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Szadai L, Bartha A, Parada IP, Lakatos A, Pál D, Lengyel AS, de Almeida NP, Jánosi ÁJ, Nogueira F, Szeitz B, Doma V, Woldmar N, Guedes J, Ujfaludi Z, Pahi ZG, Pankotai T, Kim Y, Győrffy B, Baldetorp B, Welinder C, Szasz AM, Betancourt L, Gil J, Appelqvist R, Kwon HJ, Kárpáti S, Kuras M, Murillo JR, Németh IB, Malm J, Fenyö D, Pawłowski K, Horvatovich P, Wieslander E, Kemény LV, Domont G, MarkoVarga G, Sanchez A. Predicting immune checkpoint therapy response in three independent metastatic melanoma cohorts. bioRxiv 2024:2024.05.01.592032. [PMID: 38746333 PMCID: PMC11092593 DOI: 10.1101/2024.05.01.592032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
While Immune checkpoint inhibition (ICI) therapy shows significant efficacy in metastatic melanoma, only about 50% respond, lacking reliable predictive methods. We introduce a panel of six proteins aimed at predicting response to ICI therapy. Evaluating previously reported proteins in two untreated melanoma cohorts, we used a published predictive model (EaSIeR score) to identify potential proteins distinguishing responders and non-responders. Six proteins initially identified in the ICI cohort correlated with predicted response in the untreated cohort. Additionally, three proteins correlated with patient survival, both at the protein, and at the transcript levels, in an independent immunotherapy treated cohort. Our study identifies predictive biomarkers across three melanoma cohorts, suggesting their use in therapeutic decision-making. Abstract Figure
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Nygren D, Torisson G, Happonen L, Mellhammar L, Linder A, Elf J, Yan H, Welinder C, Holm K. Proteomic Characterization of Plasma in Lemierre's Syndrome. Thromb Haemost 2024; 124:432-440. [PMID: 37857346 PMCID: PMC11038868 DOI: 10.1055/a-2195-3927] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 10/18/2023] [Indexed: 10/21/2023]
Abstract
BACKGROUND The underlying mechanisms of thrombosis in Lemierre's syndrome and other septic thrombophlebitis are incompletely understood. Therefore, in this case control study we aimed to generate hypotheses on its pathogenesis by studying the plasma proteome in patients with these conditions. METHODS All patients with Lemierre's syndrome in the Skåne Region, Sweden, were enrolled prospectively during 2017 to 2021 as cases. Age-matched patients with other severe infections were enrolled as controls. Patient plasma samples were analyzed using label-free data-independent acquisition liquid chromatography tandem mass spectrometry. Differentially expressed proteins in Lemierre's syndrome versus other severe infections were highlighted. Functions of differentially expressed proteins were defined based on a literature search focused on previous associations with thrombosis. RESULTS Eight patients with Lemierre's syndrome and 15 with other severe infections were compared. Here, 20/449 identified proteins were differentially expressed between the groups. Of these, 14/20 had functions previously associated with thrombosis. Twelve of 14 had a suggested prothrombotic effect in Lemierre's syndrome, whereas 2/14 had a suggested antithrombotic effect. CONCLUSION Proteins involved in several thrombogenic pathways were differentially expressed in Lemierre's syndrome compared to other severe infections. Among identified proteins, several were associated with endothelial damage, platelet activation, and degranulation, and warrant further targeted studies.
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Affiliation(s)
- David Nygren
- Division of Infection Medicine, Lund University, Lund, Sweden
- Department of Infectious Diseases, Skåne University Hospital, Lund/Malmö, Sweden
| | - Gustav Torisson
- Department of Infectious Diseases, Skåne University Hospital, Lund/Malmö, Sweden
- Department of Translational Medicine, Clinical Infection Medicine, Lund University, Malmö, Sweden
| | - Lotta Happonen
- Division of Infection Medicine, Lund University, Lund, Sweden
| | - Lisa Mellhammar
- Division of Infection Medicine, Lund University, Lund, Sweden
- Department of Infectious Diseases, Skåne University Hospital, Lund/Malmö, Sweden
| | - Adam Linder
- Division of Infection Medicine, Lund University, Lund, Sweden
- Department of Infectious Diseases, Skåne University Hospital, Lund/Malmö, Sweden
| | - Johan Elf
- Center of Thrombosis and Haemostasis, Skåne University Hospital, Malmö, Sweden
| | - Hong Yan
- The Swedish National Infrastructure for Biological Mass Spectrometry (BioMS), Lund University, Lund, Sweden
| | - Charlotte Welinder
- The Swedish National Infrastructure for Biological Mass Spectrometry (BioMS), Lund University, Lund, Sweden
| | - Karin Holm
- Division of Infection Medicine, Lund University, Lund, Sweden
- Department of Infectious Diseases, Skåne University Hospital, Lund/Malmö, Sweden
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Källberg E, Mehmeti-Ajradini M, Björk Gunnarsdottir F, Göransson M, Bergenfelz C, Allaoui Fredriksson R, Hagerling C, Johansson ME, Welinder C, Jirström K, Leandersson K. AIRE is expressed in breast cancer TANs and TAMs to regulate the extrinsic apoptotic pathway and inflammation. J Leukoc Biol 2024; 115:664-678. [PMID: 38060995 DOI: 10.1093/jleuko/qiad152] [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: 08/15/2023] [Revised: 11/02/2023] [Accepted: 11/19/2023] [Indexed: 04/02/2024] Open
Abstract
The autoimmune regulator (AIRE) is a transcriptional regulator expressed in the thymus and is necessary for maintaining immunological self-tolerance. Extrathymic AIRE expression is rare, and a role for AIRE in tumor-associated innate immune cells has not yet been established. In this study, we show that AIRE is expressed in human pro-tumor neutrophils. In breast cancer, AIRE was primarily located to tumor-associated neutrophils (TANs), and to a lesser extent to tumor-associated macrophages (TAMs) and tumor cells. Expression of AIRE in TAN/TAMs, but not in cancer cells, was associated with an adverse prognosis. We show that the functional role for AIRE in neutrophils and macrophages is to regulate expression of immune mediators and the extrinsic apoptotic pathway involving the Fas/TNFR death receptors and cathepsin G. Here, we propose that the role for AIRE in TAN/TAMs in breast tumors is to regulate cell death and inflammation, thus promoting tumor progression.
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Affiliation(s)
- Eva Källberg
- Cancer Immunology, Department of Translational Medicine, Lund University, Jan Waldenströmsg 35, 214 28 Malmö, Sweden
| | - Meliha Mehmeti-Ajradini
- Cancer Immunology, Department of Translational Medicine, Lund University, Jan Waldenströmsg 35, 214 28 Malmö, Sweden
| | - Frida Björk Gunnarsdottir
- Cancer Immunology, Department of Translational Medicine, Lund University, Jan Waldenströmsg 35, 214 28 Malmö, Sweden
| | - Marcus Göransson
- Cancer Immunology, Department of Translational Medicine, Lund University, Jan Waldenströmsg 35, 214 28 Malmö, Sweden
| | - Caroline Bergenfelz
- Cancer Immunology, Department of Translational Medicine, Lund University, Jan Waldenströmsg 35, 214 28 Malmö, Sweden
| | - Roni Allaoui Fredriksson
- Cancer Immunology, Department of Translational Medicine, Lund University, Jan Waldenströmsg 35, 214 28 Malmö, Sweden
| | - Catharina Hagerling
- Cancer Immunology, Department of Translational Medicine, Lund University, Jan Waldenströmsg 35, 214 28 Malmö, Sweden
| | - Martin E Johansson
- Sahlgrenska Center for Cancer Research, Department of Biomedicine, Vasaparken Universitetsplatsen 1, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Charlotte Welinder
- Mass Spectrometry, Department for Clinical Sciences, Lund University, Sölvegatan 19, 221 84 Lund, Sweden
| | - Karin Jirström
- Oncology and Therapeutic Pathology, Department of Clinical Sciences Lund, Lund University, Sölvegatan 19, 221 84 Lund, Sweden
| | - Karin Leandersson
- Cancer Immunology, Department of Translational Medicine, Lund University, Jan Waldenströmsg 35, 214 28 Malmö, Sweden
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de Oliveira KG, Bång-Rudenstam A, Beyer S, Boukredine A, Talbot H, Governa V, Johansson MC, Månsson AS, Forsberg-Nilsson K, Bengzon J, Malmström J, Welinder C, Belting M. Decoding of the surfaceome and endocytome in primary glioblastoma cells identifies potential target antigens in the hypoxic tumor niche. Acta Neuropathol Commun 2024; 12:35. [PMID: 38414005 PMCID: PMC10898066 DOI: 10.1186/s40478-024-01740-z] [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: 12/13/2023] [Accepted: 02/08/2024] [Indexed: 02/29/2024] Open
Abstract
Immunotherapies with antibody-drug-conjugates (ADC) and CAR-T cells, targeted at tumor surface antigens (surfaceome), currently revolutionize clinical oncology. However, target identification warrants a better understanding of the surfaceome and how it is modulated by the tumor microenvironment. Here, we decode the surfaceome and endocytome and its remodeling by hypoxic stress in glioblastoma (GBM), the most common and aggressive brain tumor in adults. We employed a comprehensive approach for global and dynamic profiling of the surfaceome and endocytosed (endocytome) proteins and their regulation by hypoxia in patient-derived GBM cultures. We found a heterogeneous surface-endocytome profile and a divergent response to hypoxia across GBM cultures. We provide a quantitative ranking of more than 600 surface resident and endocytosed proteins, and their regulation by hypoxia, serving as a resource to the cancer research community. As proof-of-concept, the established target antigen CD44 was identified as a commonly and abundantly expressed surface protein with high endocytic activity. Among hypoxia induced proteins, we reveal CXADR, CD47, CD81, BSG, and FXYD6 as potential targets of the stressed GBM niche. We could validate these findings by immunofluorescence analyses in patient tumors and by increased expression in the hypoxic core of GBM spheroids. Selected candidates were finally confronted by treatment studies, showing their high capacity for internalization and ADC delivery. Importantly, we highlight the limited correlation between transcriptomics and proteomics, emphasizing the critical role of membrane protein enrichment strategies and quantitative mass spectrometry. Our findings provide a comprehensive understanding of the surface-endocytome and its remodeling by hypoxia in GBM as a resource for exploration of targets for immunotherapeutic approaches in GBM.
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Affiliation(s)
- Kelin Gonçalves de Oliveira
- Department of Clinical Sciences, Lund, Section of Oncology, Lund University, Barngatan 4, 221 85, Lund, Sweden
| | - Anna Bång-Rudenstam
- Department of Clinical Sciences, Lund, Section of Oncology, Lund University, Barngatan 4, 221 85, Lund, Sweden
| | - Sarah Beyer
- Department of Clinical Sciences, Lund, Section of Oncology, Lund University, Barngatan 4, 221 85, Lund, Sweden
| | - Axel Boukredine
- Department of Clinical Sciences, Lund, Section of Oncology, Lund University, Barngatan 4, 221 85, Lund, Sweden
| | - Hugo Talbot
- Department of Clinical Sciences, Lund, Section of Oncology, Lund University, Barngatan 4, 221 85, Lund, Sweden
| | - Valeria Governa
- Department of Clinical Sciences, Lund, Section of Oncology, Lund University, Barngatan 4, 221 85, Lund, Sweden
| | - Maria C Johansson
- Department of Clinical Sciences, Lund, Section of Oncology, Lund University, Barngatan 4, 221 85, Lund, Sweden
| | - Ann-Sofie Månsson
- Department of Clinical Sciences, Lund, Section of Oncology, Lund University, Barngatan 4, 221 85, Lund, Sweden
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Division of Cancer and Stem Cells, University of Nottingham Biodiscovery Institute, Nottingham, UK
| | - Johan Bengzon
- Department of Clinical Sciences, Section of Neurosurgery, Lund University, Lund, Sweden
| | - Johan Malmström
- Department of Clinical Sciences, Division of Infection Medicine, Lund University, Lund, Sweden
| | - Charlotte Welinder
- Department of Clinical Sciences, Lund, Section of Oncology, Lund University, Barngatan 4, 221 85, Lund, Sweden
| | - Mattias Belting
- Department of Clinical Sciences, Lund, Section of Oncology, Lund University, Barngatan 4, 221 85, Lund, Sweden.
- Department of Hematology, Oncology and Radiophysics, Skåne University Hospital, Lund, Sweden.
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Akula S, Welinder C, Fu Z, Olsson AK, Hellman L. Identification of the Major Protein Components of Human and Cow Saliva. Int J Mol Sci 2023; 24:16838. [PMID: 38069163 PMCID: PMC10705902 DOI: 10.3390/ijms242316838] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/21/2023] [Accepted: 11/26/2023] [Indexed: 12/18/2023] Open
Abstract
Cows produce saliva in very large quantities to lubricate and facilitate food processing. Estimates indicate an amount of 50-150 L per day. Human saliva has previously been found to contain numerous antibacterial components, such as lysozyme, histatins, members of the S-100 family and lactoferrin, to limit pathogen colonization. Cows depend on a complex microbial community in their digestive system for food digestion. Our aim here was to analyze how this would influence the content of their saliva. We therefore sampled saliva from five humans and both nose secretions and saliva from six cows and separated the saliva on SDS-PAGE gradient gels and analyzed the major protein bands with LC-MS/MS. The cow saliva was found to be dominated by a few major proteins only, carbonic anhydrase 6, a pH-stabilizing enzyme and the short palate, lung and nasal epithelium carcinoma-associated protein 2A (SPLUNC2A), also named bovine salivary protein 30 kDa (BSP30) or BPIFA2B. This latter protein has been proposed to play a role in local antibacterial response by binding bacterial lipopolysaccharides (LPSs) and inhibiting bacterial growth but may instead, according to more recent data, primarily have surfactant activity. Numerous peptide fragments of mucin-5B were also detected in different regions of the gel in the MS analysis. Interestingly, no major band on gel was detected representing any of the antibacterial proteins, indicating that cows may produce them at very low levels that do not harm the microbial flora of their digestive system. The nose secretions of the cows primarily contained the odorant protein, a protein thought to be involved in enhancing the sense of smell of the olfactory receptors and the possibility of quickly sensing potential poisonous food components. High levels of secretory IgA were also found in one sample of cow mouth drippings, indicating a strong upregulation during an infection. The human saliva was more complex, containing secretory IgA, amylase, carbonic anhydrase 6, lysozyme, histatins and a number of other less abundant proteins, indicating a major difference to the saliva of cows that show very low levels of antibacterial components, most likely to not harm the microbial flora of the rumen.
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Affiliation(s)
- Srinivas Akula
- Department of Cell and Molecular Biology, Uppsala University, The Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden; (S.A.); (Z.F.)
| | - Charlotte Welinder
- Department of Clinical Sciences Lund, Division of Mass Spectrometry, Lund University, SE-221 00 Lund, Sweden;
| | - Zhirong Fu
- Department of Cell and Molecular Biology, Uppsala University, The Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden; (S.A.); (Z.F.)
| | - Anna-Karin Olsson
- Department of Medical Biochemistry and Microbiology, The Biomedical Center, Box 582, SE-751 23 Uppsala, Sweden;
| | - Lars Hellman
- Department of Cell and Molecular Biology, Uppsala University, The Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden; (S.A.); (Z.F.)
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Zhou J, Welinder C, Ekström P. The Phosphoproteome of the Rd1 Mouse Retina, a Model of Inherited Photoreceptor Degeneration, Changes after Protein Kinase G Inhibition. Int J Mol Sci 2023; 24:9836. [PMID: 37372984 DOI: 10.3390/ijms24129836] [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: 05/04/2023] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023] Open
Abstract
Retinitis pigmentosa (RP) is a frequent cause of blindness among the working population in industrial countries due to the inheritable death of photoreceptors. Though gene therapy was recently approved for mutations in the RPE65 gene, there is in general no effective treatment presently. Previously, abnormally high levels of cGMP and overactivation of its dependent protein kinase (PKG) have been suggested as causative for the fatal effects on photoreceptors, making it meaningful to explore the cGMP-PKG downstream signaling for more pathological insights and novel therapeutic target development purposes. Here, we manipulated the cGMP-PKG system in degenerating retinas from the rd1 mouse model pharmacologically via adding a PKG inhibitory cGMP-analogue to organotypic retinal explant cultures. A combination of phosphorylated peptide enrichment and mass spectrometry was then applied to study the cGMP-PKG-dependent phosphoproteome. We identified a host of novel potential cGMP-PKG downstream substrates and related kinases using this approach and selected the RAF1 protein, which may act as both a substrate and a kinase, for further validation. This showed that the RAS/RAF1/MAPK/ERK pathway may be involved in retinal degeneration in a yet unclarified mechanism, thus deserving further investigation in the future.
