| 1. |
- Fagerberg, Linn, et al.
(författare)
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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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Ingår i: Molecular & Cellular Proteomics. - 1535-9476 .- 1535-9484. ; 13:2, s. 397-406
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Tidskriftsartikel (refereegranskat)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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| 2. |
- Danielsson, Marcus, et al.
(författare)
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Longitudinal changes in the frequency of mosaic chromosome Y loss in peripheral blood cells of aging men varies profoundly between individuals
- 2020
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Ingår i: European Journal of Human Genetics. - : Springer Science and Business Media LLC. - 1018-4813 .- 1476-5438. ; 28:3, s. 349-357
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Tidskriftsartikel (refereegranskat)abstract
- Mosaic loss of chromosome Y (LOY) is the most common somatic genetic aberration and is associated with increased risk for all-cause mortality, various forms of cancer and Alzheimer's disease, as well as other common human diseases. By tracking LOY frequencies in subjects from which blood samples have been serially collected up to five times during up to 22 years, we observed a pronounced intra-individual variation of changes in the frequency of LOY within individual men over time. We observed that in some individuals the frequency of LOY in blood clearly progressed over time and that in other men, the frequency was constant or showed other types of longitudinal development. The predominant method used for estimating LOY is calculation of the median Log R Ratio of probes located in the male specific part of chromosome Y (mLRRY) from intensity data generated by SNP-arrays, which is difficult to interpret due to its logarithmic and inversed scale. We present here a formula to transform mLRRY-values to percentage of LOY that is a more comprehensible unit. The formula was derived using measurements of LOY from matched samples analysed using SNP-array, whole genome sequencing and a new AMELX/AMELY-based assay for droplet digital PCR. The methods described could be applied for analyses of the vast amount of SNP-array data already generated in the scientific community, allowing further discoveries of LOY associated diseases and outcomes.
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| 3. |
- Dumanski, Jan P., et al.
(författare)
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Immune cells lacking Y chromosome show dysregulation of autosomal gene expression
- 2021
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Ingår i: Cellular and Molecular Life Sciences (CMLS). - : Springer. - 1420-682X .- 1420-9071. ; 78:8, s. 4019-4033
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Tidskriftsartikel (refereegranskat)abstract
- Epidemiological investigations show that mosaic loss of chromosome Y (LOY) in leukocytes is associated with earlier mortality and morbidity from many diseases in men. LOY is the most common acquired mutation and is associated with aberrant clonal expansion of cells, yet it remains unclear whether this mosaicism exerts a direct physiological effect. We studied DNA and RNA from leukocytes in sorted- and single-cells in vivo and in vitro. DNA analyses of sorted cells showed that men diagnosed with Alzheimer’s disease was primarily affected with LOY in NK cells whereas prostate cancer patients more frequently displayed LOY in CD4 + T cells and granulocytes. Moreover, bulk and single-cell RNA sequencing in leukocytes allowed scoring of LOY from mRNA data and confirmed considerable variation in the rate of LOY across individuals and cell types. LOY-associated transcriptional effect (LATE) was observed in ~ 500 autosomal genes showing dysregulation in leukocytes with LOY. The fraction of LATE genes within specific cell types was substantially larger than the fraction of LATE genes shared between different subsets of leukocytes, suggesting that LOY might have pleiotropic effects. LATE genes are involved in immune functions but also encode proteins with roles in other diverse biological processes. Our findings highlight a surprisingly broad role for chromosome Y, challenging the view of it as a “genetic wasteland”, and support the hypothesis that altered immune function in leukocytes could be a mechanism linking LOY to increased risk for disease.
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| 4. |
- Forsberg, Lars A., 1974-, et al.
(författare)
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Mosaic loss of chromosome Y in leukocytes matters
- 2019
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 51:1, s. 4-7
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 5. |
- Lindell, Johan, et al.
(författare)
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"And like that I'm talking to a Girl from China, you know" : Cultural capital and the classification of media as avenues of cosmopolitan cultivation
- 2015
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Ingår i: Book of Abstracts. ; , s. 60-60
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Konferensbidrag (refereegranskat)abstract
- The phenomenon of a “mediated cosmopolitanism” has mainly been studied from a perspective that attempts to discern the extent to which various messages of the media succeed or fail in establishing moral solidarity with “the distant other”. This perspective misses two crucial points worthy of pursuing when attempting to understand the relationship between media and cosmopolitanism. Firstly, it still remains rather unclear what sense audiences and users make of the globalizing potential of the contemporary media landscape. Secondly, cosmopolitanism cannot solely be conceptualized as a moral obligation across vast distances, but needs also to be understood as a form of capital, as social fields become increasingly transnational. By understanding users and audiences of potentially global media as contextualized social agents we engage with the relationship between cosmopolitanism and the media from a new vantage point. In departing from the media-centric tendencies in the research area, we turn to the question of how classified social agents classify the contemporary media landscape as gateways to the wider world. What emerges in our qualitative and quantitative data is a pattern of social reproduction – agents strong on cultural capital are particularly prone to approach the media landscape as an avenue for the generation of cosmopolitan capital. There is thus reason to question the universalizing rhetoric pertaining to notions of a “mediated cosmopolitanism” and study the ways in which agents’ orientations in the media landscape are part of strategies of social reproduction.
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| 6. |
- Lindell, Johan, 1985-, et al.
