| 1. |
- Åhrman, Emma, et al.
(författare)
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Quantitative proteomic characterization of the lung extracellular matrix in chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis
- 2018
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Ingår i: Journal of Proteomics. - : Elsevier BV. - 1874-3919. ; 189, s. 23-33
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Tidskriftsartikel (refereegranskat)abstract
- Remodeling of the extracellular matrix (ECM) is a common feature in lung diseases such as chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF). Here, we applied a sequential tissue extraction strategy to describe disease-specific remodeling of human lung tissue in disease, using end-stages of COPD and IPF. Our strategy was based on quantitative comparison of the disease proteomes, with specific focus on the matrisome, using data-independent acquisition and targeted data analysis (SWATH-MS). Our work provides an in-depth proteomic characterization of human lung tissue during impaired tissue remodeling. In addition, we show important quantitative and qualitative effects of the solubility of matrisome proteins. COPD was characterized by a disease-specific increase in ECM regulators, metalloproteinase inhibitor 3 (TIMP3) and matrix metalloproteinase 28 (MMP-28), whereas for IPF, impairment in cell adhesion proteins, such as collagen VI and laminins, was most prominent. For both diseases, we identified increased levels of proteins involved in the regulation of endopeptidase activity, with several proteins belonging to the serpin family. The established human lung quantitative proteome inventory and the construction of a tissue-specific protein assay library provides a resource for future quantitative proteomic analyses of human lung tissues. Significance: We present a sequential tissue extraction strategy to determine changes in extractability of matrisome proteins in end-stage COPD and IPF compared to healthy control tissue. Extensive quantitative analysis of the proteome changes of the disease states revealed altered solubility of matrisome proteins involved in ECM regulators and cell-ECM communication. The results highlight disease-specific remodeling mechanisms associated with COPD and IPF.
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| 2. |
- De Marchi, Tommaso, et al.
(författare)
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Proteogenomic Workflow Reveals Molecular Phenotypes Related to Breast Cancer Mammographic Appearance
- 2021
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Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 20:5, s. 2983-3001
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Tidskriftsartikel (refereegranskat)abstract
- Proteogenomic approaches have enabled the generat̲ion of novel information levels when compared to single omics studies although burdened by extensive experimental efforts. Here, we improved a data-independent acquisition mass spectrometry proteogenomic workflow to reveal distinct molecular features related to mammographic appearances in breast cancer. Our results reveal splicing processes detectable at the protein level and highlight quantitation and pathway complementarity between RNA and protein data. Furthermore, we confirm previously detected enrichments of molecular pathways associated with estrogen receptor-dependent activity and provide novel evidence of epithelial-to-mesenchymal activity in mammography-detected spiculated tumors. Several transcript-protein pairs displayed radically different abundances depending on the overall clinical properties of the tumor. These results demonstrate that there are differentially regulated protein networks in clinically relevant tumor subgroups, which in turn alter both cancer biology and the abundance of biomarker candidates and drug targets.
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| 3. |
- De Marchi, Tommaso, et al.
(författare)
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Proteogenomics decodes the evolution of human ipsilateral breast cancer
- 2023
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 6:1
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Tidskriftsartikel (refereegranskat)abstract
- Ipsilateral breast tumor recurrence (IBTR) is a clinically important event, where an isolated in-breast recurrence is a potentially curable event but associated with an increased risk of distant metastasis and breast cancer death. It remains unclear if IBTRs are associated with molecular changes that can be explored as a resource for precision medicine strategies. Here, we employed proteogenomics to analyze a cohort of 27 primary breast cancers and their matched IBTRs to define proteogenomic determinants of molecular tumor evolution. Our analyses revealed a relationship between hormonal receptors status and proliferation levels resulting in the gain of somatic mutations and copy number. This in turn re-programmed the transcriptome and proteome towards a highly replicating and genomically unstable IBTRs, possibly enhanced by APOBEC3B. In order to investigate the origins of IBTRs, a second analysis that included primaries with no recurrence pinpointed proliferation and immune infiltration as predictive of IBTR. In conclusion, our study shows that breast tumors evolve into different IBTRs depending on hormonal status and proliferation and that immune cell infiltration and Ki-67 are significantly elevated in primary tumors that develop IBTR. These results can serve as a starting point to explore markers to predict IBTR formation and stratify patients for adjuvant therapy.
