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Lereim RR, Nytrova P, Guldbrandsen A, Havrdova EK, Myhr KM, Barsnes H, Berven FS. Natalizumab promotes anti-inflammatory and repair effects in multiple sclerosis. PLoS One 2024; 19:e0300914. [PMID: 38527011 PMCID: PMC10962820 DOI: 10.1371/journal.pone.0300914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/06/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND Multiple sclerosis is an inflammatory and degenerative disease of the central nervous system leading to demyelination and axonal loss. Relapsing-remitting multiple sclerosis (RRMS) is commonly treated by anti-inflammatory drugs, where one of the most effective drugs to date is the monoclonal antibody natalizumab. METHODS The cerebrospinal fluid (CSF) proteome was analyzed in 56 patients with RRMS before and after natalizumab treatment, using label-free mass spectrometry and a subset of the changed proteins were verified by parallel reaction monitoring in a new cohort of 20 patients, confirming the majority of observed changes. RESULTS A total of 287 differentially abundant proteins were detected including (i) the decrease of proteins with roles in immunity, such as immunoglobulin heavy constant mu, chitinase-3-like protein 1 and chitotriosidase, (ii) an increase of proteins involved in metabolism, such as lactate dehydrogenase A and B and malate-dehydrogenase cytoplasmic, and (iii) an increase of proteins associated with the central nervous system, including lactadherin and amyloid precursor protein. Comparison with the CSF-PR database provided evidence that natalizumab counters protein changes commonly observed in RRMS. Furthermore, vitamin-D binding protein and apolipoprotein 1 and 2 were unchanged during treatment with natalizumab, implying that these may be involved in disease activity unaffected by natalizumab. CONCLUSIONS Our study revealed that some of the previously suggested biomarkers for MS were affected by the natalizumab treatment while others were not. Proteins not previously suggested as biomarkers were also found affected by the treatment. In sum, the results provide new information on how the natalizumab treatment impacts the CSF proteome of MS patients, and points towards processes affected by the treatment. These findings ought to be explored further to disclose potential novel disease mechanisms and predict treatment responses.
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Affiliation(s)
- Ragnhild Reehorst Lereim
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
- Computational Biology Unit (CBU), Department of Informatics, University of Bergen, Bergen, Norway
| | - Petra Nytrova
- Department of Neurology and Center for Clinical Neuroscience, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Astrid Guldbrandsen
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
- Computational Biology Unit (CBU), Department of Informatics, University of Bergen, Bergen, Norway
| | - Eva Kubala Havrdova
- Department of Neurology and Center for Clinical Neuroscience, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Kjell-Morten Myhr
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Harald Barsnes
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
- Computational Biology Unit (CBU), Department of Informatics, University of Bergen, Bergen, Norway
| | - Frode S. Berven
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
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2
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Tijms BM, Vromen EM, Mjaavatten O, Holstege H, Reus LM, van der Lee S, Wesenhagen KEJ, Lorenzini L, Vermunt L, Venkatraghavan V, Tesi N, Tomassen J, den Braber A, Goossens J, Vanmechelen E, Barkhof F, Pijnenburg YAL, van der Flier WM, Teunissen CE, Berven FS, Visser PJ. Cerebrospinal fluid proteomics in patients with Alzheimer's disease reveals five molecular subtypes with distinct genetic risk profiles. Nat Aging 2024; 4:33-47. [PMID: 38195725 PMCID: PMC10798889 DOI: 10.1038/s43587-023-00550-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/29/2023] [Indexed: 01/11/2024]
Abstract
Alzheimer's disease (AD) is heterogenous at the molecular level. Understanding this heterogeneity is critical for AD drug development. Here we define AD molecular subtypes using mass spectrometry proteomics in cerebrospinal fluid, based on 1,058 proteins, with different levels in individuals with AD (n = 419) compared to controls (n = 187). These AD subtypes had alterations in protein levels that were associated with distinct molecular processes: subtype 1 was characterized by proteins related to neuronal hyperplasticity; subtype 2 by innate immune activation; subtype 3 by RNA dysregulation; subtype 4 by choroid plexus dysfunction; and subtype 5 by blood-brain barrier impairment. Each subtype was related to specific AD genetic risk variants, for example, subtype 1 was enriched with TREM2 R47H. Subtypes also differed in clinical outcomes, survival times and anatomical patterns of brain atrophy. These results indicate molecular heterogeneity in AD and highlight the need for personalized medicine.
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Affiliation(s)
- Betty M Tijms
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands.
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands.
| | - Ellen M Vromen
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
| | - Olav Mjaavatten
- Proteomics Unit at the University of Bergen, Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Henne Holstege
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
- Department of Clinical Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
| | - Lianne M Reus
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sven van der Lee
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
- Genomics of Neurodegenerative Diseases and Aging, Human Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
| | - Kirsten E J Wesenhagen
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
| | - Luigi Lorenzini
- Department of Radiology and Nuclear Medicine, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neuroimaging, Amsterdam, the Netherlands
| | - Lisa Vermunt
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
- Neurochemistry Laboratory, Department of Laboratory Medicine, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
| | - Vikram Venkatraghavan
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
| | - Niccoló Tesi
- Genomics of Neurodegenerative Diseases and Aging, Human Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Delft, the Netherlands
| | - Jori Tomassen
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
| | - Anouk den Braber
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | | | | | - Frederik Barkhof
- Department of Radiology and Nuclear Medicine, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Queen Square Institute of Neurology and Centre for Medical Image Computing, University College London, London, UK
| | - Yolande A L Pijnenburg
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
| | - Wiesje M van der Flier
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
- Epidemiology & Data Science, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
| | - Charlotte E Teunissen
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
- Neurochemistry Laboratory, Department of Laboratory Medicine, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
| | - Frode S Berven
- Proteomics Unit at the University of Bergen, Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Pieter Jelle Visser
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
- Alzheimer Center Limburg, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, Stockholm, Sweden
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Bartaula-Brevik S, Leitch C, Hernandez-Valladares M, Aasebø E, Berven FS, Selheim F, Brenner AK, Rye KP, Hagen M, Reikvam H, McCormack E, Bruserud Ø, Tvedt THA. Vacuolar ATPase Is a Possible Therapeutic Target in Acute Myeloid Leukemia: Focus on Patient Heterogeneity and Treatment Toxicity. J Clin Med 2023; 12:5546. [PMID: 37685612 PMCID: PMC10488188 DOI: 10.3390/jcm12175546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/20/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023] Open
Abstract
Vacuolar ATPase (V-ATPase) is regarded as a possible target in cancer treatment. It is expressed in primary acute myeloid leukemia cells (AML), but the expression varies between patients and is highest for patients with a favorable prognosis after intensive chemotherapy. We therefore investigated the functional effects of two V-ATPase inhibitors (bafilomycin A1, concanamycin A) for primary AML cells derived from 80 consecutive patients. The V-ATPase inhibitors showed dose-dependent antiproliferative and proapoptotic effects that varied considerably between patients. A proteomic comparison of primary AML cells showing weak versus strong antiproliferative effects of V-ATPase inhibition showed a differential expression of proteins involved in intracellular transport/cytoskeleton functions, and an equivalent phosphoproteomic comparison showed a differential expression of proteins that regulate RNA processing/function together with increased activity of casein kinase 2. Patients with secondary AML, i.e., a heterogeneous subset with generally adverse prognosis and previous cytotoxic therapy, myeloproliferative neoplasia or myelodysplastic syndrome, were characterized by a strong antiproliferative effect of V-ATPase inhibition and also by a specific mRNA expression profile of V-ATPase interactome proteins. Furthermore, the V-ATPase inhibition altered the constitutive extracellular release of several soluble mediators (e.g., chemokines, interleukins, proteases, protease inhibitors), and increased mediator levels in the presence of AML-supporting bone marrow mesenchymal stem cells was then observed, especially for patients with secondary AML. Finally, animal studies suggested that the V-ATPase inhibitor bafilomycin had limited toxicity, even when combined with cytarabine. To conclude, V-ATPase inhibition has antileukemic effects in AML, but this effect varies between patients.
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Affiliation(s)
- Sushma Bartaula-Brevik
- Acute Leukemia Research Group, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (S.B.-B.); (M.H.-V.); (E.A.); (A.K.B.); (K.P.R.); (M.H.); (H.R.); (T.H.A.T.)
| | - Calum Leitch
- Department of Clinical Science, Centre for Pharmacy, University of Bergen, 5015 Bergen, Norway; (C.L.); (E.M.)
| | - Maria Hernandez-Valladares
- Acute Leukemia Research Group, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (S.B.-B.); (M.H.-V.); (E.A.); (A.K.B.); (K.P.R.); (M.H.); (H.R.); (T.H.A.T.)
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5009 Bergen, Norway; (F.S.B.); (F.S.)
- The Department of Biomedicine, University of Bergen, 5009 Bergen, Norway
- Department of Physical Chemistry, University of Granada, Avenida de la Fuente Nueva S/N, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18012 Granada, Spain
| | - Elise Aasebø
- Acute Leukemia Research Group, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (S.B.-B.); (M.H.-V.); (E.A.); (A.K.B.); (K.P.R.); (M.H.); (H.R.); (T.H.A.T.)
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5009 Bergen, Norway; (F.S.B.); (F.S.)
- The Department of Biomedicine, University of Bergen, 5009 Bergen, Norway
| | - Frode S. Berven
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5009 Bergen, Norway; (F.S.B.); (F.S.)
- The Department of Biomedicine, University of Bergen, 5009 Bergen, Norway
| | - Frode Selheim
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5009 Bergen, Norway; (F.S.B.); (F.S.)
- The Department of Biomedicine, University of Bergen, 5009 Bergen, Norway
| | - Annette K. Brenner
- Acute Leukemia Research Group, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (S.B.-B.); (M.H.-V.); (E.A.); (A.K.B.); (K.P.R.); (M.H.); (H.R.); (T.H.A.T.)
| | - Kristin Paulsen Rye
- Acute Leukemia Research Group, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (S.B.-B.); (M.H.-V.); (E.A.); (A.K.B.); (K.P.R.); (M.H.); (H.R.); (T.H.A.T.)
| | - Marie Hagen
- Acute Leukemia Research Group, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (S.B.-B.); (M.H.-V.); (E.A.); (A.K.B.); (K.P.R.); (M.H.); (H.R.); (T.H.A.T.)
| | - Håkon Reikvam
- Acute Leukemia Research Group, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (S.B.-B.); (M.H.-V.); (E.A.); (A.K.B.); (K.P.R.); (M.H.); (H.R.); (T.H.A.T.)
- Section for Hematology, Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway
| | - Emmet McCormack
- Department of Clinical Science, Centre for Pharmacy, University of Bergen, 5015 Bergen, Norway; (C.L.); (E.M.)
| | - Øystein Bruserud
- Acute Leukemia Research Group, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (S.B.-B.); (M.H.-V.); (E.A.); (A.K.B.); (K.P.R.); (M.H.); (H.R.); (T.H.A.T.)
- Section for Hematology, Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway
| | - Tor Henrik Anderson Tvedt
- Acute Leukemia Research Group, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (S.B.-B.); (M.H.-V.); (E.A.); (A.K.B.); (K.P.R.); (M.H.); (H.R.); (T.H.A.T.)
- Section for Hematology, Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway
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Barakat A, Birkeland E, Jørstad MD, El Hajj M, Marijani M, Døskeland A, Mjaavatten O, Berven FS, Mustafa T. Proteomic analysis of peripheral blood mononuclear cells isolated from patients with pulmonary tuberculosis: A pilot study from Zanzibar, Tanzania. PLoS One 2023; 18:e0281757. [PMID: 36787336 PMCID: PMC9928017 DOI: 10.1371/journal.pone.0281757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 01/31/2023] [Indexed: 02/15/2023] Open
Abstract
This study aimed at exploring the proteomic profile of PBMCs to predict treatment response in pulmonary tuberculosis (PTB). This was a pilot study conducted among 8 adult patients from Zanzibar, Tanzania with confirmed PTB. Blood samples were collected at baseline, at 2 months of treatment, and at the end of treatment at 6 months. Proteins were extracted from PBMCs and analyzed using LC-MS/MS based label free quantitative proteomics. Overall, 3,530 proteins were quantified across the samples, and 12 differentially expressed proteins were identified at both 2 months of treatment and at treatment completion, which were involved in cellular and metabolic processes, as well as binding and catalytic activity. Seven were downregulated proteins (HSPA1B/HSPA1A, HSPH1, HSP90AA1, lipopolysaccharide-binding protein, complement component 9, calcyclin-binding protein, and protein transport protein Sec31A), and 5 proteins were upregulated (SEC14 domain and spectrin repeat-containing protein 1, leucine-rich repeat-containing 8 VRAC subunit D, homogentisate 1,2-dioxygenase, NEDD8-activating enzyme E1 regulatory subunit, and N-acetylserotonin O-methyltransferase-like protein). The results showed that proteome analysis of PBMCs can be used as a novel technique to identify protein abundance change with anti-tuberculosis treatment. The novel proteins elucidated in this work may provide new insights for understanding PTB pathogenesis, treatment, and prognosis.
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Affiliation(s)
- Ahmed Barakat
- Centre for International Health, Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Even Birkeland
- Proteomics Unit at University of Bergen (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Melissa D. Jørstad
- Centre for International Health, Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | - Magalie El Hajj
- Centre for International Health, Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
- Department of Medical Affairs, Partner 4 Health, Paris, France
| | - Msafiri Marijani
- Department of Diagnostic Services, Mnazi Mmoja Hospital, Zanzibar, The United Republic of Tanzania
| | - Anne Døskeland
- Proteomics Unit at University of Bergen (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Olav Mjaavatten
- Proteomics Unit at University of Bergen (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Frode S. Berven
- Proteomics Unit at University of Bergen (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Tehmina Mustafa
- Centre for International Health, Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
- * E-mail:
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5
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Yilmaz O, Jensen AM, Harboe T, Møgster M, Jensen RM, Mjaavatten O, Birkeland E, Spriet E, Sandven L, Furmanek T, Berven FS, Wargelius A, Norberg B. 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. BMC Genomics 2022; 23:635. [PMID: 36071374 PMCID: PMC9450261 DOI: 10.1186/s12864-022-08859-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 08/30/2022] [Indexed: 11/24/2022] Open
Abstract
Background Tandem mass tag spectrometry (TMT labeling-LC-MS/MS) was utilized to examine the global proteomes of Atlantic halibut eggs at the 1-cell-stage post fertilization. Comparisons were made between eggs judged to be of good quality (GQ) versus poor quality (BQ) as evidenced by their subsequent rates of survival for 12 days. Altered abundance of selected proteins in BQ eggs was confirmed by parallel reaction monitoring spectrometry (PRM-LC-MS/MS). Correspondence of protein levels to expression of related gene transcripts was examined via qPCR. Potential mitochondrial differences between GQ and BQ eggs were assessed by transmission electron microscopy (TEM) and measurements of mitochondrial DNA (mtDNA) levels. Results A total of 115 proteins were found to be differentially abundant between GQ and BQ eggs. Frequency distributions of these proteins indicated higher protein folding activity in GQ eggs compared to higher transcription and protein degradation activities in BQ eggs. BQ eggs were also significantly enriched with proteins related to mitochondrial structure and biogenesis. Quantitative differences in abundance of several proteins with parallel differences in their transcript levels were confirmed in egg samples obtained over three consecutive reproductive seasons. The observed disparities in global proteome profiles suggest impairment of protein and energy homeostasis related to unfolded protein response and mitochondrial stress in BQ eggs. TEM revealed BQ eggs to contain significantly higher numbers of mitochondria, but differences in corresponding genomic mtDNA (mt-nd5 and mt-atp6) levels were not significant. Mitochondria from BQ eggs were significantly smaller with a more irregular shape and a higher number of cristae than those from GQ eggs. Conclusion The results of this study indicate that BQ Atlantic halibut eggs are impaired at both transcription and translation levels leading to endoplasmic reticulum and mitochondrial disorders. Observation of these irregularities over three consecutive reproductive seasons in BQ eggs from females of diverse background, age and reproductive experience indicates that they are a hallmark of poor egg quality. Additional research is needed to discover when in oogenesis and under what circumstances these defects may arise. The prevalence of this suite of markers in BQ eggs of diverse vertebrate species also begs investigation. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08859-0.
