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336 results on '"Berven, Frode S."'

1. Cerebrospinal fluid proteomics in patients with Alzheimer’s disease reveals five molecular subtypes with distinct genetic risk profiles

Author

Tijms, Betty M., Vromen, Ellen M., Mjaavatten, Olav, Holstege, Henne, Reus, Lianne M., van der Lee, Sven, Wesenhagen, Kirsten E. J., Lorenzini, Luigi, Vermunt, Lisa, Venkatraghavan, Vikram, Tesi, Niccoló, Tomassen, Jori, den Braber, Anouk, Goossens, Julie, Vanmechelen, Eugeen, Barkhof, Frederik, Pijnenburg, Yolande A. L., van der Flier, Wiesje M., Teunissen, Charlotte E., Berven, Frode S., and Visser, Pieter Jelle

Published
2024
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2. Quantitative proteome profiling reveals molecular hallmarks of egg quality in Atlantic halibut: impairments of transcription and protein folding impede protein and energy homeostasis during early development

Author

Yilmaz, Ozlem, Jensen, Anders Mangor, Harboe, Torstein, Møgster, Margareth, Jensen, Ragnfrid Mangor, Mjaavatten, Olav, Birkeland, Even, Spriet, Endy, Sandven, Linda, Furmanek, Tomasz, Berven, Frode S., Wargelius, Anna, and Norberg, Birgitta

Published
2022
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6. Vacuolar ATPase Is a Possible Therapeutic Target in Acute Myeloid Leukemia: Focus on Patient Heterogeneity and Treatment Toxicity

Author

Bartaula-Brevik, Sushma, primary, Leitch, Calum, additional, Hernandez-Valladares, Maria, additional, Aasebø, Elise, additional, Berven, Frode S., additional, Selheim, Frode, additional, Brenner, Annette K., additional, Rye, Kristin Paulsen, additional, Hagen, Marie, additional, Reikvam, Håkon, additional, McCormack, Emmet, additional, Bruserud, Øystein, additional, and Tvedt, Tor Henrik Anderson, additional

Published
2023
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19. Developments in biobanking workflow standardization providing sample integrity and stability

Author

Malm, Johan, Fehniger, Thomas E., Danmyr, Pia, Végvári, Ákos, Welinder, Charlotte, Lindberg, Henrik, Appelqvist, Roger, Sjödin, Karin, Wieslander, Elisabet, Laurell, Thomas, Hober, Sophia, Berven, Frode S., Fenyö, David, Wang, Xiangdong, Andrén, Per E., Edula, Goutham, Carlsohn, Elisabet, Fuentes, Manuel, Nilsson, Carol L., Dahlbäck, Magnus, Rezeli, Melinda, Erlinge, David, and Marko-Varga, György

Published
2013
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21. Association of chromosome 19 to lung cancer genotypes and phenotypes

Author

Wang, Xiangdong, Zhang, Yong, Nilsson, Carol L., Berven, Frode S., Andrén, Per E., Carlsohn, Elisabet, Horvatovich, Peter, Malm, Johan, Fuentes, Manuel, Végvári, Ákos, Welinder, Charlotte, Fehniger, Thomas E., Rezeli, Melinda, Edula, Goutham, Hober, Sophia, Nishimura, Toshihide, and Marko-Varga, György

Published
2015
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30. Proteomic Characterization of Spontaneous Stress-Induced In Vitro Apoptosis of Human Acute Myeloid Leukemia Cells

Author

Aasebø, Elise, Brenner, Annette K., Hernandez-Valladares, Maria, Birkeland, Even, Reikvam, Håkon, Selheim, Frode, Berven, Frode S., and Bruserud, Øystein

Subjects
endoplasmic reticulum, hemic and lymphatic diseases, apoptosis, acute myeloid leukemia, proteomic profile
Abstract

In vitro culture is widely used for characterization of primary human acute myeloid leukemia (AML) cells, but even when using optimized handling and culture conditions the AML cells show spontaneous in vitro apoptosis with a gradual decrease in cell viability during culture. The extent of this stress-induced apoptosis varies between patients, and a high degree of apoptosis is associated with high pre-culture BCL2 levels together with low levels of BAX and Heat Shock Proteins 30 and 90. We compared the global proteomic profiles during ongoing in vitro apoptosis for patients with high and low AML cell viability (i.e., less extensive versus extensive spontaneous apoptosis) after 48 h of culture. We identified 7902 proteins, but only 276 proteins differed significantly between patients with high (i.e., &gt, 25% viable cells, 192 upregulated and 84 downregulated peptides) and low viability after in vitro culture. Protein interaction network analysis based on these 276 protein identified three protein networks that included 18 proteins, most of these proteins were localized to the endoplasmic reticulum and several of them are involved in or are altered during the process of endoplasmic reticulum stress/unfolded protein stress response. To conclude, primary AML cells are heterogeneous with regard to degree of apoptosis in response to cellular stress, and this difference in regulation of apoptosis is associated with differences in the induction of and/or response to the unfolded protein stress response.