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| 4. |
- Elowsson Rendin, Linda, et al.
(författare)
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Matrisome Properties of Scaffolds Direct Fibroblasts in Idiopathic Pulmonary Fibrosis
- 2019
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Ingår i: International Journal of Molecular Sciences. - : MDPI AG. - 1422-0067. ; 20:16
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Tidskriftsartikel (refereegranskat)abstract
- In idiopathic pulmonary fibrosis (IPF) structural properties of the extracellular matrix (ECM) are altered and influence cellular responses through cell-matrix interactions. Scaffolds (decellularized tissue) derived from subpleural healthy and IPF lungs were examined regarding biomechanical properties and ECM composition of proteins (the matrisome). Scaffolds were repopulated with healthy fibroblasts cultured under static stretch with heavy isotope amino acids (SILAC), to examine newly synthesized proteins over time. IPF scaffolds were characterized by increased tissue density, stiffness, ultimate force, and differential expressions of matrisome proteins compared to healthy scaffolds. Collagens, proteoglycans, and ECM glycoproteins were increased in IPF scaffolds, however while specific basement membrane (BM) proteins such as laminins and collagen IV were decreased, nidogen-2 was also increased. Findings were confirmed with histology, clearly showing a disorganized BM. Fibroblasts produced scaffold-specific proteins mimicking preexisting scaffold composition, where 11 out of 20 BM proteins were differentially expressed, along with increased periostin and proteoglycans production. We demonstrate how matrisome changes affect fibroblast activity using novel approaches to study temporal differences, where IPF scaffolds support a disorganized BM and upregulation of disease-associated proteins. These matrix-directed cellular responses emphasize the IPF matrisome and specifically the BM components as important factors for disease progression.
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| 5. |
- Rolandsson Enes, Sara, et al.
(författare)
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Quantitative proteomic characterization of lung-MSC and bone marrow-MSC using DIA-mass spectrometry
- 2017
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 7:1
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Tidskriftsartikel (refereegranskat)abstract
- Mesenchymal stromal cells (MSC) are ideal candidates for cell therapies, due to their immune-regulatory and regenerative properties. We have previously reported that lung-derived MSC are tissue-resident cells with lung-specific properties compared to bone marrow-derived MSC. Assessing relevant molecular differences between lung-MSC and bone marrow-MSC is important, given that such differences may impact their behavior and potential therapeutic use. Here, we present an in-depth mass spectrometry (MS) based strategy to investigate the proteomes of lung-MSC and bone marrow-MSC. The MS-strategy relies on label free quantitative data-independent acquisition (DIA) analysis and targeted data analysis using a MSC specific spectral library. We identified several significantly differentially expressed proteins between lung-MSC and bone marrow-MSC within the cell layer (352 proteins) and in the conditioned medium (49 proteins). Bioinformatics analysis revealed differences in regulation of cell proliferation, which was functionally confirmed by decreasing proliferation rate through Cytochrome P450 stimulation. Our study reveals important differences within proteome and matrisome profiles between lung- and bone marrow-derived MSC that may influence their behavior and affect the clinical outcome when used for cell-therapy.
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| 6. |
- Rosmark, Oskar, et al.
(författare)
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Quantifying extracellular matrix turnover in human lung scaffold cultures
- 2018
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- Remodelling of the extracellular matrix is accomplished by altering the balance between matrix macromolecule production and degradation. However, it is not well understood how cells balance production of new matrix molecules and degradation of existing ones during tissue remodelling and regeneration. In this study, we used decellularized lung scaffolds repopulated with allogenic lung fibroblasts cultured with stable isotope labelled amino acids to quantify the balance between matrix production and degradation at a proteome-wide scale. Specific temporal dynamics of different matrisome proteins were found to correspond to the proliferative activity of the repopulating cells and the degree of extracellular deposition. The remodeling of the scaffold was characterized by an initial phase with cell proliferation and high production of cell adhesion proteins such as emilin-1 and fibronectin. Extended culture time resulted in increased levels of core matrisome proteins. In a comparison with monolayer cultures on plastic, culture in lung scaffolds lead to a pronounced accumulation of proteoglycans, such as versican and decorin, resulting in regeneration of an extracellular matrix with greater resemblance to native lung tissue compared to standard monolayer cultures. Collectively, the study presents a promising technique for increasing the understanding of cell- extracellular matrix interactions under healthy and diseased conditions.
