| 1. |
- Abbafati, Cristiana, et al.
(författare)
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- 2020
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Tidskriftsartikel (refereegranskat)
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| 2. |
- Wang, Zhaoming, et al.
(författare)
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Imputation and subset-based association analysis across different cancer types identifies multiple independent risk loci in the TERT-CLPTM1L region on chromosome 5p15.33
- 2014
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Ingår i: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 23:24, s. 6616-6633
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Tidskriftsartikel (refereegranskat)abstract
- Genome-wide association studies (GWAS) have mapped risk alleles for at least 10 distinct cancers to a small region of 63 000 bp on chromosome 5p15.33. This region harbors the TERT and CLPTM1L genes; the former encodes the catalytic subunit of telomerase reverse transcriptase and the latter may play a role in apoptosis. To investigate further the genetic architecture of common susceptibility alleles in this region, we conducted an agnostic subset-based meta-analysis (association analysis based on subsets) across six distinct cancers in 34 248 cases and 45 036 controls. Based on sequential conditional analysis, we identified as many as six independent risk loci marked by common single-nucleotide polymorphisms: five in the TERT gene (Region 1: rs7726159, P = 2.10 × 10(-39); Region 3: rs2853677, P = 3.30 × 10(-36) and PConditional = 2.36 × 10(-8); Region 4: rs2736098, P = 3.87 × 10(-12) and PConditional = 5.19 × 10(-6), Region 5: rs13172201, P = 0.041 and PConditional = 2.04 × 10(-6); and Region 6: rs10069690, P = 7.49 × 10(-15) and PConditional = 5.35 × 10(-7)) and one in the neighboring CLPTM1L gene (Region 2: rs451360; P = 1.90 × 10(-18) and PConditional = 7.06 × 10(-16)). Between three and five cancers mapped to each independent locus with both risk-enhancing and protective effects. Allele-specific effects on DNA methylation were seen for a subset of risk loci, indicating that methylation and subsequent effects on gene expression may contribute to the biology of risk variants on 5p15.33. Our results provide strong support for extensive pleiotropy across this region of 5p15.33, to an extent not previously observed in other cancer susceptibility loci.
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| 3. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 4. |
- Aleksandrova, Krasimira, et al.
(författare)
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Circulating C-reactive protein concentrations and risks of colon and rectal cancer : a nested case-control study within the European Prospective Investigation into Cancer and Nutrition
- 2010
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Ingår i: American Journal of Epidemiology. - : Oxford University Press (OUP). - 0002-9262 .- 1476-6256. ; 172:4, s. 407-418
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Tidskriftsartikel (refereegranskat)abstract
- The authors investigated associations between serum C-reactive protein (CRP) concentrations and colon and rectal cancer risk in a nested case-control study within the European Prospective Investigation into Cancer and Nutrition (1992-2003) among 1,096 incident cases and 1,096 controls selected using risk-set sampling and matched on study center, age, sex, time of blood collection, fasting status, menopausal status, menstrual cycle phase, and hormone replacement therapy. In conditional logistic regression with adjustment for education, smoking, nutritional factors, body mass index, and waist circumference, CRP showed a significant nonlinear association with colon cancer risk but not rectal cancer risk. Multivariable-adjusted relative risks for CRP concentrations of > or = 3.0 mg/L versus <1.0 mg/L were 1.36 (95% confidence interval (CI): 1.00, 1.85; P-trend = 0.01) for colon cancer and 1.02 (95% CI: 0.67, 1.57; P-trend = 0.65) for rectal cancer. Colon cancer risk was significantly increased in men (relative risk = 1.74, 95% CI: 1.11, 2.73; P-trend = 0.01) but not in women (relative risk = 1.06, 95% CI: 0.67, 1.68; P-trend = 0.13). Additional adjustment for C-peptide, glycated hemoglobin, and high density lipoprotein cholesterol did not attenuate these results. These data provide evidence that elevated CRP concentrations are related to a higher risk of colon cancer but not rectal cancer, predominantly among men and independently of obesity, insulin resistance, and dyslipidemia.
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| 5. |
- Bamia, Christina, et al.
