| 21. |
- Fredolini, Claudia, et al.
(författare)
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Immunocapture strategies in translational proteomics
- 2016
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Ingår i: Expert Review of Proteomics. - : Taylor & Francis. - 1478-9450 .- 1744-8387. ; 13:1, s. 83-98
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Forskningsöversikt (refereegranskat)abstract
- Aiming at clinical studies of human diseases, antibody-assisted assays have been applied to biomarker discovery and toward a streamlined translation from patient profiling to assays supporting personalized treatments. In recent years, integrated strategies to couple and combine antibodies with mass spectrometry-based proteomic efforts have emerged, allowing for novel possibilities in basic and clinical research. Described in this review are some of the field's current and emerging immunocapture approaches from an affinity proteomics perspective. Discussed are some of their advantages, pitfalls and opportunities for the next phase in clinical and translational proteomics.
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| 22. |
- Grahn, Oskar, et al.
(författare)
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Mutation of the cyclooxygenase 2 gene promoter and anastomotic leakage in colorectal cancer patients : retrospective cohort study
- 2024
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Ingår i: BJS Open. - : Oxford University Press. - 2474-9842. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- Anastomotic leakage after surgery for colorectal cancer is a serious complication, causing an increased morbidity rate and mortality rate1,2.There is a debate and conflicting evidence on whether non-steroidal anti-inflammatory drugs (NSAIDs) increase the risk of leak3,4. NSAIDs act by inhibiting cyclooxygenase (COX) enzymes, which can be subdivided into isoenzymes COX-1 and COX-2. In a seminal study by Reisinger et al.5, knocking out the COX-2 gene resulted in an increase of colonic anastomotic leaks in mice. In a complementary cohort of colorectal cancer patients5, an increased frequency of anastomotic leaks was demonstrated among those homozygous for the COX-2 gene promoter mutation −765G > C (also known as rs20417). This finding could potentially be translated into clinical use following external validation.Biological effects might not only be present among those homozygous for the minor allele of −765C/C. For example, the heterozygous state of −765G/C has been associated with a decreased postoperative inflammatory response6.The present study aimed to evaluate the prevalence of the polymorphism 765G > C in a Swedish cohort of colorectal cancer patients, and its association with postoperative peritoneal infection.
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| 23. |
- Gudmundsdottir, Valborg, et al.
(författare)
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Whole blood co-expression modules associate with metabolic traits and type 2 diabetes : an IMI-DIRECT study
- 2020
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Ingår i: Genome Medicine. - : BioMed Central. - 1756-994X .- 1756-994X. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: The rising prevalence of type 2 diabetes (T2D) poses a major global challenge. It remains unresolved to what extent transcriptomic signatures of metabolic dysregulation and T2D can be observed in easily accessible tissues such as blood. Additionally, large-scale human studies are required to further our understanding of the putative inflammatory component of insulin resistance and T2D. Here we used transcriptomics data from individuals with (n = 789) and without (n = 2127) T2D from the IMI-DIRECT cohorts to describe the co-expression structure of whole blood that mainly reflects processes and cell types of the immune system, and how it relates to metabolically relevant clinical traits and T2D.Methods: Clusters of co-expressed genes were identified in the non-diabetic IMI-DIRECT cohort and evaluated with regard to stability, as well as preservation and rewiring in the cohort of individuals with T2D. We performed functional and immune cell signature enrichment analyses, and a genome-wide association study to describe the genetic regulation of the modules. Phenotypic and trans-omics associations of the transcriptomic modules were investigated across both IMI-DIRECT cohorts.Results: We identified 55 whole blood co-expression modules, some of which clustered in larger super-modules. We identified a large number of associations between these transcriptomic modules and measures of insulin action and glucose tolerance. Some of the metabolically linked modules reflect neutrophil-lymphocyte ratio in blood while others are independent of white blood cell estimates, including a module of genes encoding neutrophil granule proteins with antibacterial properties for which the strongest associations with clinical traits and T2D status were observed. Through the integration of genetic and multi-omics data, we provide a holistic view of the regulation and molecular context of whole blood transcriptomic modules. We furthermore identified an overlap between genetic signals for T2D and co-expression modules involved in type II interferon signaling.Conclusions: Our results offer a large-scale map of whole blood transcriptomic modules in the context of metabolic disease and point to novel biological candidates for future studies related to T2D.