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| 7. |
- Stenemo, Markus, et al.
(författare)
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Cancer associated proteins in blood plasma : Determining normal variation
- 2016
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Ingår i: Proteomics. - : Wiley. - 1615-9853. ; 16:13, s. 1928-1937
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Tidskriftsartikel (refereegranskat)abstract
- Protein biomarkers have the potential to improve diagnosis, stratification of patients into treatment cohorts, follow disease progression and treatment response. One distinct group of potential biomarkers comprises proteins which have been linked to cancer, known as cancer associated proteins (CAPs). We determined the normal variation of 86 CAPs in 72 individual plasma samples collected from ten individuals using SRM mass spectrometry. Samples were collected weekly during 5 weeks from ten volunteers and over one day at nine fixed time points from three volunteers. We determined the degree of the normal variation depending on interpersonal variation, variation due to time of day, and variation over weeks and observed that the variation dependent on the time of day appeared to be the most important. Subdivision of the proteins resulted in two predominant protein groups containing 21 proteins with relatively high variation in all three factors (day, week and individual), and 22 proteins with relatively low variation in all factors. We present a strategy for prioritizing biomarker candidates for future studies based on stratification over their normal variation and have made all data publicly available. Our findings can be used to improve selection of biomarker candidates in future studies and to determine which proteins are most suitable depending on study design.
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| 8. |
- Blank, Malou, 1975, et al.
(författare)
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Mobility patterns in inland southwestern Sweden during the Neolithic and Early Bronze Age
- 2021
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Ingår i: Archaeological and Anthropological Sciences. - : Springer Science and Business Media LLC. - 1866-9557 .- 1866-9565. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, we investigate population dynamics in the Scandinavian Neolithic and Early Bronze Age in southwestern Sweden. Human mobility patterns in Falbygden were studied by applying strontium isotope analysis combined with archaeological and bioarchaeological data, including mtDNA and sex assessment on a large dataset encompassing 141 individuals from 21 megalithic graves. In combination with other archaeological and anthropological records, we investigated the temporal and spatial scale of individual movement, mobility patterns of specific categories of people and possible social drivers behind them. Our results of strontium and biomolecular analyses suggest that mobility increased in the Late Neolithic and Early Bronze Age compared to the earlier parts of the Neolithic. The data indicate individuals moving both into and away from Falbygden. Mobility patterns and contact networks also shift over time.
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| 9. |
- Bruce, Carl, et al.
(författare)
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A comparative study of covalent grafting and physical adsorption of PCL onto cellulose
- 2012
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Konferensbidrag (refereegranskat)abstract
- A growing concern for the environment has, in the past years, directed the research towards a bigger focus on new “greener” materials, such as cellulose-reinforced options. Cellulose is the most abundant organic raw material in the world and it is a versatile material. However, to be able to use it in applications where it is not inherently compatible, a modification is often necessary.1-3 One common method to achieve this modification is to graft polymers onto/from the cellulose chain. This can change the inherent properties of cellulose to attain new properties, such as dimensional stability and water repellency.3 In addition to this, it has been shown that polyectrolytes can be physiosorbed onto charged surfaces.4 Due to this, it is possible to physically modify cellulose by adsorbing a polymer through electrostatic interactions instead of attaching it with a covalent bond.5However, a more detailed investigation concerning differences of covalent and physical attachment of poly(ε-caprolactone) (PCL) onto cellulose, has to the author’s best knowledge not been performed. Therefore, this project aims to compare these two techniques. Covalently bonded PCL was grafted by surface-initiated ring opening polymerization (SI-ROP) from the cellulose. For the adsorption approach, a block copolymer consisting of PCL and a shorter segment of poly(di(methylamino)ethyl methacrylate) (PDMAEMA) was made combining ROP and atom transfer radical polymerization (ATRP). The PDMAEMA-part was then quaternized, which resulted in a cationically charged chain – a polyelectrolyte. This can then be used as an electrostatic linker allowing the PDMAEMA-PCL copolymer to be adsorbed onto the negatively charged cellulose model surface. Finally, differences between the two approaches are evaluated regarding for example surface coverage and grafting/physiosorption efficiency investigated with techniques such as atomic force microscopy (AFM).
