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- Aebersold, Ruedi, et al.
(författare)
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How many human proteoforms are there?
- 2018
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Ingår i: Nature Chemical Biology. - : NATURE PUBLISHING GROUP. - 1552-4450 .- 1552-4469. ; 14:3, s. 206-214
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Tidskriftsartikel (refereegranskat)abstract
- Despite decades of accumulated knowledge about proteins and their post-translational modifications (PTMs), numerous questions remain regarding their molecular composition and biological function. One of the most fundamental queries is the extent to which the combinations of DNA-, RNA-and PTM-level variations explode the complexity of the human proteome. Here, we outline what we know from current databases and measurement strategies including mass spectrometry-based proteomics. In doing so, we examine prevailing notions about the number of modifications displayed on human proteins and how they combine to generate the protein diversity underlying health and disease. We frame central issues regarding determination of protein-level variation and PTMs, including some paradoxes present in the field today. We use this framework to assess existing data and to ask the question, "How many distinct primary structures of proteins (proteoforms) are created from the 20,300 human genes?" We also explore prospects for improving measurements to better regularize protein-level biology and efficiently associate PTMs to function and phenotype.
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- Nik-Zainal, Serena, et al.
(författare)
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Landscape of somatic mutations in 560 breast cancer whole-genome sequences
- 2016
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 534:7605, s. 47-54
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Tidskriftsartikel (refereegranskat)abstract
- We analysed whole-genome sequences of 560 breast cancers to advance understanding of the driver mutations conferring clonal advantage and the mutational processes generating somatic mutations. We found that 93 protein-coding cancer genes carried probable driver mutations. Some non-coding regions exhibited high mutation frequencies, but most have distinctive structural features probably causing elevated mutation rates and do not contain driver mutations. Mutational signature analysis was extended to genome rearrangements and revealed twelve base substitution and six rearrangement signatures. Three rearrangement signatures, characterized by tandem duplications or deletions, appear associated with defective homologous-recombination-based DNA repair: one with deficient BRCA1 function, another with deficient BRCA1 or BRCA2 function, the cause of the third is unknown. This analysis of all classes of somatic mutation across exons, introns and intergenic regions highlights the repertoire of cancer genes and mutational processes operating, and progresses towards a comprehensive account of the somatic genetic basis of breast cancer.
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- Vermeij, L. A., et al.
(författare)
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Disease-regulated local IL-10 gene therapy diminishes synovitis and cartilage proteoglycan depletion in experimental arthritis
- 2015
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Ingår i: Annals of the Rheumatic Diseases. - : BMJ. - 0003-4967 .- 1468-2060. ; 74:11, s. 2084-2091
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Tidskriftsartikel (refereegranskat)abstract
- Objectives Rheumatoid arthritis is a chronic destructive autoimmune disease, but the course is unpredictable in individual patients. An attractive treatment would provide a disease-regulated therapy that offers personalised drug delivery. Therefore, we expressed the anti-inflammatory interleukin-10 (IL-10) gene under the control of inflammation-dependent promoters in a mouse model of arthritis. Methods Proximal promoters of S100a8, Cxcl1, Mmp13, Saa3, IL-1b and Tsg6 were selected by whole-genome expression analysis of inflamed synovial tissues from arthritic mice. Mice were injected intraarticularly in knee joints with lentiviral vectors expressing a luciferase reporter or the therapeutic protein IL-10 under control of the Saa3 or Mmp13 promoter. After 4 days, arthritis was induced by intraarticular injection of streptococcal cell walls (SCW). At different time points after arthritis induction, in vivo bioluminescent imaging was performed and knee joints were dissected for histological and RNA analysis. Results The disease-regulated promoter-luciferase reporter constructs showed different activation profiles during the course of the disease. The Saa3 and Mmp13 promoters were significantly induced at day 1 or day 4 after arthritis induction respectively and selected for further research. Overexpression of IL-10 using these two disease-inducible promoters resulted in less synovitis and markedly diminished cartilage proteoglycan depletion and in upregulation of IL-1Ra and SOCS3 gene expression. Conclusions Our study shows that promoters of genes that are expressed locally during arthritis can be candidates for disease-regulated overexpression of biologics into arthritic joints, as shown for IL-10 in SCW arthritis. The disease-inducible approach might be promising for future tailor-made local gene therapy in arthritis.
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- Vetters, J, et al.
