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Kultima, Kim
Publications (10 of 21) Show all publications
Almandoz-Gil, L., Welander, H., Ihse, E., Khoonsari, P. E., Musunuri, S., Lendel, C., . . . Bergström, J. (2018). Corrigendum to “Low molar excess of 4-oxo-2-nonenal and 4-hydroxy-2-nonenal promote oligomerization of alpha-synuclein through different pathways” [Free Rad. Biol. Med. (2017) 421–431]. Free Radical Biology & Medicine, 117, 258-258
Open this publication in new window or tab >>Corrigendum to “Low molar excess of 4-oxo-2-nonenal and 4-hydroxy-2-nonenal promote oligomerization of alpha-synuclein through different pathways” [Free Rad. Biol. Med. (2017) 421–431]
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2018 (English)In: Free Radical Biology & Medicine, ISSN 0891-5849, E-ISSN 1873-4596, Vol. 117, p. 258-258Article in journal (Other academic) Published
National Category
Biochemistry and Molecular Biology Engineering and Technology
Identifiers
urn:nbn:se:uu:diva-356238 (URN)10.1016/j.freeradbiomed.2018.02.007 (DOI)000427420600025 ()29455934 (PubMedID)
Note

Correction to: Free Radical Biology & Medicine, vol. 110, pages 421-431.

DOI: 10.1016/j.freeradbiomed.2017.07.004

WoS title: Low molar excess of 4-oxo-2-nonenal and 4-hydroxy-2-nonenal promote oligomerization of alpha-synuclein through different pathways (vol 110, pg 421, 2017)

Available from: 2018-07-27 Created: 2018-07-27 Last updated: 2018-08-15Bibliographically approved
Sandor, K., Krishnan, S., Agalave, N. M., Krock, E., Salcido, J. V., Fernandez-Zafra, T., . . . Kultima, K. (2018). Spinal injection of newly identified cerebellin-1 and cerebellin-2 peptides induce mechanical hypersensitivity in mice. Neuropeptides, 69, 53-59
Open this publication in new window or tab >>Spinal injection of newly identified cerebellin-1 and cerebellin-2 peptides induce mechanical hypersensitivity in mice
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2018 (English)In: Neuropeptides, ISSN 0143-4179, E-ISSN 1532-2785, Vol. 69, p. 53-59Article in journal (Refereed) Published
Abstract [en]

By screening for neuropeptides in the mouse spinal cord using mass spectrometry (MS), we have previously demonstrated that one of the 78 peptides that is expressed predominantly (> 6-fold) in the dorsal horn compared to the ventral spinal cord is the atypical peptide desCER [des-Serl]-cerebellin, which originates from the precursor protein cerebellin 1 (CBLN1). Furthermore, we found that intrathecal injection of desCER induces mechanical hypersensitivity in a dose dependent manner. The current study was designed to further investigate the relative expression of other CBLN derived peptides in the spinal cord and to examine whether they share similar nociceptive properties. In addition to the peptides cerebellin (CER) and desCER we identified and relatively quantified nine novel peptides originating from cerebellin precursor proteins CBLN1 (two peptides), CBLN2 (three peptides) and CBLN4 (four peptides). Ten out of eleven peptides displayed statistically significantly (p < 0.05) higher expression levels (200-350%) in the dorsal horn compared to the ventral horn. Intrathecal injection of three of the four CBLN1 and two of the three CBLN2 derived peptides induced mechanical hypersensitivity in response to von Frey filament testing in mice during the first 6 h post-injection compared to saline injected mice, while none of the four CBLN4 derived peptides altered withdrawal thresholds. This study demonstrates that high performance MS is an effective tool for detecting novel neuropeptides in CNS tissues. We show the presence of nine novel atypical peptides originating from CBLN1, CBLN2 and CBLN4 precursor proteins in the mouse dorsal horn, whereof five peptides induce pain-like behavior upon intrathecal injection. Further studies are required to investigate the mechanisms by which CBLN1 and CBLN2 derived peptides facilitate nociceptive signal transmission.

