| 41. |
- Cerhan, James R., et al.
(författare)
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Genome-wide association study identifies multiple susceptibility loci for diffuse large B cell lymphoma
- 2014
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 46:11, s. 1233-1238
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Tidskriftsartikel (refereegranskat)abstract
- Diffuse large B cell lymphoma (DLBCL) is the most common lymphoma subtype and is clinically aggressive. To identify genetic susceptibility loci for DLBCL, we conducted a meta-analysis of 3 new genome-wide association studies (GWAS) and 1 previous scan, totaling 3,857 cases and 7,666 controls of European ancestry, with additional genotyping of 9 promising SNPs in 1,359 cases and 4,557 controls. In our multi-stage analysis, five independent SNPs in four loci achieved genome-wide significance marked by rs116446171 at 6p25.3 (EXOC2; P = 2.33 x 10(-21)), rs2523607 at 6p21.33 (HLA-B; P = 2.40 x 10(-10)), rs79480871 at 2p23.3 (NCOA1; P = 4.23 x 10(-8)) and two independent SNPs, rs13255292 and rs4733601, at 8q24.21 (PVT1; P = 9.98 x 10(-13) and 3.63 x 10(-11), respectively). These data provide substantial new evidence for genetic susceptibility to this B cell malignancy and point to pathways involved in immune recognition and immune function in the pathogenesis of DLBCL.
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| 42. |
- Chavez, Juan D, et al.
(författare)
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A General Method for Targeted Quantitative Cross-Linking Mass Spectrometry.
- 2016
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 11:12
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Tidskriftsartikel (refereegranskat)abstract
- Chemical cross-linking mass spectrometry (XL-MS) provides protein structural information by identifying covalently linked proximal amino acid residues on protein surfaces. The information gained by this technique is complementary to other structural biology methods such as x-ray crystallography, NMR and cryo-electron microscopy[1]. The extension of traditional quantitative proteomics methods with chemical cross-linking can provide information on the structural dynamics of protein structures and protein complexes. The identification and quantitation of cross-linked peptides remains challenging for the general community, requiring specialized expertise ultimately limiting more widespread adoption of the technique. We describe a general method for targeted quantitative mass spectrometric analysis of cross-linked peptide pairs. We report the adaptation of the widely used, open source software package Skyline, for the analysis of quantitative XL-MS data as a means for data analysis and sharing of methods. We demonstrate the utility and robustness of the method with a cross-laboratory study and present data that is supported by and validates previously published data on quantified cross-linked peptide pairs. This advance provides an easy to use resource so that any lab with access to a LC-MS system capable of performing targeted quantitative analysis can quickly and accurately measure dynamic changes in protein structure and protein interactions.
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| 43. |
- Chen, Di, et al.
(författare)
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Angiogenesis depends upon EPHB4-mediated export of collagen IV from vascular endothelial cells
- 2022
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Ingår i: JCI Insight. - : American Society for Clinical Investigation. - 2379-3708. ; 7:4
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Tidskriftsartikel (refereegranskat)abstract
- Capillary malformation-arteriovenous malformation (CM-AVM) is a blood vascular anomaly caused by inherited loss-of-function mutations in RASA1 or EPHB4 genes, which encode p120 Ras GTPase-activating protein (p120 RasGAP/RASA1) and Ephrin receptor B4 (EPHB4). However, whether RASA1 and EPHB4 function in the same molecular signaling pathway to regulate the blood vasculature is uncertain. Here, we show that induced endothelial cell-specific (EC-specific) disruption of Ephb4 in mice resulted in accumulation of collagen IV in the EC ER, leading to EC apoptotic death and defective developmental, neonatal, and pathological angiogenesis, as reported previously in induced EC-specific RASA1-deficient mice. Moreover, defects in angiogenic responses in EPHB4-deficient mice could be rescued by drugs that inhibit signaling through the Ras pathway and drugs that promote collagen IV export from the ER. However, EPHB4-mutant mice that expressed a form of EPHB4 that is unable to physically engage RASA1 but retains protein tyrosine kinase activity showed normal angiogenic responses. These findings provide strong evidence that RASA1 and EPHB4 function in the same signaling pathway to protect against the development of CM-AVM independent of physical interaction and have important implications for possible means of treatment of this disease.
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| 44. |
- Chiang, Michael F., et al.