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Affiliation(s)
- Ozlem Yilmaz
- Institute of Marine Research, Austevoll Research Station, 5392, Storebø, Norway.
| | | | - Torstein Harboe
- Institute of Marine Research, Austevoll Research Station, 5392, Storebø, Norway
| | - Margareth Møgster
- Institute of Marine Research, Austevoll Research Station, 5392, Storebø, Norway
| | | | - Olav Mjaavatten
- Department of Biomedicine, The Proteomics Facility of the University of Bergen (PROBE), 5009, Bergen, Norway
| | - Even Birkeland
- Department of Biomedicine, The Proteomics Facility of the University of Bergen (PROBE), 5009, Bergen, Norway
| | - Endy Spriet
- Department of Biomedicine, The Molecular Imaging Center (MIC), University of Bergen, 5009, Bergen, Norway
| | - Linda Sandven
- Department of Biomedicine, The Molecular Imaging Center (MIC), University of Bergen, 5009, Bergen, Norway
| | - Tomasz Furmanek
- Institute of Marine Research, P.O. Box 1870, Nordnes, 5817, Bergen, Norway
| | - Frode S Berven
- Department of Biomedicine, The Proteomics Facility of the University of Bergen (PROBE), 5009, Bergen, Norway
| | - Anna Wargelius
- Institute of Marine Research, P.O. Box 1870, Nordnes, 5817, Bergen, Norway
| | - Birgitta Norberg
- Institute of Marine Research, Austevoll Research Station, 5392, Storebø, Norway
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Neset L, Takayidza G, Berven FS, Hernandez-Valladares M. Comparing Efficiency of Lysis Buffer Solutions and Sample Preparation Methods for Liquid Chromatography-Mass Spectrometry Analysis of Human Cells and Plasma. Molecules 2022; 27:molecules27113390. [PMID: 35684327 PMCID: PMC9181984 DOI: 10.3390/molecules27113390] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/16/2022] [Accepted: 05/21/2022] [Indexed: 12/02/2022]
Abstract
The use of a proper sample processing methodology for maximum proteome coverage and high-quality quantitative data is an important choice to make before initiating a liquid chromatography–mass spectrometry (LC–MS)-based proteomics study. Popular sample processing workflows for proteomics involve in-solution proteome digestion and single-pot, solid-phase-enhanced sample preparation (SP3). We tested them on both HeLa cells and human plasma samples, using lysis buffers containing SDS, or guanidinium hydrochloride. We also studied the effect of using commercially available depletion mini spin columns before SP3, to increase proteome coverage in human plasma samples. Our results show that the SP3 protocol, using either buffer, achieves the highest number of quantified proteins in both the HeLa cells and plasma samples. Moreover, the use of depletion mini spin columns before SP3 results in a two-fold increase of quantified plasma proteins. With additional fractionation, we quantified nearly 1400 proteins, and examined lower-abundance proteins involved in neurodegenerative pathways and mitochondrial metabolism. Therefore, we recommend the use of the SP3 methodology for biological sample processing, including those after depletion of high-abundance plasma proteins.
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Affiliation(s)
- Lasse Neset
- The Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway; (L.N.); (G.T.); (F.S.B.)
| | - Gracious Takayidza
- The Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway; (L.N.); (G.T.); (F.S.B.)
| | - Frode S. Berven
- The Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway; (L.N.); (G.T.); (F.S.B.)
| | - Maria Hernandez-Valladares
- The Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway; (L.N.); (G.T.); (F.S.B.)
- Department of Clinical Science, University of Bergen, Jonas Lies vei 87, 5021 Bergen, Norway
- Department of Physical Chemistry, University of Granada, Campus Fuentenueva s/n, 18071 Granada, Spain
- Correspondence: ; Tel.: +47-555-863-68
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7
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Aasebø E, Brenner AK, Hernandez-Valladares M, Birkeland E, Mjaavatten O, Reikvam H, Selheim F, Berven FS, Bruserud Ø. Patient Heterogeneity in Acute Myeloid Leukemia: Leukemic Cell Communication by Release of Soluble Mediators and Its Effects on Mesenchymal Stem Cells. Diseases 2021; 9:diseases9040074. [PMID: 34698165 PMCID: PMC8544451 DOI: 10.3390/diseases9040074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 01/01/2023] Open
Abstract
Acute myeloid leukemia (AML) is an aggressive bone marrow malignancy, and non-leukemic stromal cells (including mesenchymal stem cells, MSCs) are involved in leukemogenesis and show AML-supporting effects. We investigated how constitutive extracellular mediator release by primary human AML cells alters proteomic profiles of normal bone marrow MSCs. An average of 6814 proteins (range 6493−6918 proteins) were quantified for 41 MSC cultures supplemented with AML-cell conditioned medium, whereas an average of 6715 proteins (range 6703−6722) were quantified for untreated control MSCs. The AML effect on global MSC proteomic profiles varied between patients. Hierarchical clustering analysis identified 10 patients (5/10 secondary AML) showing more extensive AML-effects on the MSC proteome, whereas the other 31 patients clustered together with the untreated control MSCs and showed less extensive AML-induced effects. These two patient subsets differed especially with regard to MSC levels of extracellular matrix and mitochondrial/metabolic regulatory proteins. Less than 10% of MSC proteins were significantly altered by the exposure to AML-conditioned media; 301 proteins could only be quantified after exposure to conditioned medium and 201 additional proteins were significantly altered compared with the levels in control samples (153 increased, 48 decreased). The AML-modulated MSC proteins formed several interacting networks mainly reflecting intracellular organellar structure/trafficking but also extracellular matrix/cytokine signaling, and a single small network reflecting altered DNA replication. Our results suggest that targeting of intracellular trafficking and/or intercellular communication is a possible therapeutic strategy in AML.
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Affiliation(s)
- Elise Aasebø
- Department of Clinical Science, University of Bergen, 5020 Bergen, Norway; (E.A.); (A.K.B.); (H.R.)
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5020 Bergen, Norway; (M.H.-V.); (E.B.); (O.M.); (F.S.); (F.S.B.)
| | - Annette K. Brenner
- Department of Clinical Science, University of Bergen, 5020 Bergen, Norway; (E.A.); (A.K.B.); (H.R.)
| | - Maria Hernandez-Valladares
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5020 Bergen, Norway; (M.H.-V.); (E.B.); (O.M.); (F.S.); (F.S.B.)
| | - Even Birkeland
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5020 Bergen, Norway; (M.H.-V.); (E.B.); (O.M.); (F.S.); (F.S.B.)
| | - Olav Mjaavatten
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5020 Bergen, Norway; (M.H.-V.); (E.B.); (O.M.); (F.S.); (F.S.B.)
| | - Håkon Reikvam
- Department of Clinical Science, University of Bergen, 5020 Bergen, Norway; (E.A.); (A.K.B.); (H.R.)
- Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway
| | - Frode Selheim
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5020 Bergen, Norway; (M.H.-V.); (E.B.); (O.M.); (F.S.); (F.S.B.)
| | - Frode S. Berven
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5020 Bergen, Norway; (M.H.-V.); (E.B.); (O.M.); (F.S.); (F.S.B.)
| | - Øystein Bruserud
- Department of Clinical Science, University of Bergen, 5020 Bergen, Norway; (E.A.); (A.K.B.); (H.R.)
- Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway
- Correspondence:
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8
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Joseph JV, Magaut CR, Storevik S, Geraldo LH, Mathivet T, Latif MA, Rudewicz J, Guyon J, Gambaretti M, Haukas F, Trones A, Rømo Ystaas LA, Hossain JA, Ninzima S, Cuvellier S, Zhou W, Tomar T, Klink B, Rane L, Irving BK, Marrison J, O'Toole P, Wurdak H, Wang J, Di Z, Birkeland E, Berven FS, Winkler F, Kruyt FAE, Bikfalvi A, Bjerkvig R, Daubon T, Miletic H. TGF-β promotes microtube formation in glioblastoma through thrombospondin 1. Neuro Oncol 2021; 24:541-553. [PMID: 34543427 PMCID: PMC8972291 DOI: 10.1093/neuonc/noab212] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Microtubes (MTs), cytoplasmic extensions of glioma cells, are important cell communication structures promoting invasion and treatment resistance through network formation. MTs are abundant in chemoresistant gliomas, in particular glioblastomas (GBMs), while they are uncommon in chemosensitive IDH-mutant and 1p/19q co-deleted oligodendrogliomas. The aim of this study was to identify potential signaling pathways involved in MT formation. METHODS Bioinformatics analysis of TCGA was performed to analyze differences between GBM and oligodendroglioma. Patient-derived GBM stem cell lines were used to investigate microtube formation under TGF-βstimulation and inhibition in vitro and in vivo in an orthotopic xenograft model. RNA sequencing and proteomics were performed to detect commonalities and differences between GBM cell lines stimulated with TGF-β. RESULTS Analysis of TCGA data showed that the TGF-β pathway is highly activated in GBMs compared to oligodendroglial tumors. We demonstrated that TGF-β1 stimulation of GBM cell lines promotes enhanced MT formation and communication via Calcium signaling. Inhibition of the TGF-β pathway significantly reduced MT formation and its associated invasion in vitro and in vivo. Downstream of TGF-β, we identified thrombospondin 1 (TSP1) as a potential mediator of MT formation in GBM through SMAD activation. TSP1 was upregulated upon TGF- β stimulation and enhanced MT formation, which was inhibited by TSP1 shRNAs in vitro and in vivo. CONCLUSION TGF-β and its downstream mediator TSP1 are important mediators of the MT network in GBM and blocking this pathway could potentially help to break the complex MT driven invasion/ resistance network.
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Affiliation(s)
- Justin V Joseph
- Department of Clinical Medicine, University of Aarhus, Aarhus, Danmark.,Department of Biomedicine, University of Bergen, Bergen, Norway
| | | | - Simon Storevik
- Department of Biomedicine, University of Bergen, Bergen, Norway.,Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Luiz H Geraldo
- Inserm U970, Paris Cardiovascular Research Center, Paris, 75015 France
| | - Thomas Mathivet
- Inserm U970, Paris Cardiovascular Research Center, Paris, 75015 France
| | - Md Abdul Latif
- Department of Biomedicine, University of Bergen, Bergen, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway
| | | | - Joris Guyon
- University of Bordeaux, INSERM, LAMC, U1029, 33600, Pessac, France
| | | | - Frida Haukas
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Amalie Trones
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | | | - Jubayer A Hossain
- Department of Biomedicine, University of Bergen, Bergen, Norway.,Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Sandra Ninzima
- Department of Biomedicine, University of Bergen, Bergen, Norway.,Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Sylvain Cuvellier
- Univ. Bordeaux, CNRS, IBGC, UMR5095, 33000, Bordeaux, France Bordeaux, France
| | - Wenjing Zhou
- Department of Biomedicine, University of Bergen, Bergen, Norway.,Department of Blood Transfusion, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, PR China.,Department of Neurosurgery, Qilu Hospital of Shandong University and Institute of Brain and Brain-Inspired Science, Shandong University; Shandong Key Laboratory of Brain Function Remodeling, Jinan, 250012, China
| | - Tushar Tomar
- PamGene International B.V., BJ 's-Hertogenbosch, The Netherlands
| | - Barbara Klink
- Department of Biomedicine, University of Bergen, Bergen, Norway.,National Center of Genetics (NCG), Laboratoire national de santé (LNS), Dudelange, Luxembourg.,Department of Oncology, Luxembourg Institute of Health, LIH, Luxembourg
| | - Lalit Rane
- Department of Clinical Science, University of Bergen, Bergens, Norway
| | | | | | | | - Heiko Wurdak
- School of Medicine, University of Leeds, Leeds, UK
| | - Jian Wang
- Department of Biomedicine, University of Bergen, Bergen, Norway.,Department of Neurosurgery, Qilu Hospital of Shandong University and Institute of Brain and Brain-Inspired Science, Shandong University; Shandong Key Laboratory of Brain Function Remodeling, Jinan, 250012, China
| | - Zhang Di
- Department of Neurosurgery, Qilu Hospital of Shandong University and Institute of Brain and Brain-Inspired Science, Shandong University; Shandong Key Laboratory of Brain Function Remodeling, Jinan, 250012, China
| | - Even Birkeland
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Frode S Berven
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Frank Winkler
- Neurology Clinic and National Center for Tumor Diseases, University of Heidelberg, Heidelberg, Germany
| | - Frank A E Kruyt
- Department of Medical Oncology, University of Groningen, University Medical Centre Groningen, Groningen, Netherlands
| | - Andreas Bikfalvi
- University of Bordeaux, INSERM, LAMC, U1029, 33600, Pessac, France
| | - Rolf Bjerkvig
- Department of Biomedicine, University of Bergen, Bergen, Norway.,Department of Oncology, Luxembourg Institute of Health, LIH, Luxembourg
| | - Thomas Daubon
- Department of Biomedicine, University of Bergen, Bergen, Norway.,University of Bordeaux, INSERM, LAMC, U1029, 33600, Pessac, France.,Univ. Bordeaux, CNRS, IBGC, UMR5095, 33000, Bordeaux, France Bordeaux, France
| | - Hrvoje Miletic
- Department of Biomedicine, University of Bergen, Bergen, Norway.,Department of Pathology, Haukeland University Hospital, Bergen, Norway
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9
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Røberg-Larsen H, Lundanes E, Nyman TA, Berven FS, Wilson SR. Liquid chromatography, a key tool for the advancement of single-cell omics analysis. Anal Chim Acta 2021; 1178:338551. [PMID: 34482862 DOI: 10.1016/j.aca.2021.338551] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 04/16/2021] [Accepted: 04/17/2021] [Indexed: 11/28/2022]
Abstract
Single-cell analysis can allow for an in-depth understanding of diseases, diagnostics, and aid the development of therapeutics. However, single-cell analysis is challenging, as samples are both extremely limited in size and complex. But the concept is gaining promise, much due to novel sample preparation approaches and the ever-improving field of mass spectrometry. The mass spectrometer's output is often linked to the preceding compound separation step, typically being liquid chromatography (LC). In this review, we focus on LC's role in single-cell omics. Particle-packed nano LC columns (typically 50-100 μm inner diameter) have traditionally been the tool of choice for limited samples, and are also used for single cells. Several commercial products and systems are emerging with single cells in mind, featuring particle-packed columns or miniaturized pillar array systems. In addition, columns with inner diameters as narrow as 2 μm are being explored to maximize sensitivity. Hence, LC column down-scaling is a key focus in single-cell analysis. But narrow columns are associated with considerable technical challenges, while single cell analysis may be expected to become a "routine" service, requiring higher degrees of robustness and throughput. These challenges and expectations will increase the need and attention for the development (and even the reinvention) of alternative nano LC column formats. Therefore, monolith columns and even open tubular columns may finally find their "killer-application" in single cell analysis.
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Affiliation(s)
| | - Elsa Lundanes
- Department of Chemistry, University of Oslo, Oslo, Norway
| | - Tuula A Nyman
- Department of Immunology, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Norway
| | - Frode S Berven
- Department of Biomedicine, Proteomics Unit, University of Bergen, Bergen, Norway
| | - Steven Ray Wilson
- Department of Chemistry, University of Oslo, Oslo, Norway; Hybrid Technology Hub-Centre of Excellence, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway.
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10
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Grønningsæter IS, Reikvam H, Aasebø E, Bartaula-Brevik S, Hernandez-Valladares M, Selheim F, Berven FS, Tvedt TH, Bruserud Ø, Hatfield KJ. Effects of the Autophagy-Inhibiting Agent Chloroquine on Acute Myeloid Leukemia Cells; Characterization of Patient Heterogeneity. J Pers Med 2021; 11:jpm11080779. [PMID: 34442423 PMCID: PMC8399694 DOI: 10.3390/jpm11080779] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/06/2021] [Accepted: 08/07/2021] [Indexed: 12/12/2022] Open
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.
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Affiliation(s)
- Ida Sofie Grønningsæter
- Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway; (I.S.G.); (H.R.); (E.A.); (S.B.-B.)
- Department of Medicine, Akershus University Hospital, N-1478 Lørenskog, Norway
| | - Håkon Reikvam
- Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway; (I.S.G.); (H.R.); (E.A.); (S.B.-B.)
- Department of Medicine, Haukeland University Hospital, N-5021 Bergen, Norway;
| | - Elise Aasebø
- Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway; (I.S.G.); (H.R.); (E.A.); (S.B.-B.)
- The Proteomics Facility of the University of Bergen (PROBE), Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway; (M.H.-V.); (F.S.); (F.S.B.)
| | - Sushma Bartaula-Brevik
- Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway; (I.S.G.); (H.R.); (E.A.); (S.B.-B.)
| | - Maria Hernandez-Valladares
- The Proteomics Facility of the University of Bergen (PROBE), Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway; (M.H.-V.); (F.S.); (F.S.B.)
- The Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway
| | - Frode Selheim
- The Proteomics Facility of the University of Bergen (PROBE), Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway; (M.H.-V.); (F.S.); (F.S.B.)
- The Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway
| | - Frode S. Berven
- The Proteomics Facility of the University of Bergen (PROBE), Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway; (M.H.-V.); (F.S.); (F.S.B.)
