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- Kanai, M, et al.
(författare)
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- 2023
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swepub:Mat__t
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| 2. |
- Niemi, MEK, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 3. |
- Campbell, PJ, et al.
(författare)
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Pan-cancer analysis of whole genomes
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Tidskriftsartikel (refereegranskat)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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| 7. |
- Dahlman, I, et al.
(författare)
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Adipose tissue pathways involved in weight loss of cancer cachexia
- 2010
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Ingår i: British Journal of Cancer. - : Springer Science and Business Media LLC. - 0007-0920 .- 1532-1827. ; 102:10, s. 1541-8
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: The regulatory gene pathways that accompany loss of adipose tissue in cancer cachexia are unknown and were explored using pangenomic transcriptome profiling. METHODS: Global gene expression profiles of abdominal subcutaneous adipose tissue were studied in gastrointestinal cancer patients with (n=13) or without (n=14) cachexia. RESULTS: Cachexia was accompanied by preferential loss of adipose tissue and decreased fat cell volume, but not number. Adipose tissue pathways regulating energy turnover were upregulated, whereas genes in pathways related to cell and tissue structure (cellular adhesion, extracellular matrix and actin cytoskeleton) were downregulated in cachectic patients. Transcriptional response elements for hepatic nuclear factor-4 (HNF4) were overrepresented in the promoters of extracellular matrix and adhesion molecule genes, and adipose HNF4 mRNA was downregulated in cachexia. CONCLUSIONS: Cancer cachexia is characterised by preferential loss of adipose tissue; muscle mass is less affected. Loss of adipose tissue is secondary to a decrease in adipocyte lipid content and associates with changes in the expression of genes that regulate energy turnover, cytoskeleton and extracellular matrix, which suggest high tissue remodelling. Changes in gene expression in cachexia are reciprocal to those observed in obesity, suggesting that regulation of fat mass at least partly corresponds to two sides of the same coin.
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| 8. |
- Young, Johanna J., et al.
(författare)
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Enhanced surveillance of hospitalized COVID-19 patients in Europe : an evaluation of the I-MOVE-COVID-19 surveillance network
- 2024
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Ingår i: European Journal of Public Health. - 1101-1262. ; 34:1, s. 181-189
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Tidskriftsartikel (refereegranskat)abstract
- Background: A pre-existing, well-established European influenza surveillance network known as I-MOVE enabled the rapid implementation of a European multi-country COVID-19 hospital surveillance network for surveillance of hospitalized COVID-19 cases in early 2020. This network included 257 hospitals in 11 surveillance sites across nine countries. We aimed to identify whether the surveillance objectives were relevant to public health actions, whether the surveillance system met its objectives, where and how shortcomings could be improved, and whether the system was sustainable. Methods: We identified six key attributes (meeting objectives, usefulness, timeliness, data quality, simplicity and sustainability) to assess, using Centers for Disease Control and Prevention’s evaluation framework. We analyzed pooled datasets, held interviews and group discussions with 10 participating and coordinating sites and gathered feedback through web surveys. Results: There was overall agreement that the surveillance objectives had been met and being involved in a network of European partners had additional important benefits for stakeholders. While the publication of the outputs was not always sufficiently timely, data submission processes were considered straightforward and the key surveillance variables (age, sex, hospital admission and mortality data) were complete. The main challenges were identified as the collection of the large number of variables, limited available human resources and information governance and data protection laws. Conclusions: I-MOVE-COVID-19 delivered relevant and accurate data supporting the development and implementation of COVID-19 surveillance. Recommendations presented here identify learning opportunities to support preparedness and surveillance response for future pandemics. The applied evaluation framework in this study can be adapted for other European surveillance system evaluations.
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| 9. |
- Zammit, Carla M., et al.
(författare)
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Bioleaching in brackish waters-effect of chloride ions on the acidophile population and proteomes of model species
- 2012
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Ingår i: Applied Microbiology and Biotechnology. - New York : Springer. - 0175-7598 .- 1432-0614. ; 93:1, s. 319-329
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Tidskriftsartikel (refereegranskat)abstract
- High concentrations of chloride ions inhibit the growth of acidophilic microorganisms used in biomining, a problem particularly relevant to Western Australian and Chilean biomining operations. Despite this, little is known about the mechanisms acidophiles adopt in order to tolerate high chloride ion concentrations. This study aimed to investigate the impact of increasing concentrations of chloride ions on the population dynamics of a mixed culture during pyrite bioleaching and apply proteomics to elucidate how two species from this mixed culture alter their proteomes under chloride stress. A mixture consisting of well-known biomining microorganisms and an enrichment culture obtained from an acidic saline drain were tested for their ability to bioleach pyrite in the presence of 0, 3.5, 7, and 20 g L(-1) NaCl. Microorganisms from the enrichment culture were found to out-compete the known biomining microorganisms, independent of the chloride ion concentration. The proteomes of the Gram-positive acidophile Acidimicrobium ferrooxidans and the Gram-negative acidophile Acidithiobacillus caldus grown in the presence or absence of chloride ions were investigated. Analysis of differential expression showed that acidophilic microorganisms adopted several changes in their proteomes in the presence of chloride ions, suggesting the following strategies to combat the NaCl stress: adaptation of the cell membrane, the accumulation of amino acids possibly as a form of osmoprotectant, and the expression of a YceI family protein involved in acid and osmotic-related stress.
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