(författare)
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International Classification of Retinopathy of Prematurity, Third Edition
- 2021
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Ingår i: Ophthalmology. - : Elsevier. - 0161-6420 .- 1549-4713. ; 128:10, s. 51-68
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: The International Classification of Retinopathy of Prematurity is a consensus statement that creates a standard nomenclature for classification of retinopathy of prematurity (ROP). It was initially published in 1984, expanded in 1987, and revisited in 2005. This article presents a third revision, the International Classification of Retinopathy of Prematurity, Third Edition (ICROP3), which is now required because of challenges such as: (1) concerns about subjectivity in critical elements of disease classification; (2) innovations in ophthalmic imaging; (3) novel pharmacologic therapies (e.g., antievascular endothelial growth factor agents) with unique regression and reactivation features after treatment compared with ablative therapies; and (4) recognition that patterns of ROP in some regions of the world do not fit neatly into the current classification system.Design: Review of evidence-based literature, along with expert consensus opinion. Participants: International ROP expert committee assembled in March 2019 representing 17 countries and comprising 14 pediatric ophthalmologists and 20 retinal specialists, as well as 12 women and 22 men.Methods: The committee was initially divided into 3 subcommittees-acute phase, regression or reactivation, and imaging-each of which used iterative videoconferences and an online message board to identify key challenges and approaches. Subsequently, the entire committee used iterative videoconferences, 2 in-person multiday meetings, and an online message board to develop consensus on classification.Main Outcome Measures: Consensus statement.Results: The ICROP3 retains current definitions such as zone (location of disease), stage (appearance of disease at the avascular-vascular junction), and circumferential extent of disease. Major updates in the ICROP3 include refined classification metrics (e.g., posterior zone II, notch, subcategorization of stage 5, and recognition that a continuous spectrum of vascular abnormality exists from normal to plus disease). Updates also include the definition of aggressive ROP to replace aggressive-posterior ROP because of increasing recognition that aggressive disease may occur in larger preterm infants and beyond the posterior retina, particularly in regions of the world with limited resources. ROP regression and reactivation are described in detail, with additional description of long-term sequelae.Conclusions: These principles may improve the quality and standardization of ROP care worldwide and may provide a foundation to improve research and clinical care.
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| 45. |
- Conti, David, V, et al.
(författare)
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Trans-ancestry genome-wide association meta-analysis of prostate cancer identifies new susceptibility loci and informs genetic risk prediction
- 2021
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Ingår i: Nature Genetics. - : Springer Nature. - 1061-4036 .- 1546-1718. ; 53:1, s. 65-75
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Tidskriftsartikel (refereegranskat)abstract
- Prostate cancer is a highly heritable disease with large disparities in incidence rates across ancestry populations. We conducted a multiancestry meta-analysis of prostate cancer genome-wide association studies (107,247 cases and 127,006 controls) and identified 86 new genetic risk variants independently associated with prostate cancer risk, bringing the total to 269 known risk variants. The top genetic risk score (GRS) decile was associated with odds ratios that ranged from 5.06 (95% confidence interval (CI), 4.84-5.29) for men of European ancestry to 3.74 (95% CI, 3.36-4.17) for men of African ancestry. Men of African ancestry were estimated to have a mean GRS that was 2.18-times higher (95% CI, 2.14-2.22), and men of East Asian ancestry 0.73-times lower (95% CI, 0.71-0.76), than men of European ancestry. These findings support the role of germline variation contributing to population differences in prostate cancer risk, with the GRS offering an approach for personalized risk prediction. A meta-analysis of genome-wide association studies across different populations highlights new risk loci and provides a genetic risk score that can stratify prostate cancer risk across ancestries.
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| 46. |
- Coyle, Daisy, et al.
(författare)
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Estimating the potential impact of Australia's reformulation programme on households' sodium purchases.
- 2021
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Ingår i: BMJ Nutrition, Prevention & Health. - : BMJ Publishing Group Ltd. - 2516-5542. ; 4:1, s. 49-58
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Tidskriftsartikel (refereegranskat)abstract
- Background: On average, Australian adults consume 3500 mg sodium per day, almost twice the recommended maximum level of intake. The Australian government through the Healthy Food Partnership initiative has developed a voluntary reformulation programme with sodium targets for 27 food categories. We estimated the potential impact of this programme on household sodium purchases (mg/day per capita) and examined potential differences by income level. We also modelled and compared the effects of applying the existing UK reformulation programme targets in Australia.Methods: This study used 1 year of grocery purchase data (2018) from a nationally representative consumer panel of Australian households (Nielsen Homescan) that was linked with a packaged food and beverage database (FoodSwitch) that contains product-specific sodium information. Potential reductions in per capita sodium purchases were calculated and differences across income level were assessed by analysis of variance. All analyses were modelled to the Australian population in 2018.Results: A total of 7188 households were included in the analyses. The Healthy Food Partnership targets covered 4307/26 728 (16.1%) unique products, which represented 22.3% of all packaged foods purchased by Australian households in 2018. Under the scenario that food manufacturers complied completely with the targets, sodium purchases will be reduced by 50 mg/day per capita, equivalent to 3.5% of sodium currently purchased from packaged foods. Reductions will be greater in low-income households compared with high-income households (mean difference -7 mg/day, 95% CI -4 to -11 mg/day, p<0.001). If Australia had adopted the UK sodium targets, this would have covered 9927 unique products, resulting in a reduction in per capita sodium purchases by 110 mg/day.Conclusion: The Healthy Food Partnership reformulation programme is estimated to result in a very small reduction to sodium purchases. There are opportunities to improve the programme considerably through greater coverage and more stringent targets.