- The Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway
| | - Tor Henrik Tvedt
- Department of Medicine, Haukeland University Hospital, N-5021 Bergen, Norway;
- Department of Hematology, Oslo University Hospital—The National Hospital, N-0372 Oslo, Norway
| | - Øystein Bruserud
- Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway; (I.S.G.); (H.R.); (E.A.); (S.B.-B.)
- Department of Medicine, Haukeland University Hospital, N-5021 Bergen, Norway;
- Correspondence: (Ø.B.); (K.J.H.)
| | - Kimberley Joanne Hatfield
- Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway; (I.S.G.); (H.R.); (E.A.); (S.B.-B.)
- Department of Immunology and Transfusion Medicine, Haukeland University Hospital, N-5009 Bergen, Norway
- Correspondence: (Ø.B.); (K.J.H.)
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11
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Aasebø E, Brenner AK, Hernandez-Valladares M, Birkeland E, Berven FS, Selheim F, Bruserud Ø. Proteomic Comparison of Bone Marrow Derived Osteoblasts and Mesenchymal Stem Cells. Int J Mol Sci 2021; 22:ijms22115665. [PMID: 34073480 PMCID: PMC8198503 DOI: 10.3390/ijms22115665] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/21/2021] [Accepted: 05/22/2021] [Indexed: 02/07/2023] Open
Abstract
Mesenchymal stem cells (MSCs) can differentiate into osteoblasts, and therapeutic targeting of these cells is considered both for malignant and non-malignant diseases. We analyzed global proteomic profiles for osteoblasts derived from ten and MSCs from six healthy individuals, and we quantified 5465 proteins for the osteoblasts and 5420 proteins for the MSCs. There was a large overlap in the profiles for the two cell types; 156 proteins were quantified only in osteoblasts and 111 proteins only for the MSCs. The osteoblast-specific proteins included several extracellular matrix proteins and a network including 27 proteins that influence intracellular signaling (Wnt/Notch/Bone morphogenic protein pathways) and bone mineralization. The osteoblasts and MSCs showed only minor age- and sex-dependent proteomic differences. Finally, the osteoblast and MSC proteomic profiles were altered by ex vivo culture in serum-free media. We conclude that although the proteomic profiles of osteoblasts and MSCs show many similarities, we identified several osteoblast-specific extracellular matrix proteins and an osteoblast-specific intracellular signaling network. Therapeutic targeting of these proteins will possibly have minor effects on MSCs. Furthermore, the use of ex vivo cultured osteoblasts/MSCs in clinical medicine will require careful standardization of the ex vivo handling of the cells.
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Affiliation(s)
- Elise Aasebø
- Department of Clinical Science, University of Bergen, 5020 Bergen, Norway; (E.A.); (A.K.B.)
- Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5020 Bergen, Norway; (M.H.-V.); (E.B.); (F.S.B.); (F.S.)
| | - Annette K. Brenner
- Department of Clinical Science, University of Bergen, 5020 Bergen, Norway; (E.A.); (A.K.B.)
| | - Maria Hernandez-Valladares
- Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5020 Bergen, Norway; (M.H.-V.); (E.B.); (F.S.B.); (F.S.)
| | - Even Birkeland
- Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5020 Bergen, Norway; (M.H.-V.); (E.B.); (F.S.B.); (F.S.)
| | - Frode S. Berven
- Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5020 Bergen, Norway; (M.H.-V.); (E.B.); (F.S.B.); (F.S.)
| | - Frode Selheim
- Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5020 Bergen, Norway; (M.H.-V.); (E.B.); (F.S.B.); (F.S.)
| | - Øystein Bruserud
- Department of Clinical Science, University of Bergen, 5020 Bergen, Norway; (E.A.); (A.K.B.)
- Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway
- Correspondence:
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12
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Oveland E, Ahmad I, Lereim RR, Kroksveen AC, Barsnes H, Guldbrandsen A, Myhr KM, Bø L, Berven FS, Wergeland S. Cuprizone and EAE mouse frontal cortex proteomics revealed proteins altered in multiple sclerosis. Sci Rep 2021; 11:7174. [PMID: 33785790 PMCID: PMC8010076 DOI: 10.1038/s41598-021-86191-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 02/19/2021] [Indexed: 02/06/2023] Open
Abstract
Two pathophysiological different experimental models for multiple sclerosis were analyzed in parallel using quantitative proteomics in attempts to discover protein alterations applicable as diagnostic-, prognostic-, or treatment targets in human disease. The cuprizone model reflects de- and remyelination in multiple sclerosis, and the experimental autoimmune encephalomyelitis (EAE, MOG1-125) immune-mediated events. The frontal cortex, peripheral to severely inflicted areas in the CNS, was dissected and analyzed. The frontal cortex had previously not been characterized by proteomics at different disease stages, and novel protein alterations involved in protecting healthy tissue and assisting repair of inflicted areas might be discovered. Using TMT-labelling and mass spectrometry, 1871 of the proteins quantified overlapped between the two experimental models, and the fold change compared to controls was verified using label-free proteomics. Few similarities in frontal cortex between the two disease models were observed when regulated proteins and signaling pathways were compared. Legumain and C1Q complement proteins were among the most upregulated proteins in cuprizone and hemopexin in the EAE model. Immunohistochemistry showed that legumain expression in post-mortem multiple sclerosis brain tissue (n = 19) was significantly higher in the center and at the edge of white matter active and chronic active lesions. Legumain was associated with increased lesion activity and might be valuable as a drug target using specific inhibitors as already suggested for Parkinson's and Alzheimer's disease. Cerebrospinal fluid levels of legumain, C1q and hemopexin were not significantly different between multiple sclerosis patients, other neurological diseases, or healthy controls.
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Affiliation(s)
- Eystein Oveland
- Proteomics Unit, Department of Biomedicine, University of Bergen (PROBE), Bergen, Norway
| | - Intakhar Ahmad
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Department of Neurology, Norwegian Multiple Sclerosis Competence Centre, Haukeland University Hospital, Jonas Lies vei 65, 5021, Bergen, Norway
| | - Ragnhild Reehorst Lereim
- Proteomics Unit, Department of Biomedicine, University of Bergen (PROBE), Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Ann Cathrine Kroksveen
- Proteomics Unit, Department of Biomedicine, University of Bergen (PROBE), Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Harald Barsnes
- Proteomics Unit, Department of Biomedicine, University of Bergen (PROBE), Bergen, Norway
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Astrid Guldbrandsen
- Proteomics Unit, Department of Biomedicine, University of Bergen (PROBE), Bergen, Norway
- Department of Neurology, Norwegian Multiple Sclerosis Competence Centre, Haukeland University Hospital, Jonas Lies vei 65, 5021, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Kjell-Morten Myhr
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | - Lars Bø
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Department of Neurology, Norwegian Multiple Sclerosis Competence Centre, Haukeland University Hospital, Jonas Lies vei 65, 5021, Bergen, Norway
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | - Frode S Berven
- Proteomics Unit, Department of Biomedicine, University of Bergen (PROBE), Bergen, Norway
- Department of Neurology, Norwegian Multiple Sclerosis Competence Centre, Haukeland University Hospital, Jonas Lies vei 65, 5021, Bergen, Norway
| | - Stig Wergeland
- Department of Neurology, Norwegian Multiple Sclerosis Competence Centre, Haukeland University Hospital, Jonas Lies vei 65, 5021, Bergen, Norway.
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, Bergen, Norway.
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13
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Aasebø E, Brenner AK, Birkeland E, Tvedt THA, Selheim F, Berven FS, Bruserud Ø. The Constitutive Extracellular Protein Release by Acute Myeloid Leukemia Cells-A Proteomic Study of Patient Heterogeneity and Its Modulation by Mesenchymal Stromal Cells. Cancers (Basel) 2021; 13:cancers13071509. [PMID: 33806032 PMCID: PMC8037744 DOI: 10.3390/cancers13071509] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/20/2022] Open
Abstract
Simple Summary The formation of normal blood cells in the bone marrow is supported by a network of non-hematopoietic cells including connective tissue cells, blood vessel cells and bone-forming cells. These cell types support and regulate the growth of acute myeloid leukemia (AML) cells and communicate with leukemic cells through the release of proteins to their common extracellular microenvironment. One of the AML-supporting normal cell types is a subset of connective tissue cells called mesenchymal stem cells. In the present study, we observed that AML cells release a wide range of diverse proteins into their microenvironment, but patients differ both with regard to the number and amount of released proteins. Inhibition of this bidirectional communication through protein release between AML cells and leukemia-supporting normal cells may become a new strategy for cancer treatment. Abstract Extracellular protein release is important both for the formation of extracellular matrix and for communication between cells. We investigated the extracellular protein release by in vitro cultured normal mesenchymal stem cells (MSCs) and by primary human acute myeloid leukemia (AML) cells derived from 40 consecutive patients. We observed quantifiable levels of 3082 proteins in our study; for the MSCs, we detected 1446 proteins, whereas the number of released proteins for the AML cells showed wide variation between patients (average number 1699, range 557–2380). The proteins were derived from various cellular compartments (e.g., cell membrane, nucleus, and cytoplasms), several organelles (e.g., cytoskeleton, endoplasmatic reticulum, Golgi apparatus, and mitochondria) and had various functions (e.g., extracellular matrix and exosomal proteins, cytokines, soluble adhesion molecules, protein synthesis, post-transcriptional modulation, RNA binding, and ribonuclear proteins). Thus, AML patients were very heterogeneous both regarding the number of proteins and the nature of their extracellularly released proteins. The protein release profiles of MSCs and primary AML cells show a considerable overlap, but a minority of the proteins are released only or mainly by the MSC, including several extracellular matrix molecules. Taken together, our observations suggest that the protein profile of the extracellular bone marrow microenvironment differs between AML patients, these differences are mainly caused by the protein release by the leukemic cells but this leukemia-associated heterogeneity of the overall extracellular protein profile is modulated by the constitutive protein release by normal MSCs.
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Affiliation(s)
- Elise Aasebø
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (E.A.); (A.K.B.)
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5009 Bergen, Norway; (E.B.); (F.S.); (F.S.B.)
| | - Annette K. Brenner
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (E.A.); (A.K.B.)
| | - Even Birkeland
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5009 Bergen, Norway; (E.B.); (F.S.); (F.S.B.)
| | | | - Frode Selheim
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5009 Bergen, Norway; (E.B.); (F.S.); (F.S.B.)
| | - Frode S. Berven
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5009 Bergen, Norway; (E.B.); (F.S.); (F.S.B.)
| | - Øystein Bruserud
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5009 Bergen, Norway; (E.B.); (F.S.); (F.S.B.)
- Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway;
- Correspondence: or
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14
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Guldbrandsen A, Lereim RR, Jacobsen M, Garberg H, Kroksveen AC, Barsnes H, Berven FS. Development of robust targeted proteomics assays for cerebrospinal fluid biomarkers in multiple sclerosis. Clin Proteomics 2020; 17:33. [PMID: 32963504 PMCID: PMC7499868 DOI: 10.1186/s12014-020-09296-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 09/08/2020] [Indexed: 12/25/2022] Open
Abstract
Background Verification of cerebrospinal fluid (CSF) biomarkers for multiple sclerosis and other neurological diseases is a major challenge due to a large number of candidates, limited sample material availability, disease and biological heterogeneity, and the lack of standardized assays. Furthermore, verification studies are often based on a low number of proteins from a single discovery experiment in medium-sized cohorts, where antibodies and surrogate peptides may differ, thus only providing an indication of proteins affected by the disease and not revealing the bigger picture or concluding on the validity of the markers. We here present a standard approach for locating promising biomarker candidates based on existing knowledge, resulting in high-quality assays covering the main biological processes affected by multiple sclerosis for comparable measurements over time. Methods Biomarker candidates were located in CSF-PR (proteomics.uib.no/csf-pr), and further filtered based on estimated concentration in CSF and biological function. Peptide surrogates for internal standards were selected according to relevant criteria, parallel reaction monitoring (PRM) assays created, and extensive assay quality testing performed, i.e. intra- and inter-day variation, trypsin digestion status over time, and whether the peptides were able to separate multiple sclerosis patients and controls. Results Assays were developed for 25 proteins, represented by 72 peptides selected according to relevant guidelines and available literature and tested for assay peptide suitability. Stability testing revealed 64 peptides with low intra- and inter-day variations, with 44 also being stably digested after 16 h of trypsin digestion, and 37 furthermore showing a significant difference between multiple sclerosis and controls, thereby confirming literature findings. Calibration curves and the linear area of measurement have, so far, been determined for 17 of these peptides. Conclusions We present 37 high-quality PRM assays across 21 CSF-proteins found to be affected by multiple sclerosis, along with a recommended workflow for future development of new assays. The assays can directly be used by others, thus enabling better comparison between studies. Finally, the assays can robustly and stably monitor biological processes in multiple sclerosis patients over time, thus potentially aiding in diagnosis and prognosis, and ultimately in treatment decisions.
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Affiliation(s)
- Astrid Guldbrandsen
- Proteomics Unit, PROBE, Department of Biomedicine, University of Bergen, Bergen, Norway.,Computational Biology Unit, CBU, Department of Informatics, University of Bergen, Bergen, Norway
| | - Ragnhild Reehorst Lereim
- Proteomics Unit, PROBE, Department of Biomedicine, University of Bergen, Bergen, Norway.,Computational Biology Unit, CBU, Department of Informatics, University of Bergen, Bergen, Norway
| | - Mari Jacobsen
- Proteomics Unit, PROBE, Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Hilde Garberg
- Biobank Haukeland, Haukeland University Hospital, Bergen, Norway
| | | | - Harald Barsnes
- Proteomics Unit, PROBE, Department of Biomedicine, University of Bergen, Bergen, Norway.,Computational Biology Unit, CBU, Department of Informatics, University of Bergen, Bergen, Norway
| | - Frode S Berven
- Proteomics Unit, PROBE, Department of Biomedicine, University of Bergen, Bergen, Norway
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15
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Ahmad R, Xie L, Pyle M, Suarez MF, Broger T, Steinberg D, Ame SM, Lucero MG, Szucs MJ, MacMullan M, Berven FS, Dutta A, Sanvictores DM, Tallo VL, Bencher R, Eisinger DP, Dhingra U, Deb S, Ali SM, Mehta S, Fawzi WW, Riley ID, Sazawal S, Premji Z, Black R, Murray CJL, Rodriguez B, Carr SA, Walt DR, Gillette MA. A rapid triage test for active pulmonary tuberculosis in adult patients with persistent cough. Sci Transl Med 2020; 11:11/515/eaaw8287. [PMID: 31645455 DOI: 10.1126/scitranslmed.aaw8287] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 08/23/2019] [Indexed: 01/08/2023]
Abstract
Improved tuberculosis (TB) prevention and control depend critically on the development of a simple, readily accessible rapid triage test to stratify TB risk. We hypothesized that a blood protein-based host response signature for active TB (ATB) could distinguish it from other TB-like disease (OTD) in adult patients with persistent cough, thereby providing a foundation for a point-of-care (POC) triage test for ATB. Three adult cohorts consisting of ATB suspects were recruited. A bead-based immunoassay and machine learning algorithms identified a panel of four host blood proteins, interleukin-6 (IL-6), IL-8, IL-18, and vascular endothelial growth factor (VEGF), that distinguished ATB from OTD. An ultrasensitive POC-amenable single-molecule array (Simoa) panel was configured, and the ATB diagnostic algorithm underwent blind validation in an independent, multinational cohort in which ATB was distinguished from OTD with receiver operator characteristic-area under the curve (ROC-AUC) of 0.80 [95% confidence interval (CI), 0.75 to 0.85], 80% sensitivity (95% CI, 73 to 85%), and 65% specificity (95% CI, 57 to 71%). When host antibodies against TB antigen Ag85B were added to the panel, performance improved to 86% sensitivity and 69% specificity. A blood-based host response panel consisting of four proteins and antibodies to one TB antigen can help to differentiate ATB from other causes of persistent cough in patients with and without HIV infection from Africa, Asia, and South America. Performance characteristics approach World Health Organization (WHO) target product profile accuracy requirements and may provide the foundation for an urgently needed blood-based POC TB triage test.
