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Ostacolo K, López García de Lomana A, Larat C, Hjaltalin V, Holm KY, Hlynsdóttir SS, Soucheray M, Sooman L, Rolfsson O, Krogan NJ, Steingrimsson E, Swaney DL, Ogmundsdottir MH. ATG7(2) Interacts With Metabolic Proteins and Regulates Central Energy Metabolism. Traffic 2024; 25:e12933. [PMID: 38600522 DOI: 10.1111/tra.12933] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 03/01/2024] [Accepted: 03/10/2024] [Indexed: 04/12/2024]
Abstract
Macroautophagy/autophagy is an essential catabolic process that targets a wide variety of cellular components including proteins, organelles, and pathogens. ATG7, a protein involved in the autophagy process, plays a crucial role in maintaining cellular homeostasis and can contribute to the development of diseases such as cancer. ATG7 initiates autophagy by facilitating the lipidation of the ATG8 proteins in the growing autophagosome membrane. The noncanonical isoform ATG7(2) is unable to perform ATG8 lipidation; however, its cellular regulation and function are unknown. Here, we uncovered a distinct regulation and function of ATG7(2) in contrast with ATG7(1), the canonical isoform. First, affinity-purification mass spectrometry analysis revealed that ATG7(2) establishes direct protein-protein interactions (PPIs) with metabolic proteins, whereas ATG7(1) primarily interacts with autophagy machinery proteins. Furthermore, we identified that ATG7(2) mediates a decrease in metabolic activity, highlighting a novel splice-dependent function of this important autophagy protein. Then, we found a divergent expression pattern of ATG7(1) and ATG7(2) across human tissues. Conclusively, our work uncovers the divergent patterns of expression, protein interactions, and function of ATG7(2) in contrast to ATG7(1). These findings suggest a molecular switch between main catabolic processes through isoform-dependent expression of a key autophagy gene.
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Affiliation(s)
- Kevin Ostacolo
- Department of Anatomy, Biomedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Adrián López García de Lomana
- Department of Biochemistry and Molecular Biology, Biomedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Clémence Larat
- Department of Anatomy, Biomedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Valgerdur Hjaltalin
- Department of Anatomy, Biomedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Kristrun Yr Holm
- Department of Anatomy, Biomedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Sigríður S Hlynsdóttir
- Department of Anatomy, Biomedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Margaret Soucheray
- Gladstone Institutes, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
| | - Linda Sooman
- Department of Anatomy, Biomedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Ottar Rolfsson
- Department of Biochemistry and Molecular Biology, Biomedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Nevan J Krogan
- Gladstone Institutes, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
| | - Eirikur Steingrimsson
- Department of Biochemistry and Molecular Biology, Biomedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Danielle L Swaney
- Gladstone Institutes, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
| | - Margret H Ogmundsdottir
- Department of Anatomy, Biomedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
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2
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Arnason NA, Johannsson F, Landrö R, Hardarsson B, Gudmundsson S, Lian AM, Reseland J, Rolfsson O, Sigurjonsson OE. Protein Concentrations in Stored Pooled Platelet Concentrates Treated with Pathogen Inactivation by Amotosalen Plus Ultraviolet a Illumination. Pathogens 2022; 11:pathogens11030350. [PMID: 35335674 PMCID: PMC8954553 DOI: 10.3390/pathogens11030350] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 02/04/2023] Open
Abstract
Platelet granules contain a diverse group of proteins. Upon activation and during storage, platelets release a number of proteins into the circulation or supernatant of stored platelet concentrate (PC). The aim of this work was to investigate the effect of pathogen inactivation (PI) on a selection of proteins released in stored platelets. Materials and Methods: PCs in platelet additive solution (PAS) were produced from whole blood donations using the buffy coat (BC) method. PCs in the treatment arm were pathogen inactivated with amotosalen and UVA, while PCs in the second arm were used as an untreated platelet control. Concentrations of 36 proteins were monitored in the PCs during storage. Results: The majority of proteins increased in concentration over the storage period. In addition, 10 of the 29 proteins that showed change had significantly different concentrations between the PI treatment and the control at one or more timepoints. A subset of six proteins displayed a PI-related drop in concentration. Conclusions: PI has limited effect on protein concentration stored PC supernatant. The protein’s changes related to PI treatment with elevated concentration implicate accelerated Platelet storage lesion (PSL); in contrast, there are potential novel benefits to PI related decrease in protein concentration that need further investigation.
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Affiliation(s)
- Niels Arni Arnason
- The Blood Bank, Landspitali-The National University Hospital of Iceland, 105 Reykjavik, Iceland; (N.A.A.); (R.L.); (B.H.); (S.G.)
- School of Engineering, Reykjavik University, 105 Reykjavik, Iceland
| | - Freyr Johannsson
- Department of Medicine, University of Iceland, 105 Reykjavik, Iceland; (F.J.); (O.R.)
| | - Ragna Landrö
- The Blood Bank, Landspitali-The National University Hospital of Iceland, 105 Reykjavik, Iceland; (N.A.A.); (R.L.); (B.H.); (S.G.)
| | - Björn Hardarsson
- The Blood Bank, Landspitali-The National University Hospital of Iceland, 105 Reykjavik, Iceland; (N.A.A.); (R.L.); (B.H.); (S.G.)
| | - Sveinn Gudmundsson
- The Blood Bank, Landspitali-The National University Hospital of Iceland, 105 Reykjavik, Iceland; (N.A.A.); (R.L.); (B.H.); (S.G.)
| | - Aina-Mari Lian
- Institute of Clinical Dentistry, Faculty of Dentistry, University of Oslo, 0317 Oslo, Norway; (A.-M.L.); (J.R.)
| | - Janne Reseland
- Institute of Clinical Dentistry, Faculty of Dentistry, University of Oslo, 0317 Oslo, Norway; (A.-M.L.); (J.R.)
| | - Ottar Rolfsson
- Department of Medicine, University of Iceland, 105 Reykjavik, Iceland; (F.J.); (O.R.)
| | - Olafur E. Sigurjonsson
- The Blood Bank, Landspitali-The National University Hospital of Iceland, 105 Reykjavik, Iceland; (N.A.A.); (R.L.); (B.H.); (S.G.)
- School of Engineering, Reykjavik University, 105 Reykjavik, Iceland
- Correspondence: ; Tel.: +354-543-5523 or +354-694-9427; Fax: +354-543-5532
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3
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Wang Q, Karvelsson ST, Johannsson F, Vilhjalmsson AI, Hagen L, de Miranda Fonseca D, Sharma A, Slupphaug G, Rolfsson O. UDP-glucose dehydrogenase expression is upregulated following EMT and differentially affects intracellular glycerophosphocholine and acetylaspartate levels in breast mesenchymal cell lines. Mol Oncol 2021; 16:1816-1840. [PMID: 34942055 PMCID: PMC9067156 DOI: 10.1002/1878-0261.13172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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] [Received: 08/06/2021] [Revised: 11/04/2021] [Accepted: 12/21/2021] [Indexed: 11/07/2022] Open
Abstract
Metabolic rewiring is one of the indispensable drivers of epithelial-mesenchymal transition (EMT) involved in breast cancer metastasis. In this study, we explored the metabolic changes during spontaneous EMT in three separately established breast EMT cell models using a proteomics approach supported by metabolomic analysis. We identified common proteomic changes, including in the expression of CDH1, CDH2, VIM, LGALS1, SERPINE1, PKP3, ATP2A2, JUP, MTCH2, RPL26L1 and PLOD2. Consistently altered metabolic enzymes included: FDFT1, SORD, TSTA3 and UDP-glucose dehydrogenase (UGDH). Of these, UGDH was most prominently altered and has previously been associated with breast cancer patient survival. siRNA-mediated knockdown of UGDH resulted in delayed cell proliferation and dampened invasive potential of mesenchymal cells, and downregulated expression of the EMT transcription factor SNAI1. Metabolomic analysis revealed that siRNA-mediated knockdown of UGDH decreased intracellular glycerophosphocholine (GPC), whereas levels of acetylaspartate (NAA) increased. Finally, our data suggested that platelet-derived growth factor receptor beta (PDGFRB) signaling was activated in mesenchymal cells. siRNA-mediated knockdown of PDGFRB downregulated UGDH expression, potentially via NFkB-p65. Our results support an unexplored relationship between UGDH and GPC, both of which have previously been independently associated with breast cancer progression.
