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Shevchenko, Ganna
Publications (10 of 19) Show all publications
Richard, B. C., Bayer, T. A., Lind, S., Shevchenko, G. & Bergquist, J. (2019). A simplified and sensitive immunoprecipitation mass spectrometry protocol for the analysis of amyloid-beta peptides in brain tissue. CLINICAL MASS SPECTROMETRY, 14, 83-88
Open this publication in new window or tab >>A simplified and sensitive immunoprecipitation mass spectrometry protocol for the analysis of amyloid-beta peptides in brain tissue
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2019 (English)In: CLINICAL MASS SPECTROMETRY, ISSN 2376-9998, Vol. 14, p. 83-88Article in journal (Refereed) Published
Abstract [en]

In the field of Alzheimer's disease, there is an urgent need for novel analytical tools to identify disease-specific biomarkers and to evaluate therapeutics. Preclinical trials commonly employ amyloid beta (A beta) peptide signatures as a read-out. In this paper, we report a simplified and detailed protocol for robust immunoprecipitation of A beta in brain tissue prior to mass spectrometric detection exemplified by a study using transgenic mice. The established method employed murine monoclonal and rabbit polyclonal antibodies and was capable of yielding well-reproducible peaks of high intensity with low background signal intensities corresponding to various A beta forms.

Place, publisher, year, edition, pages
ELSEVIER, 2019
Keywords
MALDI-TOF MS, Amyloid beta peptides, Brain, Immunoprecipitation
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-398015 (URN)10.1016/j.clinms.2019.07.001 (DOI)000496422100004 ()
Funder
Swedish Foundation for Strategic Research , SB16-0039Swedish Research Council, 621-2011-4423Swedish Research Council, 2015-4870Magnus Bergvall Foundation, 2018-01726
Available from: 2019-12-04 Created: 2019-12-04 Last updated: 2019-12-04Bibliographically approved
Emami Khoonsari, P., Shevchenko, G., Herman, S., Remnestal, J., Giedraitis, V., Brundin, R., . . . Kultima, K. (2019). Improved Differential Diagnosis of Alzheimer's Disease by Integrating ELISA and Mass Spectrometry-Based Cerebrospinal Fluid Biomarkers. Journal of Alzheimer's Disease, 67(2), 639-651
Open this publication in new window or tab >>Improved Differential Diagnosis of Alzheimer's Disease by Integrating ELISA and Mass Spectrometry-Based Cerebrospinal Fluid Biomarkers
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2019 (English)In: Journal of Alzheimer's Disease, ISSN 1387-2877, E-ISSN 1875-8908, Vol. 67, no 2, p. 639-651Article in journal (Refereed) Published
Abstract [en]

Background: Alzheimer’s disease (AD) is diagnosed based on a clinical evaluation as well as analyses of classical biomarkers: Aβ42, total tau (t-tau), and phosphorylated tau (p-tau) in cerebrospinal fluid (CSF). Although the sensitivities and specificities of the classical biomarkers are fairly good for detection of AD, there is still a need to develop novel biochemical markers for early detection of AD.

Objective: We explored if integration of novel proteins with classical biomarkers in CSF can better discriminate AD from non-AD subjects.

Methods: We applied ELISA, mass spectrometry, and multivariate modeling to investigate classical biomarkers and the CSF proteome in subjects (n = 206) with 76 AD patients, 74 mild cognitive impairment (MCI) patients, 11 frontotemporal dementia (FTD) patients, and 45 non-dementia controls. The MCI patients were followed for 4–9 years and 21 of these converted to AD, whereas 53 remained stable.

Results: By combining classical CSF biomarkers with twelve novel markers, the area of the ROC curves (AUROCS) of distinguishing AD and MCI/AD converters from non-AD were 93% and 96%, respectively. The FTDs and non-dementia controls were identified versus all other groups with AUROCS of 96% and 87%, respectively.

Conclusions: Integration of new and classical CSF biomarkers in a model-based approach can improve the identification of AD, FTD, and non-dementia control subjects.