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Affiliation(s)
- Rushdy Ahmad
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
| | - Liangxia Xie
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 60 Fenwood Road, Boston, MA 02115, USA.,Wyss Institute for Biologically Inspired Engineering at Harvard University, 3 Blackfan Circle, Boston, MA 02115, USA.,Department of Chemistry, Tufts University, Medford, MA 02155, USA
| | - Margaret Pyle
- University of Maryland Medical Center, 22 South Greene Street, Baltimore, MD 21201, USA
| | - Marta F Suarez
- Daktari Diagnostics, 85 Bolton Street, Cambridge, MA 02140, USA
| | - Tobias Broger
- Foundation for Innovative New Diagnostics, 9 Chemin des Mines, 1202 Geneva, Switzerland
| | - Dan Steinberg
- Salford Systems, 9685 Via Excelencia, Suite 208, San Diego, CA 92126, USA
| | - Shaali M Ame
- Public Health Laboratory-Ivo de Carneri, Wawi, Chake Chake, Pemba 5501021, Tanzania
| | - Marilla G Lucero
- Research Institute for Tropical Medicine, 9002 Research Drive, Filinvest Corporate City, Alabang, Muntinlupa City, 1781, Metro Manila, Philippines
| | - Matthew J Szucs
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Melanie MacMullan
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Frode S Berven
- Proteomics Unit, Department of Biomedicine, University of Bergen, 5009 Bergen, Norway
| | - Arup Dutta
- Center for Public Health Kinetics, 214A Vinobapuri, Lajpat Nagar-II, New Delhi 110024, India
| | - Diozele M Sanvictores
- Research Institute for Tropical Medicine, 9002 Research Drive, Filinvest Corporate City, Alabang, Muntinlupa City, 1781, Metro Manila, Philippines
| | - Veronica L Tallo
- Research Institute for Tropical Medicine, 9002 Research Drive, Filinvest Corporate City, Alabang, Muntinlupa City, 1781, Metro Manila, Philippines
| | | | | | - Usha Dhingra
- Center for Public Health Kinetics, 214A Vinobapuri, Lajpat Nagar-II, New Delhi 110024, India
| | - Saikat Deb
- Center for Public Health Kinetics, 214A Vinobapuri, Lajpat Nagar-II, New Delhi 110024, India
| | - Said M Ali
- Public Health Laboratory-Ivo de Carneri, Wawi, Chake Chake, Pemba 5501021, Tanzania
| | - Saurabh Mehta
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, 314 Savage Hall, Ithaca, NY 14850, USA
| | - Wafaie W Fawzi
- Department of Global Health and Population, Harvard School of Public Health, 665 Huntington Avenue, Building 1, Room 1102, Boston, MA 02115, USA
| | - Ian D Riley
- The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sunil Sazawal
- Center for Public Health Kinetics, 214A Vinobapuri, Lajpat Nagar-II, New Delhi 110024, India
| | - Zul Premji
- Department of Parasitology and Entomology, Muhimbili University of Health and Allied Sciences, United Nations Road, Dar es Salaam 0702172, Tanzania
| | - Robert Black
- Institute for International Programs, Department of International Health, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD 21205, USA
| | - Christopher J L Murray
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Avenue, Suite 600, Seattle, WA 98121, USA
| | - Bill Rodriguez
- Draper Richards Kaplan Foundation, 535 Boylston Street, Boston, MA 02116, USA
| | - Steven A Carr
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - David R Walt
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 60 Fenwood Road, Boston, MA 02115, USA. .,Wyss Institute for Biologically Inspired Engineering at Harvard University, 3 Blackfan Circle, Boston, MA 02115, USA.,Department of Chemistry, Tufts University, Medford, MA 02155, USA
| | - Michael A Gillette
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA. .,Massachusetts General Hospital Division of Pulmonary and Critical Care Medicine, 55 Fruit Street, Boston, MA 02114, USA
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16
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Aasebø E, Berven FS, Hovland R, Døskeland SO, Bruserud Ø, Selheim F, Hernandez-Valladares M. The Progression of Acute Myeloid Leukemia from First Diagnosis to Chemoresistant Relapse: A Comparison of Proteomic and Phosphoproteomic Profiles. Cancers (Basel) 2020; 12:cancers12061466. [PMID: 32512867 PMCID: PMC7352627 DOI: 10.3390/cancers12061466] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 06/01/2020] [Indexed: 12/14/2022] Open
Abstract
Acute myeloid leukemia (AML) is an aggressive hematological malignancy. Nearly 50% of the patients who receive the most intensive treatment develop chemoresistant leukemia relapse. Although the leukemogenic events leading to relapse seem to differ between patients (i.e., regrowth from a clone detected at first diagnosis, progression from the original leukemic or preleukemic stem cells), a common characteristic of relapsed AML is increased chemoresistance. The aim of the present study was to investigate at the proteomic level whether leukemic cells from relapsed patients present overlapping molecular mechanisms that contribute to this chemoresistance. We used liquid chromatography–tandem mass spectrometry (LC–MS/MS) to compare the proteomic and phosphoproteomic profiles of AML cells derived from seven patients at the time of first diagnosis and at first relapse. At the time of first relapse, AML cells were characterized by increased levels of proteins important for various mitochondrial functions, such as mitochondrial ribosomal subunit proteins (MRPL21, MRPS37) and proteins for RNA processing (DHX37, RNA helicase; RPP40, ribonuclease P component), DNA repair (ERCC3, DNA repair factor IIH helicase; GTF2F1, general transcription factor), and cyclin-dependent kinase (CDK) activity. The levels of several cytoskeletal proteins (MYH14/MYL6/MYL12A, myosin chains; VCL, vinculin) as well as of proteins involved in vesicular trafficking/secretion and cell adhesion (ITGAX, integrin alpha-X; CD36, platelet glycoprotein 4; SLC2A3, solute carrier family 2) were decreased in relapsed cells. Our study introduces new targetable proteins that might direct therapeutic strategies to decrease chemoresistance in relapsed AML.
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Affiliation(s)
- Elise Aasebø
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (E.A.); (Ø.B.)
- The Department of Biomedicine, The Proteomics Unit at the University of Bergen (PROBE), University of Bergen, 5009 Bergen, Norway; (F.S.B.); (F.S.)
| | - Frode S. Berven
- The Department of Biomedicine, The Proteomics Unit at the University of Bergen (PROBE), University of Bergen, 5009 Bergen, Norway; (F.S.B.); (F.S.)
- The Department of Biomedicine, University of Bergen, 5009 Bergen, Norway;
| | - Randi Hovland
- Department for Medical Genetics, Haukeland University Hospital, 5021 Bergen, Norway;
- Department of Biological Sciences, University of Bergen, 5006 Bergen, Norway
| | | | - Øystein Bruserud
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (E.A.); (Ø.B.)
| | - Frode Selheim
- The Department of Biomedicine, The Proteomics Unit at the University of Bergen (PROBE), University of Bergen, 5009 Bergen, Norway; (F.S.B.); (F.S.)
- The Department of Biomedicine, University of Bergen, 5009 Bergen, Norway;
| | - Maria Hernandez-Valladares
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (E.A.); (Ø.B.)
- The Department of Biomedicine, The Proteomics Unit at the University of Bergen (PROBE), University of Bergen, 5009 Bergen, Norway; (F.S.B.); (F.S.)
- Correspondence: ; Tel.: +47-5558-6368
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17
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Verheggen K, Raeder H, Berven FS, Martens L, Barsnes H, Vaudel M. Anatomy and evolution of database search engines-a central component of mass spectrometry based proteomic workflows. Mass Spectrom Rev 2020; 39:292-306. [PMID: 28902424 DOI: 10.1002/mas.21543] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 07/05/2017] [Indexed: 06/07/2023]
Abstract
Sequence database search engines are bioinformatics algorithms that identify peptides from tandem mass spectra using a reference protein sequence database. Two decades of development, notably driven by advances in mass spectrometry, have provided scientists with more than 30 published search engines, each with its own properties. In this review, we present the common paradigm behind the different implementations, and its limitations for modern mass spectrometry datasets. We also detail how the search engines attempt to alleviate these limitations, and provide an overview of the different software frameworks available to the researcher. Finally, we highlight alternative approaches for the identification of proteomic mass spectrometry datasets, either as a replacement for, or as a complement to, sequence database search engines.
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Affiliation(s)
- Kenneth Verheggen
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Helge Raeder
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Norway
- Department of Pediatrics, Haukeland University Hospital, Bergen, Norway
| | - Frode S Berven
- Proteomics Unit, Department of Biomedicine, University of Bergen, Norway
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Harald Barsnes
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Norway
- Proteomics Unit, Department of Biomedicine, University of Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Norway
| | - Marc Vaudel
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Norway
- Proteomics Unit, Department of Biomedicine, University of Bergen, Norway
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
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18
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Aasebø E, Berven FS, Bartaula-Brevik S, Stokowy T, Hovland R, Vaudel M, Døskeland SO, McCormack E, Batth TS, Olsen JV, Bruserud Ø, Selheim F, Hernandez-Valladares M. Proteome and Phosphoproteome Changes Associated with Prognosis in Acute Myeloid Leukemia. Cancers (Basel) 2020; 12:cancers12030709. [PMID: 32192169 PMCID: PMC7140113 DOI: 10.3390/cancers12030709] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/05/2020] [Accepted: 03/13/2020] [Indexed: 12/12/2022] Open
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.
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Affiliation(s)
- Elise Aasebø
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (E.A.); (S.B.-B.); (T.S.); (M.V.); (Ø.B.)
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5009 Bergen, Norway; (F.S.B.); (F.S.)
| | - Frode S. Berven
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5009 Bergen, Norway; (F.S.B.); (F.S.)
- The Department of Biomedicine, University of Bergen, 5009 Bergen, Norway;
| | - Sushma Bartaula-Brevik
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (E.A.); (S.B.-B.); (T.S.); (M.V.); (Ø.B.)
| | - Tomasz Stokowy
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (E.A.); (S.B.-B.); (T.S.); (M.V.); (Ø.B.)
- Department for Medical Genetics, Haukeland University Hospital, 5021 Bergen, Norway;
| | - Randi Hovland
- Department for Medical Genetics, Haukeland University Hospital, 5021 Bergen, Norway;
- Department of Biological Sciences, University of Bergen, 5006 Bergen, Norway
| | - Marc Vaudel
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (E.A.); (S.B.-B.); (T.S.); (M.V.); (Ø.B.)
| | | | - Emmet McCormack
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway;
| | - Tanveer S. Batth
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark; (T.S.B.); (J.V.O.)
| | - Jesper V. Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark; (T.S.B.); (J.V.O.)
| | - Øystein Bruserud
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (E.A.); (S.B.-B.); (T.S.); (M.V.); (Ø.B.)
| | - Frode Selheim
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5009 Bergen, Norway; (F.S.B.); (F.S.)
- The Department of Biomedicine, University of Bergen, 5009 Bergen, Norway;
| | - Maria Hernandez-Valladares
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (E.A.); (S.B.-B.); (T.S.); (M.V.); (Ø.B.)
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5009 Bergen, Norway; (F.S.B.); (F.S.)
- Correspondence: ; Tel.: +47-5558-6368
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19
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Burger B, Lereim RR, Berven FS, Barsnes H. Detecting single amino acids and small peptides by combining isobaric tags and peptidomics. Eur J Mass Spectrom (Chichester) 2019; 25:451-456. [PMID: 31189351 DOI: 10.1177/1469066719857006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Single amino acids and small endogenous peptides play important roles in maintaining a properly functioning organism. These molecules are however currently only routinely identified in targeted approaches. In a small proof-of-concept mass spectrometry experiment, we found that by combining isobaric tags and peptidomics, and by targeting singly charged molecules, we were able to identify a significant amount of single amino acids and small endogenous peptides using a basic mass-based identification approach. While there is still room for improvement, our simple test indicates that a limited amount of extra work when setting up the mass spectrometry experiment could potentially lead to a wealth of additional information.
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Affiliation(s)
- Bram Burger
- Department of Informatics, University of Bergen, Bergen, Norway
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Ragnhild Reehorst Lereim
- Department of Informatics, University of Bergen, Bergen, Norway
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Frode S Berven
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Harald Barsnes
- Department of Informatics, University of Bergen, Bergen, Norway
- Department of Biomedicine, University of Bergen, Bergen, Norway
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20
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Hernandez-Valladares M, Wangen R, Berven FS, Guldbrandsen A. Protein Post-Translational Modification Crosstalk in Acute Myeloid Leukemia Calls for Action. Curr Med Chem 2019; 26:5317-5337. [PMID: 31241430 DOI: 10.2174/0929867326666190503164004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 11/23/2018] [Accepted: 02/01/2019] [Indexed: 01/24/2023]
Abstract
BACKGROUND Post-translational modification (PTM) crosstalk is a young research field. However, there is now evidence of the extraordinary characterization of the different proteoforms and their interactions in a biological environment that PTM crosstalk studies can describe. Besides gene expression and phosphorylation profiling of acute myeloid leukemia (AML) samples, the functional combination of several PTMs that might contribute to a better understanding of the complexity of the AML proteome remains to be discovered. OBJECTIVE By reviewing current workflows for the simultaneous enrichment of several PTMs and bioinformatics tools to analyze mass spectrometry (MS)-based data, our major objective is to introduce the PTM crosstalk field to the AML research community. RESULTS After an introduction to PTMs and PTM crosstalk, this review introduces several protocols for the simultaneous enrichment of PTMs. Two of them allow a simultaneous enrichment of at least three PTMs when using 0.5-2 mg of cell lysate. We have reviewed many of the bioinformatics tools used for PTM crosstalk discovery as its complex data analysis, mainly generated from MS, becomes challenging for most AML researchers. We have presented several non-AML PTM crosstalk studies throughout the review in order to show how important the characterization of PTM crosstalk becomes for the selection of disease biomarkers and therapeutic targets. CONCLUSION Herein, we have reviewed the advances and pitfalls of the emerging PTM crosstalk field and its potential contribution to unravel the heterogeneity of AML. The complexity of sample preparation and bioinformatics workflows demands a good interaction between experts of several areas.
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Affiliation(s)
- Maria Hernandez-Valladares
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Jonas Lies vei 87, N-5021 Bergen, Norway.,The Proteomics Unit at the University of Bergen, Department of Biomedicine, Building for Basic Biology, Faculty of Medicine, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway
| | - Rebecca Wangen
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Jonas Lies vei 87, N-5021 Bergen, Norway.,The Proteomics Unit at the University of Bergen, Department of Biomedicine, Building for Basic Biology, Faculty of Medicine, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway.,Department of Internal Medicine, Hematology Section, Haukeland University Hospital, Jonas Lies vei 65, N-5021 Bergen, Norway
| | - Frode S Berven
- The Proteomics Unit at the University of Bergen, Department of Biomedicine, Building for Basic Biology, Faculty of Medicine, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway
| | - Astrid Guldbrandsen
- The Proteomics Unit at the University of Bergen, Department of Biomedicine, Building for Basic Biology, Faculty of Medicine, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway.,Computational Biology Unit, Department of Informatics, Faculty of Mathematics and Natural Sciences, University of Bergen, Thormøhlensgt 55, N-5008 Bergen, Norway
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21
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Nepstad I, Hatfield KJ, Grønningsæter IS, Aasebø E, Hernandez-Valladares M, Hagen KM, Rye KP, Berven FS, Selheim F, Reikvam H, Bruserud Ø. Effects of insulin and pathway inhibitors on the PI3K-Akt-mTOR phosphorylation profile in acute myeloid leukemia cells. Signal Transduct Target Ther 2019; 4:20. [PMID: 31240133 PMCID: PMC6582141 DOI: 10.1038/s41392-019-0050-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 02/05/2019] [Accepted: 04/04/2019] [Indexed: 12/17/2022] Open
Abstract
The phosphatidylinositol 3-kinase (PI3K)-Akt-mechanistic target of rapamycin (mTOR) pathway is constitutively activated in human acute myeloid leukemia (AML) cells and is regarded as a possible therapeutic target. Insulin is an agonist of this pathway and a growth factor for AML cells. We characterized the effect of insulin on the phosphorylation of 10 mediators in the main track of the PI3K-Akt-mTOR pathway in AML cells from 76 consecutive patients. The overall results showed that insulin significantly increased the phosphorylation of all investigated mediators. However, insulin effects on the pathway activation profile varied among patients, and increased phosphorylation in all mediators was observed only in a minority of patients; in other patients, insulin had divergent effects. Global gene expression profiling and proteomic/phosphoproteomic comparisons suggested that AML cells from these two patient subsets differed with regard to AML cell differentiation, transcriptional regulation, RNA metabolism, and cellular metabolism. Strong insulin-induced phosphorylation was associated with weakened antiproliferative effects of metabolic inhibitors. PI3K, Akt, and mTOR inhibitors also caused divergent effects on the overall pathway phosphorylation profile in the presence of insulin, although PI3K and Akt inhibition caused a general reduction in Akt pT308 and 4EBP1 pT36/pT45 phosphorylation. For Akt inhibition, the phosphorylation of upstream mediators was generally increased or unaltered. In contrast, mTOR inhibition reduced mTOR pS2448 and S6 pS244 phosphorylation but increased Akt pT308 phosphorylation. In conclusion, the effects of both insulin and PI3K-Akt-mTOR inhibitors differ between AML patient subsets, and differences in insulin responsiveness are associated with differential susceptibility to metabolic targeting.