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Affiliation(s)
- Qiong Wang
- Center for Systems Biology, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland, Sturlugata 8, 101, Reykjavik, Iceland
| | - Sigurdur Trausti Karvelsson
- Center for Systems Biology, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland, Sturlugata 8, 101, Reykjavik, Iceland
| | - Freyr Johannsson
- Center for Systems Biology, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland, Sturlugata 8, 101, Reykjavik, Iceland
| | - Arnar Ingi Vilhjalmsson
- Center for Systems Biology, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland, Sturlugata 8, 101, Reykjavik, Iceland
| | - Lars Hagen
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, N-7491, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs hospital, Trondheim, Norway.,PROMEC Core Facility for Proteomics and Modomics, Norwegian University of Science and Technology, NTNU, and the Central Norway Regional Health Authority Norway, Norway
| | - Davi de Miranda Fonseca
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, N-7491, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs hospital, Trondheim, Norway.,PROMEC Core Facility for Proteomics and Modomics, Norwegian University of Science and Technology, NTNU, and the Central Norway Regional Health Authority Norway, Norway
| | - Animesh Sharma
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, N-7491, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs hospital, Trondheim, Norway.,PROMEC Core Facility for Proteomics and Modomics, Norwegian University of Science and Technology, NTNU, and the Central Norway Regional Health Authority Norway, Norway
| | - Geir Slupphaug
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, N-7491, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs hospital, Trondheim, Norway.,PROMEC Core Facility for Proteomics and Modomics, Norwegian University of Science and Technology, NTNU, and the Central Norway Regional Health Authority Norway, Norway
| | - Ottar Rolfsson
- Center for Systems Biology, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland, Sturlugata 8, 101, Reykjavik, Iceland
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Wang Q, Karvelsson ST, Kotronoulas A, Gudjonsson T, Halldorsson S, Rolfsson O. Glutamine-fructose-6-phosphate transaminase 2 (GFPT2) is upregulated in breast epithelial-mesenchymal transition and responds to oxidative stress. Mol Cell Proteomics 2021; 21:100185. [PMID: 34923141 PMCID: PMC8803663 DOI: 10.1016/j.mcpro.2021.100185] [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: 05/26/2021] [Revised: 10/20/2021] [Accepted: 12/13/2021] [Indexed: 12/02/2022] Open
Abstract
Breast cancer cells that have undergone partial epithelial–mesenchymal transition (EMT) are believed to be more invasive than cells that have completed EMT. To study metabolic reprogramming in different mesenchymal states, we analyzed protein expression following EMT in the breast epithelial cell model D492 with single-shot LFQ supported by a SILAC proteomics approach. The D492 EMT cell model contains three cell lines: the epithelial D492 cells, the mesenchymal D492M cells, and a partial mesenchymal, tumorigenic variant of D492 that overexpresses the oncogene HER2. The analysis classified the D492 and D492M cells as basal-like and D492HER2 as claudin-low. Comparative analysis of D492 and D492M to tumorigenic D492HER2 differentiated metabolic markers of migration from those of invasion. Glutamine-fructose-6-phosphate transaminase 2 (GFPT2) was one of the top dysregulated enzymes in D492HER2. Gene expression analysis of the cancer genome atlas showed that GFPT2 expression was a characteristic of claudin-low breast cancer. siRNA-mediated knockdown of GFPT2 influenced the EMT marker vimentin and both cell growth and invasion in vitro and was accompanied by lowered metabolic flux through the hexosamine biosynthesis pathway (HBP). Knockdown of GFPT2 decreased cystathionine and sulfide:quinone oxidoreductase (SQOR) in the transsulfuration pathway that regulates H2S production and mitochondrial homeostasis. Moreover, GFPT2 was within the regulation network of insulin and EGF, and its expression was regulated by reduced glutathione (GSH) and suppressed by the oxidative stress regulator GSK3-β. Our results demonstrate that GFPT2 controls growth and invasion in the D492 EMT model, is a marker for oxidative stress, and associated with poor prognosis in claudin-low breast cancer. GFPT2 is upregulated following EMT. GFPT2 is a marker for claudin-low breast cancer. GFPT2 affects vimentin, cell proliferation, and cell invasion. GFPT2 responds to oxidative stress. GFPT2 is regulated by insulin and EGF.
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Affiliation(s)
- Qiong Wang
- Center for Systems Biology, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland
| | - Sigurdur Trausti Karvelsson
- Center for Systems Biology, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland
| | - Aristotelis Kotronoulas
- Center for Systems Biology, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland
| | - Thorarinn Gudjonsson
- Stem Cell Research Unit, Biomedical Center, Department of Anatomy, Faculty of Medicine, School of Health Sciences, University of Iceland, Vatnsmyrarvegi 16, 101 Reykjavík, Iceland
| | - Skarphedinn Halldorsson
- Center for Systems Biology, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland
| | - Ottar Rolfsson
- Center for Systems Biology, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland.
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5
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Kotronoulas A, de Lomana ALG, Karvelsson ST, Heijink M, Stone Ii R, Giera M, Rolfsson O. Lipid mediator profiles of burn wound healing: Acellular cod fish skin grafts promote the formation of EPA and DHA derived lipid mediators following seven days of treatment. Prostaglandins Leukot Essent Fatty Acids 2021; 175:102358. [PMID: 34753002 DOI: 10.1016/j.plefa.2021.102358] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 09/16/2021] [Accepted: 10/20/2021] [Indexed: 12/09/2022]
Abstract
The use of acellular fish skin grafts (FSG) for the treatment of burn wounds is becoming more common due to its beneficial wound healing properties. In our previous study we demonstarted that FSG is a scaffold biomaterial that is rich in eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) conjugated to phosphatidylcholines. Here we investigated whether EPA and DHA derived lipid mediators are influenced during the healing of burn wounds treated with FSG. Deep partial and full thickness burn wounds (DPT and FT, respectively) were created on Yorkshire pigs (n = 4). DPT were treated with either FSG or fetal bovine dermis while FT were treated either with FSG or cadaver skin initially and followed by a split thickness skin graft. Punch biopsies were collected on days 7, 14, 21, 28 and 60 and analyzed in respect of changes to approximately 45 derivatives of EPA, DHA, arachidonic acid (AA), and linoleic acid (LA) employing UPLC-MS/MS methodology. Nine EPA and DHA lipid mediators, principally mono-hydroxylated derivatives such as 18-HEPE and 17-HDHA, were significantly higher on day 7 in the DPT when treated with FSG. A similar but non-significant trend was observed for the FT. The results suggest that the use of FSG in burn wound treatment can alter the formation of EPA and DHA mono hydroxylated lipid mediators in comparison to other grafts of mammalian origin. The differences observed during the first seven days after treatment indicates that FSG affects the early stages of wound healing.
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Affiliation(s)
| | | | | | - Marieke Heijink
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), the Netherlands
| | - Randolph Stone Ii
- US Army Institute of Surgical Research, JBSA Fort Sam Houston, TX, USA
| | - Martin Giera
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), the Netherlands
| | - Ottar Rolfsson
- Center for Systems Biology, University of Iceland, Reykjavik, Iceland.
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6
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Karvelsson ST, Sigurdsson A, Seip K, Grinde MT, Wang Q, Johannsson F, Mælandsmo GM, Moestue SA, Rolfsson O, Halldorsson S. EMT-Derived Alterations in Glutamine Metabolism Sensitize Mesenchymal Breast Cells to mTOR Inhibition. Mol Cancer Res 2021; 19:1546-1558. [PMID: 34088869 DOI: 10.1158/1541-7786.mcr-20-0962] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 03/16/2021] [Accepted: 05/24/2021] [Indexed: 11/16/2022]
Abstract
Epithelial-to-mesenchymal transition (EMT) is a fundamental developmental process with strong implications in cancer progression. Understanding the metabolic alterations associated with EMT may open new avenues of treatment and prevention. Here we used 13C carbon analogs of glucose and glutamine to examine differences in their utilization within central carbon and lipid metabolism following EMT in breast epithelial cell lines. We found that there are inherent differences in metabolic profiles before and after EMT. We observed EMT-dependent re-routing of the TCA-cycle, characterized by increased mitochondrial IDH2-mediated reductive carboxylation of glutamine to lipid biosynthesis with a concomitant lowering of glycolytic rates and glutamine-dependent glutathione (GSH) generation. Using weighted correlation network analysis, we identified cancer drugs whose efficacy against the NCI-60 Human Tumor Cell Line panel is significantly associated with GSH abundance and confirmed these in vitro. We report that EMT-linked alterations in GSH synthesis modulate the sensitivity of breast epithelial cells to mTOR inhibitors. IMPLICATIONS: EMT in breast cells causes an increased demand for glutamine for fatty acid biosynthesis, altering its contribution to glutathione biosynthesis, which sensitizes the cells to mTOR inhibitors.