Place, publisher, year, edition, pages
IOS PRESS, 2019
Keywords
Alzheimer's disease, cerebrospinal fluid, ELISA, mass spectrometry, mild cognitive impairment, proteomics
National Category
Neurology Geriatrics
Identifiers
urn:nbn:se:uu:diva-377711 (URN)10.3233/JAD-180855 (DOI)000457779300016 ()30614806 (PubMedID)
Funder
VINNOVAGun och Bertil Stohnes StiftelseÅke Wiberg FoundationStiftelsen Gamla Tjänarinnor
Available from: 2019-03-08 Created: 2019-03-08 Last updated: 2019-04-29Bibliographically approved
Heras, G., Namuduri, A. V., Traini, L., Shevchenko, G., Falk, A., Bergström Lind, S., . . . Gastaldello, S. (2019). Muscle RING-finger protein-1 (MuRF1) functions and cellular localization are regulated by SUMO1 post-translational modification. Journal of Molecular Cell Biology, 11(5), 356-370
Open this publication in new window or tab >>Muscle RING-finger protein-1 (MuRF1) functions and cellular localization are regulated by SUMO1 post-translational modification
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2019 (English)In: Journal of Molecular Cell Biology, ISSN 1674-2788, E-ISSN 1759-4685, Vol. 11, no 5, p. 356-370Article in journal (Refereed) Published
Abstract [en]

The muscle RING-finger protein-1 (MuRF1) is an E3 ubiquitin ligase expressed in skeletal and cardiac muscle tissues and it plays important roles in muscle remodeling. Upregulation of MuRF1 gene transcription participates in skeletal muscle atrophy, on contrary downregulation of protein expression leads to cardiac hypertrophy. MuRF1 gene point mutations have been found to generate protein aggregate myopathies defined as muscle disorder characterized by protein accumulation in muscle fibers. We have discovered that MuRF1 turned out to be also a target for a new post-translational modification arbitrated by conjugation of SUMO1 and it is mediated by the SUMO ligases E2 UBC9 and the E3 PIASγ/4. SUMOylation takes place at lysine 238 localized at the second coiled-coil protein domain that is required for efficient substrate interaction for polyubiquitination. We provided evidence that SUMOylation is essential for MuRF1 nuclear translocation and its mitochondria accumulation is enhanced in hyperglycemic conditions delivering a stabilization of the overall SUMOylated proteins in cultured myocytes. Thus, our findings add this SUMO1 post-translational modification as a new concept to understand muscle disorders related to the defect in MuRF1 activity.

Keywords
TRIM 63 /MuRF 1, muscle remodeling, SUMO, protein degradation, hyperglycemia
National Category
Physiology
Identifiers
urn:nbn:se:uu:diva-361135 (URN)10.1093/jmcb/mjy036 (DOI)000482800300003 ()29868881 (PubMedID)
Funder
Swedish Research Council, 20133074Åke Wiberg Foundation, M14-0127Magnus Bergvall Foundation, 2015-01200Magnus Bergvall Foundation, 2016-01675Carl Tryggers foundation , CST 15:57
Available from: 2018-09-21 Created: 2018-09-21 Last updated: 2019-10-02Bibliographically approved
Abu Hamdeh, S., Shevchenko, G., Mi, J., Musunuri, S., Bergquist, J. & Marklund, N. (2018). Proteomic differences between focal and diffuse traumatic brain injury in human brain tissue. Scientific Reports, 8, Article ID 6807.
Open this publication in new window or tab >>Proteomic differences between focal and diffuse traumatic brain injury in human brain tissue
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2018 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 6807Article in journal (Refereed) Published
Abstract [en]

The early molecular response to severe traumatic brain injury (TBI) was evaluated using biopsies of structurally normal-appearing cortex, obtained at location for intracranial pressure (ICP) monitoring, from 16 severe TBI patients. Mass spectrometry (MS; label free and stable isotope dimethyl labeling) quantitation proteomics showed a strikingly different molecular pattern in TBI in comparison to cortical biopsies from 11 idiopathic normal pressure hydrocephalus patients. Diffuse TBI showed increased expression of peptides related to neurodegeneration (Tau and Fascin, p < 0.05), reduced expression related to antioxidant defense (Glutathione S-transferase Mu 3, Peroxiredoxin-6, Thioredoxin-dependent peroxide reductase; p < 0.05) and increased expression of potential biomarkers (e.g. Neurogranin, Fatty acid-binding protein, heart p < 0.05) compared to focal TBI. Proteomics of human brain biopsies displayed considerable molecular heterogeneity among the different TBI subtypes with consequences for the pathophysiology and development of targeted treatments for TBI.