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| 10. |
- Bruce, Carl, et al.
(författare)
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A comparative study of covalent grafting and physical adsorption of PCL onto cellulose
- 2011
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Konferensbidrag (refereegranskat)abstract
- In the past years, a growing concern for the environment has forced the research to focus more on new “greener” materials. The most abundant organic raw material in the world is cellulose. This, in combination with the versatility of the material, makes it interesting as a green option in various applications. However, to be able to take advantage of all characteristics possessed by cellulose, i.e., use it in applications where it is not inherently compatible, modification is often necessary.1-3 One common method used for modifying cellulose is grafting of polymers onto/from the cellulose chain. This offers a way of changing the inherent properties of cellulose to attain new properties, such as dimensional stability and water repellency.3Additionally, it has been shown that polyectrolytes can be physiosorbed onto charged surfaces.4 This has made it possible to physically modify cellulose by adsorbing a polymer through electrostatic interactions instead of attaching it with a covalent bond.5 However, a more detailed investigation concerning the differences, such as surface coverage and grafting/physiosorption efficiency, between a covalent and physical attachment of a polymer has to the author’s best knowledge earlier not been performed. Therefore, this project aims to compare these two techniques. A block copolymer consisting of poly(ε-caprolactone) (PCL) and poly(di(methylamino)ethyl methacrylate) (PDMAEMA) is made, see figure 1 for 1H-NMR-spectrum.Figure 1. The 1H-NMR-spectrum of PCL-block-PDMAEMA (in CDCl3).The PDMAEMA-part is then quaternized (figure 2), which results in a charged chain – a polyelectrolyte.Figure 2.The quaternization of the PDMAEMA block to obtain cationic charges.The charges allow for the PDMAEMA-PCL copolymer to be adsorbed onto a cellulose surface. Finally, to evaluate and compare the differences between the covalent and the physical surface modification, regarding for example surface coverage, grafting/physiosorption efficiency, adhesion and matrix compatibility, various characterization methods are employed: fourier transform infrared spectroscopy (FTIR), contact angle measurements (CA), micro adhesion measurement apparatus (MAMA), force measurements using atomic force microscopy (AFM) and macroscopic peel tests using dynamical mechanical analysis (DMA) or Instron.Figure 3. A schematic drawing of covalent attachment and physical adsorption of PCL onto cellulose.Further work after preparation of fibres may include such steps as making of fiber-reinforced composites, out of both chemically and physically modified fibres, where for example differences concerning mechanical properties would be investigated.References(1) Lönnberg, H.; Fogelström, L.; Berglund, L.; Malmström, E.; Hult, A. European Polymer Journal 2008, 44, 2991.(2) Lönnberg, H.; Zhou, Q.; Brumer, H., 3rd; Teeri Tuula, T.; Malmström, E.; Hult, A. Biomacromolecules 2006, 7, 2178.(3) Roy, D.; Semsarilar, M.; Guthrie, J. T.; Perrier, S. Chemical Society Reviews 2009, 38, 2046.(4) Decher, G.; Hong, J. D. Berichte der Bunsen-Gesellschaft 1991, 95, 1430.(5) Utsel, S.; Carlmark, A.; Pettersson, T.; Bergström, M.; Malmström, E.; Wågberg, L. Abstracts of Papers, 241st ACS National Meeting & Exposition, Anaheim, CA, United States, March 27-31, 2011 2011, CELL.
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