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| 24. |
- Hellström, Cecilia, et al.
(författare)
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High-density serum/plasma reverse phase protein arrays
- 2017
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Ingår i: Serum/Plasma Proteomics. - New York, NY : Humana Press. ; , s. 229-238
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Bokkapitel (refereegranskat)abstract
- In-depth exploration and characterization of human serum and plasma proteomes is an attractive strategy for the identification of potential prognostic or diagnostic biomarkers. The possibility of analyzing larger numbers of samples in a high-throughput fashion has markedly increased with affinity-based microarrays, thus providing higher statistical power to these biomarker studies. Here, we describe a protocol for high-density serum and plasma reverse phase protein arrays (RPPAs). We demonstrate how a biobank of 12,392 samples was immobilized and analyzed on a single microarray slide, allowing high-quality profiling of abundant target proteins across all samples in one assay.
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| 25. |
- Hong, Mun-Gwan, et al.
(författare)
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A genome-wide assessment of variability in human serum metabolism
- 2013
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Ingår i: Human Mutation. - : Hindawi Limited. - 1059-7794 .- 1098-1004. ; 34:3, s. 515-524
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Tidskriftsartikel (refereegranskat)abstract
- The study of the genetic regulation of metabolism in human serum samples can contribute to a better understanding of the intermediate biological steps that lead from polymorphism to disease. Here, we conducted a genome-wide association study (GWAS) to discover metabolic quantitative trait loci (mQTLs) utilizing samples from a study of prostate cancer in Swedish men, consisting of 402 individuals (214 cases and 188 controls) in a discovery set and 489 case-only samples in a replication set. A global nontargeted metabolite profiling approach was utilized resulting in the detection of 6,138 molecular features followed by targeted identification of associated metabolites. Seven replicating loci were identified (PYROXD2, FADS1, PON1, CYP4F2, UGT1A8, ACADL, and LIPC) with associated sequence variants contributing significantly to trait variance for one or more metabolites (P = 10(-13) -10(-91)). Regional mQTL enrichment analyses implicated two loci that included FADS1 and a novel locus near PDGFC. Biological pathway analysis implicated ACADM, ACADS, ACAD8, ACAD10, ACAD11, and ACOXL, reflecting significant enrichment of genes with acyl-CoA dehydrogenase activity. mQTL SNPs and mQTL-harboring genes were over-represented across GWASs conducted to date, suggesting that these data may have utility in tracing the molecular basis of some complex disease associations.
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| 26. |
- Hong, Mun-Gwan, et al.
(författare)
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Evidence that the gene encoding insulin degrading enzyme influences human lifespan.
- 2008
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Ingår i: Human molecular genetics. - : Oxford University Press (OUP). - 1460-2083 .- 0964-6906. ; 17:15, s. 2370-8
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Tidskriftsartikel (refereegranskat)abstract
- Studies in model organisms have demonstrated that components of insulin and insulin-like signaling pathways are involved in the regulation of lifespan but the relevance of those findings to humans has remained obscure. Here we provide evidence suggesting that variants of the gene encoding insulin-degrading enzyme (IDE) may be influencing human lifespan. We have employed a variety of models and diverse samples that reproducibly indicate the relative change in IDE genotype frequency across the age spectrum as well as allow the detection of association with age-at-death. A tenable molecular basis of this is suggested by the observation of genetic association with both fasting plasma insulin levels and IDE mRNA expression. Across populations the emergent genetic model is indicative of over-dominance, where heterozygotes of critical markers have increased IDE mRNA expression and insulin levels, and this is reflected in diminished heterozygosity at advanced age. A critical and replicating feature of this study is that change in IDE genotype frequency with advancing age appears to be occurring only in men, and this is supported in that insulin levels are only associated with IDE in men. Results suggest a relationship between a gene that is intimately involved in insulin metabolism and the determination of lifespan in humans, but over-dominance and gender specificity will be important parameters to consider clarifying the biological importance of these findings.