(författare)
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The ubiquitin-editing enzyme A20 controls NK cell homeostasis through regulation of mTOR activity and TNF
- 2019
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Ingår i: The Journal of experimental medicine. - : Rockefeller University Press. - 1540-9538 .- 0022-1007. ; 216:9, s. 2010-2023
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Tidskriftsartikel (refereegranskat)abstract
- The ubiquitin-editing enzyme A20 is a well-known regulator of immune cell function and homeostasis. In addition, A20 protects cells from death in an ill-defined manner. While most studies focus on its role in the TNF-receptor complex, we here identify a novel component in the A20-mediated decision between life and death. Loss of A20 in NK cells led to spontaneous NK cell death and severe NK cell lymphopenia. The few remaining NK cells showed an immature, hyperactivated phenotype, hallmarked by the basal release of cytokines and cytotoxic molecules. NK-A20−/− cells were hypersensitive to TNF-induced cell death and could be rescued, at least partially, by a combined deficiency with TNF. Unexpectedly, rapamycin, a well-established inhibitor of mTOR, also strongly protected NK-A20−/− cells from death, and further studies revealed that A20 restricts mTOR activation in NK cells. This study therefore maps A20 as a crucial regulator of mTOR signaling and underscores the need for a tightly balanced mTOR pathway in NK cell homeostasis.
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- Revelli, A., et al.
(författare)
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Spin-orbit entangled j=1/2 moments in Ba(2)CWeIrO(6) : A frustrated fcc quantum magnet
- 2019
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Ingår i: Physical Review B. - : American Physical Society. - 2469-9950 .- 2469-9969. ; 100:8
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Tidskriftsartikel (refereegranskat)abstract
- We establish the double perovskite Ba2CeIrO6 as a nearly ideal model system for j = 1/2 moments, with resonant inelastic x-ray scattering indicating that the ideal j = 1/2 state contributes by more than 99% to the ground-state wave function. The local j = 1/2 moments form an fcc lattice and are found to order antiferromagnetically at T-N = 14 K, more than an order of magnitude below the Curie-Weiss temperature. Model calculations show that the geometric frustration of the fcc Heisenberg antiferromagnet is further enhanced by a next-nearest neighbor exchange, and a significant size of the latter is indicated by ab initio theory. Our theoretical analysis shows that magnetic order is driven by a bond-directional Kitaev exchange and by local distortions via a strong magnetoelastic effect. Both, the suppression of frustration by Kitaev exchange and the strong magnetoelastic effect are typically not expected for j = 1/2 compounds making Ba2CeIrO6 a riveting example for the rich physics of spin-orbit entangled Mott insulators.
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| 12. |
- Revelli, A., et al.
(författare)
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Spin-orbit entangled j=1/2 moments in Ba2CeIrO6 : A frustrated fcc quantum magnet
- 2019
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Ingår i: Physical Review B. - 2469-9950 .- 2469-9969. ; 100:8
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Tidskriftsartikel (refereegranskat)abstract
- We establish the double perovskite Ba2CeIrO6 as a nearly ideal model system for j = 1/2 moments, with resonant inelastic x-ray scattering indicating that the ideal j = 1/2 state contributes by more than 99% to the ground-state wave function. The local j = 1/2 moments form an fcc lattice and are found to order antiferromagnetically at T-N = 14 K, more than an order of magnitude below the Curie-Weiss temperature. Model calculations show that the geometric frustration of the fcc Heisenberg antiferromagnet is further enhanced by a next-nearest neighbor exchange, and a significant size of the latter is indicated by ab initio theory. Our theoretical analysis shows that magnetic order is driven by a bond-directional Kitaev exchange and by local distortions via a strong magnetoelastic effect. Both, the suppression of frustration by Kitaev exchange and the strong magnetoelastic effect are typically not expected for j = 1/2 compounds making Ba2CeIrO6 a riveting example for the rich physics of spin-orbit entangled Mott insulators.
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- Shlien, Adam, et al.
(författare)
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Direct Transcriptional Consequences of Somatic Mutation in Breast Cancer
- 2016
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Ingår i: Cell Reports. - : Elsevier BV. - 2211-1247. ; 16:7, s. 2032-2046
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Tidskriftsartikel (refereegranskat)abstract
- Disordered transcriptomes of cancer encompass direct effects of somatic mutation on transcription, coordinated secondary pathway alterations, and increased transcriptional noise. To catalog the rules governing how somatic mutation exerts direct transcriptional effects, we developed an exhaustive pipeline for analyzing RNA sequencing data, which we integrated with whole genomes from 23 breast cancers. Using X-inactivation analyses, we found that cancer cells are more transcriptionally active than intermixed stromal cells. This is especially true in estrogen receptor (ER)-negative tumors. Overall, 59% of substitutions were expressed. Nonsense mutations showed lower expression levels than expected, with patterns characteristic of nonsense-mediated decay. 14% of 4,234 rearrangements caused transcriptional abnormalities, including exon skips, exon reusage, fusions, and premature polyadenylation. We found productive, stable transcription from sense-to-antisense gene fusions and gene-to-intergenic rearrangements, suggesting that these mutation classes drive more transcriptional disruption than previously suspected. Systematic integration of transcriptome with genome data reveals the rules by which transcriptional machinery interprets somatic mutation.
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