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Affiliation(s)
- Ina Nepstad
- Section for Hematology, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Kimberley Joanne Hatfield
- Section for Hematology, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Immunology and Transfusion Medicine, Haukeland University Hospital, Bergen, Norway
| | - Ida Sofie Grønningsæter
- Section for Hematology, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Elise Aasebø
- Section for Hematology, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Biomedicine, Faculty of Medicine and Dentistry, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Maria Hernandez-Valladares
- Section for Hematology, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Biomedicine, Faculty of Medicine and Dentistry, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Karen Marie Hagen
- Section for Hematology, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Kristin Paulsen Rye
- Section for Hematology, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Frode S. Berven
- Department of Biomedicine, Faculty of Medicine and Dentistry, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Frode Selheim
- Department of Biomedicine, Faculty of Medicine and Dentistry, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Håkon Reikvam
- Section for Hematology, Department of Clinical Science, University of Bergen, Bergen, Norway
- Section for Hematology, Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Øystein Bruserud
- Section for Hematology, Department of Clinical Science, University of Bergen, Bergen, Norway
- Section for Hematology, Department of Medicine, Haukeland University Hospital, Bergen, Norway
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22
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Zhang-James Y, Vaudel M, Mjaavatten O, Berven FS, Haavik J, Faraone SV. Effect of disease-associated SLC9A9 mutations on protein-protein interaction networks: implications for molecular mechanisms for ADHD and autism. ACTA ACUST UNITED AC 2019; 11:91-105. [PMID: 30927234 DOI: 10.1007/s12402-018-0281-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 11/27/2018] [Indexed: 12/20/2022]
Abstract
Na+/H+ Exchanger 9 (NHE9) is an endosomal membrane protein encoded by the Solute Carrier 9A, member 9 gene (SLC9A9). SLC9A9 has been implicated in attention deficit hyperactivity disorder (ADHD), autism spectrum disorders (ASDs), epilepsy, multiple sclerosis and cancers. To better understand the function of NHE9 and the effects of disease-associated variants on protein-protein interactions, we conducted a quantitative analysis of the NHE9 interactome using co-immunoprecipitation and isobaric labeling-based quantitative mass spectrometry. We identified 100 proteins that interact with NHE9. These proteins were enriched in known functional pathways for NHE9: the endocytosis, protein ubiquitination and phagosome pathways, as well as some novel pathways including oxidative stress, mitochondrial dysfunction, mTOR signaling, cell death and RNA processing pathways. An ADHD-associated mutation (A409P) significantly altered NHE9's interactions with a subset of proteins involved in caveolae-mediated endocytosis and MAP2K2-mediated downstream signaling. An ASD nonsense mutation in SLC9A9, R423X, produced no-detectable amount of NHE9, suggesting the overall loss of NHE9 functional networks. In addition, seven of the NHE9 interactors are products of known autism candidate genes (Simons Foundation Autism Research Initiative, SFARI Gene) and 90% of the NHE9 interactome overlap with SFARI protein interaction network PIN (p < 0.0001), supporting the role of NHE9 interactome in ASDs molecular mechanisms. Our results provide a detailed understanding of the functions of protein NHE9 and its disrupted interactions, possibly underlying ADHD and ASDs. Furthermore, our methodological framework proved useful for functional characterization of disease-associated genetic variants and suggestion of druggable targets.
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Affiliation(s)
- Yanli Zhang-James
- Departments of Psychiatry, SUNY Upstate Medical University, 750 East Adams St., Syracuse, NY, 13210, USA
| | - Marc Vaudel
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Olav Mjaavatten
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Frode S Berven
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Jan Haavik
- Department of Biomedicine, University of Bergen, Bergen, Norway.,K.G. Jebsen Centre for Research on Neuropsychiatric Disorders, University of Bergen, Bergen, Norway.,Division of Psychiatry, Haukeland University Hospital, Bergen, Norway
| | - Stephen V Faraone
- Departments of Psychiatry, SUNY Upstate Medical University, 750 East Adams St., Syracuse, NY, 13210, USA. .,Neuroscience and Physiology, SUNY Upstate Medical University, 750 East Adams St., Syracuse, NY, 13210, USA.
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23
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Yang M, Kohler M, Heyder T, Forsslund H, Garberg HK, Karimi R, Grunewald J, Berven FS, Nyrén S, Magnus Sköld C, Wheelock ÅM. Proteomic profiling of lung immune cells reveals dysregulation of phagocytotic pathways in female-dominated molecular COPD phenotype. Respir Res 2018. [PMID: 29514663 PMCID: PMC5842633 DOI: 10.1186/s12931-017-0699-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Background Smoking is the main risk factor for chronic obstructive pulmonary disease (COPD). Women with COPD who smoke experienced a higher risk of hospitalization and worse decline of lung function. Yet the mechanisms of these gender-related differences in clinical presentations in COPD remain unknown. The aim of our study is to identify proteins and molecular pathways associated with COPD pathogenesis, with emphasis on elucidating molecular gender difference. Method We employed shotgun isobaric tags for relative and absolute quantitation (iTRAQ) proteome analyses of bronchoalveolar lavage (BAL) cells from smokers with normal lung function (n = 25) and early stage COPD patients (n = 18). Multivariate modeling, pathway enrichment analysis, and correlation with clinical characteristics were performed to identify specific proteins and pathways of interest. Results More pronounced alterations both at the protein- and pathway- levels were observed in female COPD patients, involving dysregulation of the FcγR-mediated phagocytosis-lysosomal axis and increase in oxidative stress. Alterations in pathways of the phagocytosis-lysosomal axis associated with a female-dominated COPD phenotype correlated well with specific clinical features: FcγR-mediated phagocytosis correlated with FEV1/FVC, the lysosomal pathway correlated with CT < −950 Hounsfield Units (HU), and regulation of actin cytoskeleton correlated with FEV1 and FEV1/FVC in female COPD patients. Alterations observed in the corresponding male cohort were minor. Conclusion The identified molecular pathways suggest dysregulation of several phagocytosis-related pathways in BAL cells in female COPD patients, with correlation to both the level of obstruction (FEV1/FVC) and disease severity (FEV1) as well as emphysema (CT < −950 HU) in women. Trial registration No.: NCT02627872, retrospectively registered on December 9, 2015. Electronic supplementary material The online version of this article (10.1186/s12931-017-0699-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mingxing Yang
- Respiratory Medicine Unit, Department of Medicine Solna & Center for Molecular Medicine, Karolinska Institutet, Lung Research Lab L4:01, SE-171 76, Stockholm, Sweden.
| | - Maxie Kohler
- Respiratory Medicine Unit, Department of Medicine Solna & Center for Molecular Medicine, Karolinska Institutet, Lung Research Lab L4:01, SE-171 76, Stockholm, Sweden
| | - Tina Heyder
- Respiratory Medicine Unit, Department of Medicine Solna & Center for Molecular Medicine, Karolinska Institutet, Lung Research Lab L4:01, SE-171 76, Stockholm, Sweden
| | - Helena Forsslund
- Respiratory Medicine Unit, Department of Medicine Solna & Center for Molecular Medicine, Karolinska Institutet, Lung Research Lab L4:01, SE-171 76, Stockholm, Sweden
| | - Hilde K Garberg
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Reza Karimi
- Respiratory Medicine Unit, Department of Medicine Solna & Center for Molecular Medicine, Karolinska Institutet, Lung Research Lab L4:01, SE-171 76, Stockholm, Sweden
| | - Johan Grunewald
- Respiratory Medicine Unit, Department of Medicine Solna & Center for Molecular Medicine, Karolinska Institutet, Lung Research Lab L4:01, SE-171 76, Stockholm, Sweden
| | - Frode S Berven
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Sven Nyrén
- Department of Molecular Medicine and Surgery, Division of Radiology, Karolinska Institutet, Karolinska University Hospital, Solna, Stockholm, Sweden
| | - C Magnus Sköld
- Respiratory Medicine Unit, Department of Medicine Solna & Center for Molecular Medicine, Karolinska Institutet, Lung Research Lab L4:01, SE-171 76, Stockholm, Sweden
| | - Åsa M Wheelock
- Respiratory Medicine Unit, Department of Medicine Solna & Center for Molecular Medicine, Karolinska Institutet, Lung Research Lab L4:01, SE-171 76, Stockholm, Sweden.
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24
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Opsahl JA, Vaudel M, Guldbrandsen A, Aasebø E, Van Pesch V, Franciotta D, Myhr KM, Barsnes H, Berle M, Torkildsen Ø, Kroksveen AC, Berven FS. Label-free analysis of human cerebrospinal fluid addressing various normalization strategies and revealing protein groups affected by multiple sclerosis. Proteomics 2016; 16:1154-65. [PMID: 26841090 DOI: 10.1002/pmic.201500284] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 12/08/2015] [Accepted: 01/28/2016] [Indexed: 11/05/2022]
Abstract
The aims of the study were to: (i) identify differentially regulated proteins in cerebrospinal fluid (CSF) between multiple sclerosis (MS) patients and non-MS controls; (ii) examine the effect of matching the CSF samples on either total protein amount or volume, and compare four protein normalization strategies for CSF protein quantification. CSF from MS patients (n = 37) and controls (n = 64), consisting of other noninflammatory neurological diseases (n = 50) and non neurological spinal anesthetic subjects (n = 14), were analyzed using label-free proteomics, quantifying almost 800 proteins. In total, 122 proteins were significantly regulated (p < 0.05), where 77 proteins had p-value <0.01 or AUC value >0.75. Hierarchical clustering indicated that there were two main groups of MS patients, those with increased levels of inflammatory response proteins and decreased levels of proteins involved in neuronal tissue development (n = 30), and those with normal protein levels for both of these protein groups (n = 7). The main subgroup of controls clustering with the MS patients showing increased inflammation and decreased neuronal tissue development were patients suffering from chronic fatigue. Our data indicate that the preferable way to quantify proteins in CSF is to first match the samples on total protein amount and then normalize the data based on the median intensities, preferably from the CNS-enriched proteins.
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Affiliation(s)
- Jill A Opsahl
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway.,The KG Jebsen Centre for MS-research, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Marc Vaudel
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Astrid Guldbrandsen
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway.,The KG Jebsen Centre for MS-research, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Elise Aasebø
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Vincent Van Pesch
- Neurology Department, Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Diego Franciotta
- Laboratory of Neuroimmunology, IRCCS, "C. Mondino" National Neurological Institute, Pavia, Italy
| | - Kjell-Morten Myhr
- The KG Jebsen Centre for MS-research, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Harald Barsnes
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Magnus Berle
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway.,Surgical Clinic, Haukeland University Hospital, Bergen, Norway
| | - Øivind Torkildsen
- The KG Jebsen Centre for MS-research, Department of Clinical Medicine, University of Bergen, Bergen, Norway.,The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | - Ann C Kroksveen
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway.,The KG Jebsen Centre for MS-research, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Frode S Berven
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway.,The KG Jebsen Centre for MS-research, Department of Clinical Medicine, University of Bergen, Bergen, Norway
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25
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Guldbrandsen A, Farag Y, Kroksveen AC, Oveland E, Lereim RR, Opsahl JA, Myhr KM, Berven FS, Barsnes H. CSF-PR 2.0: An Interactive Literature Guide to Quantitative Cerebrospinal Fluid Mass Spectrometry Data from Neurodegenerative Disorders. Mol Cell Proteomics 2016; 16:300-309. [PMID: 27890865 DOI: 10.1074/mcp.o116.064477] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 11/18/2016] [Indexed: 01/23/2023] Open
Abstract
The rapidly growing number of biomedical studies supported by mass spectrometry based quantitative proteomics data has made it increasingly difficult to obtain an overview of the current status of the research field. A better way of organizing the biomedical proteomics information from these studies and making it available to the research community is therefore called for. In the presented work, we have investigated scientific publications describing the analysis of the cerebrospinal fluid proteome in relation to multiple sclerosis, Parkinson's disease and Alzheimer's disease. Based on a detailed set of filtering criteria we extracted 85 data sets containing quantitative information for close to 2000 proteins. This information was made available in CSF-PR 2.0 (http://probe.uib.no/csf-pr-2.0), which includes novel approaches for filtering, visualizing and comparing quantitative proteomics information in an interactive and user-friendly environment. CSF-PR 2.0 will be an invaluable resource for anyone interested in quantitative proteomics on cerebrospinal fluid.
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Affiliation(s)
- Astrid Guldbrandsen
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, 5009 Bergen, Norway.,§KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, 5020 Bergen, Norway
| | - Yehia Farag
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, 5009 Bergen, Norway.,§KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, 5020 Bergen, Norway
| | - Ann Cathrine Kroksveen
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, 5009 Bergen, Norway.,§KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, 5020 Bergen, Norway
| | - Eystein Oveland
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, 5009 Bergen, Norway.,§KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, 5020 Bergen, Norway
| | - Ragnhild R Lereim
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, 5009 Bergen, Norway.,§KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, 5020 Bergen, Norway
| | - Jill A Opsahl
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, 5009 Bergen, Norway.,§KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, 5020 Bergen, Norway
| | - Kjell-Morten Myhr
- §KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, 5020 Bergen, Norway.,¶Norwegian Multiple Sclerosis Registry and Biobank, Haukeland University Hospital, 5021 Bergen, Norway
| | - Frode S Berven
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, 5009 Bergen, Norway; .,§KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, 5020 Bergen, Norway.,‖Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital, 5021 Bergen, Norway
| | - Harald Barsnes
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, 5009 Bergen, Norway.,**Department of Clinical Science, University of Bergen, 5020 Bergen, Norway.,‡‡Computational Biology Unit, Department of Informatics, University of Bergen, 5020 Bergen, Norway
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26
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Wang X, Zhang Y, Nilsson CL, Berven FS, Andrén PE, Carlsohn E, Horvatovich P, Malm J, Fuentes M, Végvári Á, Welinder C, Fehniger TE, Rezeli M, Edula G, Hober S, Nishimura T, Marko-Varga G. Association of chromosome 19 to lung cancer genotypes and phenotypes. Cancer Metastasis Rev 2016; 34:217-26. [PMID: 25982285 DOI: 10.1007/s10555-015-9556-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The Chromosome 19 Consortium, a part of the Chromosome-Centric Human Proteome Project (C-HPP, http://www.C-HPP.org ), is tasked with the understanding chromosome 19 functions at the gene and protein levels, as well as their roles in lung oncogenesis. Comparative genomic hybridization (CGH) studies revealed chromosome aberration in lung cancer subtypes, including ADC, SCC, LCC, and SCLC. The most common abnormality is 19p loss and 19q gain. Sixty-four aberrant genes identified in previous genomic studies and their encoded protein functions were further validated in the neXtProt database ( http://www.nextprot.org/ ). Among those, the loss of tumor suppressor genes STK11, MUM1, KISS1R (19p13.3), and BRG1 (19p13.13) is associated with lung oncogenesis or remote metastasis. Gene aberrations include translocation t(15, 19) (q13, p13.1) fusion oncogene BRD4-NUT, DNA repair genes (ERCC1, ERCC2, XRCC1), TGFβ1 pathway activation genes (TGFB1, LTBP4), Dyrk1B, and potential oncogenesis protector genes such as NFkB pathway inhibition genes (NFKBIB, PPP1R13L) and EGLN2. In conclusion, neXtProt is an effective resource for the validation of gene aberrations identified in genomic studies. It promises to enhance our understanding of lung cancer oncogenesis.
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Affiliation(s)
- Xiangdong Wang
- Zhongshan Hospital, Shanghai Institute of Clinical Bioinformatics, Fudan University, Shanghai, China,
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27
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Kroksveen AC, Guldbrandsen A, Vaudel M, Lereim RR, Barsnes H, Myhr KM, Torkildsen Ø, Berven FS. In-Depth Cerebrospinal Fluid Quantitative Proteome and Deglycoproteome Analysis: Presenting a Comprehensive Picture of Pathways and Processes Affected by Multiple Sclerosis. J Proteome Res 2016; 16:179-194. [PMID: 27728768 DOI: 10.1021/acs.jproteome.6b00659] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
In the current study, we conducted a quantitative in-depth proteome and deglycoproteome analysis of cerebrospinal fluid (CSF) from relapsing-remitting multiple sclerosis (RRMS) and neurological controls using mass spectrometry and pathway analysis. More than 2000 proteins and 1700 deglycopeptides were quantified, with 484 proteins and 180 deglycopeptides significantly changed between pools of RRMS and pools of controls. Approximately 300 of the significantly changed proteins were assigned to various biological processes including inflammation, extracellular matrix organization, cell adhesion, immune response, and neuron development. Ninety-six significantly changed deglycopeptides mapped to proteins that were not found changed in the global protein study. In addition, four mapped to the proteins oligo-myelin glycoprotein and noelin, which were found oppositely changed in the global study. Both are ligands to the nogo receptor, and the glycosylation of these proteins appears to be affected by RRMS. Our study gives the most extensive overview of the RRMS affected processes observed from the CSF proteome to date, and the list of differential proteins will have great value for selection of biomarker candidates for further verification.
