| 11. |
- Mathema, Vivek Bhakta, et al.
(författare)
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Deep learning facilitates multi-data type analysis and predictive biomarker discovery in cancer precision medicine
- 2023
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Ingår i: Computational and Structural Biotechnology Journal. - : Elsevier. - 2001-0370. ; 21, s. 1372-1382
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Forskningsöversikt (refereegranskat)abstract
- Cancer progression is linked to gene-environment interactions that alter cellular homeostasis. The use of biomarkers as early indicators of disease manifestation and progression can substantially improve diagnosis and treatment. Large omics datasets generated by high-throughput profiling technologies, such as microarrays, RNA sequencing, whole-genome shotgun sequencing, nuclear magnetic resonance, and mass spectrometry, have enabled data-driven biomarker discoveries. The identification of differentially expressed traits as molecular markers has traditionally relied on statistical techniques that are often limited to linear parametric modeling. The heterogeneity, epigenetic changes, and high degree of polymorphism observed in oncogenes demand biomarker-assisted personalized medication schemes. Deep learning (DL), a major subunit of machine learning (ML), has been increasingly utilized in recent years to investigate various diseases. The combination of ML/DL approaches for performance optimization across multi-omics datasets produces robust ensemble-learning prediction models, which are becoming useful in precision medicine. This review focuses on the recent development of ML/DL methods to provide integrative solutions in discovering cancer-related biomarkers, and their utilization in precision medicine.
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| 12. |
- McGlinchey, Aidan J, 1984-, et al.
(författare)
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Prenatal exposure to perfluoroalkyl substances modulates neonatal serum phospholipids, increasing risk of type 1 diabetes
- 2020
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Ingår i: Environment International. - : Elsevier. - 0160-4120 .- 1873-6750. ; 143
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Tidskriftsartikel (refereegranskat)abstract
- In the last decade, increasing incidence of type 1 diabetes (T1D) stabilized in Finland, a phenomenon that coincides with tighter regulation of perfluoroalkyl substances (PFAS). Here, we quantified PFAS to examine their effects, during pregnancy, on lipid and immune-related markers of T1D risk in children. In a mother-infant cohort (264 dyads), high PFAS exposure during pregnancy associated with decreased cord serum phospholipids and progression to T1D-associated islet autoantibodies in the offspring. This PFAS-lipid association appears exacerbated by increased human leukocyte antigen-conferred risk of T1D in infants. Exposure to a single PFAS compound or a mixture of organic pollutants in non-obese diabetic mice resulted in a lipid profile characterized by a similar decrease in phospholipids, a marked increase of lithocholic acid, and accelerated insulitis. Our findings suggest that PFAS exposure during pregnancy contributes to risk and pathogenesis of T1D in offspring.
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| 13. |
- Olafsdottir, Torunn, et al.
(författare)
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Comparative Systems Analyses Reveal Molecular Signatures of Clinically tested Vaccine Adjuvants
- 2016
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322 .- 2045-2322. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- A better understanding of the mechanisms of action of human adjuvants could inform a rational development of next generation vaccines for human use. Here, we exploited a genome wide transcriptomics analysis combined with a systems biology approach to determine the molecular signatures induced by four clinically tested vaccine adjuvants, namely CAF01, IC31, GLA-SE and Alum in mice. We report signature molecules, pathways, gene modules and networks, which are shared by or otherwise exclusive to these clinical-grade adjuvants in whole blood and draining lymph nodes of mice. Intriguingly, co-expression analysis revealed blood gene modules highly enriched for molecules with documented roles in T follicular helper (TFH) and germinal center (GC) responses. We could show that all adjuvants enhanced, although with different magnitude and kinetics, TFH and GC B cell responses in draining lymph nodes. These results represent, to our knowledge, the first comparative systems analysis of clinically tested vaccine adjuvants that may provide new insights into the mechanisms of action of human adjuvants.
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| 14. |
- Oresic, Matej, 1967-, et al.