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| 27. |
- Hong, Mun-Gwan, et al.
(författare)
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Genome-wide and gene-based association implicates FRMD6 in Alzheimer disease
- 2012
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Ingår i: Human Mutation. - : Hindawi Limited. - 1059-7794 .- 1098-1004. ; 33:3, s. 521-529
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Tidskriftsartikel (refereegranskat)abstract
- Genome-wide association studies (GWAS) that allow for allelic heterogeneity may facilitate the discovery of novel genes not detectable by models that require replication of a single variant site. One strategy to accomplish this is to focus on genes rather than markers as units of association, and so potentially capture a spectrum of causal alleles that differ across populations. Here, we conducted a GWAS of Alzheimer disease (AD) in 2,586 Swedes and performed gene-based meta-analysis with three additional studies from France, Canada, and the United States, in total encompassing 4,259 cases and 8,284 controls. Implementing a newly designed gene-based algorithm, we identified two loci apart from the region around APOE that achieved study-wide significance in combined samples, the strongest finding being for FRMD6 on chromosome 14q (P = 2.6 × 10(-14)) and a weaker signal for NARS2 that is immediately adjacent to GAB2 on chromosome 11q (P = 7.8 × 10(-9)). Ontology-based pathway analyses revealed significant enrichment of genes involved in glycosylation. Results suggest that gene-based approaches that accommodate allelic heterogeneity in GWAS can provide a complementary avenue for gene discovery and may help to explain a portion of the missing heritability not detectable with single nucleotide polymorphisms (SNPs) derived from marker-specific meta-analysis.
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| 28. |
- Hong, Mun-Gwan
(författare)
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Genomics and bioinformatics strategies in the study of aging and Alzheimer disease
- 2011
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- To understand complex phenotypes, medical research has evolved from the study of single genes and proteins to approaches that encompass more comprehensive catalogues of molecules. Among the more widely used are genome-wide expression and high-throughput genotyping, the latter primarily making use of single nucleotide polymorphisms (SNPs) in what has been termed genome-wide association studies (GWAS). Because of the scale of the data sets that are being produced, unique problems have emerged that necessitate the extensive use of bioinformatics tools. This thesis has entailed the analysis of several such large data sets in the context of biological pathways and introduces several bioinformatics solutions. Paper III, IV, and V deal with this topic. This thesis is primarily oriented around the study of Alzheimer disease (AD) and aging. The questions about the etiology of AD are often concurrent with questions about the biology of aging. This thesis pursues insight on genomic factors pertaining to both inquiries, acknowledging that both the AD state and aging itself are complex and multi-factorial. Two constituent papers (I and III) address aging and two papers (II and V) deal with genetic models in the study of AD. In paper I, we examined the association of age with several genetic markers in the insulin degrading enzyme (IDE) and explored possible molecular mechanisms. In contrast to women, both age-at-sampling and age-at-death of the males were significantly lower in individuals that were heterozygous at genetic loci spanning the IDE locus. Plasma insulin levels and the expression levels of the gene were found to be higher in those same heterozygous males. In paper II, SNPs in 25 genes involved in cholesterol metabolism were tested for association with AD and dementia. Genetic markers in a large linkage disequilibrium block spanning SREBF1, TOM1L2, and ATPAF2 were significantly associated with disease. Gene expression and gene network analyses supported the findings. In paper III, we investigated the biological pathway basis of age in human brain and lymphocytes. Mitochondrial genes were negatively regulated in both tissue samples, while the protein translation genes appeared to decrease in lymphocytes but increase in brain. Those observations indicated that there are common themes across tissues, but also tissue specific changes in gene regulation. We also examined the genomic architecture of the age-regulated genes, and found that the expression of non-compact genes tend to decrease with advancing age. A large number of genome-wide association studies (GWAS) have now been performed over the past few years. In paper IV, we developed a program that automates the conversion of SNPs to representative gene lists in order to facilitate the exploration of biological pathway in the context of GWAS. In paper V, we employed the software developed in study IV to identify biological pathways enriched among the genes that were significantly associated from a GWAS of AD. Genes involved in intracellular protein transmembrane transport were found to be significantly overrepresented. These results highlighted the possibility that TOMM40 contributes to AD pathology together with other translocases. Through this thesis, several biological relationships have been identified linking AD and aging. Genetic markers in IDE, a gene previously claimed to be associated with AD, also associate with age. With advancing age, mitochondrial gene expression deteriorates significantly. TOMM40 may contribute the AD pathology, together with other genes that encode proteins of the intracellular transmembrane protein transport pathway. Methodologically, pathway analyses were conducted successfully with the program, ProxyGeneLD. This enabled discoveries and discussion of the challenges that face the exploration of GWAS data sets in a pathway context. In the future, more sophisticated bioinformatics tools and enhanced gene annotation may lead to the discovery of the molecular mechanisms that dominate complex diseases and traits.