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Affiliation(s)
- Ann Cathrine Kroksveen
- Proteomics Unit (PROBE), Department of Biomedicine, ‡The KG Jebsen Centre for MS Research, Department of Clinical Medicine, §KG Jebsen Center for Diabetes Research, Department of Clinical Science, and ⊥Computational Biology Unit, Department of Informatics, University of Bergen , Bergen N-5009, Norway.,Center for Medical Genetics and Molecular Medicine and ∥The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital , Bergen N-5021, Norway
| | - Astrid Guldbrandsen
- Proteomics Unit (PROBE), Department of Biomedicine, ‡The KG Jebsen Centre for MS Research, Department of Clinical Medicine, §KG Jebsen Center for Diabetes Research, Department of Clinical Science, and ⊥Computational Biology Unit, Department of Informatics, University of Bergen , Bergen N-5009, Norway.,Center for Medical Genetics and Molecular Medicine and ∥The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital , Bergen N-5021, Norway
| | - Marc Vaudel
- Proteomics Unit (PROBE), Department of Biomedicine, ‡The KG Jebsen Centre for MS Research, Department of Clinical Medicine, §KG Jebsen Center for Diabetes Research, Department of Clinical Science, and ⊥Computational Biology Unit, Department of Informatics, University of Bergen , Bergen N-5009, Norway.,Center for Medical Genetics and Molecular Medicine and ∥The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital , Bergen N-5021, Norway
| | - Ragnhild Reehorst Lereim
- Proteomics Unit (PROBE), Department of Biomedicine, ‡The KG Jebsen Centre for MS Research, Department of Clinical Medicine, §KG Jebsen Center for Diabetes Research, Department of Clinical Science, and ⊥Computational Biology Unit, Department of Informatics, University of Bergen , Bergen N-5009, Norway.,Center for Medical Genetics and Molecular Medicine and ∥The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital , Bergen N-5021, Norway
| | - Harald Barsnes
- Proteomics Unit (PROBE), Department of Biomedicine, ‡The KG Jebsen Centre for MS Research, Department of Clinical Medicine, §KG Jebsen Center for Diabetes Research, Department of Clinical Science, and ⊥Computational Biology Unit, Department of Informatics, University of Bergen , Bergen N-5009, Norway.,Center for Medical Genetics and Molecular Medicine and ∥The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital , Bergen N-5021, Norway
| | - Kjell-Morten Myhr
- Proteomics Unit (PROBE), Department of Biomedicine, ‡The KG Jebsen Centre for MS Research, Department of Clinical Medicine, §KG Jebsen Center for Diabetes Research, Department of Clinical Science, and ⊥Computational Biology Unit, Department of Informatics, University of Bergen , Bergen N-5009, Norway.,Center for Medical Genetics and Molecular Medicine and ∥The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital , Bergen N-5021, Norway
| | - Øivind Torkildsen
- Proteomics Unit (PROBE), Department of Biomedicine, ‡The KG Jebsen Centre for MS Research, Department of Clinical Medicine, §KG Jebsen Center for Diabetes Research, Department of Clinical Science, and ⊥Computational Biology Unit, Department of Informatics, University of Bergen , Bergen N-5009, Norway.,Center for Medical Genetics and Molecular Medicine and ∥The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital , Bergen N-5021, Norway
| | - Frode S Berven
- Proteomics Unit (PROBE), Department of Biomedicine, ‡The KG Jebsen Centre for MS Research, Department of Clinical Medicine, §KG Jebsen Center for Diabetes Research, Department of Clinical Science, and ⊥Computational Biology Unit, Department of Informatics, University of Bergen , Bergen N-5009, Norway.,Center for Medical Genetics and Molecular Medicine and ∥The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital , Bergen N-5021, Norway
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28
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Lereim RR, Oveland E, Xiao Y, Torkildsen Ø, Wergeland S, Myhr KM, Sun SC, Berven FS. The Brain Proteome of the Ubiquitin Ligase Peli1 Knock-Out Mouse during Experimental Autoimmune Encephalomyelitis. ACTA ACUST UNITED AC 2016; 9:209-219. [PMID: 27746629 PMCID: PMC5061044 DOI: 10.4172/jpb.1000408] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The ubiquitin ligase Peli1 has previously been suggested as a potential treatment target in multiple sclerosis. In the multiple sclerosis disease model, experimental autoimmune encephalomyelitis, Peli1 knock-out led to less activated microglia and less inflammation in the central nervous system. Despite being important in microglia, Peli1 expression has also been detected in glial and neuronal cells. In the present study the overall brain proteomes of Peli1 knock-out mice and wild-type mice were compared prior to experimental autoimmune encephalomyelitis induction, at onset of the disease and at disease peak. Brain samples from the frontal hemisphere, peripheral from the extensive inflammatory foci, were analyzed using TMT-labeling of sample pools, and the discovered proteins were verified in individual mice using label-free proteomics. The greatest proteomic differences between Peli1 knock-out and wild-type mice were observed at the disease peak. In Peli1 knock-out a higher degree of antigen presentation, increased activity of adaptive and innate immune cells and alterations to proteins involved in iron metabolism were observed during experimental autoimmune encephalomyelitis. These results unravel global effects to the brain proteome when abrogating Peli1 expression, underlining the importance of Peli1 as a regulator of the immune response also peripheral to inflammatory foci during experimental autoimmune encephalomyelitis. The proteomics data is available in PRIDE with accession PXD003710.
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Affiliation(s)
- Ragnhild Reehorst Lereim
- Proteomics Unit, Department of Biomedicine, University of Bergen, Norway; Kristian Gerhard Jebsen MS Research Centre, Department of Clinical Medicine, University of Bergen, Bergen Norway
| | - Eystein Oveland
- Proteomics Unit, Department of Biomedicine, University of Bergen, Norway; Kristian Gerhard Jebsen MS Research Centre, Department of Clinical Medicine, University of Bergen, Bergen Norway
| | - Yichuan Xiao
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA; Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University, Shanghai 200031, China
| | - Øivind Torkildsen
- Kristian Gerhard Jebsen MS Research Centre, Department of Clinical Medicine, University of Bergen, Bergen Norway; Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | - Stig Wergeland
- Kristian Gerhard Jebsen MS Research Centre, Department of Clinical Medicine, University of Bergen, Bergen Norway; Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | - Kjell-Morten Myhr
- Kristian Gerhard Jebsen MS Research Centre, Department of Clinical Medicine, University of Bergen, Bergen Norway; Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | - Shao-Cong Sun
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Frode S Berven
- Proteomics Unit, Department of Biomedicine, University of Bergen, Norway; Kristian Gerhard Jebsen MS Research Centre, Department of Clinical Medicine, University of Bergen, Bergen Norway; Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital, Bergen, Norway
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29
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Hernandez-Valladares M, Aasebø E, Selheim F, Berven FS, Bruserud Ø. Selecting Sample Preparation Workflows for Mass Spectrometry-Based Proteomic and Phosphoproteomic Analysis of Patient Samples with Acute Myeloid Leukemia. Proteomes 2016; 4:proteomes4030024. [PMID: 28248234 PMCID: PMC5217354 DOI: 10.3390/proteomes4030024] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 08/09/2016] [Accepted: 08/12/2016] [Indexed: 12/31/2022] Open
Abstract
Global mass spectrometry (MS)-based proteomic and phosphoproteomic studies of acute myeloid leukemia (AML) biomarkers represent a powerful strategy to identify and confirm proteins and their phosphorylated modifications that could be applied in diagnosis and prognosis, as a support for individual treatment regimens and selection of patients for bone marrow transplant. MS-based studies require optimal and reproducible workflows that allow a satisfactory coverage of the proteome and its modifications. Preparation of samples for global MS analysis is a crucial step and it usually requires method testing, tuning and optimization. Different proteomic workflows that have been used to prepare AML patient samples for global MS analysis usually include a standard protein in-solution digestion procedure with a urea-based lysis buffer. The enrichment of phosphopeptides from AML patient samples has previously been carried out either with immobilized metal affinity chromatography (IMAC) or metal oxide affinity chromatography (MOAC). We have recently tested several methods of sample preparation for MS analysis of the AML proteome and phosphoproteome and introduced filter-aided sample preparation (FASP) as a superior methodology for the sensitive and reproducible generation of peptides from patient samples. FASP-prepared peptides can be further fractionated or IMAC-enriched for proteome or phosphoproteome analyses. Herein, we will review both in-solution and FASP-based sample preparation workflows and encourage the use of the latter for the highest protein and phosphorylation coverage and reproducibility.
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Affiliation(s)
- Maria Hernandez-Valladares
- Department of Biomedicine, Faculty of Medicine and Dentistry, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway.
| | - Elise Aasebø
- Department of Biomedicine, Faculty of Medicine and Dentistry, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway.
| | - Frode Selheim
- Department of Biomedicine, Faculty of Medicine and Dentistry, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway.
| | - Frode S Berven
- Department of Biomedicine, Faculty of Medicine and Dentistry, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway.
| | - Øystein Bruserud
- Department of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway.
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Finne K, Marti HP, Leh S, Skogstrand T, Vethe H, Tenstad O, Berven FS, Scherer A, Vikse BE. Proteomic Analysis of Minimally Damaged Renal Tubular Tissue from Two-Kidney-One-Clip Hypertensive Rats Demonstrates Extensive Changes Compared to Tissue from Controls. Nephron Clin Pract 2016; 132:70-80. [PMID: 26745798 DOI: 10.1159/000442825] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 11/25/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Tubular atrophy and interstitial fibrosis mark the final stage in most forms of progressive kidney diseases. Little is known regarding changes in the tubular proteome. In this study, we investigated changes in the tubular proteome of normal or minimally damaged tubular tissue in the non-clipped kidney from rats with two-kidney one-clip (2K1C) hypertension. METHODS Formalin-fixed paraffin-embedded kidney sections from four 2K1C rats with hypertensive kidney damage and 6 sham rats were used. Tubulointerstitial tissue without discernable interstitial expansion or pronounced tubular alterations was microdissected and this was assumed to represent an early stage of chronic tubular damage in 2K1C. Samples were analyzed by mass spectrometry and relative protein abundances were compared between 2K1C and sham. RESULTS A total of 1,160 proteins were identified with at least 2 unique peptides, allowing for relative quantitation between samples. Among these, 151 proteins were more abundant, and 192 proteins were less abundant in 2K1C compared with sham. Transgelin, vimentin and creatine kinase B-type were among the proteins that were most increased in 2K1C. Ingenuity Pathway Analysis showed increased abundance of proteins related to Rho signaling and protein turnover (eIF2 signaling and protein ubiquitination), and decreased abundance of proteins related to fatty acid β-oxidation. CONCLUSION Tubular tissue from normal or minimally damaged hypertensive kidney damage demonstrate extensive proteomic changes with upregulation of pathways associated with progressive kidney damage, such as Rho signaling and protein turnover. Thus, proteomics presents itself to be a promising tool for the discovery of early damage markers from not yet morphologically visible tubular damage.
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Abstract
Targeting subproteomes is a good strategy to decrease the complexity of a sample, for example in body fluid biomarker studies. Glycoproteins are proteins with carbohydrates of varying size and structure attached to the polypeptide chain, and it has been shown that glycosylation plays essential roles in several vital cellular processes, making glycosylation a particularly interesting field of study. Here, we describe a method for the enrichment of glycosylated peptides from trypsin digested proteins in human cerebrospinal fluid. We also describe how to perform the data analysis on the mass spectrometry data for such samples, focusing on site-specific identification of glycosylation sites, using user friendly open source software.
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Affiliation(s)
- Astrid Guldbrandsen
- Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway
- KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Harald Barsnes
- Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway
- KG Jebsen Center for Diabetes Research, Department of Clinical Sciences, University of Bergen, Bergen, Norway
| | - Ann Cathrine Kroksveen
- Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway
- KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Frode S Berven
- Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway
- KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | - Marc Vaudel
- Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway.
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Vaudel M, Verheggen K, Csordas A, Raeder H, Berven FS, Martens L, Vizcaíno JA, Barsnes H. Exploring the potential of public proteomics data. Proteomics 2016; 16:214-25. [PMID: 26449181 PMCID: PMC4738454 DOI: 10.1002/pmic.201500295] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 08/25/2015] [Accepted: 09/28/2015] [Indexed: 12/22/2022]
Abstract
In a global effort for scientific transparency, it has become feasible and good practice to share experimental data supporting novel findings. Consequently, the amount of publicly available MS-based proteomics data has grown substantially in recent years. With some notable exceptions, this extensive material has however largely been left untouched. The time has now come for the proteomics community to utilize this potential gold mine for new discoveries, and uncover its untapped potential. In this review, we provide a brief history of the sharing of proteomics data, showing ways in which publicly available proteomics data are already being (re-)used, and outline potential future opportunities based on four different usage types: use, reuse, reprocess, and repurpose. We thus aim to assist the proteomics community in stepping up to the challenge, and to make the most of the rapidly increasing amount of public proteomics data.
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Affiliation(s)
- Marc Vaudel
- Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Kenneth Verheggen
- Medical Biotechnology Center, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Attila Csordas
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Helge Raeder
- Department of Clinical Science, KG Jebsen Center for Diabetes Research, University of Bergen, Bergen, Norway
| | - Frode S Berven
- Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway
- Department of Clinical Medicine, KG Jebsen Centre for Multiple Sclerosis Research, University of Bergen, Bergen, Norway
| | - Lennart Martens
- Medical Biotechnology Center, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Juan A Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Harald Barsnes
- Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway
- Department of Clinical Science, KG Jebsen Center for Diabetes Research, University of Bergen, Bergen, Norway
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Lereim RR, Oveland E, Berven FS, Vaudel M, Barsnes H. Visualization, Inspection and Interpretation of Shotgun Proteomics Identification Results. Modern Proteomics – Sample Preparation, Analysis and Practical Applications 2016; 919:227-235. [DOI: 10.1007/978-3-319-41448-5_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Abstract
In quantitative proteomics, large lists of identified and quantified proteins are used to answer biological questions in a systemic approach. However, working with such extensive datasets can be challenging, especially when complex experimental designs are involved. Here, we demonstrate how to post-process large quantitative datasets, detect proteins of interest, and annotate the data with biological knowledge. The protocol presented can be achieved without advanced computational knowledge thanks to the user-friendly Perseus interface (available from the MaxQuant website, www.maxquant.org ). Various visualization techniques facilitating the interpretation of quantitative results in complex biological systems are also highlighted.
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Affiliation(s)
- Elise Aasebø
- Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Frode S Berven
- Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway
- KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | - Frode Selheim
- Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Harald Barsnes
- Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Marc Vaudel
- Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway.
