| 1. |
- Campbell, PJ, et al.
(författare)
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Pan-cancer analysis of whole genomes
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Tidskriftsartikel (refereegranskat)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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| 2. |
- Ramdas, S., et al.
(författare)
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A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids
- 2022
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Ingår i: American Journal of Human Genetics. - : Elsevier BV. - 0002-9297 .- 1537-6605. ; 109:8, s. 1366-1387
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Tidskriftsartikel (refereegranskat)abstract
- A major challenge of genome-wide association studies (GWASs) is to translate phenotypic associations into biological insights. Here, we integrate a large GWAS on blood lipids involving 1.6 million individuals from five ancestries with a wide array of functional genomic datasets to discover regulatory mechanisms underlying lipid associations. We first prioritize lipid-associated genes with expression quantitative trait locus (eQTL) colocalizations and then add chromatin interaction data to narrow the search for functional genes. Polygenic enrichment analysis across 697 annotations from a host of tissues and cell types confirms the central role of the liver in lipid levels and highlights the selective enrichment of adipose-specific chromatin marks in high-density lipoprotein cholesterol and triglycerides. Overlapping transcription factor (TF) binding sites with lipid-associated loci identifies TFs relevant in lipid biology. In addition, we present an integrative framework to prioritize causal variants at GWAS loci, producing a comprehensive list of candidate causal genes and variants with multiple layers of functional evidence. We highlight two of the prioritized genes, CREBRF and RRBP1, which show convergent evidence across functional datasets supporting their roles in lipid biology.
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| 3. |
- Mishra, A., et al.
(författare)
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Stroke genetics informs drug discovery and risk prediction across ancestries
- 2022
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 611, s. 115-123
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Tidskriftsartikel (refereegranskat)abstract
- Previous genome-wide association studies (GWASs) of stroke - the second leading cause of death worldwide - were conducted predominantly in populations of European ancestry(1,2). Here, in cross-ancestry GWAS meta-analyses of 110,182 patients who have had a stroke (five ancestries, 33% non-European) and 1,503,898 control individuals, we identify association signals for stroke and its subtypes at 89 (61 new) independent loci: 60 in primary inverse-variance-weighted analyses and 29 in secondary meta-regression and multitrait analyses. On the basis of internal cross-ancestry validation and an independent follow-up in 89,084 additional cases of stroke (30% non-European) and 1,013,843 control individuals, 87% of the primary stroke risk loci and 60% of the secondary stroke risk loci were replicated (P < 0.05). Effect sizes were highly correlated across ancestries. Cross-ancestry fine-mapping, in silico mutagenesis analysis(3), and transcriptome-wide and proteome-wide association analyses revealed putative causal genes (such as SH3PXD2A and FURIN) and variants (such as at GRK5 and NOS3). Using a three-pronged approach(4), we provide genetic evidence for putative drug effects, highlighting F11, KLKB1, PROC, GP1BA, LAMC2 and VCAM1 as possible targets, with drugs already under investigation for stroke for F11 and PROC. A polygenic score integrating cross-ancestry and ancestry-specific stroke GWASs with vascular-risk factor GWASs (integrative polygenic scores) strongly predicted ischaemic stroke in populations of European, East Asian and African ancestry(5). Stroke genetic risk scores were predictive of ischaemic stroke independent of clinical risk factors in 52,600 clinical-trial participants with cardiometabolic disease. Our results provide insights to inform biology, reveal potential drug targets and derive genetic risk prediction tools across ancestries.
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| 11. |
- Abbafati, Cristiana, et al.
(författare)
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- 2020
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Tidskriftsartikel (refereegranskat)
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| 12. |
- Mahajan, Anubha, et al.