Place, publisher, year, edition, pages
CHURCHILL LIVINGSTONE, 2018
Keywords
Mass spectrometry, Peptidomics, Neuropeptides, Cerebellin, Pain, Nociception
National Category
Neurosciences
Identifiers
urn:nbn:se:uu:diva-358169 (URN)10.1016/j.npep.2018.04.004 (DOI)000435058800007 ()29705514 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationSwedish Research Council, 2013-8373Ragnar Söderbergs stiftelse
Available from: 2018-08-27 Created: 2018-08-27 Last updated: 2018-08-27Bibliographically 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: 2018-01-13Bibliographically approved
Almandoz-Gil, L., Welander, H., Ihse, E., Khoonsari, P. E., Musunuri, S., Lendel, C., . . . Bergström, J. (2017). Low molar excess of 4-oxo-2-nonenal and 4-hydroxy-2-nonenal promote oligomerization of alpha-synuclein through different pathways. Free Radical Biology & Medicine, 110, 421-431
Open this publication in new window or tab >>Low molar excess of 4-oxo-2-nonenal and 4-hydroxy-2-nonenal promote oligomerization of alpha-synuclein through different pathways
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2017 (English)In: Free Radical Biology & Medicine, ISSN 0891-5849, E-ISSN 1873-4596, Vol. 110, p. 421-431Article in journal (Refereed) Published
Abstract [en]

Aggregated alpha-synuclein is the main component of Lewy bodies, intraneuronal inclusions found in brains with Parkinson's disease and dementia with Lewy bodies. A body of evidence implicates oxidative stress in the pathogenesis of these diseases. For example, a large excess (30:1, aldehyde:protein) of the lipid peroxidation end products 4-oxo-2-nonenal (ONE) or 4-hydroxy-2-nonenal (HNE) can induce alpha-synuclein oligomer formation. The objective of the study was to investigate the effect of these reactive aldehydes on alpha-synuclein at a lower molar excess (3:1) at both physiological (7.4) and acidic (5.4) pH. As observed by size-exclusion chromatography, ONE rapidly induced the formation of alpha-synuclein oligomers at both pH values, but the effect was less pronounced under the acidic condition. In contrast, only a small proportion of alpha-synuclein oligomers were formed with low excess HNE-treatment at physiological pH and no oligomers at all under the acidic condition. With prolonged incubation times (up to 96 h), more alpha-synuclein was oligomerized at physiological pH for both ONE and HNE. As determined by Western blot, ONE-oligomers were more SDS-stable and to a higher-degree cross-linked as compared to the HNE-induced oligomers. However, as shown by their greater sensitivity to proteinase K treatment, ONE-oligomers, exhibited a less compact structure than HNE-oligomers. As indicated by mass spectrometry, ONE modified most Lys residues, whereas HNE primarily modified the His50 residue and fewer Lys residues, albeit to a higher degree than ONE. Taken together, our data show that the aldehydes ONE and HNE can modify alpha-synuclein and induce oligomerization, even at low molar excess, but to a higher degree at physiological pH and seemingly through different pathways.

Keywords
Alpha-synuclein, Oligomers, 4-oxo-2-nonenal, 4-hydroxy-2-nonenal, Oxidative stress
National Category
Medical and Health Sciences Engineering and Technology Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-326663 (URN)10.1016/j.freeradbiomed.2017.07.004 (DOI)000406049200038 ()28690195 (PubMedID)
Funder
Swedish Research Council, 2011-4519, 2012-2172, 2010-6745Marianne and Marcus Wallenberg FoundationThe Swedish Brain FoundationSwedish Society of MedicineÅke Wiberg Foundation
Note

Correction in: Free Radical Biology and Medicine, vol. 117, pages 258-258.

DOI: 10.1016/j.freeradbiomed.2018.02.007

Available from: 2017-07-19 Created: 2017-07-19 Last updated: 2018-07-27Bibliographically approved
Herman, S., Emami Khoonsari, P., Aftab, O., Krishnan, S., Strömbom, E., Larsson, R., . . . Gustafsson, M. G. (2017). Mass spectrometry based metabolomics for in vitro systems pharmacology: pitfalls, challenges, and computational solutions.. Metabolomics, 13(7), Article ID 79.
Open this publication in new window or tab >>Mass spectrometry based metabolomics for in vitro systems pharmacology: pitfalls, challenges, and computational solutions.
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2017 (English)In: Metabolomics, ISSN 1573-3882, E-ISSN 1573-3890, Vol. 13, no 7, article id 79Article in journal (Refereed) Published
Abstract [en]

INTRODUCTION: Mass spectrometry based metabolomics has become a promising complement and alternative to transcriptomics and proteomics in many fields including in vitro systems pharmacology. Despite several merits, metabolomics based on liquid chromatography mass spectrometry (LC-MS) is a developing area that is yet attached to several pitfalls and challenges. To reach a level of high reliability and robustness, these issues need to be tackled by implementation of refined experimental and computational protocols.

