| 1. |
- Micke, Patrick, et al.
(author)
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The prognostic impact of the tumour stroma fraction : A machine learning-based analysis in 16 human solid tumour types
- 2021
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In: EBioMedicine. - : Elsevier. - 2352-3964. ; 65
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Journal article (peer-reviewed)abstract
- Background: The development of a reactive tumour stroma is a hallmark of tumour progression and pronounced tumour stroma is generally considered to be associated with clinical aggressiveness. The variability between tumour types regarding stroma fraction, and its prognosis associations, have not been systematically analysed.Methods: Using an objective machine-learning method we quantified the tumour stroma in 16 solid cancer types from 2732 patients, representing retrospective tissue collections of surgically resected primary tumours. Image analysis performed tissue segmentation into stromal and epithelial compartment based on pan-cytokeratin staining and autofluorescence patterns.Findings: The stroma fraction was highly variable within and across the tumour types, with kidney cancer showing the lowest and pancreato-biliary type periampullary cancer showing the highest stroma proportion (median 19% and 73% respectively). Adjusted Cox regression models revealed both positive (pancreato-biliary type periampullary cancer and oestrogen negative breast cancer, HR(95%CI)=0.56(0.34-0.92) and HR (95%CI)=0.41(0.17-0.98) respectively) and negative (intestinal type periampullary cancer, HR(95%CI)=3.59 (1.49-8.62)) associations of the tumour stroma fraction with survival.Interpretation: Our study provides an objective quantification of the tumour stroma fraction across major types of solid cancer. Findings strongly argue against the commonly promoted view of a general associations between high stroma abundance and poor prognosis. The results also suggest that full exploitation of the prognostic potential of tumour stroma requires analyses that go beyond determination of stroma abundance.
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| 2. |
- Corell, Alba, et al.
(author)
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Stemness and clinical features in relation to the subventricular zone in diffuse lower-grade glioma : an exploratory study
- 2022
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In: Neuro-Oncology Advances. - : Oxford University Press. - 2632-2498. ; 4:1
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Journal article (peer-reviewed)abstract
- Background The subventricular zone (SVZ) of the human brain is a site of adult stem cell proliferation and a microenvironment for neural stem cells (NSCs). It has been suggested that NSCs in the SVZ are potential cells of origin containing driver mutations of glioblastoma, but their role in the origin of diffuse lower-grade gliomas (dLGGs) is not much studied. Methods We included 188 patients >= 18 years with IDH-mutated dLGG (WHO grades 2-3) histologically diagnosed between 2007 and 2020. Tissue microarrays of tumor samples for patients between 2007 and 2016 were used for immunodetection of Nestin, SOX2, SOX9, KLF4, NANOG, CD133 cMYC, and Ki67. DNA methylation profile was used for stemness index (mDNAsi). Tumor contact with the SVZ was assessed and the distance was computed. Results Overall, 70.2% of the dLGG had SVZ contact. Tumors with SVZ contact were larger (102.4 vs 30.9 mL, P < .01), the patients were older (44.3 vs 40.4 years, P = .04) and more often had symptoms related to increased intracranial pressure (31.8% vs 7.1%, P < .01). The expression of SOX2, SOX9, Nestin, and Ki67 showed intersample variability, but no difference was found between tumors with or without SVZ contact, nor with the actual distance to the SVZ. mDNAsi was similar between groups (P = .42). Conclusions We found no statistical relationship between proximity with the SVZ and mDNAsi or expression of SOX2, SOX9, Nestin, and Ki67 in IDH-mutated dLGG. Our data suggest that the potential impact of SVZ on IDH-mutated dLGG is probably not associated with a more stemness-like tumor profile.
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| 3. |
- Dénes, Anna, et al.
(author)
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The clinical value of proneural, classical and mesenchymal protein signatures in WHO 2021 adult-type diffuse lower-grade gliomas.