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Affiliation(s)
| | - Arnar Sigurdsson
- Department of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Kotryna Seip
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | | | - Qiong Wang
- Center for Systems Biology, University of Iceland, Reykjavik, Iceland
| | - Freyr Johannsson
- Center for Systems Biology, University of Iceland, Reykjavik, Iceland
| | - Gunhild Mari Mælandsmo
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Siver Andreas Moestue
- Department of Clinical and Molecular Medicine, NTNU, Trondheim, Norway.,Department of Pharmacy, Nord University, Namsos, Norway
| | - Ottar Rolfsson
- Center for Systems Biology, University of Iceland, Reykjavik, Iceland.
| | - Skarphedinn Halldorsson
- Center for Systems Biology, University of Iceland, Reykjavik, Iceland.,Institute for Surgical Research, Vilhelm Magnus Laboratory, Oslo University Hospital, Oslo, Norway
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7
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Teitsdottir UD, Halldorsson S, Rolfsson O, Lund SH, Jonsdottir MK, Snaedal J, Petersen PH. Cerebrospinal Fluid C18 Ceramide Associates with Markers of Alzheimer's Disease and Inflammation at the Pre- and Early Stages of Dementia. J Alzheimers Dis 2021; 81:231-244. [PMID: 33814423 PMCID: PMC8203241 DOI: 10.3233/jad-200964] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [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: 12/13/2022]
Abstract
Background: Understanding how dysregulation in lipid metabolism relates to the severity of Alzheimer‘s disease (AD) pathology might be critical in developing effective treatments. Objective: To identify lipid species in cerebrospinal fluid (CSF) associated with signature AD pathology and to explore their relationships with measures reflecting AD-related processes (neurodegeneration, inflammation, deficits in verbal episodic memory) among subjects at the pre- and early symptomatic stages of dementia. Methods: A total of 60 subjects that had been referred to an Icelandic memory clinic cohort were classified as having CSF AD (n = 34) or non-AD (n = 26) pathology profiles. Untargeted CSF lipidomic analysis was performed using ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS) for the detection of mass-to-charge ratio (m/z) features. CSF proteins reflecting neurodegeneration (neurofilament light [NFL]) and inflammation (chitinase-3-like protein 1 [YKL-40], S100 calcium-binding protein B [S100B], glial fibrillary acidic protein [GFAP]) were also measured. Rey Auditory Verbal Learning (RAVLT) and Story tests were used for the assessment of verbal episodic memory. Results: Eight out of 1008 features were identified as best distinguishing between the CSF profile groups. Of those, only the annotation of the m/z feature assigned to lipid species C18 ceramide was confirmed with a high confidence. Multiple regression analyses, adjusted for age, gender, and education, demonstrated significant associations of CSF core AD markers (Aβ42: st.β= –0.36, p = 0.007; T-tau: st.β= 0.41, p = 0.005) and inflammatory marker S100B (st.β= 0.51, p = 0.001) with C18 ceramide levels. Conclusion: Higher levels of C18 ceramide associated with increased AD pathology and inflammation, suggesting its potential value as a therapeutic target.
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Affiliation(s)
- Unnur D Teitsdottir
- Faculty of Medicine, Department of Anatomy, Biomedical Center, University of Iceland, Reykjavik, Iceland
| | | | - Ottar Rolfsson
- Center for Systems Biology, University of Iceland, Reykjavik, Iceland
| | | | - Maria K Jonsdottir
- Department of Psychology, Reykjavik University, Reykjavik, Iceland.,Department of Psychiatry, Landspitali -National University Hospital, Reykjavik, Iceland
| | - Jon Snaedal
- Memory Clinic, Department of Geriatric Medicine, Landspitali - National University Hospital, Reykjavik, Iceland
| | - Petur H Petersen
- Faculty of Medicine, Department of Anatomy, Biomedical Center, University of Iceland, Reykjavik, Iceland
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8
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Steinhaeuser SS, Morera E, Budkova Z, Schepsky A, Wang Q, Rolfsson O, Riedel A, Krueger A, Hilmarsdottir B, Maelandsmo GM, Valdimarsdottir B, Sigurdardottir AK, Agnarsson BA, Jonasson JG, Ingthorsson S, Traustadottir GA, Oskarsson T, Gudjonsson T. ECM1 secreted by HER2-overexpressing breast cancer cells promotes formation of a vascular niche accelerating cancer cell migration and invasion. J Transl Med 2020; 100:928-944. [PMID: 32203150 DOI: 10.1038/s41374-020-0415-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 02/07/2023] Open
Abstract
The tumor microenvironment is increasingly recognized as key player in cancer progression. Investigating heterotypic interactions between cancer cells and their microenvironment is important for understanding how specific cell types support cancer. Forming the vasculature, endothelial cells (ECs) are a prominent cell type in the microenvironment of both normal and neoplastic breast gland. Here, we sought out to analyze epithelial-endothelial cross talk in the breast using isogenic non-tumorigenic vs. tumorigenic breast epithelial cell lines and primary ECs. The cellular model used here consists of D492, a breast epithelial cell line with stem cell properties, and two isogenic D492-derived EMT cell lines, D492M and D492HER2. D492M was generated by endothelial-induced EMT and is non-tumorigenic while D492HER2 is tumorigenic, expressing the ErbB2/HER2 oncogene. To investigate cellular cross talk, we used both conditioned medium (CM) and 2D/3D co-culture systems. Secretome analysis of D492 cell lines was performed using mass spectrometry and candidate knockdown (KD), and overexpression (OE) was done using siRNA and CRISPRi/CRISPRa technology. D492HER2 directly enhances endothelial network formation and activates a molecular axis in ECs promoting D492HER2 migration and invasion, suggesting an endothelial feedback response. Secretome analysis identified extracellular matrix protein 1 (ECM1) as potential angiogenic inducer in D492HER2. Confirming its involvement, KD of ECM1 reduced the ability of D492HER2-CM to increase endothelial network formation and induce the endothelial feedback, while recombinant ECM1 (rECM1) increased both. Interestingly, NOTCH1 and NOTCH3 expression was upregulated in ECs upon treatment with D492HER2-CM or rECM1 but not by CM from D492HER2 with ECM1 KD. Blocking endothelial NOTCH signaling inhibited the increase in network formation and the ability of ECs to promote D492HER2 migration and invasion. In summary, our data demonstrate that cancer-secreted ECM1 induces a NOTCH-mediated endothelial feedback promoting cancer progression by enhancing migration and invasion. Targeting this interaction may provide a novel possibility to improve cancer treatment.
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Affiliation(s)
- Sophie Sarah Steinhaeuser
- Department of Anatomy, Stem Cell Research Unit, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Erika Morera
- Department of Anatomy, Stem Cell Research Unit, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Zuzana Budkova
- Department of Anatomy, Stem Cell Research Unit, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Alexander Schepsky
- Department of Anatomy, Stem Cell Research Unit, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Qiong Wang
- Center for Systems Biology, University of Iceland, Reykjavik, Iceland
| | - Ottar Rolfsson
- Center for Systems Biology, University of Iceland, Reykjavik, Iceland
| | - Angela Riedel
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120, Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Aileen Krueger
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120, Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Bylgja Hilmarsdottir
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Gunhild Mari Maelandsmo
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Bryndis Valdimarsdottir
- Department of Anatomy, Stem Cell Research Unit, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Anna Karen Sigurdardottir
- Department of Anatomy, Stem Cell Research Unit, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Bjarni Agnar Agnarsson
- Department of Pathology, Landspitali-University Hospital, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Jon Gunnlaugur Jonasson
- Department of Pathology, Landspitali-University Hospital, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Saevar Ingthorsson
- Department of Anatomy, Stem Cell Research Unit, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Gunnhildur Asta Traustadottir
- Department of Anatomy, Stem Cell Research Unit, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Thordur Oskarsson
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120, Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
| | - Thorarinn Gudjonsson
- Department of Anatomy, Stem Cell Research Unit, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland. .,Center for Systems Biology, University of Iceland, Reykjavik, Iceland. .,Department of Laboratory Hematology, Landspitali-University Hospital, Reykjavik, Iceland.