(författare)
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Dietary patterns and survival of older Europeans : the EPIC-Elderly Study (European Prospective Investigation into Cancer and Nutrition)
- 2007
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Ingår i: Public Health Nutrition. - : Cambridge University Press. - 1368-9800 .- 1475-2727. ; 10:6, s. 590-598
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Tidskriftsartikel (refereegranskat)abstract
- Objective: To investigate the association of a posteriori dietary patterns with overall survival of older Europeans.Design and setting: This is a multi-centre cohort study. Cox regression analysis was used to investigate the association of the prevailing, a posteriori-derived, plant-based dietary pattern with all-cause mortality in a population of subjects who were 60 years or older at recruitment to the European Prospective Investigation into Cancer and Nutrition (EPIC-Elderly cohort). Analyses controlled for all known potential risk factors.Subjects: In total, 74 607 men and women, 60 years or older at enrolment and without previous coronary heart disease, stroke or cancer, with complete information about dietary intakes and potentially confounding variables, and with known survival status as of December 2003, were included in the analysis.Results: An increase in the score which measures the adherence to the plant-based diet was associated with a lower overall mortality, a one standard deviation increment corresponding to a statistically significant reduction of 14% (95% confidence interval 5–23%). In country-specific analyses the apparent association was stronger in Greece, Spain, Denmark and The Netherlands, and absent in the UK and Germany.Conclusions: Greater adherence to the plant-based diet that was defined a posteriori in this population of European elders is associated with lower all-cause mortality. This dietary score is moderately positively correlated with the Modified Mediterranean Diet Score that has been constructed a priori and was also shown to be beneficial for the survival of the same EPIC-Elderly cohort.
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| 6. |
- Beecham, Ashley H, et al.
(författare)
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Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis.
- 2013
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Ingår i: Nature genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 45:11, s. 1353-60
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Tidskriftsartikel (refereegranskat)abstract
- Using the ImmunoChip custom genotyping array, we analyzed 14,498 subjects with multiple sclerosis and 24,091 healthy controls for 161,311 autosomal variants and identified 135 potentially associated regions (P < 1.0 × 10(-4)). In a replication phase, we combined these data with previous genome-wide association study (GWAS) data from an independent 14,802 subjects with multiple sclerosis and 26,703 healthy controls. In these 80,094 individuals of European ancestry, we identified 48 new susceptibility variants (P < 5.0 × 10(-8)), 3 of which we found after conditioning on previously identified variants. Thus, there are now 110 established multiple sclerosis risk variants at 103 discrete loci outside of the major histocompatibility complex. With high-resolution Bayesian fine mapping, we identified five regions where one variant accounted for more than 50% of the posterior probability of association. This study enhances the catalog of multiple sclerosis risk variants and illustrates the value of fine mapping in the resolution of GWAS signals.
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| 7. |
- Benskin, Jonathan, et al.
(författare)
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Manufacturing Origin of Perfluorooctanoate (PFOA) in Atlantic and Canadian Arctic Seawater
- 2012
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Ingår i: Environmental Science and Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 46:2, s. 677-685
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Tidskriftsartikel (refereegranskat)abstract
- The extent to which different manufacturing sources and long-range transport pathways contribute to perfluorooctanoate (PFOA) in the world’s oceans, particularly in remote locations, is widely debated. Here, the relative contribution of historic (i.e., electrochemically fluorinated) and contemporary (i.e., telomer) manufacturing sources was assessed for PFOA in various seawater samples by an established isomer profiling technique. The ratios of individual branched PFOA isomers were indistinguishable from those in authentic historic standards in 93% of the samples examined, indicating that marine processes had little influence on isomer profiles, and that isomer profiling is a valid source apportionment tool for seawater. Eastern Atlantic PFOA was largely (83−98%) of historic origin, but this decreased to only 33% close to the Eastern U.S. seaboard. Similarly, PFOA in the Norwegian Sea was near exclusively historic, but the relative contribution decreased to ∼50% near the Baltic Sea. Such observations of contemporary PFOA in coastal source regions coincided with elevated concentrations, suggesting that the continued production and use of PFOA is currently adding to the marine burden of this contaminant. In the Arctic, a spatial trend was observed whereby PFOA in seawater originating from the Atlantic was predominantly historic (up to 99%), whereas water in the Archipelago (i.e., from the Pacific) was predominantly of contemporary origin (as little as 17% historic). These data help to explain reported temporal and spatial trends from Arctic wildlife biomonitoring, and suggest that the dominant PFOA source(s) to the Pacific and Canadian Arctic Archipelago are either (a) from direct emissions of contemporary PFOA via manufacturing or use in Asia, or (b) from atmospheric transport and oxidation of contemporary PFOA-precursors.
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| 8. |
- Benskin, Jonathan P., et al.