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Affiliation(s)
- Jiaming Zhou
- Ophthalmology, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, 221 00 Lund, Sweden
| | - Charlotte Welinder
- Mass Spectrometry, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, 221 00 Lund, Sweden
| | - Per Ekström
- Ophthalmology, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, 221 00 Lund, Sweden
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Rasmussen M, Tolone A, Paquet-Durand F, Welinder C, Schwede F, Ekström P. The photoreceptor protective cGMP-analog Rp-8-Br-PET-cGMPS interacts with cGMP-interactors PKGI, PDE1, PDE6, and PKAI in the degenerating mouse retina. J Comp Neurol 2023; 531:935-951. [PMID: 36989379 DOI: 10.1002/cne.25475] [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: 02/28/2023] [Revised: 07/12/2022] [Accepted: 03/06/2023] [Indexed: 03/31/2023]
Abstract
The inherited eye disease retinitis pigmentosa (RP) causes the loss of photoreceptors by a still unknown cell death mechanism. During this degeneration, cyclic guanosine-3',5'-monophosphate (cGMP) levels become elevated, leading to over-activation of the cGMP-binding protein cGMP-dependent protein kinase (PKG). cGMP analogs selectively modified to have inhibitory actions on PKG have aided in impeding photoreceptor death, and one such cGMP analog is Rp-8-Br-PET-cGMPS. However, cGMP analogs have previously been shown to interact with numerous targets, so to better understand the therapeutic action of Rp-8-Br-PET-cGMPS, it is necessary to elucidate its target-selectivity and hence what potential cellular mechanism(s) it may affect within the photoreceptors. Here, we, therefore, applied affinity chromatography together with mass spectrometry to isolate and identify Rp-8-Br-PET-cGMPS interactors from retinas derived from three different murine RP models (i.e., rd1, rd2, and rd10 mice). Our findings revealed that Rp-8-Br-PET-cGMPS bound seven known cGMP-binding proteins, including PKG1β, PDE1β, PDE1c, PDE6α, and PKA1α. Furthermore, an additional 28 proteins were found to be associated with Rp-8-Br-PET-cGMPS. This latter group included MAPK1/3, which is known to connect with cGMP/PKG in other systems. However, in organotypic retinal cultures, Rp-8-Br-PET-cGMPS had no effect on photoreceptor MAPK1/3 expression or activity. To summarize, Rp-8-Br-PET-cGMPS is more target specific compared to regular cGMP.
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Affiliation(s)
- Michel Rasmussen
- Faculty of Medicine, Department of Clinical Sciences Lund, Lund University, Ophthalmology, Lund, Sweden
| | - Arianna Tolone
- Insitute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | | | - Charlotte Welinder
- Faculty of Medicine, Department of Clinical Sciences Lund, Mass Spectrometry, Lund University, Lund, Sweden
| | - Frank Schwede
- BIOLOG Life Science Institute GmbH & Co. KG, Bremen, Germany
| | - Per Ekström
- Faculty of Medicine, Department of Clinical Sciences Lund, Lund University, Ophthalmology, Lund, Sweden
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Nuñez-Diaz C, Pocevičiūtė D, Schultz N, Welinder C, Swärd K, Wennström M. Contraction of human brain vascular pericytes in response to islet amyloid polypeptide is reversed by pramlintide. Mol Brain 2023; 16:25. [PMID: 36793056 PMCID: PMC9933335 DOI: 10.1186/s13041-023-01013-1] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 02/05/2023] [Indexed: 02/17/2023] Open
Abstract
The islet amyloid polypeptide (IAPP), a pancreas-produced peptide, has beneficial functions in its monomeric form. However, IAPP aggregates, related to type 2 diabetes mellitus (T2DM), are toxic not only for the pancreas, but also for the brain. In the latter, IAPP is often found in vessels, where it is highly toxic for pericytes, mural cells that have contractile properties and regulate capillary blood flow. In the current study, we use a microvasculature model, where human brain vascular pericytes (HBVP) are co-cultured together with human cerebral microvascular endothelial cells, to demonstrate that IAPP oligomers (oIAPP) alter the morphology and contractility of HBVP. Contraction and relaxation of HBVP was verified using the vasoconstrictor sphingosine-1-phosphate (S1P) and vasodilator Y27632, where the former increased, and the latter decreased, the number of HBVP with round morphology. Increased number of round HBVP was also seen after oIAPP stimulation, and the effect was reverted by the IAPP analogue pramlintide, Y27632, and the myosin inhibitor blebbistatin. Inhibition of the IAPP receptor with the antagonist AC187 only reverted IAPP effects partially. Finally, we demonstrate by immunostaining of human brain tissue against laminin that individuals with high amount of brain IAPP levels show significantly lower capillary diameter and altered mural cell morphology compared to individuals with low brain IAPP levels. These results indicate that HBVP, in an in vitro model of microvasculature, respond morphologically to vasoconstrictors, dilators, and myosin inhibitors. They also suggest that oIAPP induces contraction of these mural cells and that pramlintide can reverse such contraction.
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Affiliation(s)
- Cristina Nuñez-Diaz
- grid.4514.40000 0001 0930 2361Cognitive Disorder Research Unit, Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - Dovilė Pocevičiūtė
- grid.4514.40000 0001 0930 2361Cognitive Disorder Research Unit, Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - Nina Schultz
- grid.4514.40000 0001 0930 2361Cognitive Disorder Research Unit, Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - The Netherlands Brain Bank
- grid.419918.c0000 0001 2171 8263Netherlands Institute for Neuroscience, Meibergdreef 47, 1105 BA Amsterdam, The Netherlands
| | - Charlotte Welinder
- grid.4514.40000 0001 0930 2361Faculty of Medicine, Department of Clinical Sciences, Lund, Mass Spectrometry, Lund University, Lund, Sweden
| | - Karl Swärd
- grid.4514.40000 0001 0930 2361Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Malin Wennström
- Cognitive Disorder Research Unit, Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden.
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Rao KU, Li P, Welinder C, Tenland E, Gourdon P, Sturegård E, Ho JCS, Godaly G. Mechanisms of a Mycobacterium tuberculosis Active Peptide. Pharmaceutics 2023; 15:pharmaceutics15020540. [PMID: 36839864 PMCID: PMC9958537 DOI: 10.3390/pharmaceutics15020540] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/10/2023] Open
Abstract
Multidrug-resistant tuberculosis (MDR) continues to pose a threat to public health. Previously, we identified a cationic host defense peptide with activity against Mycobacterium tuberculosis in vivo and with a bactericidal effect against MDR M. tuberculosis at therapeutic concentrations. To understand the mechanisms of this peptide, we investigated its interactions with live M. tuberculosis and liposomes as a model. Peptide interactions with M. tuberculosis inner membranes induced tube-shaped membranous structures and massive vesicle formation, thus leading to bubbling cell death and ghost cell formation. Liposomal studies revealed that peptide insertion into inner membranes induced changes in the peptides' secondary structure and that the membranes were pulled such that they aggregated without permeabilization, suggesting that the peptide has a strong inner membrane affinity. Finally, the peptide targeted essential proteins in M. tuberculosis, such as 60 kDa chaperonins and elongation factor Tu, that are involved in mycolic acid synthesis and protein folding, which had an impact on bacterial proliferation. The observed multifaceted targeting provides additional support for the therapeutic potential of this peptide.
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Affiliation(s)
- Komal Umashankar Rao
- Department of Microbiology, Immunology and Glycobiology, Institution of Laboratory Medicine, Lund University, SE-22362 Lund, Sweden
| | - Ping Li
- Department of Experimental Medical Science, Lund University, SE-22362 Lund, Sweden
| | - Charlotte Welinder
- Swedish National Infrastructure for Biological Mass Spectrometry, Lund University, SE-22362 Lund, Sweden
| | - Erik Tenland
- Department of Microbiology, Immunology and Glycobiology, Institution of Laboratory Medicine, Lund University, SE-22362 Lund, Sweden
| | - Pontus Gourdon
- Department of Experimental Medical Science, Lund University, SE-22362 Lund, Sweden
- Department of Biomedical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Erik Sturegård
- Department of Clinical Microbiology, Institution of Translational Medicine, Lund University, SE-21428 Malmö, Sweden
| | - James C. S. Ho
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637553, Singapore
| | - Gabriela Godaly
- Department of Microbiology, Immunology and Glycobiology, Institution of Laboratory Medicine, Lund University, SE-22362 Lund, Sweden
- Correspondence:
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Tanner L, Bergwik J, Bhongir RKV, Puthia M, Lång P, Ali MN, Welinder C, Önnerfjord P, Erjefält JS, Palmberg L, Andersson G, Egesten A. Tartrate resistant acid phosphatase 5 (TRAP5) mediates immune cell recruitment in a murine model of pulmonary bacterial infection. Front Immunol 2022; 13:1079775. [PMID: 36569898 PMCID: PMC9779928 DOI: 10.3389/fimmu.2022.1079775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 11/18/2022] [Indexed: 12/13/2022] Open
Abstract
Introduction During airway infection, upregulation of proinflammatory cytokines and subsequent immune cell recruitment is essential to mitigate bacterial infection. Conversely, during prolonged and non-resolving airway inflammation, neutrophils contribute to tissue damage and remodeling. This occurs during diseases including cystic fibrosis (CF) and COPD where bacterial pathogens, not least Pseudomonas aeruginosa, contribute to disease progression through long-lasting infections. Tartrate-resistant acid phosphatase (TRAP) 5 is a metalloenzyme expressed by alveolar macrophages and one of its target substrates is the phosphoglycoprotein osteopontin (OPN). Methods We used a knockout mouse strain (Trap5-/-) and BALB/c-Tg (Rela-luc)31Xen mice paired with siRNA administration or functional protein add-back to elucidate the role of Trap5 during bacterial infection. In a series of experiments, Trap5-/- and wild-type control mice received intratracheal administration of P.aerugniosa (Xen41) or LPS, with mice monitored using intravital imaging (IVIS). In addition, multiplex cytokine immunoassays, flow cytometry, multispectral analyses, histological staining were performed. Results In this study, we found that Trap5-/- mice had impaired clearance of P. aeruginosa airway infection and reduced recruitment of immune cells (i.e. neutrophils and inflammatory macrophages). Trap5 knockdown using siRNA resulted in a decreased activation of the proinflammatory transcription factor NF-κB in reporter mice and a subsequent decrease of proinflammatory gene expression. Add-back experiments of enzymatically active TRAP5 to Trap5-/- mice restored immune cell recruitment and bacterial killing. In human CF lung tissue, TRAP5 of alveolar macrophages was detected in proximity to OPN to a higher degree than in normal lung tissue, indicating possible interactions. Discussion Taken together, the findings of this study suggest a key role for TRAP5 in modulating airway inflammation. This could have bearing in diseases such as CF and COPD where excessive neutrophilic inflammation could be targeted by pharmacological inhibitors of TRAP5.
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Affiliation(s)
- Lloyd Tanner
- Respiratory Medicine, Allergology & Palliative Medicine, Department of Clinical Sciences Lund, Lund University and Skåne University Hospital, Lund, Sweden
| | - Jesper Bergwik
- Respiratory Medicine, Allergology & Palliative Medicine, Department of Clinical Sciences Lund, Lund University and Skåne University Hospital, Lund, Sweden
| | - Ravi K. V. Bhongir
- Respiratory Medicine, Allergology & Palliative Medicine, Department of Clinical Sciences Lund, Lund University and Skåne University Hospital, Lund, Sweden
| | - Manoj Puthia
- Department of Dermatology and Venereology, Lund University and Skåne University Hospital, Lund, Sweden,Department of Clinical Sciences Lund, Lund University and Skåne University Hospital, Lund, Sweden
| | - Pernilla Lång
- Division of Pathology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Mohamad N. Ali
- Respiratory Medicine, Allergology & Palliative Medicine, Department of Clinical Sciences Lund, Lund University and Skåne University Hospital, Lund, Sweden
| | - Charlotte Welinder
- Swedish National Infrastructure for Biological Mass Spectrometry (BioMS), Lund University, Lund, Sweden
| | - Patrik Önnerfjord
- Molecular Skeletal Biology, Section for Rheumatology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Jonas S. Erjefält
- Unit of Airway Inflammation, Experimental Medical Sciences, Lund University, Lund, Sweden
| | - Lena Palmberg
- Work Environment Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Solna, Sweden
| | - Göran Andersson
- Division of Pathology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Arne Egesten
- Respiratory Medicine, Allergology & Palliative Medicine, Department of Clinical Sciences Lund, Lund University and Skåne University Hospital, Lund, Sweden,*Correspondence: Arne Egesten,
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11
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Governa V, Talbot H, Gonçalves de Oliveira K, Cerezo-Magaña M, Bång-Rudenstam A, Forsberg-Nilsson K, Malmström J, Bengzon J, Welinder C, Belting M. P12.02.A Landscape of surfaceome and endocytome in human glioma is divergent and depends on cellular spatial organization. Neuro Oncol 2022. [DOI: 10.1093/neuonc/noac174.267] [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: 11/13/2022] Open
Abstract
Abstract
Background
Cell-surface proteins have a key role in drug development, and tumor cell-surface proteins integrated with the plasma membrane (tumor surfaceome, TS) have attracted considerable attention as targets for immunotherapies in cancer. Checkpoint inhibitor blocking antibodies, antibody drug conjugates (ADCs), and CAR-T cells are all directed at the TS. However, a remaining challenge is the lack of strategies to comprehensively map potential TS target antigens for the design of more rational, individualized treatments. Of particular relevance, ADC and other intracellular drug delivery strategies rely on targets that functionally engage in endocytic internalization.
Material and Methods
With the aim to address these challenges and to provide insight into the complexity of the TS, we have developed a versatile technology for TS mapping (TS-MAP). As proof-of-concept, we focused on primary brain tumors that remain among the most aggressive forms of cancer, and for which attempts to conquer the most common variant, glioblastoma (GBM) have failed so far. TS-MAP is compatible with primary 3D cultures and intact patient glioma tumors with preserved tissue architecture, and specifically identifies proteins capable of endocytosis as tractable targets for ADCs and other modalities requiring toxic payload internalization. Moreover, we have curated a TS classifier (SURFME) for categorization of bona fide membrane proteins.
Results
We show how cellular spatial organization (2D vs. 3D) fundamentally transforms the surfaceome and endocytome in glioma with general implications for target screening approaches. The TS-MAP platform was further applied to profile the surfaceome and endocytome landscape in a cohort of freshly resected patient gliomas. We found a highly diverse TS repertoire between patient tumors, not directly associated with grade and histology, which highlights the need for individualized approaches.
Conclusions
The TS-MAP platform and SURFME classifier should be widely applicable to a variety of brain tumors. Our findings in GBM provide new layers of understanding fundamental to the future development of immunotherapy strategies, as well as new procedures for proteomics-based target identification aimed at a better understanding of how to harness the TS for personalized immunotherapy. Our results reflect the oncogenetic multiclonality and transcriptional diversity of gliomas, which warrants future studies that elucidate how the oncogenetic profile and spatial organization synergize to shape the full complexity of the tumor microenvironment.
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12
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Linge P, Jern A, Tydén H, Gullstrand B, Yan H, Welinder C, Kahn R, Jonsen A, Semple J, Bengtsson A. POS0458 ENRICHMENT OF COMPLEMENT, IMMUNOGLOBULINS, AND AUTOANTIBODY TARGETS IN THE PROTEOME OF PLATELETS FROM PATIENTS WITH SYSTEMIC LUPUS ERYTHEMATOSUS (SLE). Ann Rheum Dis 2022. [DOI: 10.1136/annrheumdis-2022-eular.2572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BackgroundSystemic Lupus Erythematosus (SLE) is characterized by autoimmunity towards apoptotic/necrotic cells, complement activation and excessive amounts of circulating immune complexes. Platelets are recognized as immune cells that interacts with innate and adaptive immune functions. They are activated in SLE patients and contribute to an increased susceptibility to thrombosis [1]. Decreased platelet size has been observed in patients with SLE [2], but the mechanism(s) remains unclear. In this study, we have analyzed the complete proteome of platelets with normal and decreased size from SLE patients and from healthy controls (HC).ObjectivesOur aim was to find clues that could explain the morphological differences observed in platelets from SLE patients and to better characterize the role of platelets in SLE.MethodsWe included 23 consecutive patients with SLE, median SLEDAI-2K score was 2, and 10 HC. Blood count, serum complement levels and the presence of antiphospholipid or dsDNA antibodies were analyzed in all patients. Platelet size (forward scatter) and activation status (CD154, PAC1, CD32, PAR1, CD62P and Annexin V) was determined using flow cytometry. The proteome of 10 platelet isolates from SLE (five with smallest and the five with largest average size) and five HC were analyzed using liquid chromatography with tandem mass spectrometry (LC-MS/MS). Data were analyzed using ANOVA, t-test, hierarchical cluster analysis, protein interactions using the STRING software and correlation analysis using spearman correlation.ResultsWe identified a total of 2572 proteins from the platelet isolates. Out of the identified proteins, 396 had significantly different levels, meeting an ANOVA q-value ≤ 0.01. Pairwise t-test analysis, using a fold difference (FD) of ≥ 1.5 and a p-value of ≤ 0.05 as cut off reveled significant differences in the distribution of proteins between groups. Platelets of both SLE groups (small and normal sized) shared higher levels of forty proteins and twenty proteins were reduced, compared to HC. Cytoskeletal functions were overrepresentation in the group of reduced proteins, while proteins with higher levels in platelets from SLE patients included proteins associated with complement and autoantibody targets such as Beta-2-glycoprotein 1, Annexin A5, and Prothrombin. Platelets from SLE patients also shared an abundance in immunoglobulin proteins, with even greater accumulation in the normal sized platelets. SLE platelet heavy constant alpha 1 (r -0.85, p=0.003), heavy constant mu (r -0.64, p=0.05) and heavy constant gamma 3 (r -0.80, p=0.008) was inversely correlated with complement C4 in serum and heavy constant gamma 2 (r -0.648, p=0.049) with complement C3.ConclusionThis study revealed an accumulation of complement proteins, immunoglobulins and known autoantigens in platelets from SLE patients compared to HC. The signature was largely independent of platelet size, but the enrichment of proteins involved in SLE pathogenesis indicates that the composition is influenced by SLE disease mechanisms. This was supported by the inverse correlation between platelet immunoglobulin and serum levels of complement protein C3 and C4. Platelets are known to interact with complement and express the low-affinity immunoglobulin gamma Fc region receptor IIA (CD32), suggesting a role in the clearance of immune complexes [3]. Future studies will have to determine if platelets play a role in the turnover of complement and immune complexes and the potential role of platelets as a source of autoantigens.References[1]Linge, P., et al., The non-haemostatic role of platelets in systemic lupus erythematosus. Nat Rev Rheumatol, 2018. 14(4): p. 195-213.[2]Lood, C., et al., Decreased platelet size is associated with platelet activation and anti-phospholipid syndrome in systemic lupus erythematosus. Rheumatology (Oxford), 2017. 56(3): p. 408-416.[3]Huang, Z.Y., et al., Human platelet FcgammaRIIA and phagocytes in immune-complex clearance. Mol Immunol, 2011. 48(4): p. 691-6.Disclosure of InterestsPetrus Linge: None declared, Andreas Jern: None declared, Helena Tydén: None declared, Birgitta Gullstrand: None declared, Hong Yan: None declared, Charlotte Welinder: None declared, Robin Kahn: None declared, Andreas Jonsen Consultant of: Astra Zeneca and glaxosmithkline, John Semple: None declared, Anders Bengtsson: None declared.