(författare)
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Exposure to environmental contaminants is associated with sex-specific disturbances of hepatic lipid metabolism in non-alcoholic fatty liver disease
- 2021
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Ingår i: Journal of Hepatology. - : Elsevier. - 0168-8278 .- 1600-0641. ; 75:Suppl. 2, s. S605-S606
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Background and aims: Liver has a vital role in metabolism, distribution, and excretion of exogenous chemicals. The endocrine disrupting chemicals (EDCs) may act as a‘second hit’in the progression of NAFLD, advancing the earlier stages of liver pathology such as steatosis to more severe stages. A specific class of ECDs that have been linked with NAFLD are perfluorinated alkyl substances (PFAS), a class of commonly used industrial chemicals that humans are widelyexposed to. Due to the their structural similarity with fatty acids, PFAS may disrupt hepatic lipid metabolism. Furthermore, functionally, PFAS share some features with bile acids, including similar enterohepatic circulation. Nevertheless, human data linking PFAS exposure and lipid metabolism in the liver are currently lacking. The principal aim of our study was to define the impact of PFAS exposure on hepatic metabolism, with specific focus on bile acid and lipid metabolism.Method: In a well-characterized human NAFLD cohort of 105 individuals, we investigated the impact of PFAS exposure on liver metabolism in the individuals with NAFLD. Average BMI was 45.65 ± 5.99 kg/m2, with liver fat content varying between 0% and 80%. We comprehensively characterized both hepatic (liver biopsy) and serum metabolome using four analytical platforms, and measured PFAS in serum. We investigated the association between the NAFLD (liver fat %, NASH grade, fibrosis stage, insulin resistance), PFAS exposure, and metabolome.Results: PFAS exposurewas associated with NAFLD (Figure) as well as with changes in hepatic lipid and bile acid metabolism. Importantly, we observed sex-specific association between chemical exposure and NAFLD, linked with sex-specific changes in both hepatic and circulating metabolome. We noticed differences not only in the exposure profiles between the males and females, but, notably, also the impact of the exposure, as characterized both with the impact on metabolome but also on clinical parameters was clearly different between the males and females.Conclusion: Our results implicate that females may be more sensitive to the harmful impacts of PFAS. The results also suggest that the changes reported in the lipid metabolism due to PFAS exposure may be secondary to the interplay of PFAS and bile acids
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| 15. |
- Petersen, Anders Ø., et al.
(författare)
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Conjugated C-6 hydroxylated bile acids in serum relate to human metabolic health and gut Clostridia species
- 2021
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Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Knowledge about in vivo effects of human circulating C-6 hydroxylated bile acids (BAs), also called muricholic acids, is sparse. It is unsettled if the gut microbiome might contribute to their biosynthesis. Here, we measured a range of serum BAs and related them to markers of human metabolic health and the gut microbiome. We examined 283 non-obese and obese Danish adults from the MetaHit study. Fasting concentrations of serum BAs were quantified using ultra-performance liquid chromatography-tandem mass-spectrometry. The gut microbiome was characterized with shotgun metagenomic sequencing and genome-scale metabolic modeling. We find that tauro- and glycohyocholic acid correlated inversely with body mass index (P = 4.1e-03, P = 1.9e-05, respectively), waist circumference (P = 0.017, P = 1.1e-04, respectively), body fat percentage (P = 2.5e-03, P = 2.3e-06, respectively), insulin resistance (P = 0.051, P = 4.6e-4, respectively), fasting concentrations of triglycerides (P = 0.06, P = 9.2e-4, respectively) and leptin (P = 0.067, P = 9.2e-4). Tauro- and glycohyocholic acids, and tauro-a-muricholic acid were directly linked with a distinct gut microbial community primarily composed of Clostridia species (P = 0.037, P = 0.013, P = 0.027, respectively). We conclude that serum conjugated C-6-hydroxylated BAs associate with measures of human metabolic health and gut communities of Clostridia species. The findings merit preclinical interventions and human feasibility studies to explore the therapeutic potential of these BAs in obesity and type 2 diabetes.
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| 16. |
- Ribeiro, Henrique Caracho, et al.