Published
2021
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31. Effects of the Autophagy-Inhibiting Agent Chloroquine on Acute Myeloid Leukemia Cells

Author

Grønningsæter, Ida Sofie, Reikvam, Håkon, Aasebø, Elise, Bartaula-Brevik, Sushma, Hernandez-Valladares, Maria, Selheim, Frode, Berven, Frode S., Tvedt, Tor Henrik, Bruserud, Øystein, and Hatfield, Kimberley Joanne

Subjects
chloroquine, hemic and lymphatic diseases, proliferation, chemokine, apoptosis, cytokine, acute myeloid leukemia, protein profiling
Abstract

Autophagy is a highly conserved cellular degradation process that prevents cell damage and promotes cell survival, and clinical efforts have exploited autophagy inhibition as a therapeutic strategy in cancer. Chloroquine is a well-known antimalarial agent that inhibits late-stage autophagy. We evaluated the effects of chloroquine on cell viability and proliferation of acute myeloid leukemia acute myeloid leukemia (AML) cells derived from 81 AML patients. Our results show that chloroquine decreased AML cell viability and proliferation for the majority of patients. Furthermore, a subgroup of AML patients showed a greater susceptibility to chloroquine, and using hierarchical cluster analysis, we identified 99 genes upregulated in this patient subgroup, including several genes related to leukemogenesis. The combination of chloroquine with low-dose cytarabine had an additive inhibitory effect on AML cell proliferation. Finally, a minority of patients showed increased extracellular constitutive mediator release in the presence of chloroquine, which was associated with strong antiproliferative effects of chloroquine as well as cytarabine. We conclude that chloroquine has antileukemic activity and should be further explored as a therapeutic drug against AML in combination with other cytotoxic or metabolic drugs, however, due to the patient heterogeneity, chloroquine therapy will probably be effective only for selected patients.

Published
2021
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35. TGF-β promotes microtube formation in glioblastoma through thrombospondin 1

Author

Joseph, Justin V, primary, Magaut, Capucine R, additional, Storevik, Simon, additional, Geraldo, Luiz H, additional, Mathivet, Thomas, additional, Latif, Md Abdul, additional, Rudewicz, Justine, additional, Guyon, Joris, additional, Gambaretti, Matteo, additional, Haukas, Frida, additional, Trones, Amalie, additional, Rømo Ystaas, Lars A, additional, Hossain, Jubayer A, additional, Ninzima, Sandra, additional, Cuvellier, Sylvain, additional, Zhou, Wenjing, additional, Tomar, Tushar, additional, Klink, Barbara, additional, Rane, Lalit, additional, Irving, Bronwyn K, additional, Marrison, Joanne, additional, O’Toole, Peter, additional, Wurdak, Heiko, additional, Wang, Jian, additional, Di, Zhang, additional, Birkeland, Even, additional, Berven, Frode S, additional, Winkler, Frank, additional, Kruyt, Frank A E, additional, Bikfalvi, Andreas, additional, Bjerkvig, Rolf, additional, Daubon, Thomas, additional, and Miletic, Hrvoje, additional

Published
2021
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41. Additional file 11 of Development of robust targeted proteomics assays for cerebrospinal fluid biomarkers in multiple sclerosis

Author

Guldbrandsen, Astrid, Lereim, Ragnhild Reehorst, Jacobsen, Mari, Garberg, Hilde, Kroksveen, Ann Cathrine, Barsnes, Harald, and Berven, Frode S.

Abstract

Additional file 11: Table S9. Overview of the tests for stability, digestion and MS vs. OND experiments, for the 25 proteins. The colours and numbers refer to the peptides passing the specific test. Green: protein passed with two or more peptides; yellow: passed with one peptide; and, red: either no peptides passed (0) or none were tested (-).

Published
2020
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43. Pretreatment of mass spectral profiles: application to proteomic data

Author

Arneberg, Reidar, Rajalahti, Tarja, Flikka, Kristian, Berven, Frode S., Kroksveen, Ann C., Berle, Magnus, Myhr, Kjell-Morten, Vedeler, Christian A., Ulvik, Rune J., and Kvalheim, Olav M.