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13
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Linge CP, Jern A, Tydén H, Gullstrand B, Yan H, Welinder C, Kahn R, Jönssen A, Semple JW, Bengtsson AA. Enrichment of complement, immunoglobulins and autoantibody targets in the proteome of platelets from patients with Systemic Lupus Erythematosus (SLE). Thromb Haemost 2022; 122:1486-1501. [PMID: 35419777 PMCID: PMC9420555 DOI: 10.1055/a-1825-2915] [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] [Indexed: 11/04/2022]
Abstract
Background
Systemic lupus erythematosus (SLE) is a complex disease characterized by autoimmunity toward apoptotic cells, excessive amounts of circulating immune complexes, and complement activation. A decreased platelet size has been observed in SLE and their nonhemostatic functions may play an active role in the disease. The main objective of this study was to find clues that could explain their decreased size and functional role, analyzing the entire platelet proteome.
Methods
Platelets were isolated from 23 patients with SLE. The five individuals with the highest and lowest average platelet forward scatter were selected for further analysis. Platelet protein content was analyzed using liquid chromatography with tandem mass spectrometry (LC-MS/MS) and compared with platelets from five healthy controls. Data are available via ProteomeXchange with identifier PXD031202.
Results
Out of 2,572 proteins identified, 396 had significantly different levels (ANOVA
q
-value ≤ 0.01). Forty proteins, including immunoglobulin-, complement- and phosphatidylserine-binding proteins had higher abundance in platelets from SLE patients, largely independent of size (fold difference of ≥1.5 and a
t
-test
p
-value of ≤0.05 as cut-off). Functional characterization revealed increased degranulation and skewed hemostatic balance in platelets from SLE patients. In the SLE proteome, immunoglobulin proteins were negatively correlated to serum complement C3 and C4 and the highest relative levels were detected in platelets of normal size.
Conclusion
Platelets from SLE patients shared a specific protein profile, including immunoglobulins, complement proteins, and autoantigens, largely independent of the platelet size and in agreement with an integrated role for platelets in SLE.
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Affiliation(s)
- Carl Petrus Linge
- Department of Clinical Sciences Lund, Lund University Section for Molecular Skeletal Biology and Rheumatology, Lund, Sweden
| | - Andreas Jern
- Department of Clinical Sciences, Lund University Section for Molecular Skeletal Biology and Rheumatology, Lund, Sweden
| | - Helena Tydén
- Department of Clinical Sciences, Lund University Section for Molecular Skeletal Biology and Rheumatology, Lund, Sweden
| | - Birgitta Gullstrand
- Department of Clinical Sciences, Lund University Section for Molecular Skeletal Biology and Rheumatology, Lund, Sweden
| | - Hong Yan
- BioMS, Swedish National Infrastructure for Biological Mass Spectrometry, Lund, Sweden
| | - Charlotte Welinder
- Department of Clinical Sciences Lund, Lund University Department of Oncology and Pathology, Lund, Sweden
| | - Robin Kahn
- Wallenberg Center for Molecular Medicin, Lund University Faculty of Medicine, Lund, Sweden.,Paediatrics, Lund University Faculty of Medicine, Lund, Sweden
| | - Andreas Jönssen
- Department of Clinical Sciences Lund, Lund University Section for Molecular Skeletal Biology and Rheumatology, Lund, Sweden
| | - John W Semple
- Transfusion Medicine, Lunds Universitet, Lund, Sweden
| | - Anders A Bengtsson
- Department of Clinical Sciences, Lund University Section for Molecular Skeletal Biology and Rheumatology, Lund, Sweden
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14
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Arve-Butler S, Mossberg A, Schmidt T, Welinder C, Yan H, Berthold E, Król P, Kahn R. Neutrophils Lose the Capacity to Suppress T Cell Proliferation Upon Migration Towards Inflamed Joints in Juvenile Idiopathic Arthritis. Front Immunol 2022; 12:795260. [PMID: 35095871 PMCID: PMC8792960 DOI: 10.3389/fimmu.2021.795260] [Citation(s) in RCA: 2] [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: 10/14/2021] [Accepted: 12/23/2021] [Indexed: 02/03/2023] Open
Abstract
Neutrophils are highly abundant in synovial fluid of rheumatic inflamed joints. In oligoarticular juvenile idiopathic arthritis (JIA), synovial fluid neutrophils have impaired effector functions and altered phenotype. We hypothesized that these alterations might impact the immunoregulatory interplay between neutrophils and T cells. In this study we analyzed the suppressive effect of neutrophils, isolated from blood and synovial fluid of oligoarticular JIA patients, on CD4+ T cells activated by CD3/CD28 stimulation. JIA blood neutrophils suppressed T cell proliferation but synovial fluid neutrophils from several patients did not. The loss of T cell suppression was replicated in an in vitro transmigration assay, where healthy control neutrophils migrated into synovial fluid through transwell inserts with endothelial cells and synoviocytes. Non-migrated neutrophils suppressed proliferation of activated CD4+ T cells, but migrated neutrophils had no suppressive effect. Neutrophil suppression of T cells was partly dependent on reactive oxygen species (ROS), demonstrated by impaired suppression in presence of catalase. Migrated neutrophils had reduced ROS production compared to non-migrated neutrophils. A proteomic analysis of transwell-migrated neutrophils identified alterations in proteins related to neutrophil ROS production and degranulation, and biological processes involving protein transport, cell-cell contact and inflammation. In conclusion, neutrophils in synovial fluid of children with JIA have impaired capacity to suppress activated T cells, which may be due to reduced oxidative burst and alterations in proteins related to cell-cell contact and inflammation. The lack of T cell suppression by neutrophils in synovial fluid may contribute to local inflammation and autoimmune reactions in the JIA joint.
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Affiliation(s)
- Sabine Arve-Butler
- Department of Rheumatology, Clinical Sciences Lund, Lund University, Lund, Sweden.,Wallenberg Center for Molecular Medicine, Lund University, Lund, Sweden
| | - Anki Mossberg
- Wallenberg Center for Molecular Medicine, Lund University, Lund, Sweden.,Department of Pediatrics, Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Tobias Schmidt
- Wallenberg Center for Molecular Medicine, Lund University, Lund, Sweden.,Department of Pediatrics, Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Charlotte Welinder
- Department of Clinical Sciences, Division of Oncology, Lund University, Lund, Sweden
| | - Hong Yan
- Swedish National Infrastructure for Biological Mass Spectrometry, Biological Mass Spectrometry (BioMS), Lund, Sweden
| | - Elisabet Berthold
- Department of Rheumatology, Clinical Sciences Lund, Lund University, Lund, Sweden.,Wallenberg Center for Molecular Medicine, Lund University, Lund, Sweden
| | - Petra Król
- Department of Pediatrics, Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Robin Kahn
- Wallenberg Center for Molecular Medicine, Lund University, Lund, Sweden.,Department of Pediatrics, Clinical Sciences Lund, Lund University, Lund, Sweden
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15
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Rasmussen M, Welinder C, Schwede F, Ekström P. The stereospecific interaction sites and target specificity of cGMP analogs in mouse cortex. Chem Biol Drug Des 2021; 99:206-221. [PMID: 34687134 DOI: 10.1111/cbdd.13976] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 09/29/2021] [Accepted: 10/16/2021] [Indexed: 11/30/2022]
Abstract
cGMP interactors play a role in several pathologies and may be targets for cGMP analog-based drugs, but the success of targeting depends on the biochemical stereospecificity between the cGMP-analog and the interactor. The stereospecificity between general cGMP analogs-or such that are selectivity-modified to obtain, for example, inhibitory actions on a specific target, like the cGMP-dependent protein kinase-have previously been investigated. However, the importance of stereospecificity for cGMP-analog binding to interactors is not known. We, therefore, applied affinity chromatography on mouse cortex proteins utilizing analogs with cyclic phosphate (8-AET-cGMP, 2-AH-cGMP, 2'-AHC-cGMP) and selectivity-modified analogs with sulfur-containing cyclic phosphorothioates (Rp/Sp-8-AET-cGMPS, Rp/Sp-2'-AHC-cGMPS) immobilized to agaroses. The results illustrate the cGMP analogs' stereospecific binding for PKG, PKA regulatory subunits and PKA catalytic subunits, PDEs, and EPAC2 and the involvement of these in various KEGG pathways. For the seven agaroses, PKG, PKA regulatory subunits, and PKA catalytic subunits were more prone to be enriched by 2-AH-, 8-AET-, Rp-8-AET-, and Sp-8-AET-cGMP, whereas PDEs and EPAC2 were more likely to be enriched by 2-AH-, Rp-2'-AHC-, and Rp-8-AET-cGMP. Our findings help elucidate the stereospecific-binding sites essential for the interaction between individual cGMP analogs and cGMP-binding proteins, as well as the cGMP analogs' target specificity, which are two crucial parameters in drug design.
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Affiliation(s)
- Michel Rasmussen
- Faculty of Medicine, Department of Clinical Sciences Lund, Ophthalmology, Lund University, Lund, Sweden
| | - Charlotte Welinder
- Faculty of Medicine, Department of Clinical Sciences Lund, Oncology, Lund University, Lund, Sweden
| | - Frank Schwede
- BIOLOG Life Science Institute GmbH & Co. KG, Bremen, Germany
| | - Per Ekström
- Faculty of Medicine, Department of Clinical Sciences Lund, Ophthalmology, Lund University, Lund, Sweden
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16
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Betancourt LH, Gil J, Sanchez A, Doma V, Kuras M, Murillo JR, Velasquez E, Çakır U, Kim Y, Sugihara Y, Parada IP, Szeitz B, Appelqvist R, Wieslander E, Welinder C, de Almeida NP, Woldmar N, Marko‐Varga M, Eriksson J, Pawłowski K, Baldetorp B, Ingvar C, Olsson H, Lundgren L, Lindberg H, Oskolas H, Lee B, Berge E, Sjögren M, Eriksson C, Kim D, Kwon HJ, Knudsen B, Rezeli M, Malm J, Hong R, Horvath P, Szász AM, Tímár J, Kárpáti S, Horvatovich P, Miliotis T, Nishimura T, Kato H, Steinfelder E, Oppermann M, Miller K, Florindi F, Zhou Q, Domont GB, Pizzatti L, Nogueira FCS, Szadai L, Németh IB, Ekedahl H, Fenyö D, Marko‐Varga G. The Human Melanoma Proteome Atlas-Complementing the melanoma transcriptome. Clin Transl Med 2021; 11:e451. [PMID: 34323402 PMCID: PMC8299047 DOI: 10.1002/ctm2.451] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/17/2021] [Accepted: 05/20/2021] [Indexed: 12/12/2022] Open
Abstract
The MM500 meta-study aims to establish a knowledge basis of the tumor proteome to serve as a complement to genome and transcriptome studies. Somatic mutations and their effect on the transcriptome have been extensively characterized in melanoma. However, the effects of these genetic changes on the proteomic landscape and the impact on cellular processes in melanoma remain poorly understood. In this study, the quantitative mass-spectrometry-based proteomic analysis is interfaced with pathological tumor characterization, and associated with clinical data. The melanoma proteome landscape, obtained by the analysis of 505 well-annotated melanoma tumor samples, is defined based on almost 16 000 proteins, including mutated proteoforms of driver genes. More than 50 million MS/MS spectra were analyzed, resulting in approximately 13,6 million peptide spectrum matches (PSMs). Altogether 13 176 protein-coding genes, represented by 366 172 peptides, in addition to 52 000 phosphorylation sites, and 4 400 acetylation sites were successfully annotated. This data covers 65% and 74% of the predicted and identified human proteome, respectively. A high degree of correlation (Pearson, up to 0.54) with the melanoma transcriptome of the TCGA repository, with an overlap of 12 751 gene products, was found. Mapping of the expressed proteins with quantitation, spatiotemporal localization, mutations, splice isoforms, and PTM variants was proven not to be predicted by genome sequencing alone. The melanoma tumor molecular map was complemented by analysis of blood protein expression, including data on proteins regulated after immunotherapy. By adding these key proteomic pillars, the MM500 study expands the knowledge on melanoma disease.
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17
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Betancourt LH, Gil J, Kim Y, Doma V, Çakır U, Sanchez A, Murillo JR, Kuras M, Parada IP, Sugihara Y, Appelqvist R, Wieslander E, Welinder C, Velasquez E, de Almeida NP, Woldmar N, Marko‐Varga M, Pawłowski K, Eriksson J, Szeitz B, Baldetorp B, Ingvar C, Olsson H, Lundgren L, Lindberg H, Oskolas H, Lee B, Berge E, Sjögren M, Eriksson C, Kim D, Kwon HJ, Knudsen B, Rezeli M, Hong R, Horvatovich P, Miliotis T, Nishimura T, Kato H, Steinfelder E, Oppermann M, Miller K, Florindi F, Zhou Q, Domont GB, Pizzatti L, Nogueira FCS, Horvath P, Szadai L, Tímár J, Kárpáti S, Szász AM, Malm J, Fenyö D, Ekedahl H, Németh IB, Marko‐Varga G. The human melanoma proteome atlas-Defining the molecular pathology. Clin Transl Med 2021; 11:e473. [PMID: 34323403 PMCID: PMC8255060 DOI: 10.1002/ctm2.473] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 03/12/2021] [Revised: 06/03/2021] [Accepted: 06/08/2021] [Indexed: 01/19/2023] Open
Abstract
The MM500 study is an initiative to map the protein levels in malignant melanoma tumor samples, focused on in-depth histopathology coupled to proteome characterization. The protein levels and localization were determined for a broad spectrum of diverse, surgically isolated melanoma tumors originating from multiple body locations. More than 15,500 proteoforms were identified by mass spectrometry, from which chromosomal and subcellular localization was annotated within both primary and metastatic melanoma. The data generated by global proteomic experiments covered 72% of the proteins identified in the recently reported high stringency blueprint of the human proteome. This study contributes to the NIH Cancer Moonshot initiative combining detailed histopathological presentation with the molecular characterization for 505 melanoma tumor samples, localized in 26 organs from 232 patients.
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18
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Butler DSC, Cafaro C, Putze J, Wan MLY, Tran TH, Ambite I, Ahmadi S, Kjellström S, Welinder C, Chao SM, Dobrindt U, Svanborg C. A bacterial protease depletes c-MYC and increases survival in mouse models of bladder and colon cancer. Nat Biotechnol 2021; 39:754-764. [PMID: 33574609 DOI: 10.1038/s41587-020-00805-3] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 12/15/2020] [Indexed: 01/12/2023]
Abstract
Is the oncogene MYC upregulated or hyperactive? In the majority of human cancers, finding agents that target c-MYC has proved difficult. Here we report specific bacterial effector molecules that inhibit cellular MYC (c-MYC) in human cells. We show that uropathogenic Escherichia coli (UPEC) degrade the c-MYC protein and attenuate MYC expression in both human cells and animal tissues. c-MYC protein was rapidly degraded by both cell-free bacterial lysates and the purified bacterial protease Lon. In mice, intravesical or peroral delivery of Lon protease delayed tumor progression and increased survival in MYC-dependent bladder and colon cancer models, respectively. These results suggest that bacteria have evolved strategies to control c-MYC tissue levels in the host and that the Lon protease shows promise for therapeutic targeting of c-MYC in cancer.