(författare)
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Perfluoroalkyl Acids in the Atlantic and Canadian Arctic Oceans
- 2012
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Ingår i: Environmental Science and Technology. - : American Chemical Society. - 0013-936X .- 1520-5851. ; 46:11, s. 5815-5823
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Tidskriftsartikel (refereegranskat)abstract
- We report here on the spatial distribution of C-4, C-6, and C-8 perfluoroalkyl sulfonates, C-6-C-14 perfluoroalkyl carboxylates, and perfluorooctanesulfonamide in the Atlantic and Arctic Oceans, including previously unstudied coastal waters of North and South America, and the Canadian Arctic Archipelago. Perfluorooctanoate (PFOA) and perfluorooctanesulfonate (PFOS) were typically the dominant perfluoroalkyl acids (PFAAs) in Atlantic water. In the midnorthwest Atlantic/Gulf Stream, sum PFAA concentrations (Sigma PFAAs) were low (77-190 pg/L) but increased rapidly upon crossing into U.S. coastal water (up to 5800 pg/L near Rhode Island). Sigma PFAAs in the northeast Atlantic were highest north of the Canary Islands (280-980 pg/L) and decreased with latitude. In the South Atlantic, concentrations increased near Rio de la Plata (Argentina/Uruguay; 350-540 pg/L Sigma PFAAs), possibly attributable to insecticides containing N-ethyl perfluorooctanesulfonamide, or proximity to Montevideo and Buenos Aires. In all other southern hemisphere locations, Sigma PFAAs were less than210 pg/L. PFOA/PFOS ratios were typically greater than= 1 in the northern hemisphere, similar to 1 near the equator, and less than= 1 in the southern hemisphere. In the Canadian Arctic, Sigma PFAAs ranged from 40 to 250 pg/L, with perfluoroheptanoate, PFOA, and PFOS among the PFAAs detected at the highest concentrations. PFOA/PFOS ratios (typically greater thangreater than1) decreased from Baffin Bay to the Amundsen Gulf; possibly attributable to increased atmospheric inputs. These data help validate global emissions models and contribute to understanding of long-range transport pathways and sources of PFAAs to remote regions.
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| 9. |
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| 10. |
- Boysen, Lena R., et al.
(författare)
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Global climate response to idealized deforestation in CMIP6 models
- 2020
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Ingår i: Biogeosciences. - : Copernicus GmbH. - 1726-4189. ; 17, s. 5615-5638
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Tidskriftsartikel (refereegranskat)abstract
- Changes in forest cover have a strong effect on climate through the alteration of surface biogeophysical and biogeochemical properties that affect energy, water and carbon exchange with the atmosphere. To quantify biogeophysical and biogeochemical effects of deforestation in a consistent setup, nine Earth system models (ESMs) carried out an idealized experiment in the framework of the Coupled Model Intercomparison Project, phase 6 (CMIP6). Starting from their pre-industrial state, models linearly replace 20×106 km2 of forest area in densely forested regions with grasslands over a period of 50 years followed by a stabilization period of 30 years. Most of the deforested area is in the tropics, with a secondary peak in the boreal region. The effect on global annual near-surface temperature ranges from no significant change to a cooling by 0.55 ∘C, with a multi-model mean of −0.22±0.21 ∘C. Five models simulate a temperature increase over deforested land in the tropics and a cooling over deforested boreal land. In these models, the latitude at which the temperature response changes sign ranges from 11 to 43∘ N, with a multi-model mean of 23∘ N. A multi-ensemble analysis reveals that the detection of near-surface temperature changes even under such a strong deforestation scenario may take decades and thus longer than current policy horizons. The observed changes emerge first in the centre of deforestation in tropical regions and propagate edges, indicating the influence of non-local effects. The biogeochemical effect of deforestation are land carbon losses of 259±80 PgC that emerge already within the first decade. Based on the transient climate response to cumulative emissions (TCRE) this would yield a warming by 0.46 ± 0.22 ∘C, suggesting a net warming effect of deforestation. Lastly, this study introduces the “forest sensitivity” (as a measure of climate or carbon change per fraction or area of deforestation), which has the potential to provide lookup tables for deforestation–climate emulators in the absence of strong non-local climate feedbacks. While there is general agreement across models in their response to deforestation in terms of change in global temperatures and land carbon pools, the underlying changes in energy and carbon fluxes diverge substantially across models and geographical regions. Future analyses of the global deforestation experiments could further explore the effect on changes in seasonality of the climate response as well as large-scale circulation changes to advance our understanding and quantification of deforestation effects in the ESM frameworks.
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