| 1. |
- 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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| 2. |
- Berndt, Sonja I., et al.
(författare)
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Genome-wide association study identifies multiple risk loci for chronic lymphocytic leukemia
- 2013
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 45:8, s. 868-U202
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Tidskriftsartikel (refereegranskat)abstract
- Genome-wide association studies (GWAS) have previously identified 13 loci associated with risk of chronic lymphocytic leukemia or small lymphocytic lymphoma (CLL). To identify additional CLL susceptibility loci, we conducted the largest meta-analysis for CLL thus far, including four GWAS with a total of 3,100 individuals with CLL (cases) and 7,667 controls. In the meta-analysis, we identified ten independent associated SNPs in nine new loci at 10q23.31 (ACTA2 or FAS (ACTA2/FAS), P = 1.22 x 10(-14)), 18q21.33 (BCL2, P = 7.76 x 10(-11)), 11p15.5 (C11orf21, P = 2.15 x 10(-10)), 4q25 (LEF1, P = 4.24 x 10(-10)), 2q33.1 (CASP10 or CASP8 (CASP10/CASP8), P = 2.50 x 10(-9)), 9p21.3 (CDKN2B-AS1, P = 1.27 x 10(-8)), 18q21.32 (PMAIP1, P = 2.51 x 10(-8)), 15q15.1 (BMF, P = 2.71 x 10(-10)) and 2p22.2 (QPCT, P = 1.68 x 10(-8)), as well as an independent signal at an established locus (2q13, ACOXL, P = 2.08 x 10(-18)). We also found evidence for two additional promising loci below genome-wide significance at 8q22.3 (ODF1, P = 5.40 x 10(-8)) and 5p15.33 (TERT, P = 1.92 x 10(-7)). Although further studies are required, the proximity of several of these loci to genes involved in apoptosis suggests a plausible underlying biological mechanism.
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| 3. |
- Skibola, Christine F, et al.
(författare)
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Genome-wide Association Study Identifies Five Susceptibility Loci for Follicular Lymphoma outside the HLA Region.
- 2014
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Ingår i: American Journal of Human Genetics. - : Elsevier BV. - 0002-9297 .- 1537-6605. ; 95:4, s. 462-471
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Tidskriftsartikel (refereegranskat)abstract
- Genome-wide association studies (GWASs) of follicular lymphoma (FL) have previously identified human leukocyte antigen (HLA) gene variants. To identify additional FL susceptibility loci, we conducted a large-scale two-stage GWAS in 4,523 case subjects and 13,344 control subjects of European ancestry. Five non-HLA loci were associated with FL risk: 11q23.3 (rs4938573, p = 5.79 × 10(-20)) near CXCR5; 11q24.3 (rs4937362, p = 6.76 × 10(-11)) near ETS1; 3q28 (rs6444305, p = 1.10 × 10(-10)) in LPP; 18q21.33 (rs17749561, p = 8.28 × 10(-10)) near BCL2; and 8q24.21 (rs13254990, p = 1.06 × 10(-8)) near PVT1. In an analysis of the HLA region, we identified four linked HLA-DRβ1 multiallelic amino acids at positions 11, 13, 28, and 30 that were associated with FL risk (pomnibus = 4.20 × 10(-67) to 2.67 × 10(-70)). Additional independent signals included rs17203612 in HLA class II (odds ratio [ORper-allele] = 1.44; p = 4.59 × 10(-16)) and rs3130437 in HLA class I (ORper-allele = 1.23; p = 8.23 × 10(-9)). Our findings further expand the number of loci associated with FL and provide evidence that multiple common variants outside the HLA region make a significant contribution to FL risk.
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| 4. |
- 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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| 5. |
- Smedby, Karin E., et al.