Subjects
Spectra (Spectroscopy) -- Technology application, Mass spectrometry -- Methods, Proteomics -- Methods, Technology application, Chemistry
Abstract

Mass spectral profiles are influenced by several factors that have no relation to compositional differences between samples: baseline effects, shifts in mass-to-charge ratio (m/z) (synchronization/alignment problem), structured noise (heteroscedasticity), and, differences in signal intensifies (normalization problem). Different procedures for pretreatment of whole mass spectral profiles described by almost 50 000 m/z values are investigated in order to find optimal approaches with respect to revealing the information content in the data. In order to quantitatively assess the impact of different procedures for pretreatment of mass spectral profiles, we use factorial designs with the ratio between intergroup and intragroup (replicate) variance as response. We have examined the influence of smoothing, binning, alignment/synchronization, noise pattern, and normalization on data interpretation. Our analysis shows that the spectral profiles have to be corrected for heteroscedastic noise prior to normalization. An nth root transform, where n is a small, positive integer, is used to create a homoscedastic noise structure without destroying the linear correlation structures describing individual components when using whole mass spectral profiles. The choice of n is decided by a simple graphic procedure using replicate information. Log transform is shown to change the heteroscedastic noise structure from being dominant in high-intensity regions, to produce the largest noise in the low-intensity regions. In addition, log transform has a negative effect on the collinearity in the profiles. Factorial designs reveal strong interactions between several of the pretreatment steps, e.g., noise structure and normalization. This underlines the limited usability of looking at the different pretreatment steps in isolation. Binning turns out to be able to substitute smoothing of spectra by, for example, moving average or Savitsky-Golay, while, at the same time, reducing the data point description of the profiles by 1 order of magnitude. Thus, if the sampling density is high, binning seems to be an attractive option for data reduction without the risk of losing information accompanying the integration of profiles into peaks. In the absence of smoothing, binning should be executed prior to alignment. If binning is not performed, the order of pretreatment should be smoothing, alignment, nth root transform, and normalization.

Published
2007

44. Proteome and Phosphoproteome Changes Associated with Prognosis in Acute Myeloid Leukemia

Author

Aasebø, Elise, Berven, Frode S, Bartaula-Brevik, Sushma, Stokowy, Tomasz, Hovland, Randi, Vaudel, Marc, Døskeland, Stein Ove, McCormack, Emmet, Batth, Tanveer S, Olsen, Jesper V, Bruserud, Øystein, Selheim, Frode, Hernandez-Valladares, Maria, Aasebø, Elise, Berven, Frode S, Bartaula-Brevik, Sushma, Stokowy, Tomasz, Hovland, Randi, Vaudel, Marc, Døskeland, Stein Ove, McCormack, Emmet, Batth, Tanveer S, Olsen, Jesper V, Bruserud, Øystein, Selheim, Frode, and Hernandez-Valladares, Maria

Abstract

Acute myeloid leukemia (AML) is a hematological cancer that mainly affects the elderly. Although complete remission (CR) is achieved for the majority of the patients after induction and consolidation therapies, nearly two-thirds relapse within a short interval. Understanding biological factors that determine relapse has become of major clinical interest in AML. We utilized liquid chromatography tandem mass spectrometry (LC-MS/MS) to identify the protein changes and protein phosphorylation events associated with AML relapse in primary cells from 41 AML patients at time of diagnosis. Patients were defined as relapse-free if they had not relapsed within a five-year clinical follow-up after AML diagnosis. Relapse was associated with increased expression of RNA processing proteins and decreased expression of V-ATPase proteins. We also observed an increase in phosphorylation events catalyzed by cyclin-dependent kinases (CDKs) and casein kinase 2 (CSK2). The biological relevance of the proteome findings was supported by cell proliferation assays using inhibitors of V-ATPase (bafilomycin), CSK2 (CX-4945), CDK4/6 (abemaciclib) and CDK2/7/9 (SNS-032). While bafilomycin preferentially inhibited the cells from relapse patients, the kinase inhibitors were less efficient in these cells. This suggests that therapy against the upregulated kinases could also target the factors inducing their upregulation rather than their activity. This study, therefore, presents markers that could help predict AML relapse and direct therapeutic strategies.

Published
2020

50. Proteome and Phosphoproteome Changes Associated with Prognosis in Acute Myeloid Leukemia

Author

Aasebø, Elise, primary, Berven, Frode S., additional, Bartaula-Brevik, Sushma, additional, Stokowy, Tomasz, additional, Hovland, Randi, additional, Vaudel, Marc, additional, Døskeland, Stein Ove, additional, McCormack, Emmet, additional, Batth, Tanveer S., additional, Olsen, Jesper V., additional, Bruserud, Øystein, additional, Selheim, Frode, additional, and Hernandez-Valladares, Maria, additional

Published
2020
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