National Category
Neurosciences Neurology
Identifiers
urn:nbn:se:uu:diva-341912 (URN)10.1038/s41598-018-25060-0 (DOI)000431113100005 ()29717219 (PubMedID)
Funder
The Swedish Brain FoundationVINNOVASwedish Research CouncilLars Hierta Memorial FoundationStiftelsen Gamla Tjänarinnor
Available from: 2018-02-15 Created: 2018-02-15 Last updated: 2018-07-13Bibliographically approved
Abu Hamdeh, S., Shevchenko, G., Mi, J., Musunuri, S., Bergquist, J. & Marklund, N. (2018). Proteomic Differences Between Focal And Diffuse Traumatic Brain Injury In Human Brain Tissue. Paper presented at 3rd Joint Symposium of the International-and-National-Neurotrauma-Societies-and-AANS/CNS-Section on Neurotrauma and Critical Care, AUG 11-16, 2018, Toronto, CANADA. Journal of Neurotrauma, 35(16), A238-A239
Open this publication in new window or tab >>Proteomic Differences Between Focal And Diffuse Traumatic Brain Injury In Human Brain Tissue
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2018 (English)In: Journal of Neurotrauma, ISSN 0897-7151, E-ISSN 1557-9042, Vol. 35, no 16, p. A238-A239Article in journal, Meeting abstract (Other academic) Published
Place, publisher, year, edition, pages
MARY ANN LIEBERT, INC, 2018
Keywords
Biomarker, White Matter
National Category
Neurology Neurosciences
Identifiers
urn:nbn:se:uu:diva-363873 (URN)000441527400640 ()
Conference
3rd Joint Symposium of the International-and-National-Neurotrauma-Societies-and-AANS/CNS-Section on Neurotrauma and Critical Care, AUG 11-16, 2018, Toronto, CANADA
Available from: 2018-11-14 Created: 2018-11-14 Last updated: 2018-11-14Bibliographically approved
Nikitidou, E., Emami Khoonsari, P., Shevchenko, G., Ingelsson, M., Kultima, K. & Erlandsson, A. (2017). Increased Release of Apolipoprotein E in Extracellular Vesicles Following Amyloid-β Protofibril Exposure of Neuroglial Co-Cultures. Journal of Alzheimer's Disease, 60(1), 305-321
Open this publication in new window or tab >>Increased Release of Apolipoprotein E in Extracellular Vesicles Following Amyloid-β Protofibril Exposure of Neuroglial Co-Cultures
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2017 (English)In: Journal of Alzheimer's Disease, ISSN 1387-2877, E-ISSN 1875-8908, Vol. 60, no 1, p. 305-321Article in journal (Refereed) Published
Abstract [en]

Extracellular vesicles (EVs), including exosomes and larger microvesicles, have been implicated to play a role in several conditions, including Alzheimer's disease (AD). Since the EV content mirrors the intracellular environment, it could contribute with important information about ongoing pathological processes and may be a useful source for biomarkers, reflecting the disease progression. The aim of the present study was to analyze the protein content of EVs specifically released from a mixed co-culture of primary astrocytes, neurons, and oligodendrocytes treated with synthetic amyloid-beta (A beta(42)) protofibrils. The EV isolation was performed by ultracentrifugation and validated by transmission electron microscopy. Mass spectrometry analysis of the EV content revealed a total of 807 unique proteins, of which five displayed altered levels in A beta(42) protofibril exposed cultures. The most prominent protein was apolipoprotein E (apoE), and by western blot analysis we could confirm a threefold increase of apoE in EVs from A beta(42) protofibril exposed cells, compared to unexposed cells. Moreover, immunoprecipitation studies demonstrated that apoE was primarily situated inside the EVs, whereas immunocytochemistry indicated that the EVs most likely derived from the astrocytes and the neurons in the culture. The identified A beta-induced sorting of apoE into EVs from cultured neuroglial cells suggests a possible role for intercellular transfer of apoE in AD pathology and encourage future studies to fully elucidate the clinical relevance of this event.

Keywords
Alzheimer’s disease, amyloid-beta, apolipoprotein E, astrocytes, exosomes, extracellular vesicles, mass spectrometry, neurons, shedding microvesicles
National Category
Medical and Health Sciences Neurosciences
Identifiers
urn:nbn:se:uu:diva-331137 (URN)10.3233/JAD-170278 (DOI)000408582800025 ()
Funder
Swedish Research CouncilStiftelsen Gamla TjänarinnorÅke Wiberg Foundation
Available from: 2017-10-11 Created: 2017-10-11 Last updated: 2019-04-29Bibliographically approved
Emami Khoonsari, P., Haggmark, A., Lönnberg, M., Mikus, M., Kilander, L., Lannfelt, L., . . . Shevchenko, G. (2016). Analysis of the Cerebrospinal Fluid Proteome in Alzheimer's Disease. PLoS ONE, 11(3), Article ID e0150672.
Open this publication in new window or tab >>Analysis of the Cerebrospinal Fluid Proteome in Alzheimer's Disease
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2016 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 3, article id e0150672Article in journal (Refereed) Published
Abstract [en]