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Affiliation(s)
- Daniel S C Butler
- Department of Laboratory Medicine, Division of Microbiology, Immunology and Glycobiology, Lund University, Lund, Sweden
| | - Caterina Cafaro
- Department of Laboratory Medicine, Division of Microbiology, Immunology and Glycobiology, Lund University, Lund, Sweden
| | - Johannes Putze
- Institute of Hygiene, University of Münster, Münster, Germany
| | - Murphy Lam Yim Wan
- Department of Laboratory Medicine, Division of Microbiology, Immunology and Glycobiology, Lund University, Lund, Sweden
| | - Thi Hien Tran
- Department of Laboratory Medicine, Division of Microbiology, Immunology and Glycobiology, Lund University, Lund, Sweden
| | - Ines Ambite
- Department of Laboratory Medicine, Division of Microbiology, Immunology and Glycobiology, Lund University, Lund, Sweden
| | - Shahram Ahmadi
- Department of Laboratory Medicine, Division of Microbiology, Immunology and Glycobiology, Lund University, Lund, Sweden
| | - Sven Kjellström
- Department of Clinical Sciences, BioMS, Lund University, Lund, Sweden
| | - Charlotte Welinder
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Sing Ming Chao
- Department of Paediatrics, Nephrology Service, KK Women's and Children's Hospital, Singapore, Singapore
| | - Ulrich Dobrindt
- Institute of Hygiene, University of Münster, Münster, Germany
| | - Catharina Svanborg
- Department of Laboratory Medicine, Division of Microbiology, Immunology and Glycobiology, Lund University, Lund, Sweden.
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19
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Bergwik J, Kristiansson A, Welinder C, Göransson O, Hansson SR, Gram M, Erlandsson L, Åkerström B. Knockout of the radical scavenger α 1-microglobulin in mice results in defective bikunin synthesis, endoplasmic reticulum stress and increased body weight. Free Radic Biol Med 2021; 162:160-170. [PMID: 32092411 DOI: 10.1016/j.freeradbiomed.2020.02.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 11/19/2019] [Revised: 02/14/2020] [Accepted: 02/19/2020] [Indexed: 01/22/2023]
Abstract
α1-microglobulin (A1M) is a ubiquitous protein with reductase and radical- and heme-binding properties. The protein is mainly expressed in the liver and encoded by the α1-microglobulin-bikunin precursor (AMBP) gene together with the plasma proteinase inhibitor bikunin. The AMBP polypeptide is translated, glycosylated and the C-terminal bikunin part linked via a chondroitin sulfate glycosaminoglycan chain to one or two heavy chains in the endoplasmic reticulum (ER) and Golgi compartments. After proteolytic cleavage, the A1M protein and complexed bikunin parts are secreted separately. The complete physiological role of A1M, and the reason for the co-synthesis with bikunin, are both still unknown. The aim of this work was to develop an A1M knockout (A1M-KO) mouse model lacking expression of A1M, but with a preserved bikunin expression, and to study the phenotypic traits in these mice, with a focus on hepatic endoplasmic reticulum (ER) function. The bikunin expression was increased in the A1M-KO mouse livers, while the bikunin levels in plasma were decreased, indicating a defective biosynthesis of bikunin. The A1M-KO livers also showed an increased expression of transducers of the unfolded protein response (UPR), indicating an increased ER-stress in the livers. At twelve months of age, the A1M-KO mice also displayed an increased body weight, and an increased liver weight and lipid accumulation. Moreover, the KO mice showed an increased expression of endogenous antioxidants in the liver, but not in the kidneys. Together, these results suggest a physiological role of A1M as a regulator of the intracellular redox environment and more specifically the ER folding and posttranslational modification processes, particularly in the liver.
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Affiliation(s)
- Jesper Bergwik
- Section for Infection Medicine, Department of Clinical Sciences in Lund, Lund University, Lund, Sweden
| | - Amanda Kristiansson
- Section for Infection Medicine, Department of Clinical Sciences in Lund, Lund University, Lund, Sweden
| | - Charlotte Welinder
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Olga Göransson
- Protein Phosphorylation Unit, Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Stefan R Hansson
- Section for Obstetrics and Gynecology, Department of Clinical Sciences in Lund, Lund University, Lund, Sweden
| | - Magnus Gram
- Section for Infection Medicine, Department of Clinical Sciences in Lund, Lund University, Lund, Sweden
| | - Lena Erlandsson
- Section for Obstetrics and Gynecology, Department of Clinical Sciences in Lund, Lund University, Lund, Sweden
| | - Bo Åkerström
- Section for Infection Medicine, Department of Clinical Sciences in Lund, Lund University, Lund, Sweden.
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Rasmussen M, Welinder C, Schwede F, Ekström P. The cGMP system in normal and degenerating mouse neuroretina: New proteins with cGMP interaction potential identified by a proteomics approach. J Neurochem 2020; 157:2173-2186. [PMID: 33230839 PMCID: PMC8359485 DOI: 10.1111/jnc.15251] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 11/19/2020] [Accepted: 11/20/2020] [Indexed: 12/17/2022]
Abstract
The hereditary disease Retinitis pigmentosa results in severe vision loss due to photoreceptor degeneration by unclear mechanisms. In several disease models, the second messenger cGMP accumulates in the degenerating photoreceptors, where it may over‐activate specific cGMP‐interacting proteins, like cGMP‐dependent protein kinase. Moreover, interventions that counteract the activity of these proteins lead to reduced photoreceptor cell death. Yet there is little or no information whether other than such regular cGMP‐interactors are present in the retina, which we, therefore, investigated in wild‐type and retinal degeneration (rd1, rd10, and rd2) mouse models. An affinity chromatography based proteomics approach that utilized immobilized cGMP analogs was applied to enrich and select for regular and potentially new cGMP‐interacting proteins as identified by mass spectrometry. This approach revealed 12 regular and 10 potentially new retinal cGMP‐interacting proteins (e.g., EPAC2 and CaMKIIα). Several of the latter were found to be expressed in the photoreceptors and to have proximity to cGMP and may thus be of interest when defining prospective therapeutic targets or biomarkers for retinal degeneration.
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Affiliation(s)
- Michel Rasmussen
- Faculty of Medicine, Department of Clinical Sciences Lund, Lund University, Ophthalmology, Lund, Sweden
| | - Charlotte Welinder
- Faculty of Medicine, Department of Clinical Sciences Lund, Oncology, Lund University, Lund, Sweden
| | - Frank Schwede
- BIOLOG Life Science Institute GmbH & Co. KG, Bremen, Germany
| | - Per Ekström
- Faculty of Medicine, Department of Clinical Sciences Lund, Lund University, Ophthalmology, Lund, Sweden
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21
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Sanchez A, Kuras M, Murillo JR, Pla I, Pawlowski K, Szasz AM, Gil J, Nogueira FCS, Perez-Riverol Y, Eriksson J, Appelqvist R, Miliotis T, Kim Y, Baldetorp B, Ingvar C, Olsson H, Lundgren L, Ekedahl H, Horvatovich P, Sugihara Y, Welinder C, Wieslander E, Kwon HJ, Domont GB, Malm J, Rezeli M, Betancourt LH, Marko-Varga G. Novel functional proteins coded by the human genome discovered in metastases of melanoma patients. Cell Biol Toxicol 2020; 36:261-272. [PMID: 31599373 PMCID: PMC7320927 DOI: 10.1007/s10565-019-09494-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 05/21/2019] [Accepted: 09/02/2019] [Indexed: 12/18/2022]
Abstract
In the advanced stages, malignant melanoma (MM) has a very poor prognosis. Due to tremendous efforts in cancer research over the last 10 years, and the introduction of novel therapies such as targeted therapies and immunomodulators, the rather dark horizon of the median survival has dramatically changed from under 1 year to several years. With the advent of proteomics, deep-mining studies can reach low-abundant expression levels. The complexity of the proteome, however, still surpasses the dynamic range capabilities of current analytical techniques. Consequently, many predicted protein products with potential biological functions have not yet been verified in experimental proteomic data. This category of 'missing proteins' (MP) is comprised of all proteins that have been predicted but are currently unverified. As part of the initiative launched in 2016 in the USA, the European Cancer Moonshot Center has performed numerous deep proteomics analyses on samples from MM patients. In this study, nine MPs were clearly identified by mass spectrometry in MM metastases. Some MPs significantly correlated with proteins that possess identical PFAM structural domains; and other MPs were significantly associated with cancer-related proteins. This is the first study to our knowledge, where unknown and novel proteins have been annotated in metastatic melanoma tumour tissue.
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Affiliation(s)
- Aniel Sanchez
- Section for Clinical Chemistry, Department of Translational Medicine, Skåne University Hospital Malmö, Lund University, 205 02, Malmö, Sweden.
| | - Magdalena Kuras
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Jimmy Rodriguez Murillo
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Indira Pla
- Section for Clinical Chemistry, Department of Translational Medicine, Skåne University Hospital Malmö, Lund University, 205 02, Malmö, Sweden
| | - Krzysztof Pawlowski
- Section for Clinical Chemistry, Department of Translational Medicine, Skåne University Hospital Malmö, Lund University, 205 02, Malmö, Sweden
- Biology, Warsaw University of Life Sciences, Warsaw, Poland
| | - A Marcell Szasz
- Cancer Center, Semmelweis University, Budapest, 1083, Hungary
| | - Jeovanis Gil
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Fábio C S Nogueira
- Proteomics Unit, Department of Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratory of Proteomics, LADETEC, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Yasset Perez-Riverol
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD Hinxton, Cambridge, UK
| | - Jonatan Eriksson
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Roger Appelqvist
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | | | - Yonghyo Kim
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Bo Baldetorp
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Christian Ingvar
- Department of Surgery, Clinical Sciences, Skåne University Hospital, Lund University, Lund, Sweden
| | - Håkan Olsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Lotta Lundgren
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
- Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Henrik Ekedahl
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Peter Horvatovich
- Department of Analytical Biochemistry, Faculty of Science and Engineering, University of Groningen, Groningen, The Netherlands
| | - Yutaka Sugihara
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Charlotte Welinder
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Elisabet Wieslander
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Ho Jeong Kwon
- Department of Biotechnology, Yonsei University, Seoul, South Korea
| | - Gilberto B Domont
- Proteomics Unit, Department of Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Johan Malm
- Section for Clinical Chemistry, Department of Translational Medicine, Skåne University Hospital Malmö, Lund University, 205 02, Malmö, Sweden
| | - Melinda Rezeli
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Lazaro Hiram Betancourt
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden.
| | - György Marko-Varga
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
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22
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Mohlin S, Hansson K, Radke K, Martinez S, Blanco-Aparicio C, Garcia-Ruiz C, Welinder C, Esfandyari J, O'Neill M, Pastor J, von Stedingk K, Bexell D. Anti-tumor effects of PIM/PI3K/mTOR triple kinase inhibitor IBL-302 in neuroblastoma. EMBO Mol Med 2020; 12:e11749. [PMID: 31916402 PMCID: PMC6949485 DOI: 10.15252/emmm.201911749] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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23
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Betancourt LH, Szasz AM, Kuras M, Rodriguez Murillo J, Sugihara Y, Pla I, Horvath Z, Pawłowski K, Rezeli M, Miharada K, Gil J, Eriksson J, Appelqvist R, Miliotis T, Baldetorp B, Ingvar C, Olsson H, Lundgren L, Horvatovich P, Welinder C, Wieslander E, Kwon HJ, Malm J, Nemeth IB, Jönsson G, Fenyö D, Sanchez A, Marko-Varga G. The Hidden Story of Heterogeneous B-raf V600E Mutation Quantitative Protein Expression in Metastatic Melanoma-Association with Clinical Outcome and Tumor Phenotypes. Cancers (Basel) 2019; 11:E1981. [PMID: 31835364 PMCID: PMC6966659 DOI: 10.3390/cancers11121981] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [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: 10/30/2019] [Revised: 11/23/2019] [Accepted: 12/03/2019] [Indexed: 02/07/2023] Open
Abstract
In comparison to other human cancer types, malignant melanoma exhibits the greatest amount of heterogeneity. After DNA-based detection of the BRAF V600E mutation in melanoma patients, targeted inhibitor treatment is the current recommendation. This approach, however, does not take the abundance of the therapeutic target, i.e., the B-raf V600E protein, into consideration. As shown by immunohistochemistry, the protein expression profiles of metastatic melanomas clearly reveal the existence of inter- and intra-tumor variability. Nevertheless, the technique is only semi-quantitative. To quantitate the mutant protein there is a fundamental need for more precise techniques that are aimed at defining the currently non-existent link between the levels of the target protein and subsequent drug efficacy. Using cutting-edge mass spectrometry combined with DNA and mRNA sequencing, the mutated B-raf protein within metastatic tumors was quantitated for the first time. B-raf V600E protein analysis revealed a subjacent layer of heterogeneity for mutation-positive metastatic melanomas. These were characterized into two distinct groups with different tumor morphologies, protein profiles and patient clinical outcomes. This study provides evidence that a higher level of expression in the mutated protein is associated with a more aggressive tumor progression. Our study design, comprised of surgical isolation of tumors, histopathological characterization, tissue biobanking, and protein analysis, may enable the eventual delineation of patient responders/non-responders and subsequent therapy for malignant melanoma.
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Affiliation(s)
- Lazaro Hiram Betancourt
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical, Engineering, Lund University, BMC D13, 221 84 Lund, Sweden; (L.H.B.); (Z.H.); (M.R.); (J.G.); (J.E.); (R.A.); (G.M.-V.)
| | - A. Marcell Szasz
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical, Engineering, Lund University, BMC D13, 221 84 Lund, Sweden; (L.H.B.); (Z.H.); (M.R.); (J.G.); (J.E.); (R.A.); (G.M.-V.)
- Cancer Center, Semmelweis University, Budapest 1083, Hungary
| | - Magdalena Kuras
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02 Malmö, Sweden; (M.K.); (I.P.); (K.P.); (J.M.); (A.S.)
| | - Jimmy Rodriguez Murillo
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17 177 Stockholm, Sweden; (J.R.M.); (Y.S.)
| | - Yutaka Sugihara
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17 177 Stockholm, Sweden; (J.R.M.); (Y.S.)
| | - Indira Pla
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02 Malmö, Sweden; (M.K.); (I.P.); (K.P.); (J.M.); (A.S.)
| | - Zsolt Horvath
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical, Engineering, Lund University, BMC D13, 221 84 Lund, Sweden; (L.H.B.); (Z.H.); (M.R.); (J.G.); (J.E.); (R.A.); (G.M.-V.)
| | - Krzysztof Pawłowski
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02 Malmö, Sweden; (M.K.); (I.P.); (K.P.); (J.M.); (A.S.)
- Department of Biochemistry and Microbiology, Warsaw University of Life Sciences, 02-787 Warsaw, Poland
| | - Melinda Rezeli
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical, Engineering, Lund University, BMC D13, 221 84 Lund, Sweden; (L.H.B.); (Z.H.); (M.R.); (J.G.); (J.E.); (R.A.); (G.M.-V.)
| | - Kenichi Miharada
- Department of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, Sölvegatan 17, 221 84 Lund, Sweden;
| | - Jeovanis Gil
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical, Engineering, Lund University, BMC D13, 221 84 Lund, Sweden; (L.H.B.); (Z.H.); (M.R.); (J.G.); (J.E.); (R.A.); (G.M.-V.)
| | - Jonatan Eriksson
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical, Engineering, Lund University, BMC D13, 221 84 Lund, Sweden; (L.H.B.); (Z.H.); (M.R.); (J.G.); (J.E.); (R.A.); (G.M.-V.)
| | - Roger Appelqvist
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical, Engineering, Lund University, BMC D13, 221 84 Lund, Sweden; (L.H.B.); (Z.H.); (M.R.); (J.G.); (J.E.); (R.A.); (G.M.-V.)
| | - Tasso Miliotis
- Translational Science, Cardiovascular Renal and Metabolism, IMED Biotech Unit, AstraZeneca, 431 50 Gothenburg, Sweden;
| | - Bo Baldetorp
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85 Lund, Sweden; (B.B.); (H.O.); (L.L.); (C.W.); (E.W.); (G.J.)
| | - Christian Ingvar
- Department of Surgery, Clinical Sciences, Lund University, Skåne University Hospital, 222 42 Lund, Sweden;
| | - Håkan Olsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85 Lund, Sweden; (B.B.); (H.O.); (L.L.); (C.W.); (E.W.); (G.J.)
| | - Lotta Lundgren
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85 Lund, Sweden; (B.B.); (H.O.); (L.L.); (C.W.); (E.W.); (G.J.)
| | - Peter Horvatovich
- Department of Analytical Biochemistry, Faculty of Science and Engineering, University of Groningen, 9712 CP Groningen, The Netherlands;
| | - Charlotte Welinder
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85 Lund, Sweden; (B.B.); (H.O.); (L.L.); (C.W.); (E.W.); (G.J.)
| | - Elisabet Wieslander
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85 Lund, Sweden; (B.B.); (H.O.); (L.L.); (C.W.); (E.W.); (G.J.)
| | - Ho Jeong Kwon
- Department of Biotechnology, Yonsei University, Seoul 03722, Korea;
| | - Johan Malm
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02 Malmö, Sweden; (M.K.); (I.P.); (K.P.); (J.M.); (A.S.)
| | - Istvan Balazs Nemeth
- Department of Dermatology and Allergology, University of Szeged, H-6720 Szeged, Hungary;
| | - Göran Jönsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85 Lund, Sweden; (B.B.); (H.O.); (L.L.); (C.W.); (E.W.); (G.J.)
| | - David Fenyö
- Institute for Systems Genetics, NYU School of Medicine, 550 1st Ave, New York, NY 10016, USA;
| | - Aniel Sanchez
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02 Malmö, Sweden; (M.K.); (I.P.); (K.P.); (J.M.); (A.S.)
| | - György Marko-Varga
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical, Engineering, Lund University, BMC D13, 221 84 Lund, Sweden; (L.H.B.); (Z.H.); (M.R.); (J.G.); (J.E.); (R.A.); (G.M.-V.)