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9
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Yi Z, Su Y, Cherek P, Nelson DR, Lin J, Rolfsson O, Wu H, Salehi-Ashtiani K, Brynjolfsson S, Fu W. Combined artificial high-silicate medium and LED illumination promote carotenoid accumulation in the marine diatom Phaeodactylum tricornutum. Microb Cell Fact 2019; 18:209. [PMID: 31791335 PMCID: PMC6889666 DOI: 10.1186/s12934-019-1263-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [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: 09/08/2019] [Accepted: 11/28/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Diatoms, which can accumulate large amounts of carotenoids, are a major group of microalgae and the dominant primary producer in marine environments. Phaeodactylum tricornutum, a model diatom species, acquires little silicon for its growth although silicon is known to contribute to gene regulation and play an important role in diatom intracellular metabolism. In this study, we explored the effects of artificial high-silicate medium (i.e. 3.0 mM sodium metasilicate) and LED illumination conditions on the growth rate and pigment accumulation in P. tricornutum, which is the only known species so far that can grow without silicate. It's well known that light-emitting diodes (LEDs) as novel illuminants are emerging to be superior monochromatic light sources for algal cultivation with defined and efficient red and blue lights. RESULTS Firstly, we cultivated P. tricornutum in a synthetic medium supplemented with either 0.3 mM or 3.0 mM silicate. The morphology and size of diatom cells were examined: the proportion of the oval and triradiate cells decreased while the fusiform cells increased with more silicate addition in high-silicate medium; the average length of fusiform cells also slightly changed from 14.33 µm in 0.3 mM silicate medium to 12.20 µm in 3.0 mM silicate medium. Then we cultivated P. tricornutum under various intensities of red light in combination with the two different levels of silicate in the medium. Higher biomass productivity also achieved in 3.0 mM silicate medium than in 0.3 mM silicate medium under red LED light irradiation at 128 μmol/m2/s or higher light intensity. Increasing silicate reversed the down-regulation of fucoxanthin and chlorophyll a under high red-light illumination (i.e. 255 μmol/m2/s). When doubling the light intensity, fucoxanthin content decreased under red light but increased under combined red and blue (50:50) lights while chlorophyll a content reduced under both conditions. Fucoxanthin accumulation and biomass productivity increased with enhanced red and blue (50:50) lights. CONCLUSION High-silicate medium and blue light increased biomass and fucoxanthin production in P. tricornutum under high light conditions and this strategy may be beneficial for large-scale production of fucoxanthin in diatoms.
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Affiliation(s)
- Zhiqian Yi
- Center for Systems Biology and Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, School of Engineering and Natural Sciences, University of Iceland, Reykjavík, 101, Iceland.,Department of Orthopaedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.,Biomedical Center and Department of Anatomy, Faulty of Medicine, University of Iceland, Reykjavík, 101, Iceland
| | - Yixi Su
- Center for Systems Biology and Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, School of Engineering and Natural Sciences, University of Iceland, Reykjavík, 101, Iceland
| | - Paulina Cherek
- Biomedical Center and Department of Anatomy, Faulty of Medicine, University of Iceland, Reykjavík, 101, Iceland
| | - David R Nelson
- Center for Genomics and Systems Biology and Division of Science and Math, New York University Abu Dhabi, 129188, Abu Dhabi, United Arab Emirates
| | - Jianping Lin
- Key Laboratory of Biomass Chemical Engineering of the Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Ottar Rolfsson
- Center for Systems Biology and Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, School of Engineering and Natural Sciences, University of Iceland, Reykjavík, 101, Iceland
| | - Hua Wu
- Department of Orthopaedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Kourosh Salehi-Ashtiani
- Center for Genomics and Systems Biology and Division of Science and Math, New York University Abu Dhabi, 129188, Abu Dhabi, United Arab Emirates
| | - Sigurdur Brynjolfsson
- Center for Systems Biology and Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, School of Engineering and Natural Sciences, University of Iceland, Reykjavík, 101, Iceland
| | - Weiqi Fu
- Center for Systems Biology and Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, School of Engineering and Natural Sciences, University of Iceland, Reykjavík, 101, Iceland. .,Center for Genomics and Systems Biology and Division of Science and Math, New York University Abu Dhabi, 129188, Abu Dhabi, United Arab Emirates.
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10
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Arnason NA, Johannson F, Landrö R, Hardarsson B, Irsch J, Gudmundsson S, Rolfsson O, Sigurjonsson OE. Pathogen inactivation with amotosalen plus UVA illumination minimally impacts microRNA expression in platelets during storage under standard blood banking conditions. Transfusion 2019; 59:3727-3735. [PMID: 31674051 DOI: 10.1111/trf.15575] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 09/15/2019] [Accepted: 10/03/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND To reduce the risk of transfusion transmission infection, nucleic acid targeted methods have been developed to inactivate pathogens in PCs. miRNAs have been shown to play an important role in platelet function, and changes in the abundance of specific miRNAs during storage have been observed, as have perturbation effects related to pathogen inactivation (PI) methods. The aim of this work was to investigate the effects of PI on selected miRNAs during storage. STUDY DESIGN AND METHODS Using a pool and split strategy, 3 identical buffy coat PC units were generated from a pool of 24 whole blood donors. Each unit received a different treatment: 1) Untreated platelet control in platelet additive solution (C-PAS); 2) Amotosalen-UVA-treated platelets in PAS (PI-PAS); and 3) untreated platelets in donor plasma (U-PL). PCs were stored for 7 days under standard blood banking conditions. Standard platelet quality control (QC) parameters and 25 selected miRNAs were analyzed. RESULTS During the 7-day storage period, differences were found in several QC parameters relating to PI treatment and storage in plasma, but overall the three treatments were comparable. Out of 25 miRNA tested changes in regulation of 5 miRNA in PI-PAS and 3 miRNA U-PL where detected compared to C-PAS. A statistically significant difference was observed in down regulations miR-96-5p on Days 2 and 4, 61.9% and 61.8%, respectively, in the PI-PAS treatment. CONCLUSION Amotosalen-UVA treatment does not significantly alter the miRNA profile of platelet concentrates generated and stored using standard blood banking conditions.
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Affiliation(s)
- Niels Arni Arnason
- The Blood Bank, Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland
| | - Freyr Johannson
- Department of Medicine, University of Iceland, Reykjavik, Iceland
| | - Ragna Landrö
- The Blood Bank, Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland
| | - Björn Hardarsson
- The Blood Bank, Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland
| | | | - Sveinn Gudmundsson
- The Blood Bank, Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland
| | - Ottar Rolfsson
- Department of Medicine, University of Iceland, Reykjavik, Iceland
| | - Olafur E Sigurjonsson
- The Blood Bank, Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland.,School of Science and Engineering, Reykjavik University, Reykjavik, Iceland
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11
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Arason AJ, Joelsson JP, Valdimarsdottir B, Sigurdsson S, Gudjonsson A, Halldorsson S, Johannsson F, Rolfsson O, Lehmann F, Ingthorsson S, Cherek P, Gudmundsson GH, Gardarsson FR, Page CP, Baldursson O, Gudjonsson T, Kricker JA. Azithromycin induces epidermal differentiation and multivesicular bodies in airway epithelia. Respir Res 2019; 20:129. [PMID: 31234850 PMCID: PMC6591972 DOI: 10.1186/s12931-019-1101-3] [Citation(s) in RCA: 10] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 06/14/2019] [Indexed: 02/07/2023] Open
Abstract
Background Azithromycin (Azm) is a macrolide recognized for its disease-modifying effects and reduction in exacerbation of chronic airway diseases. It is not clear whether the beneficial effects of Azm are due to its anti-microbial activity or other pharmacological actions. We have shown that Azm affects the integrity of the bronchial epithelial barrier measured by increased transepithelial electrical resistance. To better understand these effects of Azm on bronchial epithelia we have investigated global changes in gene expression. Methods VA10 bronchial epithelial cells were treated with Azm and cultivated in air-liquid interface conditions for up to 22 days. RNA was isolated at days 4, 10 and 22 and analyzed using high-throughput RNA sequencing. qPCR and immunostaining were used to confirm key findings from bioinformatic analyses. Detailed assessment of cellular changes was done using microscopy, followed by characterization of the lipidomic profiles of the multivesicular bodies present. Results Bioinformatic analysis revealed that after 10 days of treatment genes encoding effectors of sterol and cholesterol metabolism were prominent. Interestingly, expression of genes associated with epidermal barrier differentiation, KRT1, CRNN, SPINK5 and DSG1, increased significantly at day 22. Together with immunostaining, these results suggest an epidermal differentiation pattern. We also found that Azm induced the formation of multivesicular and lamellar bodies in two different airway epithelial cell lines. Lipidomic analysis revealed that Azm was entrapped in multivesicular bodies linked to different types of lipids, most notably palmitate and stearate. Furthermore, targeted analysis of lipid species showed accumulation of phosphatidylcholines, as well as ceramide derivatives. Conclusions Taken together, we demonstrate how Azm might confer its barrier enhancing effects, via activation of epidermal characteristics and changes to intracellular lipid dynamics. These effects of Azm could explain the unexpected clinical benefit observed during Azm-treatment of patients with various lung diseases affecting barrier function. Electronic supplementary material The online version of this article (10.1186/s12931-019-1101-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ari Jon Arason
- Stem Cell Research Unit, BioMedical Center, School of Health Sciences, University of Iceland, Reykjavík, Iceland.,EpiEndo Pharmaceuticals, Reykjavík, Iceland
| | - Jon Petur Joelsson
- Stem Cell Research Unit, BioMedical Center, School of Health Sciences, University of Iceland, Reykjavík, Iceland
| | - Bryndis Valdimarsdottir
- Stem Cell Research Unit, BioMedical Center, School of Health Sciences, University of Iceland, Reykjavík, Iceland.,EpiEndo Pharmaceuticals, Reykjavík, Iceland
| | - Snaevar Sigurdsson
- Stem Cell Research Unit, BioMedical Center, School of Health Sciences, University of Iceland, Reykjavík, Iceland
| | - Alexander Gudjonsson
- Stem Cell Research Unit, BioMedical Center, School of Health Sciences, University of Iceland, Reykjavík, Iceland
| | | | - Freyr Johannsson
- Center for Systems Biology, University of Iceland, Reykjavík, Iceland
| | - Ottar Rolfsson
- Center for Systems Biology, University of Iceland, Reykjavík, Iceland
| | | | - Saevar Ingthorsson
- Stem Cell Research Unit, BioMedical Center, School of Health Sciences, University of Iceland, Reykjavík, Iceland.,EpiEndo Pharmaceuticals, Reykjavík, Iceland
| | - Paulina Cherek
- Department of Anatomy, Faculty of Medicine, University of Iceland, Reykjavík, Iceland
| | - Gudmundur H Gudmundsson
- BioMedical Center, Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | | | - Clive P Page
- EpiEndo Pharmaceuticals, Reykjavík, Iceland.,Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, UK
| | - Olafur Baldursson
- EpiEndo Pharmaceuticals, Reykjavík, Iceland.,Department of Respiratory Medicine, Landspitali-University Hospital, Reykjavík, Iceland
| | - Thorarinn Gudjonsson
- Stem Cell Research Unit, BioMedical Center, School of Health Sciences, University of Iceland, Reykjavík, Iceland.,Department of Laboratory Hematology, Landspitali-University Hospital, Iceland, Reykjavík, Iceland.,EpiEndo Pharmaceuticals, Reykjavík, Iceland
| | - Jennifer A Kricker
- Stem Cell Research Unit, BioMedical Center, School of Health Sciences, University of Iceland, Reykjavík, Iceland. .,EpiEndo Pharmaceuticals, Reykjavík, Iceland.