Alzheimer's disease is a neurodegenerative disorder accounting for more than 50% of cases of dementia. Diagnosis of Alzheimer's disease relies on cognitive tests and analysis of amyloid beta, protein tau, and hyperphosphorylated tau in cerebrospinal fluid. Although these markers provide relatively high sensitivity and specificity for early disease detection, they are not suitable for monitor of disease progression. In the present study, we used label-free shotgun mass spectrometry to analyse the cerebrospinal fluid proteome of Alzheimer's disease patients and non-demented controls to identify potential biomarkers for Alzheimer's disease. We processed the data using five programs (DecyderMS, Maxquant, OpenMS, PEAKS, and Sieve) and compared their results by means of reproducibility and peptide identification, including three different normalization methods. After depletion of high abundant proteins we found that Alzheimer's disease patients had lower fraction of low-abundance proteins in cerebrospinal fluid compared to healthy controls (p<0.05). Consequently, global normalization was found to be less accurate compared to using spiked-in chicken ovalbumin for normalization. In addition, we determined that Sieve and OpenMS resulted in the highest reproducibility and PEAKS was the programs with the highest identification performance. Finally, we successfully verified significantly lower levels (p<0.05) of eight proteins (A2GL, APOM, C1QB, C1QC, C1S, FBLN3, PTPRZ, and SEZ6) in Alzheimer's disease compared to controls using an antibody-based detection method. These proteins are involved in different biological roles spanning from cell adhesion and migration, to regulation of the synapse and the immune system.

National Category
Neurology Geriatrics
Identifiers
urn:nbn:se:uu:diva-283774 (URN)10.1371/journal.pone.0150672 (DOI)000371990100049 ()26950848 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationMarianne and Marcus Wallenberg FoundationThe Swedish Brain FoundationSwedish Research Council FormasSwedish Research Council, P29797-1Swedish Research Council, 621-2011-4423
Available from: 2016-04-14 Created: 2016-04-14 Last updated: 2019-04-29Bibliographically approved
Musunuri, S., Kultima, K., Richard, B. C., Ingelsson, M., Lannfelt, L., Bergquist, J. & Shevchenko, G. (2015). Micellar extraction possesses a new advantage for the analysis of Alzheimer's disease brain proteome. Analytical and Bioanalytical Chemistry, 407(4), 1041-1057
Open this publication in new window or tab >>Micellar extraction possesses a new advantage for the analysis of Alzheimer's disease brain proteome
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2015 (English)In: Analytical and Bioanalytical Chemistry, ISSN 1618-2642, E-ISSN 1618-2650, Vol. 407, no 4, p. 1041-1057Article in journal (Refereed) Published
Abstract [en]

Integral membrane proteins (MPs), such as transporters, receptors, and ion channels, are of great interest because of their participation in various vital cellular functions including cell-cell interactions, ion transport, and signal transduction. However, studies of MPs are complicated because of their hydrophobic nature, heterogeneity, and low abundance. Cloud-point extraction (CPE) with the non-ionic surfactant Triton X-114 was performed to simultaneously extract and phase separate hydrophobic and hydrophilic proteins from Alzheimer's disease (AD) and unaffected control brain tissue. Quantitative proteomics analysis of temporal neocortex samples of AD patients and controls was performed using a shotgun approach based on stable isotope dimethyl labeling (DML) quantification technique followed by nanoLC-MS/MS analysis. A total of 1096 unique proteins were identified and quantified, with 40.3 % (211/524) predicted as integral MPs with at least one transmembrane domain (TMD) found in the detergent phase, and 10 % (80/798) in the detergent-depleted phase. Among these, 62 proteins were shown to be significantly altered (p-value < 0.05), in AD versus control samples. In the detergent fraction, we found 10 hydrophobic transmembrane proteins containing up to 14 putative TMDs that were significantly up- or down-regulated in AD compared with control brains. Changes in four of these proteins, alpha-enolase (ENOA), lysosome-associated membrane glycoprotein 1 (LAMP1), 14-3-3 protein gamma (1433G), and sarcoplasmic/endoplasmic reticulum calcium ATPase2 (AT2A2) were validated by immunoblotting. Our results emphasize that separating hydrophobic MPs in CPE contributes to an increased understanding of the underlying molecular mechanisms in AD. Such knowledge can become useful for the development of novel disease biomarkers.