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24
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Indira Chandran V, Welinder C, Gonçalves de Oliveira K, Cerezo-Magaña M, Månsson AS, Johansson MC, Marko-Varga G, Belting M. Global extracellular vesicle proteomic signature defines U87-MG glioma cell hypoxic status with potential implications for non-invasive diagnostics. J Neurooncol 2019; 144:477-488. [PMID: 31414377 PMCID: PMC6764937 DOI: 10.1007/s11060-019-03262-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 08/06/2019] [Indexed: 12/17/2022]
Abstract
Purpose Glioblastoma multiforme (GBM) is the most common and lethal of primary malignant brain tumors. Hypoxia constitutes a major determining factor for the poor prognosis of high-grade glioma patients, and is known to contribute to the development of treatment resistance. Therefore, new strategies to comprehensively profile and monitor the hypoxic status of gliomas are of high clinical relevance. Here, we have explored how the proteome of secreted extracellular vesicles (EVs) at the global level may reflect hypoxic glioma cells. Methods We have employed shotgun proteomics and label free quantification to profile EVs isolated from human high-grade glioma U87-MG cells cultured at normoxia or hypoxia. Parallel reaction monitoring was used to quantify the identified, hypoxia-associated EV proteins. To determine the potential biological significance of hypoxia-associated proteins, the cumulative Z score of identified EV proteins was compared with GBM subtypes from HGCC and TCGA databases. Results In total, 2928 proteins were identified in EVs, out of which 1654 proteins overlapped with the ExoCarta EV-specific database. We found 1034 proteins in EVs that were unique to the hypoxic status of U87-MG cells. We subsequently identified an EV protein signature, “HYPSIGNATURE”, encompassing nine proteins that strongly represented the hypoxic situation and exhibited close proximity to the mesenchymal GBM subtype. Conclusions We propose, for the first time, an EV protein signature that could comprehensively reflect the hypoxic status of high-grade glioma cells. The presented data provide proof-of-concept for targeted proteomic profiling of glioma derived EVs, which should motivate future studies exploring its utility in non-invasive diagnosis and monitoring of brain tumor patients. Electronic supplementary material The online version of this article (10.1007/s11060-019-03262-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vineesh Indira Chandran
- Department of Clinical Sciences, Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden.
| | - Charlotte Welinder
- Department of Clinical Sciences, Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | | | - Myriam Cerezo-Magaña
- Department of Clinical Sciences, Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Ann-Sofie Månsson
- Department of Clinical Sciences, Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Maria C Johansson
- Department of Clinical Sciences, Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Gyorgy Marko-Varga
- Department of Biomedical Engineering, Clinical Protein Science & Imaging, Biomedical Center, Lund University, Lund, Sweden
| | - Mattias Belting
- Department of Clinical Sciences, Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden.,Department of Hematology, Oncology and Radiophysics, Skåne University Hospital, Lund, Sweden.,Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
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25
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Gil J, Betancourt LH, Pla I, Sanchez A, Appelqvist R, Miliotis T, Kuras M, Oskolas H, Kim Y, Horvath Z, Eriksson J, Berge E, Burestedt E, Jönsson G, Baldetorp B, Ingvar C, Olsson H, Lundgren L, Horvatovich P, Murillo JR, Sugihara Y, Welinder C, Wieslander E, Lee B, Lindberg H, Pawłowski K, Kwon HJ, Doma V, Timar J, Karpati S, Szasz AM, Németh IB, Nishimura T, Corthals G, Rezeli M, Knudsen B, Malm J, Marko-Varga G. Clinical protein science in translational medicine targeting malignant melanoma. Cell Biol Toxicol 2019; 35:293-332. [PMID: 30900145 PMCID: PMC6757020 DOI: 10.1007/s10565-019-09468-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [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: 12/04/2018] [Accepted: 02/13/2019] [Indexed: 02/06/2023]
Abstract
Melanoma of the skin is the sixth most common type of cancer in Europe and accounts for 3.4% of all diagnosed cancers. More alarming is the degree of recurrence that occurs with approximately 20% of patients lethally relapsing following treatment. Malignant melanoma is a highly aggressive skin cancer and metastases rapidly extend to the regional lymph nodes (stage 3) and to distal organs (stage 4). Targeted oncotherapy is one of the standard treatment for progressive stage 4 melanoma, and BRAF inhibitors (e.g. vemurafenib, dabrafenib) combined with MEK inhibitor (e.g. trametinib) can effectively counter BRAFV600E-mutated melanomas. Compared to conventional chemotherapy, targeted BRAFV600E inhibition achieves a significantly higher response rate. After a period of cancer control, however, most responsive patients develop resistance to the therapy and lethal progression. The many underlying factors potentially causing resistance to BRAF inhibitors have been extensively studied. Nevertheless, the remaining unsolved clinical questions necessitate alternative research approaches to address the molecular mechanisms underlying metastatic and treatment-resistant melanoma. In broader terms, proteomics can address clinical questions far beyond the reach of genomics, by measuring, i.e. the relative abundance of protein products, post-translational modifications (PTMs), protein localisation, turnover, protein interactions and protein function. More specifically, proteomic analysis of body fluids and tissues in a given medical and clinical setting can aid in the identification of cancer biomarkers and novel therapeutic targets. Achieving this goal requires the development of a robust and reproducible clinical proteomic platform that encompasses automated biobanking of patient samples, tissue sectioning and histological examination, efficient protein extraction, enzymatic digestion, mass spectrometry-based quantitative protein analysis by label-free or labelling technologies and/or enrichment of peptides with specific PTMs. By combining data from, e.g. phosphoproteomics and acetylomics, the protein expression profiles of different melanoma stages can provide a solid framework for understanding the biology and progression of the disease. When complemented by proteogenomics, customised protein sequence databases generated from patient-specific genomic and transcriptomic data aid in interpreting clinical proteomic biomarker data to provide a deeper and more comprehensive molecular characterisation of cellular functions underlying disease progression. In parallel to a streamlined, patient-centric, clinical proteomic pipeline, mass spectrometry-based imaging can aid in interrogating the spatial distribution of drugs and drug metabolites within tissues at single-cell resolution. These developments are an important advancement in studying drug action and efficacy in vivo and will aid in the development of more effective and safer strategies for the treatment of melanoma. A collaborative effort of gargantuan proportions between academia and healthcare professionals has led to the initiation, establishment and development of a cutting-edge cancer research centre with a specialisation in melanoma and lung cancer. The primary research focus of the European Cancer Moonshot Lund Center is to understand the impact that drugs have on cancer at an individualised and personalised level. Simultaneously, the centre increases awareness of the relentless battle against cancer and attracts global interest in the exceptional research performed at the centre.
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Affiliation(s)
- Jeovanis Gil
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden.
| | - Lazaro Hiram Betancourt
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden.
| | - Indira Pla
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02, Malmö, Sweden
| | - Aniel Sanchez
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02, Malmö, Sweden
| | - Roger Appelqvist
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Tasso Miliotis
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Translational Science, Cardiovascular Renal and Metabolism, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Magdalena Kuras
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Henriette Oskolas
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Yonghyo Kim
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Zsolt Horvath
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Jonatan Eriksson
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Ethan Berge
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Elisabeth Burestedt
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Göran Jönsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Bo Baldetorp
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Christian Ingvar
- Department of Surgery, Clinical Sciences, Lund University, SUS, Lund, Sweden
| | - Håkan Olsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Lotta Lundgren
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
- Department of Haematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Peter Horvatovich
- Department of Analytical Biochemistry, Faculty of Science and Engineering, University of Groningen, Groningen, The Netherlands
| | - Jimmy Rodriguez Murillo
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Yutaka Sugihara
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Charlotte Welinder
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Elisabet Wieslander
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Boram Lee
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Henrik Lindberg
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Krzysztof Pawłowski
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Department of Experimental Design and Bioinformatics, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Ho Jeong Kwon
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Chemical Genomics Global Research Lab, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Viktoria Doma
- Second Department of Pathology, Semmelweis University, Budapest, Hungary
| | - Jozsef Timar
- Second Department of Pathology, Semmelweis University, Budapest, Hungary
| | - Sarolta Karpati
- Department of Dermatology, Semmelweis University, Budapest, Hungary
| | - A Marcell Szasz
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
- Cancer Center, Semmelweis University, Budapest, 1083, Hungary
- MTA-TTK Momentum Oncology Biomarker Research Group, Hungarian Academy of Sciences, Budapest, 1117, Hungary
| | - István Balázs Németh
- Department of Dermatology and Allergology, University of Szeged, Szeged, H-6720, Hungary
| | - Toshihide Nishimura
- Clinical Translational Medicine Informatics, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
- Department of Surgery, Tokyo Medical University, 6-7-1 Nishishinjiku Shinjiku-ku, Tokyo, Japan
| | - Garry Corthals
- Van't Hoff Institute of Molecular Sciences, 1090 GS, Amsterdam, The Netherlands
| | - Melinda Rezeli
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Beatrice Knudsen
- Biomedical Sciences and Pathology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Johan Malm
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02, Malmö, Sweden
| | - György Marko-Varga
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Chemical Genomics Global Research Lab, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
- Department of Surgery, Tokyo Medical University, 6-7-1 Nishishinjiku Shinjiku-ku, Tokyo, Japan
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26
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Mohlin S, Hansson K, Radke K, Martinez S, Blanco-Apiricio C, Garcia-Ruiz C, Welinder C, Esfandyari J, O'Neill M, Pastor J, von Stedingk K, Bexell D. Anti-tumor effects of PIM/PI3K/mTOR triple kinase inhibitor IBL-302 in neuroblastoma. EMBO Mol Med 2019; 11:e10058. [PMID: 31310053 PMCID: PMC6685085 DOI: 10.15252/emmm.201810058] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [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: 11/12/2018] [Revised: 06/04/2019] [Accepted: 06/24/2019] [Indexed: 11/12/2022] Open
Abstract
The PI3K pathway is a major driver of cancer progression. However, clinical resistance to PI3K inhibition is common. IBL‐302 is a novel highly specific triple PIM, PI3K, and mTOR inhibitor. Screening IBL‐302 in over 700 cell lines representing 47 tumor types identified neuroblastoma as a strong candidate for PIM/PI3K/mTOR inhibition. IBL‐302 was more effective than single PI3K inhibition in vitro, and IBL‐302 treatment of neuroblastoma patient‐derived xenograft (PDX) cells induced apoptosis, differentiated tumor cells, and decreased N‐Myc protein levels. IBL‐302 further enhanced the effect of the common cytotoxic chemotherapies cisplatin, doxorubicin, and etoposide. Global genome, proteome, and phospho‐proteome analyses identified crucial biological processes, including cell motility and apoptosis, targeted by IBL‐302 treatment. While IBL‐302 treatment alone reduced tumor growth in vivo, combination therapy with low‐dose cisplatin inhibited neuroblastoma PDX growth. Complementing conventional chemotherapy treatment with PIM/PI3K/mTOR inhibition has the potential to improve clinical outcomes and reduce severe late effects in children with high‐risk neuroblastoma.
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Affiliation(s)
- Sofie Mohlin
- Division of Pediatrics, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Karin Hansson
- Department of Laboratory Medicine, Translational Cancer Research, Lund University Cancer Center, Lund University, Lund, Sweden
| | - Katarzyna Radke
- Department of Laboratory Medicine, Translational Cancer Research, Lund University Cancer Center, Lund University, Lund, Sweden
| | - Sonia Martinez
- Experimental Therapeutics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Carmen Blanco-Apiricio
- Experimental Therapeutics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Cristian Garcia-Ruiz
- Department of Laboratory Medicine, Translational Cancer Research, Lund University Cancer Center, Lund University, Lund, Sweden
| | - Charlotte Welinder
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Javanshir Esfandyari
- Department of Laboratory Medicine, Translational Cancer Research, Lund University Cancer Center, Lund University, Lund, Sweden
| | | | - Joaquin Pastor
- Experimental Therapeutics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Kristoffer von Stedingk
- Division of Pediatrics, Department of Clinical Sciences, Lund University, Lund, Sweden.,Department of Oncogenomics, University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Daniel Bexell
- Department of Laboratory Medicine, Translational Cancer Research, Lund University Cancer Center, Lund University, Lund, Sweden
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27
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Betancourt LH, Pawłowski K, Eriksson J, Szasz AM, Mitra S, Pla I, Welinder C, Ekedahl H, Broberg P, Appelqvist R, Yakovleva M, Sugihara Y, Miharada K, Ingvar C, Lundgren L, Baldetorp B, Olsson H, Rezeli M, Wieslander E, Horvatovich P, Malm J, Jönsson G, Marko-Varga G. Improved survival prognostication of node-positive malignant melanoma patients utilizing shotgun proteomics guided by histopathological characterization and genomic data. Sci Rep 2019; 9:5154. [PMID: 30914758 PMCID: PMC6435712 DOI: 10.1038/s41598-019-41625-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 08/20/2018] [Accepted: 03/13/2019] [Indexed: 12/18/2022] Open
Abstract
Metastatic melanoma is one of the most common deadly cancers, and robust biomarkers are still needed, e.g. to predict survival and treatment efficiency. Here, protein expression analysis of one hundred eleven melanoma lymph node metastases using high resolution mass spectrometry is coupled with in-depth histopathology analysis, clinical data and genomics profiles. This broad view of protein expression allowed to identify novel candidate protein markers that improved prediction of survival in melanoma patients. Some of the prognostic proteins have not been reported in the context of melanoma before, and few of them exhibit unexpected relationship to survival, which likely reflects the limitations of current knowledge on melanoma and shows the potential of proteomics in clinical cancer research.
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Affiliation(s)
| | - Krzysztof Pawłowski
- Lund University, Lund, Sweden.
- Warsaw University of Life Sciences SGGW, Warszawa, Poland.
| | | | - A Marcell Szasz
- Lund University, Lund, Sweden
- National Koranyi Institute of Pulmonology, Budapest, Hungary
- Semmelweis University, Budapest, Hungary
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Peter Horvatovich
- Lund University, Lund, Sweden
- University of Groningen, Groningen, The Netherlands
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28
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Indira Chandran V, Welinder C, Månsson AS, Offer S, Freyhult E, Pernemalm M, Lund SM, Pedersen S, Lehtiö J, Marko-Varga G, Johansson MC, Englund E, Sundgren PC, Belting M. Ultrasensitive Immunoprofiling of Plasma Extracellular Vesicles Identifies Syndecan-1 as a Potential Tool for Minimally Invasive Diagnosis of Glioma. Clin Cancer Res 2019; 25:3115-3127. [PMID: 30679164 DOI: 10.1158/1078-0432.ccr-18-2946] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 11/16/2018] [Accepted: 01/16/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE Liquid biopsy has great potential to improve the management of brain tumor patients at high risk of surgery-associated complications. Here, the aim was to explore plasma extracellular vesicle (plEV) immunoprofiling as a tool for noninvasive diagnosis of glioma. EXPERIMENTAL DESIGN PlEV isolation and analysis were optimized using advanced mass spectrometry, nanoparticle tracking analysis, and electron microscopy. We then established a new procedure that combines size exclusion chromatography isolation and proximity extension assay-based ultrasensitive immunoprofiling of plEV proteins that was applied on a well-defined glioma study cohort (n = 82). RESULTS Among potential candidates, we for the first time identify syndecan-1 (SDC1) as a plEV constituent that can discriminate between high-grade glioblastoma multiforme (GBM, WHO grade IV) and low-grade glioma [LGG, WHO grade II; area under the ROC curve (AUC): 0.81; sensitivity: 71%; specificity: 91%]. These findings were independently validated by ELISA. Tumor SDC1 mRNA expression similarly discriminated between GBM and LGG in an independent glioma patient population from The Cancer Genome Atlas cohort (AUC: 0.91; sensitivity: 79%; specificity: 91%). In experimental studies with GBM cells, we show that SDC1 is efficiently sorted to secreted EVs. Importantly, we found strong support of plEVSDC1 originating from GBM tumors, as plEVSDC1 correlated with SDC1 protein expression in matched patient tumors, and plEVSDC1 was decreased postoperatively depending on the extent of surgery. CONCLUSIONS Our studies support the concept of circulating plEVs as a tool for noninvasive diagnosis and monitoring of gliomas and should move this field closer to the goal of improving the management of cancer patients.