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12
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Eiriksson FF, Rolfsson O, Ogmundsdottir HM, Haraldsson GG, Thorsteinsdottir M, Halldorsson S. Altered plasmalogen content and fatty acid saturation following epithelial to mesenchymal transition in breast epithelial cell lines. Int J Biochem Cell Biol 2018; 103:99-104. [DOI: 10.1016/j.biocel.2018.08.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 06/27/2018] [Accepted: 08/06/2018] [Indexed: 12/21/2022]
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13
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Magnusson S, Baldursson BT, Kjartansson H, Rolfsson O, Sigurjonsson GF. Regenerative and Antibacterial Properties of Acellular Fish Skin Grafts and Human Amnion/Chorion Membrane: Implications for Tissue Preservation in Combat Casualty Care. Mil Med 2018; 182:383-388. [PMID: 28291503 DOI: 10.7205/milmed-d-16-00142] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Improvised explosive devices and new directed energy weapons are changing warfare injuries from penetrating wounds to large surface area thermal and blast injuries. Acellular fish skin is used for tissue repair and during manufacturing subjected to gentle processing compared to biologic materials derived from mammals. This is due to the absence of viral and prion disease transmission risk, preserving natural structure and composition of the fish skin graft. OBJECTIVES The aim of this study was to assess properties of acellular fish skin relevant for severe battlefield injuries and to compare those properties with those of dehydrated human amnion/chorion membrane. METHODS We evaluated cell ingrowth capabilities of the biological materials with microscopy techniques. Bacterial barrier properties were tested with a 2-chamber model. RESULTS The microstructure of the acellular fish skin is highly porous, whereas the microstructure of dehydrated human amnion/chorion membrane is mostly nonporous. The fish skin grafts show superior ability to support 3-dimensional ingrowth of cells compared to dehydrated human amnion/chorion membrane (p < 0.0001) and the fish skin is a bacterial barrier for 24 to 48 hours. CONCLUSION The unique biomechanical properties of the acellular fish skin graft make it ideal to be used as a conformal cover for severe trauma and burn wounds in the battlefield.
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Affiliation(s)
| | | | | | - Ottar Rolfsson
- Center for Systems Biology, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland
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14
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Righetti L, Bergmann A, Galaverna G, Rolfsson O, Paglia G, Dall'Asta C. Ion mobility-derived collision cross section database: Application to mycotoxin analysis. Anal Chim Acta 2018. [PMID: 29523251 DOI: 10.1016/j.aca.2018.01.047] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The recent hyphenation of ion mobility spectrometry (IMS) with high resolution mass spectrometry (HRMS) has risen as a powerful technique for both targeted and non-targeted screening, reducing background noise and allowing separation of isomeric and isobaric compounds. Nevertheless, such an approach remains largely unexplored in food safety applications, such as mycotoxin analysis. To implement ion mobility in routinely MS-based mycotoxin workflows, searchable databases with collusion cross section (CCS) values and accurate mass-values are required. This paper provides for the first time a traveling-wave IMS (TWIMS)-derived CCS database for mycotoxins, including more than 100 CCS values. The measurements showed high reproducibility (RSD < 2%) across different instrumental conditions as well as several complex cereal matrices, showing a mean inter-matrix precision of RSD <0.9%. As a proof of concept, the database was applied to the analysis of several spiked as well as naturally incurred cereal-based samples. In addition, the effect of adducts on the drift time was studied in a series of mycotoxins in order to understand potential deviations from expected drift time behaviors. Overall, our study confirmed that CCS values represent a physicochemical property that can be used alongside the traditional molecular identifiers of precursor ion accurate mass, fragment ions, isotopic pattern, and retention time.
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Affiliation(s)
- Laura Righetti
- Department of Food Science, University of Parma, Viale delle Scienze 17/A, I-43124 Parma, Italy
| | - Andreas Bergmann
- Center for Systems Biology, Medical Department, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland
| | - Gianni Galaverna
- Department of Food Science, University of Parma, Viale delle Scienze 17/A, I-43124 Parma, Italy
| | - Ottar Rolfsson
- Center for Systems Biology, Medical Department, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland
| | - Giuseppe Paglia
- Center of Biomedicine, European Academy of Bolzano/Bozen, Via Galvani 31, Bolzano 39100, Italy
| | - Chiara Dall'Asta
- Department of Food Science, University of Parma, Viale delle Scienze 17/A, I-43124 Parma, Italy.
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15
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Yurkovich JT, Zielinski DC, Yang L, Paglia G, Rolfsson O, Sigurjónsson ÓE, Broddrick JT, Bordbar A, Wichuk K, Brynjólfsson S, Palsson S, Gudmundsson S, Palsson BO. Quantitative time-course metabolomics in human red blood cells reveal the temperature dependence of human metabolic networks. J Biol Chem 2017; 292:19556-19564. [PMID: 29030425 DOI: 10.1074/jbc.m117.804914] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [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: 06/30/2017] [Revised: 09/21/2017] [Indexed: 11/06/2022] Open
Abstract
The temperature dependence of biological processes has been studied at the levels of individual biochemical reactions and organism physiology (e.g. basal metabolic rates) but has not been examined at the metabolic network level. Here, we used a systems biology approach to characterize the temperature dependence of the human red blood cell (RBC) metabolic network between 4 and 37 °C through absolutely quantified exo- and endometabolomics data. We used an Arrhenius-type model (Q10) to describe how the rate of a biochemical process changes with every 10 °C change in temperature. Multivariate statistical analysis of the metabolomics data revealed that the same metabolic network-level trends previously reported for RBCs at 4 °C were conserved but accelerated with increasing temperature. We calculated a median Q10 coefficient of 2.89 ± 1.03, within the expected range of 2-3 for biological processes, for 48 individual metabolite concentrations. We then integrated these metabolomics measurements into a cell-scale metabolic model to study pathway usage, calculating a median Q10 coefficient of 2.73 ± 0.75 for 35 reaction fluxes. The relative fluxes through glycolysis and nucleotide metabolism pathways were consistent across the studied temperature range despite the non-uniform distributions of Q10 coefficients of individual metabolites and reaction fluxes. Together, these results indicate that the rate of change of network-level responses to temperature differences in RBC metabolism is consistent between 4 and 37 °C. More broadly, we provide a baseline characterization of a biochemical network given no transcriptional or translational regulation that can be used to explore the temperature dependence of metabolism.