Keywords
Alzheimer's disease (AD), Cloud point extraction (CPE), Membrane proteins (MPs), Dimethyl labeling quantitative proteomics, Brain tissue
National Category
Geriatrics Analytical Chemistry
Identifiers
urn:nbn:se:uu:diva-246344 (URN)10.1007/s00216-014-8320-8 (DOI)000348436100002 ()25416231 (PubMedID)
Available from: 2015-03-10 Created: 2015-03-05 Last updated: 2019-04-29Bibliographically approved
Shevchenko, G., Konzer, A., Musunuri, S. & Bergquist, J. (2015). Neuroproteomics Tools in Clinical Practice. Biochimica et Biophysica Acta - Proteins and Proteomics, 1854(7), 705-717
Open this publication in new window or tab >>Neuroproteomics Tools in Clinical Practice
2015 (English)In: Biochimica et Biophysica Acta - Proteins and Proteomics, ISSN 1570-9639, E-ISSN 1878-1454, Vol. 1854, no 7, p. 705-717Article in journal (Refereed) Published
Abstract [en]

Abstract Neurodegenerative disorders such as Alzheimer’s disease (AD), Parkinson’s disease (PD), amyotrophic lateral sclerosis (ALS) are characterized by neuronal impairment that leads to disease-specific changes in the neuronal proteins. The early diagnosis of these disorders is difficult, thus, the need for identifying, developing and using valid clinically applicable biomarkers that meet the criteria of precision, specificity and repeatability is very vital. The application of rapidly emerging technology such as mass spectrometry (MS) in proteomics has opened new avenues to accelerate biomarker discovery, both for diagnostic as well as for prognostic purposes. This review summarizes the most recent advances in the mass spectrometry-based neuroproteomics and analyses the current and future directions in the biomarker discovery for the neurodegenerative diseases.11 This article is part of a Special Issue entitled: Neuroproteomics: Applications in Neuroscience and Neurology.

Keywords
Proteomics, Quantitative neuroproteomics, Neurodegenerative disease, Mass spectrometry
National Category
Chemical Sciences
Identifiers
urn:nbn:se:uu:diva-244132 (URN)10.1016/j.bbapap.2015.01.016 (DOI)000355036500002 ()
Available from: 2015-02-12 Created: 2015-02-12 Last updated: 2017-12-04Bibliographically approved
Elf, K., Shevchenko, G., Nygren, I., Larsson, L., Bergquist, J., Askmark, H. & Artemenko, K. (2014). Alterations in muscle proteome of patients diagnosed with amyotrophic lateral sclerosis. Journal of Proteomics, 108, 55-64
Open this publication in new window or tab >>Alterations in muscle proteome of patients diagnosed with amyotrophic lateral sclerosis
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2014 (English)In: Journal of Proteomics, ISSN 1874-3919, E-ISSN 1876-7737, Vol. 108, p. 55-64Article in journal (Refereed) Published
Abstract [en]

Amyotrophic lateral sclerosis (ALS) is a motor neuron disease characterized by progressive muscle paralysis. Currently clinical tools for ALS diagnostics do not perform well enough and their improvement is needed. The objective of this study was to identify specific protein alterations related to the development of ALS using tiny muscle biopsies. We applied a shotgun proteomics and quantitative dimethyl labeling in order to analyze the global changes in human skeletal muscle proteome of ALS versus healthy subjects for the first time. 235 proteins were quantified and 11 proteins were found significantly regulated in ALS muscles. These proteins are involved in muscle development and contraction, metabolic processes, enzyme activity, regulation of apoptosis and transport activity. In order to eliminate a risk to confuse ALS with other denervations, muscle biopsies of patients with postpolio syndrome and Charcot Marie Tooth disease (negative controls) were compared to those of ALS and controls. Only few proteins significantly regulated in ALS patients compared to controls were affected differently in negative controls. These proteins (BTB and kelch domain-containing protein 10, myosin light chain 3, glycogen debranching enzyme, transitional endoplasmic reticulum ATPase), individually or as a panel, could be selected for estimation of ALS diagnosis and development. Biological significance ALS is a devastating neurodegenerative disease, and luckily, very rare: only one to two people out of 100,000 develop ALS yearly. This fact, however, makes studies of ALS very challenging since it is very difficult to collect the representative set of clinical samples and this may take up to several years. In this study we collected the muscle biopsies from 12 ALS patients and compared the ALS muscle proteome against the one from control subjects. We suggested the efficient method for such comprehensive quantitative analysis by LC-MS and performed it for the first time using human ALS material. This gel- and antibody-free method can be widely applied for muscle proteome studies and has been used by us for revealing of the specific protein alterations associated with ALS.

Keywords
Amyotrophic lateral sclerosis (ALS), Dimethyl labeling quantitative proteomics, Mass spectrometry (MS), Muscle biopsy
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-230939 (URN)10.1016/j.jprot.2014.05.004 (DOI)000340315400004 ()
Available from: 2014-09-04 Created: 2014-09-01 Last updated: 2017-12-05Bibliographically approved
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