(författare)
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Multi-ancestry genetic study of type 2 diabetes highlights the power of diverse populations for discovery and translation
- 2022
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Ingår i: Nature Genetics. - : Springer Nature. - 1061-4036 .- 1546-1718. ; 54:5, s. 560-572
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Tidskriftsartikel (refereegranskat)abstract
- We assembled an ancestrally diverse collection of genome-wide association studies (GWAS) of type 2 diabetes (T2D) in 180,834 affected individuals and 1,159,055 controls (48.9% non-European descent) through the Diabetes Meta-Analysis of Trans-Ethnic association studies (DIAMANTE) Consortium. Multi-ancestry GWAS meta-analysis identified 237 loci attaining stringent genome-wide significance (P < 5 x 10(-9)), which were delineated to 338 distinct association signals. Fine-mapping of these signals was enhanced by the increased sample size and expanded population diversity of the multi-ancestry meta-analysis, which localized 54.4% of T2D associations to a single variant with >50% posterior probability. This improved fine-mapping enabled systematic assessment of candidate causal genes and molecular mechanisms through which T2D associations are mediated, laying the foundations for functional investigations. Multi-ancestry genetic risk scores enhanced transferability of T2D prediction across diverse populations. Our study provides a step toward more effective clinical translation of T2D GWAS to improve global health for all, irrespective of genetic background. Genome-wide association and fine-mapping analyses in ancestrally diverse populations implicate candidate causal genes and mechanisms underlying type 2 diabetes. Trans-ancestry genetic risk scores enhance transferability across populations.
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| 13. |
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| 14. |
- Abramowicz, H., et al.
(författare)
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Conceptual design report for the LUXE experiment
- 2021
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Ingår i: European Physical Journal-Special Topics. - : Springer Science and Business Media LLC. - 1951-6355 .- 1951-6401. ; 230:11, s. 2445-2560
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Tidskriftsartikel (refereegranskat)abstract
- This Conceptual Design Report describes LUXE (Laser Und XFEL Experiment), an experimental campaign that aims to combine the high-quality and high-energy electron beam of the European XFEL with a powerful laser to explore the uncharted terrain of quantum electrodynamics characterised by both high energy and high intensity. We will reach this hitherto inaccessible regime of quantum physics by analysing high-energy electron-photon and photon-photon interactions in the extreme environment provided by an intense laser focus. The physics background and its relevance are presented in the science case which in turn leads to, and justifies, the ensuing plan for all aspects of the experiment: Our choice of experimental parameters allows (i) field strengths to be probed where the coupling to charges becomes non-perturbative and (ii) a precision to be achieved that permits a detailed comparison of the measured data with calculations. In addition, the high photon flux predicted will enable a sensitive search for new physics beyond the Standard Model. The initial phase of the experiment will employ an existing 40 TW laser, whereas the second phase will utilise an upgraded laser power of 350 TW. All expectations regarding the performance of the experimental set-up as well as the expected physics results are based on detailed numerical simulations throughout.
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| 17. |
- van Cappellen, W., et al.
(författare)
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Apertif: Phased array feeds for the Westerbork Synthesis Radio Telescope: System overview and performance characteristics
- 2022
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 658
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Tidskriftsartikel (refereegranskat)abstract
- We describe the APERture Tile In Focus (Apertif) system, a phased array feed (PAF) upgrade of the Westerbork Synthesis Radio Telescope that transforms this telescope into a high-sensitivity, wide-field-of-view L-band imaging and transient survey instrument. Using novel PAF technology, up to 40 partially overlapping beams are formed on the sky simultaneously, significantly increasing the survey speed of the telescope. With this upgraded instrument, an imaging survey covering an area of 2300 deg2 is being performed that will deliver both continuum and spectral line datasets, of which the first data have been publicly released. In addition, a time domain transient and pulsar survey covering 15 000 deg2 is in progress. An overview of the Apertif science drivers, hardware, and software of the upgraded telescope is presented, along with its key performance characteristics.
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| 18. |
- Bogota-Angel, G., et al.
