile pool of calnexin to the MAM in addition to regulating homeostatic ER calcium signaling as well as MAM integrity. Together, these findings suggest that cytosolic, membrane and lumenal proteins combine to form a two-way switch that determines the rate of protein secretion by providing ions and metabolites and that appears to participate in the pro-apoptotic ER-mitochondria calcium transfer.
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Affiliation(s)
- Thomas Simmen
- Faculty of Medicine and Dentistry, School of Molecular and Systems Medicine, Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada.
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20
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Extending the knowledge in histochemistry and cell biology. Histochem Cell Biol 2009; 133:1-40. [PMID: 19946696 DOI: 10.1007/s00418-009-0665-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2009] [Indexed: 01/21/2023]
Abstract
Central to modern Histochemistry and Cell Biology stands the need for visualization of cellular and molecular processes. In the past several years, a variety of techniques has been achieved bridging traditional light microscopy, fluorescence microscopy and electron microscopy with powerful software-based post-processing and computer modeling. Researchers now have various tools available to investigate problems of interest from bird's- up to worm's-eye of view, focusing on tissues, cells, proteins or finally single molecules. Applications of new approaches in combination with well-established traditional techniques of mRNA, DNA or protein analysis have led to enlightening and prudent studies which have paved the way toward a better understanding of not only physiological but also pathological processes in the field of cell biology. This review is intended to summarize articles standing for the progress made in "histo-biochemical" techniques and their manifold applications.
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Vascotto C, Cesaratto L, Zeef LAH, Deganuto M, D'Ambrosio C, Scaloni A, Romanello M, Damante G, Taglialatela G, Delneri D, Kelley MR, Mitra S, Quadrifoglio F, Tell G. Genome-wide analysis and proteomic studies reveal APE1/Ref-1 multifunctional role in mammalian cells. Proteomics 2009; 9:1058-74. [PMID: 19180539 DOI: 10.1002/pmic.200800638] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Apurinic apyrimidinic endonuclease/redox effector factor 1 (APE1/Ref-1) protects cells from oxidative stress by acting as a central enzyme in base excision repair pathways of DNA lesions and through its independent activity as a redox transcriptional co-activator. Dysregulation of this protein has been associated with cancer development. At present, contrasting data have been published regarding the biological relevance of the two functions as well as the molecular mechanisms involved. Here, we combined both mRNA expression profiling and proteomic analysis to determine the molecular changes associated with APE1 loss-of-expression induced by siRNA technology. This approach identified a role of APE1 in cell growth, apoptosis, intracellular redox state, mitochondrial function, and cytoskeletal structure. Overall, our data show that APE1 acts as a hub in coordinating different and vital functions in mammalian cells, highlighting the molecular determinants of the multifunctional nature of APE1 protein.
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Affiliation(s)
- Carlo Vascotto
- Department of Biomedical Sciences and Technologies, University of Udine, Udine, Italy
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State-of-the-art technologies, current opinions and developments, and novel findings: news from the field of histochemistry and cell biology. Histochem Cell Biol 2008; 130:1205-51. [PMID: 18985372 DOI: 10.1007/s00418-008-0535-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2008] [Indexed: 10/25/2022]
Abstract
Investigations of cell and tissue structure and function using innovative methods and approaches have again yielded numerous exciting findings in recent months and have added important data to current knowledge, inspiring new ideas and hypotheses in various fields of modern life sciences. Topics and contents of comprehensive expert reviews covering different aspects in methodological advances, cell biology, tissue function and morphology, and novel findings reported in original papers are summarized in the present review.
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Fagone P, Jackowski S. Membrane phospholipid synthesis and endoplasmic reticulum function. J Lipid Res 2008; 50 Suppl:S311-6. [PMID: 18952570 DOI: 10.1194/jlr.r800049-jlr200] [Citation(s) in RCA: 304] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
This review presents an overview of mammalian phospholipid synthesis and the cellular locations of the biochemical activities that produce membrane lipid molecular species. The generalized endoplasmic reticulum compartment is a central site for membrane lipid biogenesis, and examples of the emerging relationships between alterations in lipid composition, regulation of membrane lipid biogenesis, and cellular secretory function are discussed.
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Affiliation(s)
- Paolo Fagone
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105-3678, USA
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Sadowski PG, Groen AJ, Dupree P, Lilley KS. Sub-cellular localization of membrane proteins. Proteomics 2008; 8:3991-4011. [DOI: 10.1002/pmic.200800217] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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MALDI imaging mass spectrometry for direct tissue analysis: a new frontier for molecular histology. Histochem Cell Biol 2008; 130:421-34. [PMID: 18618129 PMCID: PMC2522327 DOI: 10.1007/s00418-008-0469-9] [Citation(s) in RCA: 223] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2008] [Indexed: 12/13/2022]
Abstract
Matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) is a powerful tool for investigating the distribution of proteins and small molecules within biological systems through the in situ analysis of tissue sections. MALDI-IMS can determine the distribution of hundreds of unknown compounds in a single measurement and enables the acquisition of cellular expression profiles while maintaining the cellular and molecular integrity. In recent years, a great many advances in the practice of imaging mass spectrometry have taken place, making the technique more sensitive, robust, and ultimately useful. In this review, we focus on the current state of the art of MALDI-IMS, describe basic technological developments for MALDI-IMS of animal and human tissues, and discuss some recent applications in basic research and in clinical settings.
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