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Affiliation(s)
- Vineesh Indira Chandran
- Department of Clinical Sciences, Lund, Section of Oncology and Pathology, Lund University, Lund, Sweden
| | - Charlotte Welinder
- Department of Clinical Sciences, Lund, Section of Oncology and Pathology, Lund University, Lund, Sweden.,Center of Excellence in Biological and Medical Mass Spectrometry (CEBMMS), Lund University, Lund, Sweden
| | - Ann-Sofie Månsson
- Department of Clinical Sciences, Lund, Section of Oncology and Pathology, Lund University, Lund, Sweden
| | - Svenja Offer
- Department of Clinical Sciences, Lund, Section of Oncology and Pathology, Lund University, Lund, Sweden
| | - Eva Freyhult
- National Bioinformatics Infrastructure, SciLife Lab, Uppsala, Sweden
| | - Maria Pernemalm
- Department of Oncology and Pathology, Karolinska Institute, Solna, Sweden
| | - Sigrid M Lund
- Department of Clinical Biochemistry, Aalborg University Hospital, Aalborg, Denmark
| | - Shona Pedersen
- Department of Clinical Biochemistry, Aalborg University Hospital, Aalborg, Denmark.,Faculty of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Janne Lehtiö
- Department of Oncology and Pathology, Karolinska Institute, Solna, Sweden
| | - Gyorgy Marko-Varga
- Center of Excellence in Biological and Medical Mass Spectrometry (CEBMMS), Lund University, Lund, Sweden.,Clinical Protein Science and Imaging, Biomedical Center, Department of Biomedical Engineering, Lund University, Lund, Sweden
| | - Maria C Johansson
- Department of Clinical Sciences, Lund, Section of Oncology and Pathology, Lund University, Lund, Sweden
| | - Elisabet Englund
- Department of Clinical Sciences, Lund, Section of Oncology and Pathology, Lund University, Lund, Sweden
| | - Pia C Sundgren
- Department of Clinical Sciences, Lund, Section of Diagnostic Radiology, Lund University, Lund, Sweden.,Lund BioImaging Centre, Lund University, Lund, Sweden.,Department of Medical Imaging and Function, Skåne University Hospital, Lund, Lund, Sweden
| | - Mattias Belting
- Department of Clinical Sciences, Lund, Section of Oncology and Pathology, Lund University, Lund, Sweden. .,Department of Hematology, Oncology and Radiophysics, Skåne University Hospital, Lund, Sweden.,Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
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29
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Wendel U, Persson N, Risinger C, Bengtsson E, Nodin B, Danielsson L, Welinder C, Nordin Fredrikson G, Jansson B, Blixt O. A novel monoclonal antibody targeting carboxymethyllysine, an advanced glycation end product in atherosclerosis and pancreatic cancer. PLoS One 2018; 13:e0191872. [PMID: 29420566 PMCID: PMC5805250 DOI: 10.1371/journal.pone.0191872] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [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: 10/24/2017] [Accepted: 01/13/2018] [Indexed: 12/12/2022] Open
Abstract
Advanced glycation end products are formed by non-enzymatic reactions between proteins and carbohydrates, causing irreversible lysine and arginine alterations that severely affect protein structure and function. The resulting modifications induce inflammation by binding to scavenger receptors. An increase in advanced glycation end products is observed in a number of diseases e.g. atherosclerosis and cancer. Since advanced glycation end products also are present in healthy individuals, their detection and quantification are of great importance for usage as potential biomarkers. Current methods for advanced glycation end product detection are though limited and solely measure total glycation. This study describes a new epitope-mapped single chain variable fragment, D1-B2, against carboxymethyllysine, produced from a phage library that was constructed from mouse immunizations. The phage library was selected against advanced glycation end product targets using a phage display platform. Characterization of its binding pattern was performed using large synthetic glycated peptide and protein libraries displayed on microarray slides. D1-B2 showed a preference for an aspartic acid, three positions N-terminally from a carboxymethyllysine residue and also bound to a broad collection of glycated proteins. Positive immunohistochemical staining of mouse atherosclerotic plaques and of a tissue microarray of human pancreatic tumors confirmed the usability of the new scFv for advanced glycation end product detection in tissues. This study demonstrates a promising methodology for high-throughput generation of epitope-mapped monoclonal antibodies against AGE.
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Affiliation(s)
- Ulrika Wendel
- Chemical Glyco-Biology Laboratory, Department of Chemistry, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Nina Persson
- Chemical Glyco-Biology Laboratory, Department of Chemistry, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Christian Risinger
- Chemical Glyco-Biology Laboratory, Department of Chemistry, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Eva Bengtsson
- Department of Clinical Sciences Malmö, Scania University Hospital, Malmö Lund University, Malmö, Sweden
| | - Björn Nodin
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Lena Danielsson
- Clinical Chemistry and Pharmacology, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Charlotte Welinder
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Centre of Excellence in Biological and Medical Mass Spectrometry “CEBMMS”, Biomedical Centre D13, Lund University, Lund, Sweden
| | - Gunilla Nordin Fredrikson
- Department of Clinical Sciences Malmö, Scania University Hospital, Malmö Lund University, Malmö, Sweden
| | - Bo Jansson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Ola Blixt
- Chemical Glyco-Biology Laboratory, Department of Chemistry, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
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30
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Hu D, Ansari D, Pawłowski K, Zhou Q, Sasor A, Welinder C, Kristl T, Bauden M, Rezeli M, Jiang Y, Marko-Varga G, Andersson R. Proteomic analyses identify prognostic biomarkers for pancreatic ductal adenocarcinoma. Oncotarget 2018. [PMID: 29515771 PMCID: PMC5839402 DOI: 10.18632/oncotarget.23929] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy. Here we show that shotgun and targeted protein sequencing can be used to identify potential prognostic biomarkers in formalin-fixed paraffin-embedded specimens from 9 patients with PDAC with “short” survival (<12 months) and 10 patients with “long” survival (>45 months) undergoing surgical resection. A total of 24 and 147 proteins were significantly upregulated [fold change ≥2 or ≤0.5 and P<0.05; or different detection frequencies (≥5 samples)] in patients with “short” survival (including GLUT1) and “long” survival (including C9orf64, FAM96A, CDH1 and CDH17), respectively. STRING analysis of these proteins indicated a tight protein-protein interaction network centered on TP53. Ingenuity pathway analysis linked proteins representing “activated stroma factors” and “basal tumor factors” to poor prognosis of PDAC. It also highlighted TCF1 and CTNNB1 as possible upstream regulators. Further parallel reaction monitoring verified that seven proteins were upregulated in patients with “short” survival (MMP9, CLIC3, MMP8, PRTN3, P4HA2, THBS1 and FN1), while 18 proteins were upregulated in patients with “long” survival, including EPCAM, LGALS4, VIL1, CLCA1 and TPPP3. Thus, we verified 25 protein biomarker candidates for PDAC prognosis at the tissue level. Furthermore, an activated stroma status and protein-protein interactions with TP53 might be linked to poor prognosis of PDAC.
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Affiliation(s)
- Dingyuan Hu
- Lund University, Faculty of Medicine, Department of Clinical Sciences Lund (Surgery), Lund, Sweden.,Department of Gastroenterology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Daniel Ansari
- Lund University, Skane University Hospital, Department of Clinical Sciences Lund (Surgery), Lund, Sweden
| | - Krzysztof Pawłowski
- Department of Experimental Design and Bioinformatics, Warsaw University of Life Sciences, Warsaw, Poland.,Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Qimin Zhou
- Lund University, Faculty of Medicine, Department of Clinical Sciences Lund (Surgery), Lund, Sweden
| | - Agata Sasor
- Department of Pathology, Skåne University Hospital, Lund, Sweden
| | - Charlotte Welinder
- Lund University, Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund, Sweden
| | - Theresa Kristl
- Lund University, Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund, Sweden
| | - Monika Bauden
- Lund University, Faculty of Medicine, Department of Clinical Sciences Lund (Surgery), Lund, Sweden
| | - Melinda Rezeli
- Department of Biomedical Engineering, Clinical Protein Science and Imaging, Lund University, Lund, Sweden
| | - Yi Jiang
- Department of Gastroenterology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - György Marko-Varga
- Department of Biomedical Engineering, Clinical Protein Science and Imaging, Lund University, Lund, Sweden
| | - Roland Andersson
- Lund University, Skane University Hospital, Department of Clinical Sciences Lund (Surgery), Lund, Sweden
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31
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Persson N, Stuhr-Hansen N, Risinger C, Mereiter S, Polónia A, Polom K, Kovács A, Roviello F, Reis CA, Welinder C, Danielsson L, Jansson B, Blixt O. Epitope mapping of a new anti-Tn antibody detecting gastric cancer cells. Glycobiology 2017; 27:635-645. [DOI: 10.1093/glycob/cwx033] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/11/2017] [Indexed: 12/15/2022] Open
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32
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Welinder C, Pawłowski K, Szasz AM, Yakovleva M, Sugihara Y, Malm J, Jönsson G, Ingvar C, Lundgren L, Baldetorp B, Olsson H, Rezeli M, Laurell T, Wieslander E, Marko-Varga G. Correlation of histopathologic characteristics to protein expression and function in malignant melanoma. PLoS One 2017; 12:e0176167. [PMID: 28445515 PMCID: PMC5405986 DOI: 10.1371/journal.pone.0176167] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [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: 10/31/2016] [Accepted: 04/06/2017] [Indexed: 12/11/2022] Open
Abstract
Background Metastatic melanoma is still one of the most prevalent skin cancers, which upon progression has neither a prognostic marker nor a specific and lasting treatment. Proteomic analysis is a versatile approach with high throughput data and results that can be used for characterizing tissue samples. However, such analysis is hampered by the complexity of the disease, heterogeneity of patients, tumors, and samples themselves. With the long term aim of quest for better diagnostics biomarkers, as well as predictive and prognostic markers, we focused on relating high resolution proteomics data to careful histopathological evaluation of the tumor samples and patient survival information. Patients and methods Regional lymph node metastases obtained from ten patients with metastatic melanoma (stage III) were analyzed by histopathology and proteomics using mass spectrometry. Out of the ten patients, six had clinical follow-up data. The protein deep mining mass spectrometry data was related to the histopathology tumor tissue sections adjacent to the area used for deep-mining. Clinical follow-up data provided information on disease progression which could be linked to protein expression aiming to identify tissue-based specific protein markers for metastatic melanoma and prognostic factors for prediction of progression of stage III disease. Results In this feasibility study, several proteins were identified that positively correlated to tumor tissue content including IF6, ARF4, MUC18, UBC12, CSPG4, PCNA, PMEL and MAGD2. The study also identified MYC, HNF4A and TGFB1 as top upstream regulators correlating to tumor tissue content. Other proteins were inversely correlated to tumor tissue content, the most significant being; TENX, EHD2, ZA2G, AOC3, FETUA and THRB. A number of proteins were significantly related to clinical outcome, among these, HEXB, PKM and GPNMB stood out, as hallmarks of processes involved in progression from stage III to stage IV disease and poor survival. Conclusion In this feasibility study, promising results show the feasibility of relating proteomics to histopathology and clinical outcome, and insight thus can be gained into the molecular processes driving the disease. The combined analysis of histological features including the sample cellular composition with protein expression of each metastasis enabled the identification of novel, differentially expressed proteins. Further studies are necessary to determine whether these putative biomarkers can be utilized in diagnostics and prognostic prediction of metastatic melanoma.
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Affiliation(s)
- Charlotte Welinder
- Division of Oncology and Pathology, Dept. of Clinical Sciences Lund, Lund University, Lund, Sweden
- Centre of Excellence in Biological and Medical Mass Spectrometry “CEBMMS”, Biomedical Centre D13, Lund University, Lund, Sweden
| | - Krzysztof Pawłowski
- Faculty of Agriculture and Biology, Dept. of Experimental Design and Bioinformatics, Warsaw University of Life Sciences, Warszawa, Poland
- Dept. of Translational Medicine, Lund University, Malmö, Sweden
| | - A. Marcell Szasz
- Division of Oncology and Pathology, Dept. of Clinical Sciences Lund, Lund University, Lund, Sweden
- Centre of Excellence in Biological and Medical Mass Spectrometry “CEBMMS”, Biomedical Centre D13, Lund University, Lund, Sweden
- 2nd Dept. of Pathology, Semmelweis University, Budapest, Hungary
| | - Maria Yakovleva
- Centre of Excellence in Biological and Medical Mass Spectrometry “CEBMMS”, Biomedical Centre D13, Lund University, Lund, Sweden
| | - Yutaka Sugihara
- Division of Oncology and Pathology, Dept. of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Johan Malm
- Centre of Excellence in Biological and Medical Mass Spectrometry “CEBMMS”, Biomedical Centre D13, Lund University, Lund, Sweden
- Dept. of Translational Medicine, Lund University, Malmö, Sweden
| | - Göran Jönsson
- Division of Oncology and Pathology, Dept. of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Christian Ingvar
- Dept. of Surgery, Dept. of Clinical Sciences Lund, Lund University, Skåne University Hospital, Lund, Sweden
| | - Lotta Lundgren
- Division of Oncology and Pathology, Dept. of Clinical Sciences Lund, Lund University, Lund, Sweden
- Dept. of Oncology, Skåne University Hospital, Lund, Sweden
| | - Bo Baldetorp
- Division of Oncology and Pathology, Dept. of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Håkan Olsson
- Division of Oncology and Pathology, Dept. of Clinical Sciences Lund, Lund University, Lund, Sweden
- Dept. of Oncology, Skåne University Hospital, Lund, Sweden
- Cancer Epidemiology, Dept. of Clinical Sciences, Lund University, Lund, Sweden
| | - Melinda Rezeli
- Clinical Protein Science & Imaging, Biomedical Centre, Dept. of Biomedical Engineering, Lund University, BMC D13, Lund, Sweden
| | - Thomas Laurell
- Centre of Excellence in Biological and Medical Mass Spectrometry “CEBMMS”, Biomedical Centre D13, Lund University, Lund, Sweden
- Clinical Protein Science & Imaging, Biomedical Centre, Dept. of Biomedical Engineering, Lund University, BMC D13, Lund, Sweden
| | - Elisabet Wieslander
- Division of Oncology and Pathology, Dept. of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - György Marko-Varga
- Centre of Excellence in Biological and Medical Mass Spectrometry “CEBMMS”, Biomedical Centre D13, Lund University, Lund, Sweden
- Clinical Protein Science & Imaging, Biomedical Centre, Dept. of Biomedical Engineering, Lund University, BMC D13, Lund, Sweden
- First Dept. of Surgery, Tokyo Medical University, Tokyo, Japan
- * E-mail:
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33
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Persson N, Jansson B, Stuhr-Hansen N, Kovács A, Welinder C, Danielsson L, Blixt O. A Combinatory Antibody-Antigen Microarray Assay for High-Content Screening of Single-Chain Fragment Variable Clones from Recombinant Libraries. PLoS One 2016; 11:e0168761. [PMID: 28002485 PMCID: PMC5176327 DOI: 10.1371/journal.pone.0168761] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [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: 07/14/2016] [Accepted: 12/06/2016] [Indexed: 12/30/2022] Open
Abstract
We have developed a combinatory antibody–antigen microarray for direct screening of multiple single-chain fragment variable (scFv) clones with no need for pre-purification or enrichment before screening. The straightforward workflow allows for early selection of binders to predefined peptide and glycopeptide targets. A capture antibody is contact printed on microarray slides, side by side with the antigens of interest. A large number of scFv clones, in supernatants, are printed on top of the capture antibody and the antigen in a “spot-on-spot” print. The printed scFv clones, which bind to the capture antibody, are detected using biotinylated antigen, while the binding of scFv clones to the printed antigen is detected through a mouse anti-tag antibody. Two different analyses are thus performed on the same slide, generating two kinds of information: one on the ability of an individual scFv clone to bind to the soluble form of the antigen, which may favour selection for higher affinity rather than avidity, while the other allows the identification of large numbers of clones, simultaneously, due to the binding of scFv clones to densely presented antigens, thus providing an overall increased hit rate. The functionality of the new screening approach was illustrated through the generation of antibodies against peptides from the chaperone complex Ku70/Ku80 and the GalNAcα-serine/threonine epitope on the IgA1 alpha chain hinge region. In total, 659 scFv clones were screened with a hit rate of approximately 20%. This approach allowed the identification of functional antibodies in both cases, illustrating the usefulness and capacity of this combinatory microarray screening technique for efficient analysis and validation of antibodies at an early stage of antibody generation.
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Affiliation(s)
- Nina Persson
- Chemical Glyco-Biology Laboratory, Department of Chemistry, Copenhagen University, Copenhagen, Denmark
| | - Bo Jansson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Nicolai Stuhr-Hansen
- Chemical Glyco-Biology Laboratory, Department of Chemistry, Copenhagen University, Copenhagen, Denmark
| | - András Kovács
- Chemical Glyco-Biology Laboratory, Department of Chemistry, Copenhagen University, Copenhagen, Denmark
- Division of Clinical Chemistry and Pharmacology, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Charlotte Welinder
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Centre of Excellence in Biological and Medical Mass Spectrometry (CEBMMS), Biomedical Centre D13, Lund University, Lund, Sweden
| | - Lena Danielsson
- Division of Clinical Chemistry and Pharmacology, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Ola Blixt
- Chemical Glyco-Biology Laboratory, Department of Chemistry, Copenhagen University, Copenhagen, Denmark
- * E-mail:
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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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Menard JA, Christianson HC, Kucharzewska P, Bourseau-Guilmain E, Svensson KJ, Lindqvist E, Indira Chandran V, Kjellén L, Welinder C, Bengzon J, Johansson MC, Belting M. Metastasis Stimulation by Hypoxia and Acidosis-Induced Extracellular Lipid Uptake Is Mediated by Proteoglycan-Dependent Endocytosis. Cancer Res 2016; 76:4828-40. [PMID: 27199348 DOI: 10.1158/0008-5472.can-15-2831] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 05/05/2016] [Indexed: 01/03/2023]
Abstract
Hypoxia and acidosis are inherent stress factors of the tumor microenvironment and have been linked to increased tumor aggressiveness and treatment resistance. Molecules involved in the adaptive mechanisms that drive stress-induced disease progression constitute interesting candidates of therapeutic intervention. Here, we provide evidence of a novel role of heparan sulfate proteoglycans (HSPG) in the adaptive response of tumor cells to hypoxia and acidosis through increased internalization of lipoproteins, resulting in a lipid-storing phenotype and enhanced tumor-forming capacity. Patient glioblastoma tumors and cells under hypoxic and acidic stress acquired a lipid droplet (LD)-loaded phenotype, and showed an increased recruitment of all major lipoproteins, HDL, LDL, and VLDL. Stress-induced LD accumulation was associated with increased spheroid-forming capacity during reoxygenation in vitro and lung metastatic potential in vivo On a mechanistic level, we found no apparent effect of hypoxia on HSPGs, whereas lipoprotein receptors (VLDLR and SR-B1) were transiently upregulated by hypoxia. Importantly, however, using pharmacologic and genetic approaches, we show that stress-mediated lipoprotein uptake is highly dependent on intact HSPG expression. The functional relevance of HSPG in the context of tumor cell stress was evidenced by HSPG-dependent lipoprotein cell signaling activation through the ERK/MAPK pathway and by reversal of the LD-loaded phenotype by targeting of HSPGs. We conclude that HSPGs may have an important role in the adaptive response to major stress factors of the tumor microenvironment, with functional consequences on tumor cell signaling and metastatic potential. Cancer Res; 76(16); 4828-40. ©2016 AACR.