(författare)
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GWAS of Follicular Lymphoma Reveals Allelic Heterogeneity at 6p21.32 and Suggests Shared Genetic Susceptibility with Diffuse Large B-cell Lymphoma
- 2011
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Ingår i: PLoS Genetics. - : Public Library of Science (PLoS). - 1553-7390 .- 1553-7404. ; 7:4, s. e1001378-
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Tidskriftsartikel (refereegranskat)abstract
- Non-Hodgkin lymphoma (NHL) represents a diverse group of hematological malignancies, of which follicular lymphoma (FL) is a prevalent subtype. A previous genome-wide association study has established a marker, rs10484561 in the human leukocyte antigen (HLA) class II region on 6p21.32 associated with increased FL risk. Here, in a three-stage genome-wide association study, starting with a genome-wide scan of 379 FL cases and 791 controls followed by validation in 1,049 cases and 5,790 controls, we identified a second independent FL-associated locus on 6p21.32, rs2647012 (ORcombined = 0.64, P-combined= 2x10(-21)) located 962 bp away from rs10484561 (r(2)< 0.1 in controls). After mutual adjustment, the associations at the two SNPs remained genome-wide significant (rs2647012: ORadjusted = 0.70, P-adjusted= 4x10(-12); rs10484561: ORadjusted = 1.64, P-adjusted= 5x10(-15)). Haplotype and coalescence analyses indicated that rs2647012 arose on an evolutionarily distinct haplotype from that of rs10484561 and tags a novel allele with an opposite (protective) effect on FL risk. Moreover, in a follow-up analysis of the top 6 FL-associated SNPs in 4,449 cases of other NHL subtypes, rs10484561 was associated with risk of diffuse large B-cell lymphoma (ORcombined = 1.36, P-combined = 1.4x10(-7)). Our results reveal the presence of allelic heterogeneity within the HLA class II region influencing FL susceptibility and indicate a possible shared genetic etiology with diffuse large B-cell lymphoma. These findings suggest that the HLA class II region plays a complex yet important role in NHL.
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| 6. |
- Mischak, Harald, et al.
(författare)
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Comprehensive human urine standards for comparability and standardization in clinical proteome analysis
- 2010
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Ingår i: Proteomics - Clinical Applications. - : Wiley. - 1862-8346 .- 1862-8354. ; 4:4, s. 464-478
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: Urine proteomics is emerging as a powerful tool for biomarker discovery. The purpose of this study is the development of a well-characterized "real life" sample that can be used as reference standard in urine clinical proteomics studies. Experimental design: We report on the generation of male and female urine samples that are extensively characterized by different platforms and methods (CE-MS, LC-MS, LC-MS/MS, 1-D gel analysis in combination with nano-LC MS/MS (using LTQ-FT ultra), and 2-DE-MS) for their proteome and peptidome. In several cases analysis involved a definition of the actual biochemical entities, i.e. proteins/peptides associated with molecular mass and detected PTMs and the relative abundance of these compounds. Results: The combination of different technologies allowed coverage of a wide mass range revealing the advantages and complementarities of the different technologies. Application of these samples in "inter-laboratory" and "inter-platform" data comparison is also demonstrated. Conclusions and clinical relevance: These well-characterized urine samples are freely available upon request to enable data comparison especially in the context of biomarker discovery and validation studies. It is also expected that they will provide the basis for the comprehensive characterization of the urinary proteome.
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| 7. |
- Novak, Masuma, 1969, et al.
(författare)
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Social and health-related correlates of intergenerational and intragenerational social mobility among Swedish men and women
- 2012
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Ingår i: Public health. - : Elsevier BV. - 1476-5616 .- 0033-3506. ; 126:4, s. 349-57
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVE: To explore the pattern and determinants of inter- and intragenerational occupational mobility among Swedish men and women. STUDY DESIGN: A Swedish 14-year prospective longitudinal study (response rate 96.5%). METHODS: Detailed information on 546 men and 495 women regarding their occupation, health status, health-related behaviour, psychosocial environment at home and school, material recourses and ethnicity prior to mobility were available at 16, 21 and 30 years of age. Odds ratios and 99% confidence intervals were calculated using logistic regression to determine social mobility. RESULTS: The results indicated that being popular at school predicted upward mobility, and being less popular at school predicted downward mobility. Additionally, material deprivation, economic deprivation, shorter height (women) and poor health behavioural factors predicted downward mobility. Among this cohort, being less popular at school was more common among subjects whose parents had low socio-economic status. Occupational mobility was not influenced by ethnic background. CONCLUSIONS: Apart from height (women), health status was not associated with mobility for men or women either inter- or intragenerationally. Unfavourable school environment was a consistent predictor of mobility for both genders. The results indicate that schools should be used as a setting for interventions aimed at reducing socio-economic health inequities. Targeted school interventions that are designed to assist higher educational attainment of socio-economically disadvantaged youth would help to break the social chain of risk experienced during this time, and thereby alter their life course in ways that would reduce subsequent social inequities in health and well-being.