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Vaudel M, Barsnes H, Ræder H, Berven FS. Using Proteomics Bioinformatics Tools and Resources in Proteogenomic Studies. Advances in Experimental Medicine and Biology 2016; 926:65-75. [DOI: 10.1007/978-3-319-42316-6_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Kroksveen AC, Jaffe JD, Aasebø E, Barsnes H, Bjørlykke Y, Franciotta D, Keshishian H, Myhr KM, Opsahl JA, van Pesch V, Teunissen CE, Torkildsen Ø, Ulvik RJ, Vethe H, Carr SA, Berven FS. Quantitative proteomics suggests decrease in the secretogranin-1 cerebrospinal fluid levels during the disease course of multiple sclerosis. Proteomics 2015; 15:3361-9. [DOI: 10.1002/pmic.201400142] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 03/12/2015] [Accepted: 07/01/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Ann C. Kroksveen
- The KG Jebsen Centre for MS-research; Department of Clinical Medicine; University of Bergen; Bergen Norway
- Proteomics Unit (PROBE); Department of Biomedicine; University of Bergen; Bergen Norway
| | - Jacob D. Jaffe
- Broad Institute of MIT and Harvard; 7 Cambridge Center; Cambridge MA USA
| | - Elise Aasebø
- Proteomics Unit (PROBE); Department of Biomedicine; University of Bergen; Bergen Norway
| | - Harald Barsnes
- Proteomics Unit (PROBE); Department of Biomedicine; University of Bergen; Bergen Norway
- Computational Biology Unit, Department of Informatics; University of Bergen; Bergen Norway
| | - Yngvild Bjørlykke
- Proteomics Unit (PROBE); Department of Biomedicine; University of Bergen; Bergen Norway
- Department of Clinical Science; University of Bergen; Bergen Norway
| | - Diego Franciotta
- Laboratory of Neuroimmunology; “C. Mondino” National Neurological Institute; Pavia Italy
| | - Hasmik Keshishian
- Broad Institute of MIT and Harvard; 7 Cambridge Center; Cambridge MA USA
| | - Kjell-Morten Myhr
- The KG Jebsen Centre for MS-research; Department of Clinical Medicine; University of Bergen; Bergen Norway
- The Norwegian Multiple Sclerosis Competence Centre; Department of Neurology; Haukeland University Hospital; Bergen Norway
| | - Jill A. Opsahl
- The KG Jebsen Centre for MS-research; Department of Clinical Medicine; University of Bergen; Bergen Norway
- Proteomics Unit (PROBE); Department of Biomedicine; University of Bergen; Bergen Norway
| | - Vincent van Pesch
- Neurochemistry Unit; Institute of Neuroscience, Université Catholique de Louvain; Brussels Belgium
| | - Charlotte E. Teunissen
- Neurochemistry Laboratory and Biobank; Department of Clinical Chemistry; VU University Medical Center; Amsterdam The Netherlands
| | - Øivind Torkildsen
- The KG Jebsen Centre for MS-research; Department of Clinical Medicine; University of Bergen; Bergen Norway
- The Norwegian Multiple Sclerosis Competence Centre; Department of Neurology; Haukeland University Hospital; Bergen Norway
| | - Rune J. Ulvik
- Department of Clinical Medicine; University of Bergen; Bergen Norway
- Laboratory of Clinical Biochemistry; Haukeland University Hospital; Bergen Norway
| | - Heidrun Vethe
- Proteomics Unit (PROBE); Department of Biomedicine; University of Bergen; Bergen Norway
- Department of Clinical Science; University of Bergen; Bergen Norway
| | - Steven A. Carr
- Broad Institute of MIT and Harvard; 7 Cambridge Center; Cambridge MA USA
| | - Frode S. Berven
- The KG Jebsen Centre for MS-research; Department of Clinical Medicine; University of Bergen; Bergen Norway
- Proteomics Unit (PROBE); Department of Biomedicine; University of Bergen; Bergen Norway
- The Norwegian Multiple Sclerosis Competence Centre; Department of Neurology; Haukeland University Hospital; Bergen Norway
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Vaudel M, Barsnes H, Bjerkvig R, Bikfalvi A, Selheim F, Berven FS, Daubon T. Practical Considerations for Omics Experiments in Biomedical Sciences. Curr Pharm Biotechnol 2015; 17:105-14. [PMID: 26278526 DOI: 10.2174/1389201016666150817095348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 07/07/2015] [Accepted: 07/27/2015] [Indexed: 11/22/2022]
Abstract
Modern analytical techniques provide an unprecedented insight to biomedical samples, allowing an in depth characterization of cells or body fluids, to the level of genes, transcripts, peptides, proteins, metabolites, or metallic ions. The fine grained picture provided by such approaches holds the promise for a better understanding of complex pathologies, and consequently the personalization of diagnosis, prognosis and treatment procedures. In practice however, technical limitations restrict the resolution of the acquired data, and thus of downstream biomedical inference. As a result, the study of complex diseases like leukemia and other types of cancer is impaired by the high heterogeneity of pathologies as well as patient profiles. In this review, we propose an introduction to the general approach of characterizing samples and inferring biomedical results. We highlight the main limitations of the technique with regards to complex and heterogeneous pathologies, and provide ways to overcome these by improving the ability of experiments in discriminating samples.
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Affiliation(s)
- Marc Vaudel
- Proteomics Unit, Department of Biomedicine, University of Bergen, Norway; Jones Liesvei 91, N-5009 Bergen, Norway.
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Horvatovich P, Végvári Á, Saul J, Park JG, Qiu J, Syring M, Pirrotte P, Petritis K, Tegeler TJ, Aziz M, Fuentes M, Diez P, Gonzalez-Gonzalez M, Ibarrola N, Droste C, De Las Rivas J, Gil C, Clemente F, Hernaez ML, Corrales FJ, Nilsson CL, Berven FS, Bischoff R, Fehniger TE, LaBaer J, Marko-Varga G. In Vitro Transcription/Translation System: A Versatile Tool in the Search for Missing Proteins. J Proteome Res 2015; 14:3441-51. [PMID: 26155874 DOI: 10.1021/acs.jproteome.5b00486] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Approximately 18% of all human genes purported to encode proteins have not been directly evidenced at the protein level, according to the validation criteria established by neXtProt, and are considered to be "missing" proteins. One of the goals of the Chromosome-Centric Human Proteome Project (C-HPP) is to identify as many of these missing proteins as possible in human samples using mass spectrometry-based methods. To further this goal, a consortium of C-HPP teams (chromosomes 5, 10, 16, and 19) has joined forces to devise new strategies to identify missing proteins by use of a cell-free in vitro transcription/translation system (IVTT). The proposed strategy employs LC-MS/MS data-dependent acquisition (DDA) and targeted selective reaction monitoring (SRM) methods to scrutinize low-complexity samples derived from IVTT. The optimized assays are then applied to identify missing proteins in human cells and tissues. We describe the approach and show proof-of-concept results for development of LC-SRM assays for identification of 18 missing proteins. We believe that the IVTT system, when coupled with downstream mass spectrometric identification, can be applied to identify proteins that have eluded more traditional methods of detection.
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Affiliation(s)
- Péter Horvatovich
- Analytical Biochemistry, Department of Pharmacy, University of Groningen , A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Ákos Végvári
- Department of Pharmacology & Toxicology, The University of Texas Medical Branch , 301 University Boulevard, Galveston, Texas 77555-1074, United States
| | - Justin Saul
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Jin G Park
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Ji Qiu
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Michael Syring
- Center for Proteomics, Translational Genomics Research Institute , Phoenix, Arizona 85004, United States
| | - Patrick Pirrotte
- Center for Proteomics, Translational Genomics Research Institute , Phoenix, Arizona 85004, United States
| | - Konstantinos Petritis
- Center for Proteomics, Translational Genomics Research Institute , Phoenix, Arizona 85004, United States.,Pathology Research, Phoenix Children's Hospital , 1919 East Thomas Road, Phoenix, Arizona 85016, United States
| | - Tony J Tegeler
- Center for Proteomics, Translational Genomics Research Institute , Phoenix, Arizona 85004, United States
| | - Meraj Aziz
- Center for Proteomics, Translational Genomics Research Institute , Phoenix, Arizona 85004, United States
| | | | | | | | | | | | | | - Concha Gil
- Department of Microbiology & Proteomics Unit, University Complutense , 28040 Madrid, Spain
| | - Felipe Clemente
- Department of Microbiology & Proteomics Unit, University Complutense , 28040 Madrid, Spain
| | - Maria Luisa Hernaez
- Department of Microbiology & Proteomics Unit, University Complutense , 28040 Madrid, Spain
| | - Fernando J Corrales
- Center for Applied Medical Research (CIMA), University of Navarra, PRB2-ProteoRed-ISCIII, IDISNA, Ciberhed , 31008 Pamplona, Spain
| | - Carol L Nilsson
- Department of Pharmacology & Toxicology, The University of Texas Medical Branch , 301 University Boulevard, Galveston, Texas 77555-1074, United States
| | - Frode S Berven
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen , Postbox 7804, N-5009 Bergen, Norway.,The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital , Postbox 1400, 5021 Bergen, Norway
| | - Rainer Bischoff
- Analytical Biochemistry, Department of Pharmacy, University of Groningen , A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | | | - Joshua LaBaer
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - György Marko-Varga
- First Department of Surgery, Tokyo Medical University , 6-7-1 Nishishinjuku Shinjuku-ku, 160-0023 Tokyo, Japan
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Wang X, Zhang Y, Nilsson CL, Berven FS, Andrén PE, Carlsohn E, Horvatovich P, Malm J, Fuentes M, Végvári Á, Welinder C, Fehniger TE, Rezeli M, Edula G, Hober S, Nishimura T, Marko-Varga G. Erratum to: Association of chromosome 19 to lung cancer genotypes and phenotypes. Cancer Metastasis Rev 2015; 34:227. [PMID: 26143031 DOI: 10.1007/s10555-015-9571-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Erratum to: Cancer and Metastasis Review, DOI 10.1007/s10555-015-9556-2. There are changes in authors' affiliations and a new affiliations for Carol L. Nilsson and Thomas E. Fehniger has been added. The corresponding author also missed out to include Peter Horvatovich as a co-author of this work. The complete list of authors is now listed above.
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Affiliation(s)
- Xiangdong Wang
- Zhongshan Hospital, Shanghai Institute of Clinical Bioinformatics, Fudan University, Shanghai, China,
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Oveland E, Muth T, Rapp E, Martens L, Berven FS, Barsnes H. Viewing the proteome: how to visualize proteomics data? Proteomics 2015; 15:1341-55. [PMID: 25504833 DOI: 10.1002/pmic.201400412] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 10/23/2014] [Accepted: 12/05/2014] [Indexed: 01/18/2023]
Abstract
Proteomics has become one of the main approaches for analyzing and understanding biological systems. Yet similar to other high-throughput analysis methods, the presentation of the large amounts of obtained data in easily interpretable ways remains challenging. In this review, we present an overview of the different ways in which proteomics software supports the visualization and interpretation of proteomics data. The unique challenges and current solutions for visualizing the different aspects of proteomics data, from acquired spectra via protein identification and quantification to pathway analysis, are discussed, and examples of the most useful visualization approaches are highlighted. Finally, we offer our ideas about future directions for proteomics data visualization.
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Affiliation(s)
- Eystein Oveland
- Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway; KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, Bergen, Norway; Department of Clinical Medicine, University of Bergen, Bergen, Norway
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Kroksveen AC, Opsahl JA, Guldbrandsen A, Myhr KM, Oveland E, Torkildsen Ø, Berven FS. Cerebrospinal fluid proteomics in multiple sclerosis. Biochim Biophys Acta 2014; 1854:746-56. [PMID: 25526888 DOI: 10.1016/j.bbapap.2014.12.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 11/27/2014] [Accepted: 12/11/2014] [Indexed: 12/31/2022]
Abstract
Multiple sclerosis (MS) is an immune mediated chronic inflammatory disease of the central nervous system usually initiated during young adulthood, affecting approximately 2.5 million people worldwide. There is currently no cure for MS, but disease modifying treatment has become increasingly more effective, especially when started in the first phase of the disease. The disease course and prognosis are often unpredictable and it can be challenging to determine an early diagnosis. The detection of novel biomarkers to understand more of the disease mechanism, facilitate early diagnosis, predict disease progression, and find treatment targets would be very attractive. Over the last decade there has been an increasing effort toward finding such biomarker candidates. One promising strategy has been to use state-of-the-art quantitative proteomics approaches to compare the cerebrospinal fluid (CSF) proteome between MS and control patients or between different subgroups of MS. In this review we summarize and discuss the status of CSF proteomics in MS, including the latest findings with a focus on the last five years. This article is part of a Special Issue entitled: Neuroproteomics: Applications in Neuroscience and Neurology.
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Affiliation(s)
- Ann C Kroksveen
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Postbox 7804, N-5009 Bergen, Norway; The KG Jebsen Centre for MS-Research, Department of Clinical Medicine, University of Bergen, Postbox 7804, N-5021 Bergen, Norway
| | - Jill A Opsahl
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Postbox 7804, N-5009 Bergen, Norway; The KG Jebsen Centre for MS-Research, Department of Clinical Medicine, University of Bergen, Postbox 7804, N-5021 Bergen, Norway
| | - Astrid Guldbrandsen
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Postbox 7804, N-5009 Bergen, Norway
| | - Kjell-Morten Myhr
- The KG Jebsen Centre for MS-Research, Department of Clinical Medicine, University of Bergen, Postbox 7804, N-5021 Bergen, Norway; Department of Neurology, Haukeland University Hospital, Postbox 1400, 5021 Bergen, Norway; The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital, Postbox 1400, 5021 Bergen, Norway
| | - Eystein Oveland
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Postbox 7804, N-5009 Bergen, Norway; The KG Jebsen Centre for MS-Research, Department of Clinical Medicine, University of Bergen, Postbox 7804, N-5021 Bergen, Norway
| | - Øivind Torkildsen
- The KG Jebsen Centre for MS-Research, Department of Clinical Medicine, University of Bergen, Postbox 7804, N-5021 Bergen, Norway; Department of Neurology, Haukeland University Hospital, Postbox 1400, 5021 Bergen, Norway; The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital, Postbox 1400, 5021 Bergen, Norway
| | - Frode S Berven
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Postbox 7804, N-5009 Bergen, Norway; The KG Jebsen Centre for MS-Research, Department of Clinical Medicine, University of Bergen, Postbox 7804, N-5021 Bergen, Norway; The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital, Postbox 1400, 5021 Bergen, Norway.
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Nilsson CL, Mostovenko E, Lichti CF, Ruggles K, Fenyö D, Rosenbloom KR, Hancock WS, Paik YK, Omenn GS, LaBaer J, Kroes RA, Uhlén M, Hober S, Végvári Á, Andrén PE, Sulman EP, Lang FF, Fuentes M, Carlsohn E, Emmett MR, Moskal JR, Berven FS, Fehniger TE, Marko-Varga G. Use of ENCODE Resources to Characterize Novel Proteoforms and Missing Proteins in the Human Proteome. J Proteome Res 2014; 14:603-8. [DOI: 10.1021/pr500564q] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
| | | | | | - Kelly Ruggles
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), 1156 High Street, New York, Santa Cruz California 95064, United States
| | - David Fenyö
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), 1156 High Street, New York, Santa Cruz California 95064, United States
| | - Kate R. Rosenbloom
- Center
for Biomolecular Science and Engineering, University of California, 1156 High St, Mail Stop CBSE, Santa Cruz, California 95064, United States
| | - William S. Hancock
- College
of Science, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Young-Ki Paik
- Department
of Biochemistry, Yonsei Proteome Research Center, 50 Yonsei-Ro,
Seodaemun-gu, Seoul 120-749, South Korea
| | - Gilbert S. Omenn
- Center for
Computational Medicine and Bioinformatics, University of Michican Medical School, 100 Washtenaw Avenue, Ann
Arbor, Michigan 48109, United States
| | - Joshua LaBaer
- Biodesign
Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, Arizona 85287, United States
| | - Roger A. Kroes
- The
Falk Center for Molecular Therapeutics, McCormick School of Engineering
and Applied Sciences, Northwestern University, 1801 Maple Street, Evanston, Illinois 60201, United States
| | - Matthias Uhlén
- Biotechnology,
AlbaNova University Center, Royal Institute of Technology, Roslagstullsbacken
21, 106 91 Stockholm, Sweden
| | - Sophia Hober
- School
of Biotechnology, Department of Proteomics, Royal Institute of Technology, 106 91 Stockholm, Sweden
| | - Ákos Végvári
- Clinical Protein Science & Imaging, Biomedical Center, Department of Biomedical Engineering, Lund University, 221 84 Lund, Sweden
| | - Per E. Andrén
- Department
of Pharmaceutical Biosciences, Uppsala University, Husargatan 3, 752 37 Uppsala, Sweden
| | - Erik P. Sulman
- Department
of Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, United States
| | - Frederick F. Lang
- Department
of Neurosurgery, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, United States
| | - Manuel Fuentes
- Centro
de Investigacion del Cancer, Medicine-Immunology, CSIC-University of Salamanca, Salamanca 37007, Spain
| | - Elisabet Carlsohn
- Proteomics
Core Facility, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan
7A, Gothenburg 413 90, Sweden
| | | | - Joseph R. Moskal
- The
Falk Center for Molecular Therapeutics, McCormick School of Engineering
and Applied Sciences, Northwestern University, 1801 Maple Street, Evanston, Illinois 60201, United States
| | - Frode S. Berven
- Department
of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Thomas E. Fehniger
- Clinical Protein Science & Imaging, Biomedical Center, Department of Biomedical Engineering, Lund University, 221 84 Lund, Sweden
| | - György Marko-Varga
- Clinical Protein Science & Imaging, Biomedical Center, Department of Biomedical Engineering, Lund University, 221 84 Lund, Sweden
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Bjorlykke Y, Vethe H, Vaudel M, Barsnes H, Berven FS, Tjora E, Raeder H. Carboxyl-Ester Lipase Maturity-Onset Diabetes of the Young Disease Protein Biomarkers in Secretin-Stimulated Duodenal Juice. J Proteome Res 2014; 14:521-30. [DOI: 10.1021/pr500750z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Yngvild Bjorlykke
- KG
Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Jonas Lies Vei 65, Bergen 5021, Norway
- Department
of Pediatrics, Haukeland University Hospital, Jonas Lies vei 65, Bergen 5021, Norway
| | - Heidrun Vethe
- KG
Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Jonas Lies Vei 65, Bergen 5021, Norway
- Department
of Pediatrics, Haukeland University Hospital, Jonas Lies vei 65, Bergen 5021, Norway
| | - Marc Vaudel
- Proteomics
Unit (PROBE), Department of Biomedicine, University of Bergen, Jonas Lies vei 91, Bergen 5009, Norway
| | - Harald Barsnes
- Proteomics
Unit (PROBE), Department of Biomedicine, University of Bergen, Jonas Lies vei 91, Bergen 5009, Norway
| | - Frode S. Berven
- Proteomics
Unit (PROBE), Department of Biomedicine, University of Bergen, Jonas Lies vei 91, Bergen 5009, Norway
| | - Erling Tjora
- Department
of Pediatrics, Haukeland University Hospital, Jonas Lies vei 65, Bergen 5021, Norway
| | - Helge Raeder
- KG
Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Jonas Lies Vei 65, Bergen 5021, Norway
- Department
of Pediatrics, Haukeland University Hospital, Jonas Lies vei 65, Bergen 5021, Norway
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44
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Finne K, Vethe H, Skogstrand T, Leh S, Dahl TD, Tenstad O, Berven FS, Reed RK, Vikse BE. Proteomic analysis of formalin-fixed paraffin-embedded glomeruli suggests depletion of glomerular filtration barrier proteins in two-kidney, one-clip hypertensive rats. Nephrol Dial Transplant 2014; 29:2217-27. [PMID: 25129444 PMCID: PMC4240179 DOI: 10.1093/ndt/gfu268] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background It is well known that hypertension may cause glomerular damage, but the molecular mechanisms involved are still incompletely understood. Methods In the present study, we used formalin-fixed paraffin-embedded (FFPE) tissue to investigate changes in the glomerular proteome in the non-clipped kidney of two-kidney one-clip (2K1C) hypertensive rats, with special emphasis on the glomerular filtration barrier. 2K1C hypertension was induced in 6-week-old Wistar Hannover rats (n = 6) that were sacrificed 23 weeks later and compared with age-matched sham-operated controls (n = 6). Tissue was stored in FFPE tissue blocks and later prepared on tissue slides for laser microdissection. Glomeruli without severe morphological damage were isolated, and the proteomes were analysed using liquid chromatography–tandem mass spectrometry. Results 2K1C glomeruli showed reduced abundance of proteins important for slit diaphragm complex, such as nephrin, podocin and neph1. The podocyte foot process had a pattern of reduced abundance of transmembrane proteins but unchanged abundances of the podocyte cytoskeletal proteins synaptopodin and α-actinin-4. Lower abundance of important glomerular basement membrane proteins was seen. Possible glomerular markers of damage with increased abundance in 2K1C were transgelin, desmin and acyl-coenzyme A thioesterase 1. Conclusions Microdissection and tandem mass spectrometry could be used to investigate the proteome of isolated glomeruli from FFPE tissue. Glomerular filtration barrier proteins had reduced abundance in the non-clipped kidney of 2K1C hypertensive rats.