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Affiliation(s)
- Julien A Menard
- Department of Clinical Sciences, Section of Oncology and Pathology, Lund University, Lund, Sweden
| | - Helena C Christianson
- Department of Clinical Sciences, Section of Oncology and Pathology, Lund University, Lund, Sweden
| | - Paulina Kucharzewska
- Department of Clinical Sciences, Section of Oncology and Pathology, Lund University, Lund, Sweden
| | - Erika Bourseau-Guilmain
- Department of Clinical Sciences, Section of Oncology and Pathology, Lund University, Lund, Sweden
| | - Katrin J Svensson
- Dana-Farber Cancer Institute and Department of Cell Biology, Harvard Medical School, Boston, Massachusetts
| | - Eva Lindqvist
- Department of Clinical Sciences, Section of Oncology and Pathology, Lund University, Lund, Sweden
| | - Vineesh Indira Chandran
- Department of Clinical Sciences, Section of Oncology and Pathology, Lund University, Lund, Sweden
| | - Lena Kjellén
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Charlotte Welinder
- Department of Clinical Sciences, Section of Oncology and Pathology, Lund University, Lund, Sweden. Center of Excellence in Biological and Medical Mass Spectrometry "CEBMMS", Biomedical Centre D13, Lund University, Lund, Sweden
| | - Johan Bengzon
- Lund Stem Cell Center, Lund University, Lund, Sweden. Department of Clinical Sciences, Section of Neurosurgery, Lund University, Lund, Sweden
| | - Maria C Johansson
- Department of Clinical Sciences, Section of Oncology and Pathology, Lund University, Lund, Sweden
| | - Mattias Belting
- Department of Clinical Sciences, Section of Oncology and Pathology, Lund University, Lund, Sweden. Skåne University Hospital, Lund, Sweden.
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Yakovleva ME, Welinder C, Sugihara Y, Pawłowski K, Rezeli M, Wieslander E, Malm J, Marko-Varga G. Workflow for large-scale analysis of melanoma tissue samples. EuPA Open Proteomics 2015. [DOI: 10.1016/j.euprot.2015.07.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Malm J, Lindberg H, Erlinge D, Appelqvist R, Yakovleva M, Welinder C, Steinfelder E, Fehniger TE, Marko-Varga G. Semi-automated biobank sample processing with a 384 high density sample tube robot used in cancer and cardiovascular studies. Clin Transl Med 2015; 4:67. [PMID: 26272727 PMCID: PMC4536244 DOI: 10.1186/s40169-015-0067-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [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: 05/06/2015] [Accepted: 07/02/2015] [Indexed: 12/30/2022] Open
Abstract
Background In the postgenomic era, it has become evident that analysis of genetic and protein expression changes alone is not sufficient to understand most disease processes in e.g. cardiovascular and cancer disease. Biobanking has been identified as an important area for development and discovery of better diagnostic tools and new treatment modalities. Biobanks are developed in order to integrate the collection of clinical samples from both healthy individuals and patients and provide valuable information that will make possible improved patient care. Modern healthcare developments are intimately linked to information based on studies of patient samples from biobank archives in large scale studies. Today biobanks form important national, as well as international, networks that share and combine global resources. Methods We have developed and validated a novel biobanking workflow process that utilizes 384-tube systems with a high speed sample array robot with unique processing principles. Results The 384-tube format and robotic processing is incorporated into a cancer and cardiovascular diagnostic/prognostic research program with therapeutic interventions. Our biobank practice has gained acceptance within many hospitals and research units and is based on high-density sample storage with small aliquot sample volumes. The previous standard of 5–10 mL sample volume tubes is being replaced by smaller volumes of 50–70 μL blood fractions that typically result in hundreds of thousands of aliquot fractions in 384-tube systems. Conclusions Our novel biobanking workflow process is robust and well suited for clinical studies.
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Affiliation(s)
- Johan Malm
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02, Malmö, Sweden,
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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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Frithiof H, Welinder C, Larsson AM, Rydén L, Aaltonen K. A novel method for downstream characterization of breast cancer circulating tumor cells following CellSearch isolation. J Transl Med 2015; 13:126. [PMID: 25896421 PMCID: PMC4409738 DOI: 10.1186/s12967-015-0493-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [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: 02/04/2015] [Accepted: 04/15/2015] [Indexed: 01/05/2023] Open
Abstract
Background Enumeration of circulating tumor cells (CTCs) obtained from minimally invasive blood samples has been well established as a valuable monitoring tool in metastatic and early breast cancer, as well as in several other cancer types. The gold standard technology for detecting CTCs in blood against a backdrop of millions of leukocytes is the FDA-approved CellSearch system (Janssen Diagnostics), which relies on EpCAM-based immunomagnetic separation. Secondary characterization of these cells could enable treatment selection based on specific targets in these cells, as well as providing a real time window into the metastatic process and offering unique insights into tumor heterogeneity. The objective of this study was to develop a method for downstream characterization of CTCs following isolation with the CellSearch system. Methods An in vitro CTC model system focusing on clinically useful treatment predictive biomarkers in breast cancer, specifically the estrogen receptor α (ERα) and the human epidermal growth factor receptor 2 (HER2), was established using healthy donor blood spiked with breast cancer cell lines MCF7 (ERα+/HER2−) and SKBr3 (ERα−/HER2+). Following CTC isolation by CellSearch, the captured CTCs were further enriched and fixed on a microscope slide using the in-house-developed CTC-DropMount technique. Results The recovery rate of CTCs after CellSearch Profile analysis and CTC-DropMount was 87%. A selective and consistent triple-immunostaining protocol was optimized. Cells positive for DAPI, cytokeratin (CK) 8, 18 and 19, but negative for the leukocyte-specific marker CD45, were classified as CTCs and subsequently analyzed for ERα and HER2 expression. The method was verified in breast cancer patient samples, thus demonstrating its clinical relevance. Conclusions Our results show that it is possible to ascertain the status of important predictive biomarkers expressed in breast cancer CTCs using the newly developed CTC-DropMount technique. Downstream characterization of multiple biomarkers using a standard fluorescence microscope demonstrates that important clinical and biological information may be obtained from a single patient blood sample following either CellSearch epithelial or profile analyses. Trial registration Clinical Trials NCT01322893
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Affiliation(s)
- Henrik Frithiof
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.
| | - Charlotte Welinder
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.
| | - Anna-Maria Larsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden. .,Skåne Department of Oncology, Skåne University Hospital, Lund, Sweden.
| | - Lisa Rydén
- Division of Surgery, Department of Clinical Sciences, Lund University, Lund, Sweden. .,Department of Surgery, Skåne University Hospital, Lund, Sweden.
| | - Kristina Aaltonen
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.
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Welinder C, Pawłowski K, Sugihara Y, Yakovleva M, Jönsson G, Ingvar C, Lundgren L, Baldetorp B, Olsson H, Rezeli M, Jansson B, Laurell T, Fehniger T, Döme B, Malm J, Wieslander E, Nishimura T, Marko-Varga G. A protein deep sequencing evaluation of metastatic melanoma tissues. PLoS One 2015; 10:e0123661. [PMID: 25874936 PMCID: PMC4395420 DOI: 10.1371/journal.pone.0123661] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [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: 10/29/2014] [Accepted: 02/21/2015] [Indexed: 12/13/2022] Open
Abstract
Malignant melanoma has the highest increase of incidence of malignancies in the western world. In early stages, front line therapy is surgical excision of the primary tumor. Metastatic disease has very limited possibilities for cure. Recently, several protein kinase inhibitors and immune modifiers have shown promising clinical results but drug resistance in metastasized melanoma remains a major problem. The need for routine clinical biomarkers to follow disease progression and treatment efficacy is high. The aim of the present study was to build a protein sequence database in metastatic melanoma, searching for novel, relevant biomarkers. Ten lymph node metastases (South-Swedish Malignant Melanoma Biobank) were subjected to global protein expression analysis using two proteomics approaches (with/without orthogonal fractionation). Fractionation produced higher numbers of protein identifications (4284). Combining both methods, 5326 unique proteins were identified (2641 proteins overlapping). Deep mining proteomics may contribute to the discovery of novel biomarkers for metastatic melanoma, for example dividing the samples into two metastatic melanoma "genomic subtypes", ("pigmentation" and "high immune") revealed several proteins showing differential levels of expression. In conclusion, the present study provides an initial version of a metastatic melanoma protein sequence database producing a total of more than 5000 unique protein identifications. The raw data have been deposited to the ProteomeXchange with identifiers PXD001724 and PXD001725.
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Affiliation(s)
- Charlotte Welinder
- Oncology and Pathology, Dept. of Clinical Sciences, Lund University, Lund, Sweden
- Centre of Excellence in Biological and Medical Mass Spectrometry “CEBMMS”, Biomedical Centre D13, Lund University, Lund, Sweden
| | | | - Yutaka Sugihara
- Oncology and Pathology, Dept. of Clinical Sciences, Lund University, Lund, Sweden
| | - Maria Yakovleva
- National Korányi Institute of Pulmonology, Budapest, Hungary
- Clinical Protein Science & Imaging, Biomedical Centre, Dept. of Biomedical Engineering, Lund University, Lund, Sweden
| | - Göran Jönsson
- Oncology and Pathology, Dept. of Clinical Sciences, Lund University, Lund, Sweden
| | - Christian Ingvar
- Surgery, Dept. of Clinical Sciences, Lund University, Skåne University Hospital, Lund, Sweden
| | - Lotta Lundgren
- Oncology and Pathology, Dept. of Clinical Sciences, Lund University, Lund, Sweden
- Skåne University Hospital, Lund, Sweden
| | - Bo Baldetorp
- Oncology and Pathology, Dept. of Clinical Sciences, Lund University, Lund, Sweden
| | - Håkan Olsson
- Oncology and Pathology, Dept. of Clinical Sciences, Lund University, Lund, Sweden
- Skåne University Hospital, Lund, Sweden
- Cancer Epidemiology, Dept. of Clinical Sciences, Lund University, Lund, Sweden
| | - Melinda Rezeli
- Clinical Protein Science & Imaging, Biomedical Centre, Dept. of Biomedical Engineering, Lund University, Lund, Sweden
| | - Bo Jansson
- Oncology and Pathology, Dept. of Clinical Sciences, Lund University, Lund, Sweden
| | - Thomas Laurell
- Centre of Excellence in Biological and Medical Mass Spectrometry “CEBMMS”, Biomedical Centre D13, Lund University, Lund, Sweden
- Clinical Protein Science & Imaging, Biomedical Centre, Dept. of Biomedical Engineering, Lund University, Lund, Sweden
| | - Thomas Fehniger
- Oncology and Pathology, Dept. of Clinical Sciences, Lund University, Lund, Sweden
- Centre of Excellence in Biological and Medical Mass Spectrometry “CEBMMS”, Biomedical Centre D13, Lund University, Lund, Sweden
| | - Balazs Döme
- National Korányi Institute of Pulmonology, Budapest, Hungary
- Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - Johan Malm
- Section for Clinical Chemistry, Dept. of Laboratory Medicine, Lund University, Skåne University Hospital in Malmö, Malmö, Sweden
| | - Elisabet Wieslander
- Oncology and Pathology, Dept. of Clinical Sciences, Lund University, Lund, Sweden
| | - Toshihide Nishimura
- Oncology and Pathology, Dept. of Clinical Sciences, Lund University, Lund, Sweden
- Centre of Excellence in Biological and Medical Mass Spectrometry “CEBMMS”, Biomedical Centre D13, Lund University, Lund, Sweden
- First Dept. of Surgery, Tokyo Medical University, Tokyo, Japan
| | - György Marko-Varga
- Centre of Excellence in Biological and Medical Mass Spectrometry “CEBMMS”, Biomedical Centre D13, Lund University, Lund, Sweden
- Clinical Protein Science & Imaging, Biomedical Centre, Dept. of Biomedical Engineering, Lund University, Lund, Sweden
- First Dept. of Surgery, Tokyo Medical University, Tokyo, Japan
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Welinder C, Jansson B, Lindell G, Wenner J. Cytokeratin 20 improves the detection of circulating tumor cells in patients with colorectal cancer. Cancer Lett 2015; 358:43-6. [DOI: 10.1016/j.canlet.2014.12.024] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 12/11/2014] [Accepted: 12/11/2014] [Indexed: 12/26/2022]
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Ekblad L, Welinder C, Kjellén E, Brun E, Wennerberg J. Anti- or pro-proliferation – Conditional options for TGF-α and cetuximab in head and neck squamous cell carcinoma. Oral Oncol 2015; 51:46-52. [DOI: 10.1016/j.oraloncology.2014.08.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 08/08/2014] [Accepted: 08/30/2014] [Indexed: 10/24/2022]
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Welinder C, Jönsson GB, Ingvar C, Lundgren L, Baldetorp B, Olsson H, Breslin T, Rezeli M, Jansson B, Fehniger TE, Laurell T, Wieslander E, Pawlowski K, Marko-Varga G. Analysis of alpha-synuclein in malignant melanoma - development of a SRM quantification assay. PLoS One 2014; 9:e110804. [PMID: 25333933 PMCID: PMC4204935 DOI: 10.1371/journal.pone.0110804] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [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: 04/09/2014] [Accepted: 08/07/2014] [Indexed: 12/11/2022] Open
Abstract
Globally, malignant melanoma shows a steady increase in the incidence among cancer diseases. Malignant melanoma represents a cancer type where currently no biomarker or diagnostics is available to identify disease stage, progression of disease or personalized medicine treatment. The aim of this study was to assess the tissue expression of alpha-synuclein, a protein implicated in several disease processes, in metastatic tissues from malignant melanoma patients. A targeted Selected Reaction Monitoring (SRM) assay was developed and utilized together with stable isotope labeling for the relative quantification of two target peptides of alpha-synuclein. Analysis of alpha-synuclein protein was then performed in ten metastatic tissue samples from the Lund Melanoma Biobank. The calibration curve using peak area ratio (heavy/light) versus concentration ratios showed linear regression over three orders of magnitude, for both of the selected target peptide sequences. In support of the measurements of specific protein expression levels, we also observed significant correlation between the protein and mRNA levels of alpha-synuclein in these tissues. Investigating levels of tissue alpha-synuclein may add novel aspect to biomarker development in melanoma, help to understand disease mechanisms and ultimately contribute to discriminate melanoma patients with different prognosis.