- 2023
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In: PloS one. - : Public Library of Science (PLoS). - 1932-6203. ; 18:5
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Journal article (peer-reviewed)abstract
- Accumulating evidence shows that mesenchymal transition of glioblastomas is associated with a more aggressive course of disease and therapy resistance. In WHO2021-defined adult-type diffuse gliomas of lower grade (dLGG), the transition of the tumor phenotype over time, has not been studied. Most efforts to correlate proneural, classical or mesenchymal phenotype with outcome in dLGG were made prior to the WHO 2021 classification. Here, we set out to investigate if phenotype predicted survival and tumor recurrence in a clinical cohort of dLGGs, re-classified according to the 2021 WHO criteria.Using a TMA-based approach with five immunohistochemical markers (EGFR, p53, MERTK, CD44 and OLIG2), we investigated 183 primary and 49 recurrent tumors derived from patients with previously diagnosed dLGG. Of the 49 relapses, nine tumors recurred a second time, and one a third time.In total, 71.0% of all tumors could be subtyped. Proneural was most dominant in IDH-mut tumors (78.5%), mesenchymal more common among IDH-wt tumors (63.6%). There was a significant difference in survival between classical, proneural and mesenchymal phenotypes in the total cohort (p<0.001), but not after molecular stratification (IDH-mut: p = 0.220, IDH-wt: p = 0.623). Upon recurrence, proneural was retained in 66.7% of the proneural IDH-mut dLGGs (n = 21), whereas IDH-wt tumors (n = 10) mainly retained or gained mesenchymal phenotype. No significant difference in survival was found between IDH-mut gliomas remaining proneural and those shifting to mesenchymal phenotype (p = 0.347).Subtyping into classical, proneural and mesenchymal phenotypes by five immunohistochemical markers, was possible for the majority of tumors, but protein signatures did not correlate with patient survival in our WHO2021-stratified cohort. At recurrence, IDH-mut tumors mainly retained proneural, while IDH-wt tumors mostly retained or gained mesenchymal signatures. This phenotypic shift, associated with increased aggressiveness in glioblastoma, did not affect survival. Group sizes were, however, too small to draw any firm conclusions.
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| 4. |
- Edfors, Fredrik, et al.
(author)
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Enhanced validation of antibodies for research applications
- 2018
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In: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 9
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Journal article (peer-reviewed)abstract
- There is a need for standardized validation methods for antibody specificity and selectivity. Recently, five alternative validation pillars were proposed to explore the specificity of research antibodies using methods with no need for prior knowledge about the protein target. Here, we show that these principles can be used in a streamlined manner for enhanced validation of research antibodies in Western blot applications. More than 6,000 antibodies were validated with at least one of these strategies involving orthogonal methods, genetic knockdown, recombinant expression, independent antibodies, and capture mass spectrometry analysis. The results show a path forward for efforts to validate antibodies in an application-specific manner suitable for both providers and users.
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| 5. |
- Elmstedt, Sixten, et al.
(author)
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Cancer patients hospitalised in the last week of life risk insufficient care quality : a population-based study from the Swedish Register of Palliative Care
- 2019
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In: Acta Oncologica. - : Taylor & Francis Group. - 0284-186X .- 1651-226X. ; 58:4, s. 432-438
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Journal article (peer-reviewed)abstract
- Background: One-quarter of all cancer deaths in Sweden occur in hospitals. If the place of death affects the quality of end-of-life (EOL) is largely unknown.Methods: This population-based, retrospective study included all adults cancer deaths reported to the Swedish Register of Palliative Care in 2011-2013 (N = 41,729). Hospital deaths were compared to deaths occurring in general or specialised palliative care, or in nursing homes with respect to care quality indicators in the last week of life. Odds ratios (OR) with 95% confidence intervals (CI) were calculated with specialised palliative home care as reference.Results: Preferred place of death was unknown for 63% of hospitalised patients and consistent with the actual place of death in 25% compared to 97% in palliative home care. Hospitalised patients were less likely to be informed when death was imminent (OR: 0.3; CI: 0.28-0.33) as were their families (OR: 0.51; CI: 0.46-0.57). Validated screening tools were less often used in hospitals for assessment of pain (OR: 0.32; CI: 0.30-0.34) or other symptoms (OR: 0.31; CI: 0.28-0.34) despite similar levels of EOL symptoms. Prescriptions of as needed drugs against anxiety (OR: 0.27; CI: 0.24-0.30), nausea (OR: 0.19; CI: 0.17-0.21), or pulmonary secretions (OR: 0.29; CI: 0.26-0.32) were less prevalent in hospitals. Bereavement support was offered after 57% of hospital deaths compared to 87-97% in palliative care units and 72% in nursing homes.Conclusions: Dying in hospital was associated with inferior end-of-life care quality among cancer patients in Sweden.
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| 6. |
- Fagerberg, Linn, et al.