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Affiliation(s)
- Kenneth Finne
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Heidrun Vethe
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Trude Skogstrand
- Department of Clinical Medicine, University of Bergen, Bergen, Norway Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Sabine Leh
- Department of Clinical Medicine, University of Bergen, Bergen, Norway Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Tone D Dahl
- Department of Clinical Medicine, University of Bergen, Bergen, Norway Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Olav Tenstad
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Frode S Berven
- Department of Biomedicine, University of Bergen, Bergen, Norway The Norwegian Multiple Sclerosis National Competence Centre, Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | - Rolf K Reed
- Department of Biomedicine, University of Bergen, Bergen, Norway Centre for Cancer Biomarkers (CCBIO), University of Bergen, Bergen, Norway
| | - Bjørn Egil Vikse
- Department of Clinical Medicine, University of Bergen, Bergen, Norway Department of Medicine, Haukeland University Hospital, Bergen, Norway Department of Medicine, Haugesund Hospital, Haugesund, Norway
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45
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Aasebø E, Vaudel M, Mjaavatten O, Gausdal G, Van der Burgh A, Gjertsen BT, Døskeland SO, Bruserud Ø, Berven FS, Selheim F. Performance of super-SILAC based quantitative proteomics for comparison of different acute myeloid leukemia (AML) cell lines. Proteomics 2014; 14:1971-6. [DOI: 10.1002/pmic.201300448] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 05/30/2014] [Accepted: 07/04/2014] [Indexed: 01/06/2023]
Affiliation(s)
- Elise Aasebø
- Proteomics Unit (PROBE), Department of Biomedicine; University of Bergen; Bergen Norway
| | - Marc Vaudel
- Proteomics Unit (PROBE), Department of Biomedicine; University of Bergen; Bergen Norway
| | - Olav Mjaavatten
- Proteomics Unit (PROBE), Department of Biomedicine; University of Bergen; Bergen Norway
| | - Gro Gausdal
- Department of Biomedicine; University of Bergen; Bergen Norway
| | - Arthur Van der Burgh
- Proteomics Unit (PROBE), Department of Biomedicine; University of Bergen; Bergen Norway
| | | | | | - Øystein Bruserud
- Department of Clinical Science; University of Bergen; Bergen Norway
| | - Frode S. Berven
- Proteomics Unit (PROBE), Department of Biomedicine; University of Bergen; Bergen Norway
| | - Frode Selheim
- Proteomics Unit (PROBE), Department of Biomedicine; University of Bergen; Bergen Norway
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46
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Guldbrandsen A, Vethe H, Farag Y, Oveland E, Garberg H, Berle M, Myhr KM, Opsahl JA, Barsnes H, Berven FS. In-depth characterization of the cerebrospinal fluid (CSF) proteome displayed through the CSF proteome resource (CSF-PR). Mol Cell Proteomics 2014; 13:3152-63. [PMID: 25038066 PMCID: PMC4223498 DOI: 10.1074/mcp.m114.038554] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this study, the human cerebrospinal fluid (CSF) proteome was mapped using three different strategies prior to Orbitrap LC-MS/MS analysis: SDS-PAGE and mixed mode reversed phase-anion exchange for mapping the global CSF proteome, and hydrazide-based glycopeptide capture for mapping glycopeptides. A maximal protein set of 3081 proteins (28,811 peptide sequences) was identified, of which 520 were identified as glycoproteins from the glycopeptide enrichment strategy, including 1121 glycopeptides and their glycosylation sites. To our knowledge, this is the largest number of identified proteins and glycopeptides reported for CSF, including 417 glycosylation sites not previously reported. From parallel plasma samples, we identified 1050 proteins (9739 peptide sequences). An overlap of 877 proteins was found between the two body fluids, whereas 2204 proteins were identified only in CSF and 173 only in plasma. All mapping results are freely available via the new CSF Proteome Resource (http://probe.uib.no/csf-pr), which can be used to navigate the CSF proteome and help guide the selection of signature peptides in targeted quantitative proteomics.
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Affiliation(s)
- Astrid Guldbrandsen
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway; §KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Heidrun Vethe
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Yehia Farag
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway; ¶Department of Informatics, University of Bergen, Bergen, Norway
| | - Eystein Oveland
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway; §KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, Bergen, Norway; ‖Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Hilde Garberg
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Magnus Berle
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway; **Surgical Clinic, Haukeland University Hospital, Bergen, Norway
| | - Kjell-Morten Myhr
- §KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, Bergen, Norway; ‡‡Norwegian Multiple Sclerosis Registry and Biobank, Haukeland University Hospital, Bergen, Norway
| | - Jill A Opsahl
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway; §KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Harald Barsnes
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Frode S Berven
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway; §KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, Bergen, Norway; §§Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital, Bergen, Norway.
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47
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Haaland I, Opsahl JA, Berven FS, Reikvam H, Fredly HK, Haugse R, Thiede B, McCormack E, Lain S, Bruserud Ø, Gjertsen BT. Molecular mechanisms of nutlin-3 involve acetylation of p53, histones and heat shock proteins in acute myeloid leukemia. Mol Cancer 2014; 13:116. [PMID: 24885082 PMCID: PMC4032636 DOI: 10.1186/1476-4598-13-116] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 04/29/2014] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The small-molecule MDM2 antagonist nutlin-3 has proved to be an effective p53 activating therapeutic compound in several preclinical cancer models, including acute myeloid leukemia (AML). We and others have previously reported a vigorous acetylation of the p53 protein by nutlin-treatment. In this study we aimed to investigate the functional role of this p53 acetylation in nutlin-sensitivity, and further to explore if nutlin-induced protein acetylation in general could indicate novel targets for the enhancement of nutlin-based therapy. RESULTS Nutlin-3 was found to enhance the acetylation of p53 in the human AML cell line MOLM-13 (wild type TP53) and in TP53 null cells transfected with wild type p53 cDNA. Stable isotope labeling with amino acids in cell culture (SILAC) in combination with immunoprecipitation using an anti-acetyl-lysine antibody and mass spectrometry analysis identified increased levels of acetylated Histone H2B, Hsp27 and Hsp90 in MOLM-13 cells after nutlin-treatment, accompanied by downregulation of total levels of Hsp27 and Hsp90. Intracellular levels of heat shock proteins Hsp27, Hsp40, Hsp60, Hsp70 and Hsp90α were correlated to nutlin-sensitivity for primary AML cells (n = 40), and AML patient samples with low sensitivity to nutlin-3 tended to express higher levels of heat shock proteins than more responsive samples. Combination therapy of nutlin-3 and Hsp90 inhibitor geldanamycin demonstrated synergistic induction of apoptosis in AML cell lines and primary AML cells. Finally, TP53 null cells transfected with a p53 acetylation defective mutant demonstrated decreased heat shock protein acetylation and sensitivity to nutlin-3 compared to wild type p53 expressing cells. CONCLUSIONS Altogether, our results demonstrate that nutlin-3 induces acetylation of p53, histones and heat shock proteins, and indicate that p53 acetylation status and the levels of heat shock proteins may participate in modulation of nutlin-3 sensitivity in AML.
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MESH Headings
- Acetylation
- Antineoplastic Agents/pharmacology
- Benzoquinones/pharmacology
- Cell Line, Tumor
- Drug Synergism
- Gene Expression Regulation, Leukemic
- HSP27 Heat-Shock Proteins/genetics
- HSP27 Heat-Shock Proteins/metabolism
- HSP90 Heat-Shock Proteins/genetics
- HSP90 Heat-Shock Proteins/metabolism
- Histones/genetics
- Histones/metabolism
- Humans
- Imidazoles/pharmacology
- Lactams, Macrocyclic/pharmacology
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Piperazines/pharmacology
- Primary Cell Culture
- Signal Transduction
- Tumor Suppressor Protein p53/genetics
- Tumor Suppressor Protein p53/metabolism
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Affiliation(s)
- Ingvild Haaland
- Department of Clinical Science, Hematology Section, University of Bergen, Bergen N-5021, Norway
| | - Jill A Opsahl
- Department of Biomedicine, Proteomics Unit at University of Bergen (PROBE), University of Bergen, Bergen N-5021, Norway
| | - Frode S Berven
- Department of Biomedicine, Proteomics Unit at University of Bergen (PROBE), University of Bergen, Bergen N-5021, Norway
| | - Håkon Reikvam
- Department of Clinical Science, Hematology Section, University of Bergen, Bergen N-5021, Norway
| | - Hanne K Fredly
- Department of Clinical Science, Hematology Section, University of Bergen, Bergen N-5021, Norway
| | - Ragnhild Haugse
- Department of Clinical Science, Hematology Section, University of Bergen, Bergen N-5021, Norway
| | - Bernd Thiede
- The Biotechnology Centre of Oslo, University of Oslo, Oslo N-0317, Norway
| | - Emmet McCormack
- Department of Clinical Science, Hematology Section, University of Bergen, Bergen N-5021, Norway
- Department of Internal Medicine, Haukeland University Hospital, Bergen N-5021, Norway
| | - Sonia Lain
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm SE-171777, Sweden
| | - Øystein Bruserud
- Department of Clinical Science, Hematology Section, University of Bergen, Bergen N-5021, Norway
- Department of Internal Medicine, Haukeland University Hospital, Bergen N-5021, Norway
| | - Bjørn Tore Gjertsen
- Department of Internal Medicine, Haukeland University Hospital, Bergen N-5021, Norway
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen N-5021, Norway
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48
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Vaudel M, Barsnes H, Martens L, Berven FS. Bioinformatics for proteomics: opportunities at the interface between the scientists, their experiments, and the community. Methods Mol Biol 2014; 1156:239-48. [PMID: 24791993 DOI: 10.1007/978-1-4939-0685-7_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Within the last decade, bioinformatics has moved from command line scripts dedicated to single experiments towards production grade software integrated in experimental workflows providing a rich environment for biological investigation. Located at the interface between the scientists, their experiments, and the community, bioinformatics acts as a gateway to a wide source of information. This chapter does not list tools and methods, but rather hints at how bioinformatics can help in improving biological projects, all the way from their initial design to the dissemination of the results.
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Affiliation(s)
- Marc Vaudel
- Proteomics Unit, Department of Biomedicine, University of Bergen, Jonas Liesvei 91, Bergen, 5009, Norway,
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49
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Vaudel M, Venne AS, Berven FS, Zahedi RP, Martens L, Barsnes H. Shedding light on black boxes in protein identification. Proteomics 2014; 14:1001-5. [DOI: 10.1002/pmic.201300488] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 01/10/2014] [Accepted: 01/22/2014] [Indexed: 12/28/2022]
Affiliation(s)
- Marc Vaudel
- Proteomics Unit; Department of Biomedicine; University of Bergen; Norway
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V; Dortmund Germany
| | - A. Saskia Venne
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V; Dortmund Germany
| | - Frode S. Berven
- Proteomics Unit; Department of Biomedicine; University of Bergen; Norway
- Department of Clinical Medicine; The KG Jebsen Centre for MS-research; University of Bergen; Bergen Norway
- Department of Neurology; The Norwegian Multiple Sclerosis Competence Centre; Haukeland University Hospital; Bergen Norway
| | - René P. Zahedi
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V; Dortmund Germany
| | - Lennart Martens
- Department of Medical Protein Research; VIB; Ghent Belgium
- Department of Biochemistry; Ghent University; Ghent Belgium
| | - Harald Barsnes
- Proteomics Unit; Department of Biomedicine; University of Bergen; Norway
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50
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Lichti CF, Liu H, Shavkunov AS, Mostovenko E, Sulman EP, Ezhilarasan R, Wang Q, Kroes RA, Moskal JC, Fenyö D, Oksuz BA, Conrad CA, Lang FF, Berven FS, Végvári A, Rezeli M, Marko-Varga G, Hober S, Nilsson CL. Integrated chromosome 19 transcriptomic and proteomic data sets derived from glioma cancer stem-cell lines. J Proteome Res 2013; 13:191-9. [PMID: 24266786 DOI: 10.1021/pr400786s] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
One subproject within the global Chromosome 19 Consortium is to define chromosome 19 gene and protein expression in glioma-derived cancer stem cells (GSCs). Chromosome 19 is notoriously linked to glioma by 1p/19q codeletions, and clinical tests are established to detect that specific aberration. GSCs are tumor-initiating cells and are hypothesized to provide a repository of cells in tumors that can self-replicate and be refractory to radiation and chemotherapeutic agents developed for the treatment of tumors. In this pilot study, we performed RNA-Seq, label-free quantitative protein measurements in six GSC lines, and targeted transcriptomic analysis using a chromosome 19-specific microarray in an additional six GSC lines. The data have been deposited to the ProteomeXchange with identifier PXD000563. Here we present insights into differences in GSC gene and protein expression, including the identification of proteins listed as having no or low evidence at the protein level in the Human Protein Atlas, as correlated to chromosome 19 and GSC subtype. Furthermore, the upregulation of proteins downstream of adenovirus-associated viral integration site 1 (AAVS1) in GSC11 in response to oncolytic adenovirus treatment was demonstrated. Taken together, our results may indicate new roles for chromosome 19, beyond the 1p/19q codeletion, in the future of personalized medicine for glioma patients.
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Affiliation(s)
- Cheryl F Lichti
- Department of Pharmacology and Toxicology, UTMB Cancer Center, University of Texas Medical Branch , 301 University Boulevard, Galveston, Texas 77555, United States
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