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| 47. |
- Coyle, Daisy H, et al.
(författare)
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Contribution of major food companies and their products to household dietary sodium purchases in Australia
- 2020
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Ingår i: International Journal of Behavioral Nutrition and Physical Activity. - : BioMed Central (BMC). - 1479-5868. ; 17:1, s. 2-9
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Tidskriftsartikel (refereegranskat)abstract
- Background: The Australian federal government will soon release voluntary sodium reduction targets for 30 packaged food categories through the Healthy Food Partnership. Previous assessments of voluntary targets show variable industry engagement, and little is known about the extent that major food companies and their products contribute to dietary sodium purchases among Australian households.Methods: The aim of this cross-sectional study was to identify the relative contribution that food companies and their products made to Australian household sodium purchases in 2018, and to examine differences in sodium purchases by household income level. We used 1 year of grocery purchase data from a nationally representative consumer panel of Australian households who reported their grocery purchases (the Nielsen Homescan panel), combined with database that contains product-specific sodium content for packaged foods and beverages (FoodSwitch). The top food companies and food categories were ranked according to their contribution to household sodium purchases. Differences in per capita sodium purchases by income levels were assessed by 1-factor ANOVA. All analyses were modelled to the Australian population in 2018 using sample weights.Results: Sodium data were available from 7188 households who purchased 26,728 unique products and purchased just under 7.5 million food product units. Out of 1329 food companies, the top 10 accounted for 35% of unique products and contributed to 58% of all sodium purchased from packaged foods and beverages. The top three companies were grocery food retailers each contributing 12-15% of sodium purchases from sales of their private label products, particularly processed meat, cheese and bread. Out of the 67 food categories, the top 10 accounted for 73% of sodium purchased, particularly driven by purchases of processed meat (14%), bread (12%) and sauces (11%). Low-income Australian households purchased significantly more sodium from packaged products than high-income households per capita (452 mg/d, 95%CI: 363-540 mg/d, P < 0.001).Conclusions: A small number of food companies and food categories account for most of the dietary sodium purchased by Australian households. Prioritizing government engagement with these groups could deliver a large reduction in population sodium intake.
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| 48. |
- Coyle, Daisy H, et al.
(författare)
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Estimating the potential impact of the Australian government's reformulation targets on household sugar purchases.
- 2021
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Ingår i: International Journal of Behavioral Nutrition and Physical Activity. - : Springer Nature. - 1479-5868. ; 18:1
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Countries around the world are putting in place sugar reformulation targets for packaged foods to reduce excess sugar consumption. The Australian government released its voluntary sugar reformulation targets for nine food categories in 2020. We estimated the potential impact of these targets on household sugar purchases and examined differences by income. For comparison, we also modelled the potential impact of the UK sugar reduction targets on per capita sugar purchases as the UK has one of the most comprehensive sugar reduction strategies in the world.METHODS: Grocery purchase data from a nationally representative consumer panel (n=7,188) in Australia was linked with a large database (FoodSwitch) with product-specific sugar content information for packaged foods (n=25,261); both datasets were collected in 2018. Potential reductions in per capita sugar purchases were calculated overall and by food category. Differences in sugar reduction across income level were assessed by analysis of variance.RESULTS: In 2018, the total sugar acquired from packaged food and beverage purchases consumed at-home was 56.1 g/day per capita. Australia's voluntary reformulation targets for sugar covered 2,471/25,261 (9.8%) unique products in the FoodSwitch dataset. Under the scenario that all food companies adhered to the voluntary targets, sugar purchases were estimated to be reduced by 0.9 g/day per capita, which represents a 1.5% reduction in sugar purchased from packaged foods. However, if Australia adopted the UK targets, over twice as many products would be covered (n=4,667), and this would result in a more than four times greater reduction in sugar purchases (4.1 g/day per capita). It was also estimated that if all food companies complied with Australia's voluntary sugar targets, reductions to sugar would be slightly greater in low-income households compared with high-income households by 0.3 g/day (95%CI 0.2 - 0.4 g/day, p<0.001).CONCLUSIONS: Sugar-reduction policies have the potential to substantially reduce population sugar consumption and may help to reduce health inequalities related to excess sugar consumption. However, the current reformulation targets in Australia are estimated to achieve only a small reduction to sugar intakes, particularly in comparison to the UK's sugar reduction program.