(författare)
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Climate and geological change as drivers of Mauritiinae palm biogeography
- 2021
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Ingår i: Journal of Biogeography. - : Wiley. - 0305-0270 .- 1365-2699. ; 48:5, s. 1001-1022
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Tidskriftsartikel (refereegranskat)abstract
- Aim Forest composition and distribution are determined by a myriad of factors, including climate. As models of tropical rain forest, palms are often used as indicator taxa, particularly the Mauritiinae. We question, what characterizes the Mauritiinae pollen in the global fossil record? And when did the Mauritiinae become endemic to South America? Location Global tropics. Taxon Mauritiinae palms (Arecaceae: Lepidocaryeae). Methods Pollen trait data from extinct and extant Mauritiinae pollen were generated from light-, scanning-, and transmission electron microscopy. Statistical morphometric analysis was used to define species and their relationships to other Mauritiinae. We also compiled a comprehensive pollen database for extinct and extant Mauritiinae and mapped their global geographical distribution from Late Cretaceous to present, using GBIF and fossil data. Results Our morphometric analysis identified 18 species (11 extinct and seven extant), all exhibiting exine indentations, a synapomorphy of the subtribe. The fossil taxa and early divergent extant Lepidocaryum are all monosulcate, whereas the extant Mauritia and Mauritiella species are all monoulcerate. Paleobiogeographical maps of fossil Mauritiinae pollen occurrences suggest the taxon originated in equatorial Africa during the Cretaceous, and expanded their range to South America, and to India in the Paleocene. Range retraction started in the early Eocene with extirpation from India, and reduction in diversity in Africa culminating at the Eocene-Oligocene Transition (EOT). In contrast, in South America, the distribution is maintained, and since the Neogene Mauritiinae palms are mostly restricted to swampy, lowland habitats. Main conclusions Morphometric analysis shows that since their origin Mauritiinae pollen are relatively species poor, and Mauritiidites resembles Lepidocaryum. We also conclude that the biogeographical history of the Mauriitinae and, by extension, tropical forests was strongly affected by global climatic cooling events. In particular, the climate change at the EOT was a fundamental determinant of current tropical forest distribution.
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| 19. |
- Corvetto, Julia F., et al.
(författare)
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Private vs. public emergency visits for mental health due to heat : an indirect socioeconomic assessment of heat vulnerability and healthcare access, in Curitiba, Brazil
- 2024
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Ingår i: Science of the Total Environment. - : Elsevier. - 0048-9697 .- 1879-1026. ; 934
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Tidskriftsartikel (refereegranskat)abstract
- Few studies have explored the influence of socioeconomic status (SES) on the heat vulnerability of mental health (MH) patients. As individual socioeconomic data was unavailable, we aimed to fill this gap by using the healthcare system type as a proxy for SES. Brazilian national statistics indicate that public patients have lower SES than private. Therefore, we compared the risk of emergency department visits (EDVs) for MH between patients from both healthcare types. EDVs for MH disorders from all nine public (101,452 visits) and one large private facility (154,954) in Curitiba were assessed (2017–2021). Daily mean temperature was gathered and weighed from 3 stations. Distributed-lag non-linear model with quasi-Poisson (maximum 10-lags) was used to assess the risk. We stratified by private and public, age, and gender under moderate and extreme heat. Additionally, we calculated the attributable fraction (AF), which translates individual risks into population-representative burdens – especially useful for public policies. Random-effects meta-regression pooled the risk estimates between healthcare systems. Public patients showed significant risks immediately as temperatures started to increase. Their cumulative relative risk (RR) of MH-EDV was 7.5 % higher than the private patients (Q-Test 26.2 %) under moderate heat, suggesting their particular heat vulnerability. Differently, private patients showed significant risks only under extreme heat, when their RR became 4.3 % higher than public (Q-Test 6.2 %). These findings suggest that private patients have a relatively greater adaptation capacity to heat. However, when faced with extreme heat, their current adaptation means were potentially insufficient, so they needed and could access healthcare freely, unlike their public counterparts. MH patients would benefit from measures to reduce heat vulnerability and access barriers, increasing equity between the healthcare systems in Brazil. AF of EDVs due to extreme heat was 0.33 % (95%CI 0.16;0.50) for the total sample (859 EDVs). This corroborates that such broad population-level policies are urgently needed as climate change progresses.