(author)
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Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics
- 2014
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In: Molecular & Cellular Proteomics. - 1535-9476 .- 1535-9484. ; 13:2, s. 397-406
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Journal article (peer-reviewed)abstract
- Global classification of the human proteins with regards to spatial expression patterns across organs and tissues is important for studies of human biology and disease. Here, we used a quantitative transcriptomics analysis (RNA-Seq) to classify the tissue-specific expression of genes across a representative set of all major human organs and tissues and combined this analysis with antibody- based profiling of the same tissues. To present the data, we launch a new version of the Human Protein Atlas that integrates RNA and protein expression data corresponding to 80% of the human protein-coding genes with access to the primary data for both the RNA and the protein analysis on an individual gene level. We present a classification of all human protein-coding genes with regards to tissue-specificity and spatial expression pattern. The integrative human expression map can be used as a starting point to explore the molecular constituents of the human body.
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| 7. |
- Lindskog, Magnus, et al.
(author)
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Fluid therapy is associated with lower care quality and higher symptom burden during last days of life of patients with cancer : a population-based register study
- 2024
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In: BMC Palliative Care. - : BioMed Central (BMC). - 1472-684X. ; 23:1
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Journal article (peer-reviewed)abstract
- Background: Parenteral fluid (PF) therapy of patients in end-of-life (EOL) is controversial. The purpose of this study was to assess associations between PF, quality of the EOL care process and symptom burden in dying cancer patients, using a population-based approach.Methods: This was a nationwide retrospective register study of all adult cancer deaths with documented information on PF in the last 24 h of life as reported to the Swedish Register of Palliative Care during a three-year period (n = 41,709). Prevalence and relief of symptoms during the last week of life as well as EOL care process quality indicators were assessed in relation to PF in those patients who had a documented decision to focus on EOL care (immediately dying, n = 23,112). Odds ratios were calculated, adjusting for place of death (hospital vs. non-hospital).Results: PF was administered to 30.9% of immediately dying patients in hospitals compared to 6.5% outside of hospitals. PF was associated with a higher likelihood for breathlessness and nausea. In patients screened for EOL symptoms with a validated instrument, PF was inversely associated with the likelihood of complete relief of breathlessness, respiratory secretions, anxiety, nausea and pain. Several palliative care quality indicators were inversely associated with PF, including EOL conversations and prescriptions of injectable drugs as needed. These associations were more pronounced in hospitals.Conclusions: Parenteral fluid therapy in the last 24 h of life was associated with inferior quality of the EOL care process and with increased symptom burden in imminently dying cancer patients.
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| 8. |
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| 9. |
- Sand Lindskog, Hanna
(author)
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Local Participation in Electrification: A qualitative study of local participation in two small-scale hydropower projects in Tanzania
- 2012
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Reports (other academic/artistic)abstract
- The aim of this study is to investigate how different types and levels of participation affect the outcomes of two small-scale hydropower projects in Tanzania. It does not cover all possible aspects of participation and its relation to project outcomes, but focuses on outcomes in terms of the local actors’ perceptions of the significance of electricity, their expectations and satisfaction with the project, and their problem solving capacity for the future operation of the hydro plant.The research design is qualitative using a multiple-case study approach by conducting field studies at two sites and using data triangulation; semi-structured interviews, observations and secondary sources.The two projects in this study use both different and similar types and levels of participation in the planning, implementation and operation phases. The differences, however, are greater than the similarities. When the users’ perception of the significance of electricity and the satisfaction with the project differ, it depends mainly on the expectations created in the planning phase, the capacity of the hydropower system and the amount of users covered in the projects. Participation affects what people expect of the project and in turn also how satisfied they will become. However, participation needs to be put in relation to the financial and technical aspects in order to be effective.
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| 10. |
- Thul, Peter J., et al.
(author)
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A subcellular map of the human proteome
- 2017
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In: Science. - : American Association for the Advancement of Science. - 0036-8075 .- 1095-9203. ; 356:6340
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Journal article (peer-reviewed)abstract
- Resolving the spatial distribution of the human proteome at a subcellular level can greatly increase our understanding of human biology and disease. Here we present a comprehensive image-based map of subcellular protein distribution, the Cell Atlas, built by integrating transcriptomics and antibody-based immunofluorescence microscopy with validation by mass spectrometry. Mapping the in situ localization of 12,003 human proteins at a single-cell level to 30 subcellular structures enabled the definition of the proteomes of 13 major organelles. Exploration of the proteomes revealed single-cell variations in abundance or spatial distribution and localization of about half of the proteins to multiple compartments. This subcellular map can be used to refine existing protein-protein interaction networks and provides an important resource to deconvolute the highly complex architecture of the human cell.
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