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| 8. |
- Novak, Masuma, 1969-
(författare)
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Social inequity in health : Explanation from a life course and gender perspective
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Background: A boy child born in a Gothenburg suburb has a life expectancy that is nine years shorter than that of another child just 23 km away, and among girls the difference is five years. There is no necessary biological reason to this observed difference. In fact, like life length, most diseases follow a social gradient, even in a country like Sweden where many believe there is no class inequity. This social inequity in health tells us that some of us are not achieving our potential in health or in life length compared to our more fortunate fellow citizens. Aim: This thesis attempts to explore the patterns of health inequities and the pathways by which health inequities develop from a life course and gender perspective. In particular focuses on the importance of material, behavioural, health related and psychosocial circumstances from adolescence to adulthood in explaining social inequity in musculoskeletal disorders (MSDs), obesity, smoking, and social mobility. Method: All four papers of this thesis were based on quantitative analyses of data from a 14-year follow-up study. The baseline survey was conducted in 1981 in Luleå, Sweden. The survey included all 16-year-old pupils born in 1965. A total of 1081 pupils (575 boys and 506 girls) were surveyed. They were followed up at ages 18, 21 and 30 years with comprehensive self-administered questionnaires. The response rate was 96.5% throughout the 14-year follow-up. In addition to the questionnaires data, school records, and interviews with nurse and teachers’ were used. Results: There were no class or gender differences in MSDs and in obesity during adolescence, but significantly more girls than boys were smokers. Class and gender differences had emerged when they reached adulthood with more women reporting to have MSDs but more men being overweight and obese. Women continued to be smokers at a higher rate than men through to adulthood. When an intersection between class and gender was considered, a more complex picture emerged. For example, not all women had higher prevalence of MSDs or smoked more than men, rather men with high socioeconomic position (SEP) had lower prevalences of MSDs and smoking than women with high SEP; and these high SEP women had lower prevalences than men with low SEP. The worst-off group was women with low SEP. The obesity pattern was quite the contrary, where women with high SEP had a lower prevalence of obesity than women with low SEP; and these low SEP women had a lower prevalence than men with high SEP. The worst-off group was men with low SEP. Regarding social mobility, health status (other than height in women) and ethnic background were not associated with mobility either for men or women. The results indicated that unequal distribution of material, psychosocial, health and health related behavioural factors during adolescence, young adulthood and adulthood accounted for the observed social gradients and social mobility. However, several factors from adolescence appeared to be more important for women while recent factors were more important for men. Important adolescent factors for social inequity and downward mobility were: unfavourable material circumstances defined as low SEP of parent, unemployed family member, and had no own room during upbringing; unfavourable psychosocial circumstances defined as parental divorce, poor contact with parents, being less liked in school, and low school control; and poor health related behaviour defined as smoking and physical inactivity. Among these factors, being less liked in school showed consistent association with all outcome measures of this thesis. Being less liked by the teachers and students was found to be more common among adolescents whose parents had low SEP. Men and women who were less liked in school during their adolescence were more likely as adults to be smokers, obese (only women), and downwardly mobile. The dominant adult life factor that contributed to class inequity in MSDs for men and women was physical heavy working conditions, which attributed to an estimated 46.9% (women) and 49.5% (men) of the increased risk in MSDs of the lower SEP group. High alcohol consumption among men with low SEP was an additional factor that contributed to class inequities in health and social mobility. Conclusion: Social patterning of health in this cohort was gendered and age specific depending on the outcome measures. Unfavourable school environment in early years had long lasting negative influence on later health, health behavior and SEP. The thesis supports the notion of accumulation of risk that social inequities in health occurs due to accumulation of multiple adverse circumstances among the lower SEP group throughout their life course. Schools should be used as a setting for interventions aimed at reducing socioeconomic inequities in health. The detailed policy implications for reduction of social inequities in health among men and women are discussed.