OBJECTIVES: This study illustrates some key pitfalls in LC-MS based metabolomics and introduces an automated computational procedure to compensate for them.

METHOD: Non-cancerous mammary gland derived cells were exposed to 27 chemicals from four pharmacological classes plus a set of six pesticides. Changes in the metabolome of cell lysates were assessed after 24 h using LC-MS. A data processing pipeline was established and evaluated to handle issues including contaminants, carry over effects, intensity decay and inherent methodology variability and biases. A key component in this pipeline is a latent variable method called OOS-DA (optimal orthonormal system for discriminant analysis), being theoretically more easily motivated than PLS-DA in this context, as it is rooted in pattern classification rather than regression modeling.

RESULT: The pipeline is shown to reduce experimental variability/biases and is used to confirm that LC-MS spectra hold drug class specific information.

CONCLUSION: LC-MS based metabolomics is a promising methodology, but comes with pitfalls and challenges. Key difficulties can be largely overcome by means of a computational procedure of the kind introduced and demonstrated here. The pipeline is freely available on www.github.com/stephanieherman/MS-data-processing.

Keywords
Batch effects, Data handling, Drug metabolism, Mass spectrometry, Metabolomics
National Category
Bioinformatics (Computational Biology)
Research subject
Bioinformatics
Identifiers
urn:nbn:se:uu:diva-323946 (URN)10.1007/s11306-017-1213-z (DOI)000403779800002 ()28596718 (PubMedID)
Funder
Science for Life Laboratory - a national resource center for high-throughput molecular bioscienceSwedish Research Council
Available from: 2017-06-11 Created: 2017-06-11 Last updated: 2018-01-13Bibliographically 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: 2017-11-30Bibliographically approved
Senkowski, W., Jarvius, M., Rubin, J., Lengqvist, J., Gustafsson, M. G., Nygren, P., . . . Fryknäs, M. (2016). Large-Scale Gene Expression Profiling Platform for Identification of Context-Dependent Drug Responses in Multicellular Tumor Spheroids. CELL CHEMICAL BIOLOGY, 23(11), 1428-1438
Open this publication in new window or tab >>Large-Scale Gene Expression Profiling Platform for Identification of Context-Dependent Drug Responses in Multicellular Tumor Spheroids
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2016 (English)In: CELL CHEMICAL BIOLOGY, ISSN 2451-9448, Vol. 23, no 11, p. 1428-1438Article in journal (Refereed) Published
Abstract [en]

Cancer cell lines grown as two-dimensional (2D) cultures have been an essential model for studying cancer biology and anticancer drug discovery. However, 2D cancer cell cultures have major limitations, as they do not closely mimic the heterogeneity and tissue context of in vivo tumors. Developing three-dimensional (3D) cell cultures, such as multicellular tumor spheroids, has the potential to address some of these limitations. Here, we combined a high-throughput gene expression profiling method with a tumor spheroid-based drug-screening assay to identify context-dependent treatment responses. As a proof of concept, we examined drug responses of quiescent cancer cells to oxidative phosphorylation (OXPHOS) inhibitors. Use of multicellular tumor spheroids led to discovery that the mevalonate pathway is upregulated in quiescent cells during OXPHOS inhibition, and that OXPHOS inhibitors and mevalonate pathway inhibitors were synergistically toxic to quiescent spheroids. This work illustrates how 3D cellular models yield functional and mechanistic insights not accessible via 2D cultures.