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Affiliation(s)
- James T Yurkovich
- From the Departments of Bioengineering and.,Bioinformatics and Systems Biology Program, and
| | | | | | - Giuseppe Paglia
- Institute for Biomedicine, EURAC Research, Viale Druso Drususallee 1, 39100 Bolzano, Bozen, Italy
| | - Ottar Rolfsson
- Center for Systems Biology, University of Iceland, Sturlugata 8, IS-101 Reykjavík, Iceland
| | - Ólafur E Sigurjónsson
- The Blood Bank, Landspítali-University Hospital, Snorrabraut 60, 105 Reykjavík, Iceland.,School of Science and Engineering, Reykjavík University, Menntavegur 1, IS-101 Reykjavík, Iceland, and
| | - Jared T Broddrick
- From the Departments of Bioengineering and.,Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093
| | | | - Kristine Wichuk
- Center for Systems Biology, University of Iceland, Sturlugata 8, IS-101 Reykjavík, Iceland
| | - Sigurður Brynjólfsson
- Center for Systems Biology, University of Iceland, Sturlugata 8, IS-101 Reykjavík, Iceland
| | - Sirus Palsson
- Center for Systems Biology, University of Iceland, Sturlugata 8, IS-101 Reykjavík, Iceland.,Sinopia Biosciences, San Diego, California 92101
| | - Sveinn Gudmundsson
- The Blood Bank, Landspítali-University Hospital, Snorrabraut 60, 105 Reykjavík, Iceland
| | - Bernhard O Palsson
- From the Departments of Bioengineering and .,Bioinformatics and Systems Biology Program, and.,Center for Systems Biology, University of Iceland, Sturlugata 8, IS-101 Reykjavík, Iceland.,Pediatrics
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16
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Hilmarsdottir B, Halldorsson S, Grinde MT, Barkovskaya A, Pettersen S, Gudjonsson T, Moestue SA, Rolfsson O, Mælandsmo GM. Abstract 4412: Metabolic reprogramming in EMT - targeting regulatory nodes in mesenchymal cells. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-4412] [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] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
To combat cancer we have to avoid development of resistant and metastatic disease. Breast cancer cells can switch from an epithelial to mesenchymal phenotype through a process called epithelial to mesenchymal transition/EMT. Emerging evidence suggests that this process is vital to avoid treatment pressure and to gain metastatic capacity. Furthermore, recent literature shows that metabolic reprogramming is an essential attribute of cellular plasticity. Metabolic targeting could therefore be an attractive possibility to prevent development of resistance and metastatic dissemination. Here we tried to understand the metabolic phenotype of EMT and the mechanisms linking the metabolic programs to cellular plasticity. We also aimed to unravel compensatory metabolic pathways and use the metabolic inhibitors to sensitize breast cancer cells to conventional therapy.
To that end we have investigated the metabolic signature of the D492 EMT cell model. The D492 cell line, established from human breast epithelial progenitor cells, has retained stem cell characteristics and has the ability to undergo EMT upon stromal (endothelial) influence, forming the mesenchymal D492M cells. Thus, D492 cell system has preserved the natural flexibility of breast epithelial progenitor cells, and constitutes a unique platform to unravel the factors responsible for stromal cell-induced cellular plasticity.
We show that metabolic reprogramming is essential for induction of the mesenchymal phenotype using metabolomic profiling. Using Ultra performance liquid chromatography Mass Spectrometry and gene expression profiling we have created genome-scale metabolic models of D492 and D492M. Our data show that glycolytic flux and oxidative phosphorylation is higher in D492, however, D492M cells rely more on amino acid anaplerosis and fatty acid oxidation to fuel the TCA cycle. Glutamine and glucose tracing using NMR will give further insight into the difference in metabolism between the two cell lines.
We have used these data to find metabolic targets that lock the cells in the epithelial state or identify the means to induce lethality in the mesenchymal cells.
Using the metabolic rewiring of EMT in the D492 cell model we can understand the mechanisms responsible for treatment resistance, identify compensatory metabolic pathways during treatment and find metabolic inhibitors that will sensitize BC cells to conventional therapy.
Citation Format: Bylgja Hilmarsdottir, Skarphedinn Halldorsson, Maria T. Grinde, Anna Barkovskaya, Solveig Pettersen, Thorarinn Gudjonsson, Siver A. Moestue, Ottar Rolfsson, Gunhild M. Mælandsmo. Metabolic reprogramming in EMT - targeting regulatory nodes in mesenchymal cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4412. doi:10.1158/1538-7445.AM2017-4412
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Affiliation(s)
| | | | - Maria T. Grinde
- 3Norwegian University of Science and Technology, Trondheim, Norway
| | - Anna Barkovskaya
- 1Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Solveig Pettersen
- 1Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | | | - Siver A. Moestue
- 3Norwegian University of Science and Technology, Trondheim, Norway
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17
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Bordbar A, Yurkovich JT, Paglia G, Rolfsson O, Sigurjónsson ÓE, Palsson BO. Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics. Sci Rep 2017; 7:46249. [PMID: 28387366 PMCID: PMC5384226 DOI: 10.1038/srep46249] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [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] [Received: 12/01/2016] [Accepted: 03/14/2017] [Indexed: 02/07/2023] Open
Abstract
The increasing availability of metabolomics data necessitates novel methods for deeper data analysis and interpretation. We present a flux balance analysis method that allows for the computation of dynamic intracellular metabolic changes at the cellular scale through integration of time-course absolute quantitative metabolomics. This approach, termed "unsteady-state flux balance analysis" (uFBA), is applied to four cellular systems: three dynamic and one steady-state as a negative control. uFBA and FBA predictions are contrasted, and uFBA is found to be more accurate in predicting dynamic metabolic flux states for red blood cells, platelets, and Saccharomyces cerevisiae. Notably, only uFBA predicts that stored red blood cells metabolize TCA intermediates to regenerate important cofactors, such as ATP, NADH, and NADPH. These pathway usage predictions were subsequently validated through 13C isotopic labeling and metabolic flux analysis in stored red blood cells. Utilizing time-course metabolomics data, uFBA provides an accurate method to predict metabolic physiology at the cellular scale for dynamic systems.
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Affiliation(s)
| | - James T Yurkovich
- Bioengineering Department, University of California, San Diego, La Jolla, CA, USA.,Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
| | - Giuseppe Paglia
- Center for Systems Biology, University of Iceland, Reykjavik, Iceland
| | - Ottar Rolfsson
- Center for Systems Biology, University of Iceland, Reykjavik, Iceland
| | - Ólafur E Sigurjónsson
- Blood Bank, Landspitali-University Hospital, Reykjavik, Iceland.,School of Science and Engineering, Reykjavik University, Reykjavik, Iceland
| | - Bernhard O Palsson
- Bioengineering Department, University of California, San Diego, La Jolla, CA, USA.,Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA.,Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Novo Nordisk Foundation Center for Biosustainability, The Technical University of Denmark, Hørsholm, Denmark
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Choudhary KS, Rohatgi N, Halldorsson S, Briem E, Gudjonsson T, Gudmundsson S, Rolfsson O. EGFR Signal-Network Reconstruction Demonstrates Metabolic Crosstalk in EMT. PLoS Comput Biol 2016; 12:e1004924. [PMID: 27253373 PMCID: PMC4890760 DOI: 10.1371/journal.pcbi.1004924] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 04/17/2016] [Indexed: 01/05/2023] Open
Abstract
Epithelial to mesenchymal transition (EMT) is an important event during development and cancer metastasis. There is limited understanding of the metabolic alterations that give rise to and take place during EMT. Dysregulation of signalling pathways that impact metabolism, including epidermal growth factor receptor (EGFR), are however a hallmark of EMT and metastasis. In this study, we report the investigation into EGFR signalling and metabolic crosstalk of EMT through constraint-based modelling and analysis of the breast epithelial EMT cell model D492 and its mesenchymal counterpart D492M. We built an EGFR signalling network for EMT based on stoichiometric coefficients and constrained the network with gene expression data to build epithelial (EGFR_E) and mesenchymal (EGFR_M) networks. Metabolic alterations arising from differential expression of EGFR genes was derived from a literature review of AKT regulated metabolic genes. Signaling flux differences between EGFR_E and EGFR_M models subsequently allowed metabolism in D492 and D492M cells to be assessed. Higher flux within AKT pathway in the D492 cells compared to D492M suggested higher glycolytic activity in D492 that we confirmed experimentally through measurements of glucose uptake and lactate secretion rates. The signaling genes from the AKT, RAS/MAPK and CaM pathways were predicted to revert D492M to D492 phenotype. Follow-up analysis of EGFR signaling metabolic crosstalk in three additional breast epithelial cell lines highlighted variability in in vitro cell models of EMT. This study shows that the metabolic phenotype may be predicted by in silico analyses of gene expression data of EGFR signaling genes, but this phenomenon is cell-specific and does not follow a simple trend.