(författare)
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(Mediated) cosmopolitanism as symbolic violence
- 2014
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The notions of a “mediated cosmopolitanism”, a “global imagined community” and an “imagined cosmopolitanism” speak of a cosmopolitan opportunism gaining ground in contemporary media and communication studies. This line of research tends to epistemologically situate human beings exclusively as users or audiences of media. The risk by such a media-centric focus is to confine oneself to the question of “what the media does to people”. By understanding users and audiences of potentially global media as contextualized social agents we engage with the relationship between cosmopolitanism and the media from a different vantage point. Our media sociological perspective insists on accounting for social context, and so we turn to the question of how classified social agents classify the contemporary media landscape as gateways to the wider world. What emerges in our qualitative and quantitative data is a pattern of social reproduction by way of cultural distinction – agents strong on cultural capital is particularly prone to approach the media landscape as an avenue for cosmopolitan socialization. There is thus reason to question the universalizing rhetoric pertaining to notions of a “mediated cosmopolitanism”.
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| 7. |
- Lindell, Johan, 1985-, et al.
(författare)
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Moulding cultural capital into cosmopolitan capital : Media practices as reconversion work in a globalising world
- 2017
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Ingår i: Nordicom Review. - Göteborg : Göteborgs universitet. - 1403-1108 .- 2001-5119. ; 38:2, s. 51-64
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Tidskriftsartikel (refereegranskat)abstract
- Various media allow people to build transnational networks, learn about the world and meet people from other cultures. In other words, media may allow one to cultivate cosmopolitan capital, defined here as a distinct form of embodied cultural capital. However, far from everyone is identifying this potential. Analyses of a national survey and in-depth interviews, conducted in Sweden, disclose a tendency among those in possession of cultural capital to recognise and exploit cosmopolitan capital in their media practices. Those who are dispossessed of cultural capital are significantly less liable to approach media in this way. Relying on various media practices in order to reshape one’s cultural capital exemplifies what Bourdieu called a reconversion strategy. As social fields undergo globalisation, media offer opportunities for the privileged to remain privileged – to change in order to conserve.
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| 8. |
- Lindell, Johan, 1985-, et al.
(författare)
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Trading cultural capital for cosmopolitan capital : media practice as reconversion work in a globalizing world
- 2016
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Konferensbidrag (refereegranskat)abstract
- Various media allow people to build transnational networks, learn about the world and meet people from other cultures. In other words, media may allow one to cultivate a cosmopolitan capital. However, far from everyone is recognizing this potential. This study argues that cosmopolitan ‘readings’ of the contemporary media landscape should be understood in relation to cultural capital. Analyses from a national survey and in-depth interviews, conducted in Sweden, disclose a tendency among those in possession of cultural capital to recognize and exploit cosmopolitan capital in their media practices. Those in dispossession of cultural capital are significantly less prone to approach the media in this way. Relying on various media practices in order to exchange one capital for another exemplifies what Bourdieu called reconversion strategies. As social fields become more global, media offer opportunities for those occupying positions of relative (cultural) privilege to remain privileged – to change in order to conserve.
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| 9. |
- Mattisson, Jonas, et al.
(författare)
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Leukocytes with chromosome Y loss have reduced abundance of the cell surface immunoprotein CD99
- 2021
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Ingår i: Scientific Reports. - : Springer Nature. - 2045-2322. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Mosaic loss of chromosome Y (LOY) in immune cells is a male-specific mutation associated with increased risk for morbidity and mortality. The CD99 gene, positioned in the pseudoautosomal regions of chromosomes X and Y, encodes a cell surface protein essential for several key properties of leukocytes and immune system functions. Here we used CITE-seq for simultaneous quantification of CD99 derived mRNA and cell surface CD99 protein abundance in relation to LOY in single cells. The abundance of CD99 molecules was lower on the surfaces of LOY cells compared with cells without this aneuploidy in all six types of leukocytes studied, while the abundance of CD proteins encoded by genes located on autosomal chromosomes were independent from LOY. These results connect LOY in single cells with immune related cellular properties at the protein level, providing mechanistic insight regarding disease vulnerability in men affected with mosaic chromosome Y loss in blood leukocytes.
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| 10. |
- Thompson, Deborah J, et al.
(författare)
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Genetic predisposition to mosaic Y chromosome loss in blood
- 2019
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 575, s. 652-657
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Tidskriftsartikel (refereegranskat)abstract
- Mosaic loss of chromosome Y (LOY) in circulating white blood cells is the most common form of clonal mosaicism1-5, yet our knowledge of the causes and consequences of this is limited. Here, using a computational approach, we estimate that 20% of the male population represented in the UK Biobank study (n = 205,011) has detectable LOY. We identify 156 autosomal genetic determinants of LOY, which we replicate in 757,114 men of European and Japanese ancestry. These loci highlight genes that are involved in cell-cycle regulation and cancer susceptibility, as well as somatic drivers of tumour growth and targets of cancer therapy. We demonstrate that genetic susceptibility to LOY is associated with non-haematological effects on health in both men and women, which supports the hypothesis that clonal haematopoiesis is a biomarker of genomic instability in other tissues. Single-cell RNA sequencing identifies dysregulated expression of autosomal genes in leukocytes with LOY and provides insights into why clonal expansion of these cells may occur. Collectively, these data highlight the value of studying clonal mosaicism to uncover fundamental mechanisms that underlie cancer and other ageing-related diseases.
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