(författare)
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Metabolomic and proteomic profiling in bipolar disorder patients revealed potential molecular signatures related to hemostasis
- 2022
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Ingår i: Metabolomics. - : Springer-Verlag New York. - 1573-3882 .- 1573-3890. ; 18:8
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Tidskriftsartikel (refereegranskat)abstract
- INTRODUCTION: Bipolar disorder (BD) is a mood disorder characterized by the occurrence of depressive episodes alternating with episodes of elevated mood (known as mania). There is also an increased risk of other medical comorbidities.OBJECTIVES: This work uses a systems biology approach to compare BD treated patients with healthy controls (HCs), integrating proteomics and metabolomics data using partial correlation analysis in order to observe the interactions between altered proteins and metabolites, as well as proposing a potential metabolic signature panel for the disease.METHODS: Data integration between proteomics and metabolomics was performed using GC-MS data and label-free proteomics from the same individuals (N = 13; 5 BD, 8 HC) using generalized canonical correlation analysis and partial correlation analysis, and then building a correlation network between metabolites and proteins. Ridge-logistic regression models were developed to stratify between BD and HC groups using an extended metabolomics dataset (N = 28; 14 BD, 14 HC), applying a recursive feature elimination for the optimal selection of the metabolites.RESULTS: Network analysis demonstrated links between proteins and metabolites, pointing to possible alterations in hemostasis of BD patients. Ridge-logistic regression model indicated a molecular signature comprising 9 metabolites, with an area under the receiver operating characteristic curve (AUROC) of 0.833 (95% CI 0.817-0.914).CONCLUSION: From our results, we conclude that several metabolic processes are related to BD, which can be considered as a multi-system disorder. We also demonstrate the feasibility of partial correlation analysis for integration of proteomics and metabolomics data in a case-control study setting.
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| 17. |
- Sen, Partho, et al.
(författare)
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1-Deoxyceramides : key players in lipotoxicity and progression to type 2 diabetes?
- 2021
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Ingår i: Acta Physiologica. - : John Wiley & Sons. - 1748-1708 .- 1748-1716. ; 232:1
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Tidskriftsartikel (refereegranskat)abstract
- Ceramides are bioactive sphingolipids, comprised of sphingosine and a fatty acyl chain. They have been recognized as key mediators of lipotoxicity; a phenomenon where excess fat in adipose tissue leads to de novo synthesis of ceramides and their precursor dihydroceramides (DHCer). This occurs in adipose tissue as well as in the periphery. Accumulation of these ceramides is associated with insulin resistance, de novo lipogenesis, and inflammation1 , thus increasing the risk of cardiometabolic diseases such as type 2 diabetes (T2D) and atherosclerosis. Recently, in this journal, Hannish and colleagues reported that another, non-canonical class of ceramides, the 1-deoxyceramides (DoxCer), is highly enriched in visceral adipose tissue (VAT) as well as in serum of obese patients with T2D2 . This study also clarified previously-reported discrepancies in the literature concerning the association of DHCer with the risk of T2D, as the signals from DHCer can be easily confused with the signals from DoxCer in mass spectrometric (MS) analysis of lipids.
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| 18. |
- Sen, Partho, 1983-, et al.
(författare)
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Deep learning meets metabolomics : a methodological perspective
- 2021
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Ingår i: Briefings in Bioinformatics. - : Oxford University Press. - 1467-5463 .- 1477-4054. ; 22:2, s. 1531-1542
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Forskningsöversikt (refereegranskat)abstract
- Deep learning (DL), an emerging area of investigation in the fields of machine learning and artificial intelligence, has markedly advanced over the past years. DL techniques are being applied to assist medical professionals and researchers in improving clinical diagnosis, disease prediction and drug discovery. It is expected that DL will help to provide actionable knowledge from a variety of 'big data', including metabolomics data. In this review, we discuss the applicability of DL to metabolomics, while presenting and discussing several examples from recent research. We emphasize the use of DL in tackling bottlenecks in metabolomics data acquisition, processing, metabolite identification, as well as in metabolic phenotyping and biomarker discovery. Finally, we discuss how DL is used in genome-scale metabolic modelling and in interpretation of metabolomics data. The DL-based approaches discussed here may assist computational biologists with the integration, prediction and drawing of statistical inference about biological outcomes, based on metabolomics data.
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| 19. |
- Sen, Partho, 1983-, et al.
