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Kultima, Kim
Publications (10 of 19) Show all publications
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., Emami Khoonsari, P., 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
National Category
Medical and Health Sciences Engineering and Technology
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
Available from: 2017-07-19 Created: 2017-07-19 Last updated: 2018-02-23Bibliographically 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
Sjödin, M. O. .., Wetterhall, M., Kultima, K. & Artemenko, K. (2013). Comparative study of label and label-free techniques using shotgun proteomics for relative protein quantification. Journal of chromatography. B, 928, 83-92
Open this publication in new window or tab >>Comparative study of label and label-free techniques using shotgun proteomics for relative protein quantification
2013 (English)In: Journal of chromatography. B, ISSN 1570-0232, E-ISSN 1873-376X, Vol. 928, p. 83-92Article in journal (Refereed) Published
Abstract [en]

The analytical performance of three different strategies, iTRAQ (isobaric tag for relative and absolute quantitation), dimethyl labeling (DML) and label free (LF) for relative protein quantification using shotgun proteomics have been evaluated. The methods have been explored using samples containing (i) Bovine proteins in known ratios and (ii) Bovine proteins in known ratios spiked into E.Coli. The latter case mimics the actual conditions in a typical biological sample with a few differentially expressed proteins and a bulk of proteins with unchanged ratios. Additionally, the evaluation was performed on both Q-TOF and LTQ-FTICR mass spectrometers. LF LTQ-FTICR was found to have the highest proteome coverage (94 %) while the highest accuracy based on the artificially regulated proteins was found for DML LTQ-FTICR (54%). A good linearity (r2: 0.61-0.96) was shown for all methods within selected dynamic ranges. All methods were found to consistently underestimate bovine protein ratios when matrix proteins were added. However LF LTQ-FTICR was more tolerant towards a compression effect.  A single peptide was demonstrated to be sufficient for a reliable quantification using iTRAQ. A ranking system utilizing several parameters important for quantitative proteomics demonstrated that the overall performance of the five different methods were; DML LTQ-FTICR > iTRAQ QTOF > LF LTQ-FTICR > DML Q-TOF > LF Q-TOF.

Keywords
Relative quantification, Proteomics, Mass spectrometry, Stable isotope labeling, Label free
National Category
Analytical Chemistry
Research subject
Analytical Chemistry
Identifiers
urn:nbn:se:uu:diva-180105 (URN)10.1016/j.jchromb.2013.03.027 (DOI)000319236700011 ()
Note

De två (2) sista författarna delar sistaförfattarskapet.

Available from: 2012-08-29 Created: 2012-08-29 Last updated: 2017-12-07Bibliographically approved
Karlsson, O., Kultima, K., Wadensten, H., Nilsson, A., Roman, E., Andrén, P. E. & Brittebo, E. B. (2013). Neurotoxin-Induced Neuropeptide Perturbations in Striatum of Neonatal Rats. Journal of Proteome Research, 12(4), 1678-1690
Open this publication in new window or tab >>Neurotoxin-Induced Neuropeptide Perturbations in Striatum of Neonatal Rats
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2013 (English)In: Journal of Proteome Research, ISSN 1535-3893, E-ISSN 1535-3907, Vol. 12, no 4, p. 1678-1690Article in journal (Refereed) Published
Abstract [en]

The cyanobacterial toxin β-N-methylamino-l-alanine (BMAA) is suggested to play a role in neurodegenerative disease. We have previously shown that although the selective uptake of BMAA in the rodent neonatal striatum does not cause neuronal cell death, exposure during the neonatal development leads to cognitive impairments in adult rats. The aim of the present study was to characterize the changes in the striatal neuropeptide systems of male and female rat pups treated neonatally (postnatal days 9-10) with BMAA (40-460 mg/kg). The label-free quantification of the relative levels of endogenous neuropeptides using mass spectrometry revealed that 25 peptides from 13 neuropeptide precursors were significantly changed in the rat neonatal striatum. The exposure to noncytotoxic doses of BMAA induced a dose-dependent increase of neurosecretory protein VGF-derived peptides, and changes in the relative levels of cholecystokinin, chromogranin, secretogranin, MCH, somatostatin and cortistatin-derived peptides were observed at the highest dose. In addition, the results revealed a sex-dependent increase in the relative level of peptides derived from the proenkephalin-A and protachykinin-1 precursors, including substance P and neurokinin A, in female pups. Because several of these peptides play a critical role in the development and survival of neurons, the observed neuropeptide changes might be possible mediators of BMAA-induced behavioral changes. Moreover, some neuropeptide changes suggest potential sex-related differences in susceptibility toward this neurotoxin. The present study also suggests that neuropeptide profiling might provide a sensitive characterization of the BMAA-induced noncytotoxic effects on the developing brain.

Keywords
neurotoxin, BMAA, neonatal striatum, neuropeptide, ALS/PDC, cyanobacteria, sex differences, cortistatin
National Category
Pharmacology and Toxicology
Research subject
Toxicology; Developmental Neurosciences
Identifiers
urn:nbn:se:uu:diva-196966 (URN)10.1021/pr3010265 (DOI)000317327500013 ()23410195 (PubMedID)
Note

De två första författarna delar förstaförfattarskapet.

Available from: 2013-03-15 Created: 2013-03-15 Last updated: 2018-01-11Bibliographically approved
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