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Affiliation(s)
- Kumari Sonal Choudhary
- Center for Systems Biology, University of Iceland, Reykjavik, Iceland
- Biomedical Center, University of Iceland, Reykjavik, Iceland
| | - Neha Rohatgi
- Center for Systems Biology, University of Iceland, Reykjavik, Iceland
- Biomedical Center, University of Iceland, Reykjavik, Iceland
| | - Skarphedinn Halldorsson
- Center for Systems Biology, University of Iceland, Reykjavik, Iceland
- Biomedical Center, University of Iceland, Reykjavik, Iceland
| | - Eirikur Briem
- Biomedical Center, University of Iceland, Reykjavik, Iceland
- Stem Cell Research Unit, Department of Anatomy, School of Health Sciences, University of Iceland, Reykjavík, Iceland
- Department of Laboratory Hematology, Landspitali-University Hospital, Reykjavik, Iceland
| | - Thorarinn Gudjonsson
- Biomedical Center, University of Iceland, Reykjavik, Iceland
- Stem Cell Research Unit, Department of Anatomy, School of Health Sciences, University of Iceland, Reykjavík, Iceland
- Department of Laboratory Hematology, Landspitali-University Hospital, Reykjavik, Iceland
| | | | - Ottar Rolfsson
- Center for Systems Biology, University of Iceland, Reykjavik, Iceland
- Biomedical Center, University of Iceland, Reykjavik, Iceland
- * E-mail:
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19
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Bordbar A, Johansson PI, Paglia G, Harrison SJ, Wichuk K, Magnusdottir M, Valgeirsdottir S, Gybel-Brask M, Ostrowski SR, Palsson S, Rolfsson O, Sigurjónsson OE, Hansen MB, Gudmundsson S, Palsson BO. Identified metabolic signature for assessing red blood cell unit quality is associated with endothelial damage markers and clinical outcomes. Transfusion 2016; 56:852-62. [PMID: 26749434 DOI: 10.1111/trf.13460] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 11/03/2015] [Accepted: 11/10/2015] [Indexed: 12/23/2022]
Abstract
BACKGROUND There has been interest in determining whether older red blood cell (RBC) units have negative clinical effects. Numerous observational studies have shown that older RBC units are an independent factor for patient mortality. However, recently published randomized clinical trials have shown no difference of clinical outcome for patients receiving old or fresh RBCs. An overlooked but essential issue in assessing RBC unit quality and ultimately designing the necessary clinical trials is a metric for what constitutes an old or fresh RBC unit. STUDY DESIGN AND METHODS Twenty RBC units were profiled using quantitative metabolomics over 42 days of storage in SAGM with 3- to 4-day time intervals. Metabolic pathway usage during storage was assessed using systems biology methods. The detected time intervals of the metabolic states were compared to clinical outcomes. RESULTS Using multivariate statistics, we identified a nonlinear decay process exhibiting three distinct metabolic states (Days 0-10, 10-17, and 17-42). Hematologic variables traditionally measured in the transfusion setting (e.g., pH, hemolysis, RBC indices) did not distinguish these three states. Systemic changes in pathway usage occurred between the three states, with key pathways changing in both magnitude and direction. Finally, an association was found between the time periods of the metabolic states with the clinical outcomes of more than 280,000 patients in the country of Denmark transfused over the past 15 years and endothelial damage markers in healthy volunteers undergoing autologous transfusions. CONCLUSION The state of RBC metabolism may be a better indicator of cellular quality than traditional hematologic variables.
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Affiliation(s)
| | - Pär I Johansson
- Section for Transfusion Medicine, Capital Region Blood Bank, Rigshopitalet, University of Copenhagen, Copenhagen, Denmark
| | - Giuseppe Paglia
- Center for Systems Biology, University of Iceland, Reykjavik, Iceland
| | - Scott J Harrison
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Kristine Wichuk
- Center for Systems Biology, University of Iceland, Reykjavik, Iceland
| | | | | | - Mikkel Gybel-Brask
- Section for Transfusion Medicine, Capital Region Blood Bank, Rigshopitalet, University of Copenhagen, Copenhagen, Denmark
| | - Sisse R Ostrowski
- Section for Transfusion Medicine, Capital Region Blood Bank, Rigshopitalet, University of Copenhagen, Copenhagen, Denmark
| | - Sirus Palsson
- Sinopia Biosciences, San Diego, California.,Center for Systems Biology, University of Iceland, Reykjavik, Iceland
| | - Ottar Rolfsson
- Center for Systems Biology, University of Iceland, Reykjavik, Iceland
| | - Olafur E Sigurjónsson
- Blood Bank, Landspitali-University Hospital.,School of Science and Engineering, Reykjavik University, Reykjavik, Iceland
| | - Morten B Hansen
- Section for Transfusion Medicine, Capital Region Blood Bank, Rigshopitalet, University of Copenhagen, Copenhagen, Denmark
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20
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Stockley PG, White SJ, Dykeman E, Manfield I, Rolfsson O, Patel N, Bingham R, Barker A, Wroblewski E, Chandler-Bostock R, Weiß EU, Ranson NA, Tuma R, Twarock R. Bacteriophage MS2 genomic RNA encodes an assembly instruction manual for its capsid. Bacteriophage 2016; 6:e1157666. [PMID: 27144089 PMCID: PMC4836477 DOI: 10.1080/21597081.2016.1157666] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 02/15/2016] [Accepted: 02/17/2016] [Indexed: 12/11/2022]
Abstract
Using RNA-coat protein crosslinking we have shown that the principal RNA recognition surface on the interior of infectious MS2 virions overlaps with the known peptides that bind the high affinity translational operator, TR, within the phage genome. The data also reveal the sequences of genomic fragments in contact with the coat protein shell. These show remarkable overlap with previous predictions based on the hypothesis that virion assembly is mediated by multiple sequences-specific contacts at RNA sites termed Packaging Signals (PSs). These PSs are variations on the TR stem-loop sequence and secondary structure. They act co-operatively to regulate the dominant assembly pathway and ensure cognate RNA encapsidation. In MS2, they also trigger conformational change in the dimeric capsomere creating the A/B quasi-conformer, 60 of which are needed to complete the T=3 capsid. This is the most compelling demonstration to date that this ssRNA virus, and by implications potentially very many of them, assemble via a PS-mediated assembly mechanism.
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Affiliation(s)
- Peter G. Stockley
- Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Simon J. White
- Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Eric Dykeman
- Department of Biology and Mathematics & York Center for Complex Systems Analysis, University of York, York, UK
| | - Iain Manfield
- Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Ottar Rolfsson
- Center for Systems Biology, University of Iceland, University of Iceland Biomedical Center, Reykjavik, Iceland
| | - Nikesh Patel
- Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Richard Bingham
- Department of Biology and Mathematics & York Center for Complex Systems Analysis, University of York, York, UK
| | - Amy Barker
- Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Emma Wroblewski
- Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, UK
| | | | - Eva U. Weiß
- Department of Biology and Mathematics & York Center for Complex Systems Analysis, University of York, York, UK
| | - Neil A. Ranson
- Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Roman Tuma
- Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Reidun Twarock
- Department of Biology and Mathematics & York Center for Complex Systems Analysis, University of York, York, UK
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21
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Paglia G, Williams JP, Menikarachchi L, Thompson JW, Tyldesley-Worster R, Halldórsson S, Rolfsson O, Moseley A, Grant D, Langridge J, Palsson BO, Astarita G. Ion mobility derived collision cross sections to support metabolomics applications. Anal Chem 2014; 86:3985-93. [PMID: 24640936 PMCID: PMC4004193 DOI: 10.1021/ac500405x] [Citation(s) in RCA: 243] [Impact Index Per Article: 24.3] [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: 02/06/2023]
Abstract
Metabolomics is a rapidly evolving analytical approach in life and health sciences. The structural elucidation of the metabolites of interest remains a major analytical challenge in the metabolomics workflow. Here, we investigate the use of ion mobility as a tool to aid metabolite identification. Ion mobility allows for the measurement of the rotationally averaged collision cross-section (CCS), which gives information about the ionic shape of a molecule in the gas phase. We measured the CCSs of 125 common metabolites using traveling-wave ion mobility-mass spectrometry (TW-IM-MS). CCS measurements were highly reproducible on instruments located in three independent laboratories (RSD < 5% for 99%). We also determined the reproducibility of CCS measurements in various biological matrixes including urine, plasma, platelets, and red blood cells using ultra performance liquid chromatography (UPLC) coupled with TW-IM-MS. The mean RSD was < 2% for 97% of the CCS values, compared to 80% of retention times. Finally, as proof of concept, we used UPLC-TW-IM-MS to compare the cellular metabolome of epithelial and mesenchymal cells, an in vitro model used to study cancer development. Experimentally determined and computationally derived CCS values were used as orthogonal analytical parameters in combination with retention time and accurate mass information to confirm the identity of key metabolites potentially involved in cancer. Thus, our results indicate that adding CCS data to searchable databases and to routine metabolomics workflows will increase the identification confidence compared to traditional analytical approaches.