(författare)
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Exposure to environmental contaminants is associated with altered hepatic lipid metabolism in non-alcoholic fatty liver disease
- 2022
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Ingår i: Journal of Hepatology. - : Elsevier. - 0168-8278 .- 1600-0641. ; 76:2, s. 283-293
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Tidskriftsartikel (refereegranskat)abstract
- Background & aims: Recent experimental models and epidemiological studies suggest that specific environmental contaminants (ECs) contribute to the initiation and pathology of non-alcoholic fatty liver disease (NAFLD). However, the underlying mechanisms linking EC exposure with NAFLD remain poorly understood and there is no data on their impact on the human liver metabolome. Herein, we hypothesized that exposure to ECs, particularly perfluorinated alkyl substances (PFAS), impacts liver metabolism, specifically bile acid metabolism.Methods: In a well-characterized human NAFLD cohort of 105 individuals, we investigated the effects of EC exposure on liver metabolism. We characterized the liver (via biopsy) and circulating metabolomes using 4 mass spectrometry-based analytical platforms, and measured PFAS and other ECs in serum. We subsequently compared these results with an exposure study in a PPARa-humanized mouse model.Results: PFAS exposure appears associated with perturbation of key hepatic metabolic pathways previously found altered in NAFLD, particularly those related to bile acid and lipid metabolism. We identified stronger associations between the liver metabolome, chemical exposure and NAFLD-associated clinical variables (liver fat content, HOMA-IR), in females than males. Specifically, we observed PFAS-associated upregulation of bile acids, triacylglycerols and ceramides, and association between chemical exposure and dysregulated glucose metabolism in females. The murine exposure study further corroborated our findings, vis-à-vis a sex-specific association between PFAS exposure and NAFLD-associated lipid changes.Conclusions: Females may be more sensitive to the harmful impacts of PFAS. Lipid-related changes subsequent to PFAS exposure may be secondary to the interplay between PFAS and bile acid metabolism.Lay summary: There is increasing evidence that specific environmental contaminants, such as perfluorinated alkyl substances (PFAS), contribute to the progression of non-alcoholic fatty liver disease (NAFLD). However, it is poorly understood how these chemicals impact human liver metabolism. Here we show that human exposure to PFAS impacts metabolic processes associated with NAFLD, and that the effect is different in females and males.
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| 20. |
- Sen, Partho, 1983-, et al.
(författare)
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Exposure to environmental toxicants is associated with gut microbiome dysbiosis, insulin resistance and obesity
- 2024
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Ingår i: Environment International. - : Elsevier. - 0160-4120 .- 1873-6750. ; 186
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Tidskriftsartikel (refereegranskat)abstract
- Environmental toxicants (ETs) are associated with adverse health outcomes. Here we hypothesized that exposures to ETs are linked with obesity and insulin resistance partly through a dysbiotic gut microbiota and changes in the serum levels of secondary bile acids (BAs). Serum BAs, per- and polyfluoroalkyl substances (PFAS) and additional twenty-seven ETs were measured by mass spectrometry in 264 Danes (121 men and 143 women, aged 56.6 ± 7.3 years, BMI 29.7 ± 6.0 kg/m2) using a combination of targeted and suspect screening approaches. Bacterial species were identified based on whole-genome shotgun sequencing (WGS) of DNA extracted from stool samples. Personalized genome-scale metabolic models (GEMs) of gut microbial communities were developed to elucidate regulation of BA pathways. Subsequently, we compared findings from the human study with metabolic implications of exposure to perfluorooctanoic acid (PFOA) in PPARα-humanized mice. Serum levels of twelve ETs were associated with obesity and insulin resistance. High chemical exposure was associated with increased abundance of several bacterial species (spp.) of genus (Anaerotruncus, Alistipes, Bacteroides, Bifidobacterium, Clostridium, Dorea, Eubacterium, Escherichia, Prevotella, Ruminococcus, Roseburia, Subdoligranulum, and Veillonella), particularly in men. Conversely, females in the higher exposure group, showed a decrease abundance of Prevotella copri. High concentrations of ETs were correlated with increased levels of secondary BAs including lithocholic acid (LCA), and decreased levels of ursodeoxycholic acid (UDCA). In silico causal inference analyses suggested that microbiome-derived secondary BAs may act as mediators between ETs and obesity or insulin resistance. Furthermore, these findings were substantiated by the outcome of the murine exposure study. Our combined epidemiological and mechanistic studies suggest that multiple ETs may play a role in the etiology of obesity and insulin resistance. These effects may arise from disruptions in the microbial biosynthesis of secondary BAs.
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