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| 20. |
- Dong, WB, et al.
(författare)
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Abo1 is required for the H3K9me2 to H3K9me3 transition in heterochromatin
- 2020
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Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 10:1, s. 6055-
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Tidskriftsartikel (refereegranskat)abstract
- Heterochromatin regulation is critical for genomic stability. Different H3K9 methylation states have been discovered, with distinct roles in heterochromatin formation and silencing. However, how the transition from H3K9me2 to H3K9me3 is controlled is still unclear. Here, we investigate the role of the conserved bromodomain AAA-ATPase, Abo1, involved in maintaining global nucleosome organisation in fission yeast. We identified several key factors involved in heterochromatin silencing that interact genetically with Abo1: histone deacetylase Clr3, H3K9 methyltransferase Clr4, and HP1 homolog Swi6. Cells lacking Abo1 cultivated at 30 °C exhibit an imbalance of H3K9me2 and H3K9me3 in heterochromatin. In abo1∆ cells, the centromeric constitutive heterochromatin has increased H3K9me2 but decreased H3K9me3 levels compared to wild-type. In contrast, facultative heterochromatin regions exhibit reduced H3K9me2 and H3K9me3 levels in abo1∆. Genome-wide analysis showed that abo1∆ cells have silencing defects in both the centromeres and subtelomeres, but not in a subset of heterochromatin islands in our condition. Thus, our work uncovers a role of Abo1 in stabilising directly or indirectly Clr4 recruitment to allow the H3K9me2 to H3K9me3 transition in heterochromatin.
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| 21. |
- Kanoni, Stavroula, et al.
(författare)
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Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis.
- 2022
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Ingår i: Genome biology. - : Springer Science and Business Media LLC. - 1474-760X .- 1465-6906 .- 1474-7596. ; 23:1
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Tidskriftsartikel (refereegranskat)abstract
- Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently unknown, limiting understanding of these findings and hindering downstream translational efforts such as drug target discovery.To expand our understanding of the underlying biological pathways and mechanisms controlling blood lipid levels, we leverage a large multi-ancestry meta-analysis (N=1,654,960) of blood lipids to prioritize putative causal genes for 2286 lipid associations using six gene prediction approaches. Using phenome-wide association (PheWAS) scans, we identify relationships of genetically predicted lipid levels to other diseases and conditions. We confirm known pleiotropic associations with cardiovascular phenotypes and determine novel associations, notably with cholelithiasis risk. We perform sex-stratified GWAS meta-analysis of lipid levels and show that 3-5% of autosomal lipid-associated loci demonstrate sex-biased effects. Finally, we report 21 novel lipid loci identified on the X chromosome. Many of the sex-biased autosomal and X chromosome lipid loci show pleiotropic associations with sex hormones, emphasizing the role of hormone regulation in lipid metabolism.Taken together, our findings provide insights into the biological mechanisms through which associated variants lead to altered lipid levels and potentially cardiovascular disease risk.
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| 22. |
- Kumar, S., et al.
(författare)
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Additive-Driven Interfacial Engineering of Aluminum Metal Anode for Ultralong Cycling Life
- 2023
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Ingår i: Nano-Micro Letters. - : Springer Science and Business Media LLC. - 2311-6706 .- 2150-5551. ; 15:1
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Tidskriftsartikel (refereegranskat)abstract
- Rechargeable Al batteries (RAB) are promising candidates for safe and environmentally sustainable battery systems with low-cost investments. However, the currently used aluminum chloride-based electrolytes present a significant challenge to commercialization due to their corrosive nature. Here, we report for the first time, a novel electrolyte combination for RAB based on aluminum trifluoromethanesulfonate (Al(OTf)(3)) with tetrabutylammonium chloride (TBAC) additive in diglyme. The presence of a mere 0.1 M of TBAC in the Al(OTf)(3) electrolyte generates the charge carrying electrochemical species, which forms the basis of reaction at the electrodes. TBAC reduces the charge transfer resistance and the surface activation energy at the anode surface and also augments the dissociation of Al(OTf)(3) to generate the solid electrolyte interphase components. Our electrolyte's superiority directly translates into reduced anodic overpotential for cells that ran for 1300 cycles in Al plating/stripping tests, the longest cycling life reported to date. This unique combination of salt and additive is non-corrosive, exhibits a high flash point and is cheaper than traditionally reported RAB electrolyte combinations, which makes it commercially promising. Through this report, we address a major roadblock in the commercialization of RAB and inspire equivalent electrolyte fabrication approaches for other metal anode batteries.