National Category
Cell and Molecular Biology Cancer and Oncology
Identifiers
urn:nbn:se:uu:diva-311191 (URN)10.1016/j.chembiol.2016.09.013 (DOI)000388373200015 ()27984028 (PubMedID)
Funder
Swedish Cancer SocietySwedish Foundation for Strategic Research
Available from: 2016-12-22 Created: 2016-12-22 Last updated: 2018-01-13Bibliographically 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: 2017-12-04Bibliographically approved
Su, J., Sandor, K., Sköld, K., Hokfelt, T., Svensson, C. I. & Kultima, K. (2014). Identification and quantification of neuropeptides in naive mouse spinal cord using mass spectrometry reveals [des-Ser1]-cerebellin as a novel modulator of nociception. Journal of Neurochemistry, 130(2), 199-214
Open this publication in new window or tab >>Identification and quantification of neuropeptides in naive mouse spinal cord using mass spectrometry reveals [des-Ser1]-cerebellin as a novel modulator of nociception
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2014 (English)In: Journal of Neurochemistry, ISSN 0022-3042, E-ISSN 1471-4159, Vol. 130, no 2, p. 199-214Article in journal (Refereed) Published
Abstract [en]

Neuropeptide transmitters involved in nociceptive processes are more likely to be expressed in the dorsal than the ventral horn of the spinal cord. This study was designed to examine the relative distribution of neuropeptides between the dorsal and ventral spinal cord in naive mice using liquid chromatography, high-resolution mass spectrometry. We identified and relatively quantified 36 well-characterized full-length neuropeptides and an additional 168 not previously characterized peptides. By extraction with organic solvents we identified seven additional full-length neuropeptides. The peptide [des-Ser1]-cerebellin (desCER), originating from cerebellin precursor protein 1 (CBLN1), was predominantly expressed in the dorsal horn. Immunohistochemistry showed the presence of CBLN1 immunoreactivity with a punctate cytoplasmic pattern in neuronal cell bodies throughout the spinal gray matter. The signal was stronger in the dorsal compared to the ventral horn, with most CBLN1 positive cells present in outer laminae II/III, colocalizing with calbindin, a marker for excitatory interneurons. Intrathecal injection of desCER induced a dose-dependent mechanical hypersensitivity but not heat or cold hypersensitivity. This study provides evidence for involvement of desCER in nociception and provides a platform for continued exploration of involvement of novel neuropeptides in the regulation of nociceptive transmission.

Keywords
mass spectrometry, neuropeptides, nociception, pain, peptidomics, spinal cord
National Category
Medical Biotechnology Neurosciences Basic Medicine
Identifiers
urn:nbn:se:uu:diva-230511 (URN)10.1111/jnc.12730 (DOI)000339283200005 ()
Available from: 2014-09-08 Created: 2014-08-26 Last updated: 2018-01-11Bibliographically approved
Musunuri, S., Wetterhall, M., Ingelsson, M., Lannfelt, L., Artemenko, K., Bergquist, J., . . . Shevchenko, G. (2014). Quantification of the Brain Proteome in Alzheimer's Disease Using Multiplexed Mass Spectrometry. Journal of Proteome Research, 13(4), 2056-2068
Open this publication in new window or tab >>Quantification of the Brain Proteome in Alzheimer's Disease Using Multiplexed Mass Spectrometry
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2014 (English)In: Journal of Proteome Research, ISSN 1535-3893, E-ISSN 1535-3907, Vol. 13, no 4, p. 2056-2068Article in journal (Refereed) Published
Abstract [en]

We have compared the brain proteome in the temporal neocortex between Alzheimer's disease (AD) patients and non-AD individuals by using shotgun mass spectrometry based on a stable isotope dimethyl labeling. A total of 827 unique proteins were identified and quantitated. Of these, 227 proteins were found in at least 9 out of 10 AD/control pairs and were further subjected to statistical analysis. A total of 69 proteins showed different levels (p-value < 0.05) in AD versus control brain samples. Of these proteins, 37 were increased and 32 were decreased as compared to the non-AD subjects. Twenty-three proteins comprise novel proteins that have not previously been reported as related to AD, e.g., neuronal-specific septin-3, septin-2, septin-5, dihydropteridine reductase, and clathrin heavy chain 1. The proteins with altered levels in the AD brain represent a wide variety of pathways suggested to be involved in the disease pathogenesis, including energy metabolism, glycolysis, oxidative stress, apoptosis, signal transduction, and synaptic functioning. Apart from leading to new insights into the molecular mechanisms in AD, the findings provide us with possible novel candidates for future diagnostic and prognostic disease markers.

Keywords
Alzheimer's disease (AD), dimethyl labeling (DML), quantitative proteomics, mass spectrometry (MS), brain tissue
National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:uu:diva-224578 (URN)10.1021/pr401202d (DOI)000334016400025 ()
Available from: 2014-05-19 Created: 2014-05-14 Last updated: 2017-12-05Bibliographically approved
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