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| 29. |
- Hong, Mun-Gwan, et al.
(författare)
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Multidimensional Normalization to Minimize Plate Effects of Suspension Bead Array Data
- 2016
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Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 15:10, s. 3473-3480
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Tidskriftsartikel (refereegranskat)abstract
- Enhanced by the growing number of biobanks, biomarker studies can now be performed with reasonable statistical power by using large sets of samples. Antibody-based proteomics by means of suspension bead arrays offers one attractive approach to analyze serum, plasma, or CSF samples for such studies in microtiter plates. To expand measurements beyond single batches, with either 96 or 384 samples per plate, suitable normalization methods are required to minimize the variation between plates. Here we propose two normalization approaches utilizing MA coordinates. The multidimensional MA (multi-MA) and MA-loess both consider all samples of a microtiter plate per suspension bead array assay and thus do not require any external reference samples. We demonstrate the performance of the two MA normalization methods with data obtained from the analysis of 384 samples including both serum and plasma. Samples were randomized across 96-well sample plates, processed, and analyzed in assay plates, respectively. Using principal component analysis (PCA), we could show that plate-wise clusters found in the first two components were eliminated by multi-MA normalization as compared with other normalization methods. Furthermore, we studied the correlation profiles between random pairs of antibodies and found that both MA normalization methods substantially reduced the inflated correlation introduced by plate effects. Normalization approaches using multi-MA and MA-loess minimized batch effects arising from the analysis of several assay plates with antibody suspension bead arrays. In a simulated biomarker study, multi-MA restored associations lost due to plate effects. Our normalization approaches, which are available as R package MDimNornin, could also be useful in studies using other types of high-throughput assay data.
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| 30. |
- Hong, Mun-Gwan, et al.
(författare)
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Profiles of histidine-rich glycoprotein associate with age and risk of all-cause mortality
- 2020
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Ingår i: Life Science Alliance. - : Life Science Alliance, LLC. - 2575-1077. ; 3:10, s. e202000817-
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Tidskriftsartikel (refereegranskat)abstract
- Despite recognizing aging as a common risk factor of many human diseases, little is known about its molecular traits. To identify age-associated proteins circulating in human blood, we screened 156 individuals aged 50–92 using exploratory and multiplexed affinity proteomics assays. Profiling eight additional study sets (N = 3,987), performing antibody validation, and conducting a meta-analysis revealed a consistent age association (P = 6.61 × 10−6) for circulating histidine-rich glycoprotein (HRG). Sequence variants of HRG influenced how the protein was recognized in the immunoassays. Indeed, only the HRG profiles affected by rs9898 were associated with age and predicted the risk of mortality (HR = 1.25 per SD; 95% CI = 1.12–1.39; P = 6.45 × 10−5) during a follow-up period of 8.5 yr after blood sampling (IQR = 7.7–9.3 yr). Our affinity proteomics analysis found associations between the particular molecular traits of circulating HRG with age and all-cause mortality. The distinct profiles of this multipurpose protein could serve as an accessible and informative indicator of the physiological processes related to biological aging.
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