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| 23. |
- Parajuli, Narayan Prasad, 1989-, et al.
(författare)
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Antibiotic thermorubin tethers ribosomal subunits and impedes A-site interactions to perturb protein synthesis in bacteria
- 2023
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- Thermorubin (THB) is a long-known broad-spectrum ribosome-targeting antibiotic, but the molecular mechanism of its action was unclear. Here, our precise fast-kinetics assays in a reconstituted Escherichia coli translation system and 1.96 Å resolution cryo-EM structure of THB-bound 70S ribosome with mRNA and initiator tRNA, independently suggest that THB binding at the intersubunit bridge B2a near decoding center of the ribosome interferes with the binding of A-site substrates aminoacyl-tRNAs and class-I release factors, thereby inhibiting elongation and termination steps of bacterial translation. Furthermore, THB acts as an anti-dissociation agent that tethers the ribosomal subunits and blocks ribosome recycling, subsequently reducing the pool of active ribosomes. Our results show that THB does not inhibit translation initiation as proposed earlier and provide a complete mechanism of how THB perturbs bacterial protein synthesis. This in-depth characterization will hopefully spur efforts toward the design of THB analogs with improved solubility and effectivity against multidrug-resistant bacteria.
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| 24. |
- Parajuli, Narayan Prasad, 1989-
(författare)
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Molecular Interplay of Antibiotics on the Bacterial Ribosome
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Inhibition of protein synthesis is one of the most common modes of action for medically useful antibiotics. This thesis presents the mechanistic studies of two chemically distinct classes of antibiotics that target bacterial ribosomes –aminoglycosides and thermorubin. Arbekacin (ABK) and amikacin (AMK) are two new-generation semisynthetic aminoglycosides (AGAs) that were developed to overcome enzyme-mediated AGA resistance in bacteria. Our results demonstrate that these two antibiotics induce potent inhibitory effects on various phases of bacterial protein synthesis. The binding of ABK stalls elongating ribosomes to a state that is unfavorable for elongation factor-G (EF-G) binding, which drastically prolongs the time for translocation from ~50 milliseconds to at least 2 seconds. ABK also abolishes the accuracy of mRNA decoding and inhibits peptide release. The results of in vitro fast kinetics and structures of ABK and AMK-bound 70S ribosomes reveal that in addition to canonical binding at h44 of 16S rRNA, appended amino-hydroxy butyryl (AHB) moiety of ABK and AMK secures extra interactions at the binding pocket and provides long dwelling-time on the translating ribosome. Moreover, AMK binds at the large subunit of ribosome proximal to the 3'CCA-end of the tRNA in the P-site and inhibits the release factor-mediated peptide release. Our data suggest that AGA impose bacteriostatic effects mainly by inhibiting translocation, while they become bactericidal in combination with decoding errors. We have further characterized the molecular mechanism of action of the antibiotic thermorubin (THB) using in vitro fast kinetics and cryo-EM. We found that THB impedes elongation, termination, and ribosome recycling phases of translation. THB does so by binding to the intersubunit bridge B2a and extruding C1914 of H69 of 23S rRNA that interferes with the interactions of A-site substrates including aminoacyl-tRNAs, class-I release factors, and ribosome recycling factor. We also found that THB acts as an anti-dissociation agent that tethers the ribosomal subunits and blocks ribosome recycling, subsequently reducing the pool of active ribosomes. These studies altogether suggest that in-depth characterization of antibiotic action provides important clues that hopefully aid in the development of new antibiotics to fight against looming antibiotic resistance.
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