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| 9. |
- Schmitt, Roland, et al.
(författare)
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The Combined Role of Galactose-Deficient IgA1 and Streptococcal IgA-Binding M Protein in Inducing IL-6 and C3 Secretion from Human Mesangial Cells: Implications for IgA Nephropathy.
- 2014
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Ingår i: Journal of Immunology. - : The American Association of Immunologists. - 1550-6606 .- 0022-1767. ; 193:1, s. 317-326
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Tidskriftsartikel (refereegranskat)abstract
- IgA nephropathy (IgAN) is characterized by mesangial cell proliferation and extracellular matrix expansion associated with immune deposits consisting of galactose-deficient polymeric IgA1 and C3. We have previously shown that IgA-binding regions of streptococcal M proteins colocalize with IgA in mesangial immune deposits in patients with IgAN. In the present study, the IgA-binding M4 protein from group A Streptococcus was found to bind to galactose-deficient polymeric IgA1 with higher affinity than to other forms of IgA1, as shown by surface plasmon resonance and solid-phase immunoassay. The M4 protein was demonstrated to bind to mesangial cells not via the IgA-binding region but rather via the C-terminal region, as demonstrated by flow cytometry. IgA1 enhanced binding of M4 to mesangial cells, but not vice versa. Costimulation of human mesangial cells with M4 and galactose-deficient polymeric IgA1 resulted in a significant increase in IL-6 secretion compared with each stimulant alone. Galactose-deficient polymeric IgA1 alone, but not M4, induced C3 secretion from the cells, and costimulation enhanced this effect. Additionally, costimulation enhanced mesangial cell proliferation compared with each stimulant alone. These results indicate that IgA-binding M4 protein binds preferentially to galactose-deficient polymeric IgA1 and that these proteins together induce excessive proinflammatory responses and proliferation of human mesangial cells. Thus, tissue deposition of streptococcal IgA-binding M proteins may contribute to the pathogenesis of IgAN.
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| 10. |
- Wada, Yoshinao, et al.
(författare)
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Comparison of methods for profiling O-glycosylation: Human Proteome Organisation Human Disease Glycomics/Proteome Initiative multi-institutional study of IgA1.
- 2010
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Ingår i: Molecular & cellular proteomics. - 1535-9484. ; 9:4, s. 719-727
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Tidskriftsartikel (refereegranskat)abstract
- The Human Proteome Organisation Human Disease Glycomics/Proteome Initiative recently coordinated a multi-institutional study that evaluated methodologies that are widely used for defining the N-glycan content in glycoproteins. The study convincingly endorsed mass spectrometry as the technique of choice for glycomic profiling in the discovery phase of diagnostic research. The present study reports the extension of the Human Disease Glycomics/Proteome Initiative's activities to an assessment of the methodologies currently used for O-glycan analysis. Three samples of IgA1 isolated from the serum of patients with multiple myeloma were distributed to 15 laboratories worldwide for O-glycomics analysis. A variety of mass spectrometric and chromatographic procedures representative of current methodologies were used. Similar to the previous N-glycan study, the results convincingly confirmed the pre-eminent performance of MS for O-glycan profiling. Two general strategies were found to give the most reliable data, namely direct MS analysis of mixtures of permethylated reduced glycans in the positive ion mode and analysis of native reduced glycans in the negative ion mode using LC-MS approaches. In addition, mass spectrometric methodologies to analyze O-glycopeptides were also successful.
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