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Affiliation(s)
- Charlotte Welinder
- Division of Oncology and Pathology, Clinical Sciences, Lund University, Lund, Sweden
- Centre of Excellence in Biological and Medical Mass Spectrometry, Lund University, Lund, Sweden
- * E-mail:
| | - Göran B. Jönsson
- Division of Oncology and Pathology, Clinical Sciences, Lund University, Lund, Sweden
| | - Christian Ingvar
- Skåne University Hospital, Lund, Sweden
- Dept. of Surgery, Clinical Sciences, Lund University, Skåne University Hospital, Lund, Sweden
| | - Lotta Lundgren
- Division of Oncology and Pathology, Clinical Sciences, Lund University, Lund, Sweden
- Skåne University Hospital, Lund, Sweden
| | - Bo Baldetorp
- Division of Oncology and Pathology, Clinical Sciences, Lund University, Lund, Sweden
| | - Håkan Olsson
- Division of Oncology and Pathology, Clinical Sciences, Lund University, Lund, Sweden
- Skåne University Hospital, Lund, Sweden
- Dept. of Cancer Epidemiology, Clinical Sciences, Lund University, Lund, Sweden
| | - Thomas Breslin
- Division of Oncology and Pathology, Clinical Sciences, Lund University, Lund, Sweden
| | - Melinda Rezeli
- Clinical Protein Science & Imaging, Biomedical Center, Biomedical Engineering, Lund University, Lund, Sweden
| | - Bo Jansson
- Division of Oncology and Pathology, Clinical Sciences, Lund University, Lund, Sweden
| | - Thomas E. Fehniger
- Division of Oncology and Pathology, Clinical Sciences, Lund University, Lund, Sweden
- Centre of Excellence in Biological and Medical Mass Spectrometry, Lund University, Lund, Sweden
| | - Thomas Laurell
- Centre of Excellence in Biological and Medical Mass Spectrometry, Lund University, Lund, Sweden
- Clinical Protein Science & Imaging, Biomedical Center, Biomedical Engineering, Lund University, Lund, Sweden
| | - Elisabet Wieslander
- Division of Oncology and Pathology, Clinical Sciences, Lund University, Lund, Sweden
| | - Krzysztof Pawlowski
- Division of Oncology and Pathology, Clinical Sciences, Lund University, Lund, Sweden
- Dept. of Experimental Design and Bioinformatics, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warszawa, Poland
| | - György Marko-Varga
- Centre of Excellence in Biological and Medical Mass Spectrometry, Lund University, Lund, Sweden
- Clinical Protein Science & Imaging, Biomedical Center, Biomedical Engineering, Lund University, Lund, Sweden
- First Department of Surgery, Tokyo Medical University, Tokyo, Japan
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Sugihara Y, Végvári Á, Welinder C, Jönsson G, Ingvar C, Lundgren L, Olsson H, Breslin T, Wieslander E, Laurell T, Rezeli M, Jansson B, Nishimura T, Fehniger TE, Baldetorp B, Marko-Varga G. A new look at drugs targeting malignant melanoma-An application for mass spectrometry imaging. Proteomics 2014; 14:1963-70. [DOI: 10.1002/pmic.201300476] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 06/25/2014] [Accepted: 07/16/2014] [Indexed: 12/16/2022]
Affiliation(s)
- Yutaka Sugihara
- Department of Oncology; Clinical Sciences; Lund University and Skåne University Hospital; Lund Sweden
| | - Ákos Végvári
- Department of Biomedical Engineering; Clinical Protein Science & Imaging; Biomedical Center; Lund University; Lund Sweden
- CREATE Health; Lund University; Lund Sweden
| | - Charlotte Welinder
- Department of Oncology; Clinical Sciences; Lund University and Skåne University Hospital; Lund Sweden
| | - Göran Jönsson
- Department of Oncology; Clinical Sciences; Lund University and Skåne University Hospital; Lund Sweden
| | - Christian Ingvar
- Department of Surgery; Clinical Sciences; Lund University; Lund Sweden
| | - Lotta Lundgren
- Department of Oncology; Clinical Sciences; Lund University and Skåne University Hospital; Lund Sweden
| | - Håkan Olsson
- Department of Oncology; Clinical Sciences; Lund University and Skåne University Hospital; Lund Sweden
| | - Thomas Breslin
- Department of Oncology; Clinical Sciences; Lund University and Skåne University Hospital; Lund Sweden
| | - Elisabet Wieslander
- Department of Oncology; Clinical Sciences; Lund University and Skåne University Hospital; Lund Sweden
| | - Thomas Laurell
- Department of Biomedical Engineering; Clinical Protein Science & Imaging; Biomedical Center; Lund University; Lund Sweden
| | - Melinda Rezeli
- Department of Biomedical Engineering; Clinical Protein Science & Imaging; Biomedical Center; Lund University; Lund Sweden
| | | | - Toshihide Nishimura
- Center of Excellence in Biological and Medical Mass Spectrometry; Lund University; Lund Sweden
| | - Thomas E. Fehniger
- Department of Biomedical Engineering; Clinical Protein Science & Imaging; Biomedical Center; Lund University; Lund Sweden
- Center of Excellence in Biological and Medical Mass Spectrometry; Lund University; Lund Sweden
| | - Bo Baldetorp
- Department of Oncology; Clinical Sciences; Lund University and Skåne University Hospital; Lund Sweden
| | - György Marko-Varga
- Department of Biomedical Engineering; Clinical Protein Science & Imaging; Biomedical Center; Lund University; Lund Sweden
- Center of Excellence in Biological and Medical Mass Spectrometry; Lund University; Lund Sweden
- First Department of Surgery; Tokyo Medical University; Tokyo Japan
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Evans-Axelsson S, Vilhelmsson Timmermand O, Welinder C, Borrebaeck CAK, Strand SE, Tran TA, Jansson B, Bjartell A. Preclinical evaluation of (111)In-DTPA-INCA-X anti-Ku70/Ku80 monoclonal antibody in prostate cancer. Am J Nucl Med Mol Imaging 2014; 4:311-323. [PMID: 24982817 PMCID: PMC4074497] [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] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 05/14/2014] [Indexed: 06/03/2023]
Abstract
The aim of this investigation was to assess the Ku70/Ku80 complex as a potential target for antibody imaging of prostate cancer. We evaluated the in vivo and ex vivo tumor targeting and biodistribution of the (111)In-labeled human internalizing antibody, INCA-X ((111)In-DTPA-INCA-X antibody), in NMRI-nude mice bearing human PC-3, PC-3M-Lu2 or DU145 xenografts. DTPA-conjugated, non-labeled antibody was pre-administered at different time-points followed by a single intravenous injection of (111)In-DTPA-INCA-X. At 48, 72 and 96 h post-injection, tissues were harvested, and the antibody distribution was determined by measuring radioactivity. Preclinical SPECT/CT imaging of mice with and without the predose was performed at 48 hours post-injection of labeled DTPA-INCA-X. Biodistribution of the labeled antibody showed enriched activity in tumor, spleen and liver. Animals pre-administered with DTPA-INCA-X showed increased tumor uptake and blood content of (111)In-DTPA-INCA-X with reduced splenic and liver uptake. The in vitro and in vivo data presented show that the (111)In-labeled INCA-X antibody is internalized into prostate cancer cells and by pre-administering non-labeled DTPA-INCA-X, we were able to significantly reduce the off target binding and increase the (111)In-DTPA-INCA-X mAb uptake in PC-3, PC-3M-Lu2 and DU145 xenografts. The results are encouraging and identifying the Ku70/Ku80 antigen as a target is worth further investigation for functional imaging of prostate cancer.
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Affiliation(s)
- Susan Evans-Axelsson
- Division of Urological Cancers, Department of Clinical Sciences Malmö, Lund UniversitySweden
| | | | | | - Carl AK Borrebaeck
- Department of Immunotechnology and CREATE Health Translational Cancer Center, Lund UniversityMedicon Village, Lund, Sweden
| | - Sven-Erik Strand
- Department of Medical Radiation Physics, Clinical Sciences, Lund UniversityLund, Sweden
- Lund University Bioimaging CenterLund, Sweden
| | - Thuy A Tran
- Lund University Bioimaging CenterLund, Sweden
| | - Bo Jansson
- Department of Oncology, Clinical Sciences, Lund UniversityLund, Sweden
| | - Anders Bjartell
- Division of Urological Cancers, Department of Clinical Sciences Malmö, Lund UniversitySweden
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Ansari D, Aronsson L, Sasor A, Welinder C, Rezeli M, Marko-Varga G, Andersson R. The role of quantitative mass spectrometry in the discovery of pancreatic cancer biomarkers for translational science. J Transl Med 2014; 12:87. [PMID: 24708694 PMCID: PMC3998064 DOI: 10.1186/1479-5876-12-87] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [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: 01/14/2014] [Accepted: 03/13/2014] [Indexed: 02/06/2023] Open
Abstract
In the post-genomic era, it has become evident that genetic changes alone are not sufficient to understand most disease processes including pancreatic cancer. Genome sequencing has revealed a complex set of genetic alterations in pancreatic cancer such as point mutations, chromosomal losses, gene amplifications and telomere shortening that drive cancerous growth through specific signaling pathways. Proteome-based approaches are important complements to genomic data and provide crucial information of the target driver molecules and their post-translational modifications. By applying quantitative mass spectrometry, this is an alternative way to identify biomarkers for early diagnosis and personalized medicine. We review the current quantitative mass spectrometric technologies and analyses that have been developed and applied in the last decade in the context of pancreatic cancer. Examples of candidate biomarkers that have been identified from these pancreas studies include among others, asporin, CD9, CXC chemokine ligand 7, fibronectin 1, galectin-1, gelsolin, intercellular adhesion molecule 1, insulin-like growth factor binding protein 2, metalloproteinase inhibitor 1, stromal cell derived factor 4, and transforming growth factor beta-induced protein. Many of these proteins are involved in various steps in pancreatic tumor progression including cell proliferation, adhesion, migration, invasion, metastasis, immune response and angiogenesis. These new protein candidates may provide essential information for the development of protein diagnostics and targeted therapies. We further argue that new strategies must be advanced and established for the integration of proteomic, transcriptomic and genomic data, in order to enhance biomarker translation. Large scale studies with meta data processing will pave the way for novel and unexpected correlations within pancreatic cancer, that will benefit the patient, with targeted treatment.
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Affiliation(s)
| | | | | | | | | | | | - Roland Andersson
- Department of Surgery, Clinical Sciences Lund, Lund University, and Skåne University Hospital, SE-221 85 Lund, Sweden.
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Welinder C, Jönsson G, Ingvar C, Lundgren L, Baldetorp B, Olsson H, Breslin T, Rezeli M, Jansson B, Laurell T, Fehniger TE, Wieslander E, Pawlowski K, Marko-Varga G. Feasibility study on measuring selected proteins in malignant melanoma tissue by SRM quantification. J Proteome Res 2014; 13:1315-26. [PMID: 24490776 DOI: 10.1021/pr400876p] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Currently there are no clinically recognized molecular biomarkers for malignant melanoma (MM) for either diagnosing disease stage or measuring response to therapy. The aim of this feasibility study was to develop targeted selected reaction monitoring (SRM) assays for identifying candidate protein biomarkers in metastatic melanoma tissue lysate. In a pilot study applying the SRM assay, the tissue expression of nine selected proteins [complement 3 (C3), T-cell surface glycoprotein CD3 epsilon chain E (CD3E), dermatopontin, minichromosome maintenance complex component (MCM4), premelanosome protein (PMEL), S100 calcium binding protein A8 (S100A8), S100 calcium binding protein A13 (S100A13), transgelin-2 and S100B] was quantified in a small cohort of metastatic malignant melanoma patients. The SRM assay was developed using a TSQ Vantage triple quadrupole mass spectrometer that generated highly accurate peptide quantification. Repeated injection of internal standards spiked into matrix showed relative standard deviation (RSD) from 6% to 15%. All nine target proteins were identified in tumor lysate digests spiked with heavy peptide standards. The multiplex SRM peptide assay panel was then measured and quantified on a set of frozen MM tissue samples obtained from the Malignant Melanoma Biobank collected in Lund, Sweden. All nine proteins could be accurately quantified using the new SRM assay format. This study provides preliminary data on the heterogeneity of biomarker expression within MM patients. The S100B protein, which is clinically used as the pathology identifier of MM, was identified in 9 out of 10 MM tissue lysates. The use of the targeted SRM assay provides potential advancements in the diagnosis of MM that can aid in future assessments of disease in melanoma patients.
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Affiliation(s)
- Charlotte Welinder
- Departments of †Oncology, ∥Surgery, and ⊥Cancer Epidemiology, Clinical Sciences, and ‡Centre of Excellence in Biological and Medical Mass Spectrometry, Lund University , 221 85 Lund, Sweden
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Végvári Á, Fehniger TE, Rezeli M, Laurell T, Döme B, Jansson B, Welinder C, Marko-Varga G. Experimental models to study drug distributions in tissue using MALDI mass spectrometry imaging. J Proteome Res 2013; 12:5626-33. [PMID: 24134601 DOI: 10.1021/pr400581b] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Requirements for patient safety and improved efficacy are steadily increasing in modern healthcare and are key drivers in modern drug development. New drug characterization assays are central in providing evidence of the specificity and selectivity of drugs. Meeting this need, matrix-assisted laser desorption ionization-mass spectrometry imaging (MALDI-MSI) is used to study drug localization within microenvironmental tissue compartments. Thin sections of human lung tumor and rat xenograft tissues were exposed to pharmaceutical drugs by either spotting or submerging. These drugs, the epidermal growth factor receptor antagonists, erlotinib (Tarceva) and gefitinib (Iressa), and the acetylcholine receptor antagonist, tiotropium, were characterized by microenvironment localization. Intact tissue blocks were also immersed in drug solution, followed by sectioning. MALDI-MSI was then performed using a Thermo MALDI LTQ Orbitrap XL instrument to localize drug-distribution patterns. We propose three MALDI-MSI models measuring drug disposition that have been used to map the selected compounds within tissue compartments of tumors isolated from lung cancer patients.
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Affiliation(s)
- Ákos Végvári
- Clinical Protein Science & Imaging, Biomedical Center, Department of Measurement Technology and Industrial Electrical Engineering, Lund University , BMC C13, SE-221 84 Lund, Sweden
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Welinder C, Jönsson G, Ingvar C, Lundgren L, Olsson H, Breslin T, Végvári A, Laurell T, Rezeli M, Jansson B, Baldetorp B, Marko-Varga G. Establishing a Southern Swedish Malignant Melanoma OMICS and biobank clinical capability. Clin Transl Med 2013; 2:7. [PMID: 23445834 PMCID: PMC3599425 DOI: 10.1186/2001-1326-2-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [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] [Received: 11/12/2012] [Accepted: 02/15/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The objectives and goals of the Southern Swedish Malignant Melanoma (SSMM) are to develop, build and utilize cutting edge biobanks and OMICS platforms to better understand disease pathology and drug mechanisms. The SSMM research team is a truly cross-functional group with members from oncology, surgery, bioinformatics, proteomics, and genomics initiatives. Within the research team there are members who daily diagnose patients with suspect melanomas, do follow-ups on malignant melanoma patients and remove primary or metastatic lesions by surgery. This inter-disciplinary clinical patient care ensures a competence build as well as a best practice procedure where the patient benefits. METHODS Clinical materials from patients before, during and after treatments with clinical end points are being collected. Tissue samples as well as bio-fluid samples such as blood fractions, plasma, serum and whole blood will be archived in 384-high density sample tube formats. Standardized approaches for patient selections, patient sampling, sample-processing and analysis platforms with dedicated protein assays and genomics platforms that will hold value for the research community are used. The patient biobank archives are fully automated with novel ultralow temperature biobank storage units and used as clinical resources. RESULTS An IT-infrastructure using a laboratory information management system (LIMS) has been established, that is the key interface for the research teams in order to share and explore data generated within the project. The cross-site data repository in Lund forms the basis for sample processing, together with biological samples in southern Sweden, including blood fractions and tumor tissues. Clinical registries are associated with the biobank materials, including pathology reports on disease diagnosis on the malignant melanoma (MM) patients. CONCLUSIONS We provide data on the developments of protein profiling and targeted protein assays on isolated melanoma tumors, as well as reference blood standards that is used by the team members in the respective laboratories. These pilot data show biobank access and feasibility of performing quantitative proteomics in MM biobank repositories collected in southern Sweden. The scientific outcomes further strengthen the build of healthcare benefit in the complex challenges of malignant melanoma pathophysiology that is addressed by the novel personalized medicines entering the market.
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Affiliation(s)
- Charlotte Welinder
- Clinical Protein Science & Imaging, Biomedical Center, Dept, of Measurement Technology and Industrial Electrical Engineering, Lund University, BMC C13, Lund 221 84, Sweden.
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Nilsson CL, Berven F, Selheim F, Liu H, Moskal JR, Kroes RA, Sulman EP, Conrad CA, Lang FF, Andrén PE, Nilsson A, Carlsohn E, Lilja H, Malm J, Fenyö D, Subramaniyam D, Wang X, Gonzales-Gonzales M, Dasilva N, Diez P, Fuentes M, Végvári Á, Sjödin K, Welinder C, Laurell T, Fehniger TE, Lindberg H, Rezeli M, Edula G, Hober S, Marko-Varga G. Chromosome 19 annotations with disease speciation: a first report from the Global Research Consortium. J Proteome Res 2012; 12:135-50. [PMID: 23249167 DOI: 10.1021/pr3008607] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
A first research development progress report of the Chromosome 19 Consortium with members from Sweden, Norway, Spain, United States, China and India, a part of the Chromosome-centric Human Proteome Project (C-HPP) global initiative, is presented ( http://www.c-hpp.org ). From the chromosome 19 peptide-targeted library constituting 6159 peptides, a pilot study was conducted using a subset with 125 isotope-labeled peptides. We applied an annotation strategy with triple quadrupole, ESI-Qtrap, and MALDI mass spectrometry platforms, comparing the quality of data within and in between these instrumental set-ups. LC-MS conditions were outlined by multiplex assay developments, followed by MRM assay developments. SRM was applied to biobank samples, quantifying kallikrein 3 (prostate specific antigen) in plasma from prostate cancer patients. The antibody production has been initiated for more than 1200 genes from the entire chromosome 19, and the progress developments are presented. We developed a dedicated transcript microarray to serve as the mRNA identifier by screening cancer cell lines. NAPPA protein arrays were built to align with the transcript data with the Chromosome 19 NAPPA chip, dedicated to 90 proteins, as the first development delivery. We have introduced an IT-infrastructure utilizing a LIMS system that serves as the key interface for the research teams to share and explore data generated within the project. The cross-site data repository will form the basis for sample processing, including biological samples as well as patient samples from national Biobanks.
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Affiliation(s)
- Carol L Nilsson
- Department of Pharmacology and Toxicology, UTMB Cancer Center, University of Texas Medical Branch, Galveston, Texas 77555, United States
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