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Affiliation(s)
- Giuseppe Paglia
- Center for Systems Biology, University of Iceland , IS 101, Reykjavik, Iceland
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22
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Rolfsson O, Palsson BØ, Thiele I. The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions. BMC Syst Biol 2011; 5:155. [PMID: 21962087 PMCID: PMC3224382 DOI: 10.1186/1752-0509-5-155] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Accepted: 10/01/2011] [Indexed: 11/29/2022]
Abstract
Background Metabolic network reconstructions formalize our knowledge of metabolism. Gaps in these networks pinpoint regions of metabolism where biological components and functions are "missing." At the same time, a major challenge in the post genomic era involves characterisation of missing biological components to complete genome annotation. Results We used the human metabolic network reconstruction RECON 1 and established constraint-based modelling tools to uncover novel functions associated with human metabolism. Flux variability analysis identified 175 gaps in RECON 1 in the form of blocked reactions. These gaps were unevenly distributed within metabolic pathways but primarily found in the cytosol and often caused by compounds whose metabolic fate, rather than production, is unknown. Using a published algorithm, we computed gap-filling solutions comprised of non-organism specific metabolic reactions capable of bridging the identified gaps. These candidate solutions were found to be dependent upon the reaction environment of the blocked reaction. Importantly, we showed that automatically generated solutions could produce biologically realistic hypotheses of novel human metabolic reactions such as of the fate of iduronic acid following glycan degradation and of N-acetylglutamate in amino acid metabolism. Conclusions The results demonstrate how metabolic models can be utilised to direct hypotheses of novel metabolic functions in human metabolism; a process that we find is heavily reliant upon manual curation and biochemical insight. The effectiveness of a systems approach for novel biochemical pathway discovery in mammals is demonstrated and steps required to tailor future gap filling algorithms to mammalian metabolic networks are proposed.
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Affiliation(s)
- Ottar Rolfsson
- Center for Systems Biology, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland
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23
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Rolfsson O, Toropova K, Morton V, Francese S, Basnak G, Thompson GS, Homans SW, Ashcroft AE, Stonehouse NJ, Ranson NA, Stockley PG. RNA Packing Specificity and Folding during Assembly of the Bacteriophage MS2. Computational and Mathematical Methods in Medicine 2008; 9:339-349. [DOI: 10.1080/17486700802168445] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Using a combination of biochemistry, mass spectrometry, NMR spectroscopy and cryo-electron microscopy (cryo-EM), we have been able to show that quasi-equivalent conformer switching in the coat protein (CP) of an RNA bacteriophage (MS2) is controlled by a sequence-specific RNA–protein interaction. The RNA component of this complex is an RNA stem-loop encompassing just 19 nts from the phage genomic RNA, which is 3569 nts in length. This binding results in the conversion of a CP dimer from a symmetrical conformation to an asymmetric one. Only when both symmetrical and asymmetrical dimers are present in solution is assembly of theT = 3 phage capsid efficient. This implies that the conformers, we have characterized by NMR correspond to the two distinct quasi-equivalent conformers seen in the 3D structure of the virion. An icosahedrally-averaged single particle cryo-EM reconstruction of the wild-type phage (to ∼9 Å resolution) has revealed icosahedrally ordered density encompassing up to 90% of the single-stranded RNA genome. The RNA is seen with a novel arrangement of two concentric shells, with connections between them along the 5-fold symmetry axes. RNA in the outer shell interacts with each of the 90 CP dimers in theT = 3 capsid and although the density is icosahedrally averaged, there appears to be a different average contact at the different quasi-equivalent protein dimers: precisely the result that would be expected if protein conformer switching is RNA-mediated throughout the assembly pathway. This unprecedented RNA structure provides new constraints for models of viral assembly and we describe experiments aimed at probing these. Together, these results suggest that viral genomic RNA folding is an important factor in efficient assembly, and further suggest that RNAs that could sequester viral CPs but not fold appropriately could act as potent inhibitors of viral assembly.
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Affiliation(s)
- Ottar Rolfsson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Katerina Toropova
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Victoria Morton
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Simona Francese
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Gabriella Basnak
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Gary S. Thompson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Stephen W. Homans
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Alison E. Ashcroft
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | | | - Neil A. Ranson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Peter G. Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
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24
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Stockley PG, Rolfsson O, Thompson GS, Basnak G, Francese S, Stonehouse NJ, Homans SW, Ashcroft AE. A simple, RNA-mediated allosteric switch controls the pathway to formation of a T=3 viral capsid. J Mol Biol 2007; 369:541-52. [PMID: 17434527 PMCID: PMC7612263 DOI: 10.1016/j.jmb.2007.03.020] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2007] [Revised: 03/04/2007] [Accepted: 03/05/2007] [Indexed: 10/23/2022]
Abstract
Using mass spectrometry we have detected both assembly intermediates and the final product, the T=3 viral capsid, during reassembly of the RNA bacteriophage MS2. Assembly is only efficient when both types of quasiequivalent coat protein dimer seen in the final capsid are present in solution. NMR experiments confirm that interconversion of these conformers is allosterically regulated by sequence-specific binding of a short RNA stem-loop. Isotope pulse-chase experiments confirm that all intermediates observed are competent for further coat protein addition, i.e., they are all on the pathway to capsid formation, and that the unit of capsid growth is a coat protein dimer. The major intermediate species are dominated by stoichiometries derived from formation of the particle threefold axis, implying that there is a defined pathway toward the T=3 shell. These results provide the first experimental evidence for a detailed mechanistic explanation of the regulation of quasiequivalent capsid assembly. They suggest a direct role for the encapsidated RNA in assembly in vivo, which is consistent with the structure of the genomic RNA within wild-type phage.
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Affiliation(s)
- Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.
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25
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Styrkarsdottir U, Cazier JB, Kong A, Rolfsson O, Larsen H, Bjarnadottir E, Johannsdottir VD, Sigurdardottir MS, Bagger Y, Christiansen C, Reynisdottir I, Grant SFA, Jonasson K, Frigge ML, Gulcher JR, Sigurdsson G, Stefansson K. Linkage of osteoporosis to chromosome 20p12 and association to BMP2. PLoS Biol 2003; 1:E69. [PMID: 14691541 PMCID: PMC270020 DOI: 10.1371/journal.pbio.0000069] [Citation(s) in RCA: 199] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2003] [Accepted: 10/09/2003] [Indexed: 01/16/2023] Open
Abstract
Osteoporotic fractures are a major cause of morbidity and mortality in ageing populations. Osteoporosis, defined as low bone mineral density (BMD) and associated fractures, have significant genetic components that are largely unknown. Linkage analysis in a large number of extended osteoporosis families in Iceland, using a phenotype that combines osteoporotic fractures and BMD measurements, showed linkage to Chromosome 20p12.3 (multipoint allele-sharing LOD, 5.10; p value, 6.3 x 10(-7)), results that are statistically significant after adjusting for the number of phenotypes tested and the genome-wide search. A follow-up association analysis using closely spaced polymorphic markers was performed. Three variants in the bone morphogenetic protein 2 (BMP2) gene, a missense polymorphism and two anonymous single nucleotide polymorphism haplotypes, were determined to be associated with osteoporosis in the Icelandic patients. The association is seen with many definitions of an osteoporotic phenotype, including osteoporotic fractures as well as low BMD, both before and after menopause. A replication study with a Danish cohort of postmenopausal women was conducted to confirm the contribution of the three identified variants. In conclusion, we find that a region on the short arm of Chromosome 20 contains a gene or genes that appear to be a major risk factor for osteoporosis and osteoporotic fractures, and our evidence supports the view that BMP2 is at least one of these genes.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Yu Bagger
- 2Center for Clinical and Basic Research A/SBallerupDenmark
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