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| 49. |
- Coyle, Daisy H, et al.
(författare)
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The Contribution of Major Food Categories and Companies to Household Purchases of Added Sugar in Australia.
- 2022
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Ingår i: Journal of the Academy of Nutrition and Dietetics. - : Elsevier. - 2212-2672 .- 2212-2680. ; 122:2, s. 345-353.e3
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: The Australian Government will soon be releasing a series of sugar reformulation targets for packaged foods.OBJECTIVE: To estimate the amount of added sugar purchased from packaged food and beverages and the relative contribution that food categories and food companies made to these purchases in 2018. The secondary objective was to examine differences in purchases of added sugar across income levels.DESIGN: Cross-sectional study.PARTICIPANTS/SETTING: We used 1 year of grocery purchase data from a nationally representative panel of Australian households (the NielsenIQ Homescan panel), combined with a packaged food and beverage database (FoodSwitch).MAIN OUTCOME MEASURES: Added sugar purchases (grams per day per capita), purchase-weighted added sugar content (grams per 100 g) and total weight of products (with added sugar) purchased (grams per day per capita).STATISTICAL ANALYSES PERFORMED: Food categories and food companies were ranked according to their contribution to added sugar purchases. Differences in added sugar purchases by income levels were assessed by 1-factor analysis of variance.RESULTS: Added sugar information was available from 7188 households and across 26,291 unique foods and beverages. On average, the amount of added sugar acquired from packaged foods and beverages was (mean ± SE) 35.9 ± 0.01 g/d per capita. Low-income households purchased 11.0 g/d (95% CI: 10.9-11.0 g/d, P < .001) more added sugar from packaged products than high-income households per capita. The top 10 food categories accounted for 82.2% of added sugar purchased, largely due to purchases of chocolate and sweets, soft drinks, and ice cream and edible ices. Out of 994 food companies, the top 10 companies contributed to 62.1% of added sugar purchases.CONCLUSIONS: The Australian Government can strengthen their proposed sugar reduction program by adding further category-specific targets, prioritizing engagement with key food companies and considering a broader range of policies to reduce added sugar intakes across the Australian population.
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| 50. |
- Crosby, Jacy, et al.
(författare)
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Loss-of-Function Mutations in APOC3, Triglycerides, and Coronary Disease
- 2014
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Ingår i: New England Journal of Medicine. - 0028-4793 .- 1533-4406. ; 371:1, s. 22-31
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Tidskriftsartikel (refereegranskat)abstract
- Background Plasma triglyceride levels are heritable and are correlated with the risk of coronary heart disease. Sequencing of the protein-coding regions of the human genome (the exome) has the potential to identify rare mutations that have a large effect on phenotype. Methods We sequenced the protein-coding regions of 18,666 genes in each of 3734 participants of European or African ancestry in the Exome Sequencing Project. We conducted tests to determine whether rare mutations in coding sequence, individually or in aggregate within a gene, were associated with plasma triglyceride levels. For mutations associated with triglyceride levels, we subsequently evaluated their association with the risk of coronary heart disease in 110,970 persons. Results An aggregate of rare mutations in the gene encoding apolipoprotein C3 (APOC3) was associated with lower plasma triglyceride levels. Among the four mutations that drove this result, three were loss-of-function mutations: a nonsense mutation (R19X) and two splice-site mutations (IVS2+1G -> A and IVS3+1G -> T). The fourth was a missense mutation (A43T). Approximately 1 in 150 persons in the study was a heterozygous carrier of at least one of these four mutations. Triglyceride levels in the carriers were 39% lower than levels in noncarriers (P<1x10(-20)), and circulating levels of APOC3 in carriers were 46% lower than levels in noncarriers (P = 8x10(-10)). The risk of coronary heart disease among 498 carriers of any rare APOC3 mutation was 40% lower than the risk among 110,472 noncarriers (odds ratio, 0.60; 95% confidence interval, 0.47 to 0.75; P = 4x10(-6)). Conclusions Rare mutations that disrupt APOC3 function were associated with lower levels of plasma triglycerides and APOC3. Carriers of these mutations were found to have a reduced risk of coronary heart disease. (Funded by the National Heart, Lung, and Blood Institute and others.)
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