| 1. |
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| 2. |
- Abraham-Nordling, Mirna, et al.
(author)
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Model of the complex of Parathyroid hormone-2receptor and Tuberoinfundibular peptide of39 residues
- 2010
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In: BMC Reseach Notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 3:270
-
Journal article (peer-reviewed)abstract
- BackgroundWe aim to propose interactions between the parathyroid hormone-2 receptor (PTH2R) and its ligand the tuberoinfundibular peptide of 39 residues (TIP39) by constructing a homology model of their complex. The two related peptides parathyroid hormone (PTH) and parathyroid hormone related protein (PTHrP) are compared with the complex to examine their interactions.FindingsIn the model, the hydrophobic N-terminus of TIP39 is buried in a hydrophobic part of the central cavity between helices 3 and 7. Comparison of the peptide sequences indicates that the main discriminator between the agonistic peptides TIP39 and PTH and the inactive PTHrP is a tryptophan-phenylalanine replacement. The model indicates that the smaller phenylalanine in PTHrP does not completely occupy the binding site of the larger tryptophan residue in the other peptides. As only TIP39 causes internalisation of the receptor and the primary difference being an aspartic acid in position 7 of TIP39 that interacts with histidine 396 in the receptor, versus isoleucine/histidine residues in the related hormones, this might be a trigger interaction for the events that cause internalisation.ConclusionsA model is constructed for the complex and a trigger interaction for full agonistic activation between aspartic acid 7 of TIP39 and histidine 396 in the receptor is proposed.
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| 3. |
- Nordling, Erik, et al.
(author)
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Colonic amyloidosis, computational analysis of the major amyloidogenic species, Serum Amyloid A
- 2012
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In: Computational biology and chemistry (Print). - : Elsevier. - 1476-9271 .- 1476-928X. ; 39, s. 29-34
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Journal article (peer-reviewed)abstract
- Amyloidosis is characterized by misfolding of proteins. The clinical gastrointestinal manifestations of amyloidosis may mimic other disease, such as inflammatory bowel disease or colonic cancer. As these patients have a high risk for bleeding and poor wound healing following surgery it is important to diagnose them correctly and do a careful preoperative assessment. The most common form of colonic amyloidosis is caused by Serum Amyloid A (SAA), an acute phase protein of unknown function. It is expressed in response to inflammation and the increased levels may lead to amyloidosis. The main treatment is to suppress the acute phase response and thereby reduce production of SAA. less thanbrgreater than less thanbrgreater thanAs no structure for SAA is available we aim to perform an in silico assessment of its structural and fibrillation properties. In the paper we propose an ab initio model of the structure of SAA, which consists of a five membered helical bundle with a fold related to the tetratricopeptide repeat domain. As there are uncertainties relating to the packing of the helices, each helical region is subjected to triplicate molecular dynamics simulations to assess the integrity of the structural region. The first helix, stretching from residues 1 to 13, is the least stable according to the simulations: almost all of the helical conformation is lost during the 10 ns simulations, whereas the other helices maintain portions that remain in an helical conformation in at least 80% of the simulations. All helices are also subjected to a single 100 ns simulation to investigate how the secondary structure develops over time. In them helix 1 adopts a beta-hairpin structure similar to other fibril forming proteins. The beta-hairpin can in turn multimerise and form a mature fibril structure. The mechanism behind the conformational transition appears to be driven by interactions of side chains of charged residues, particularly Arginine 1. It exchanges interaction partners in the simulation and stabilizes intermediate conformations on the folding pathway to the final beta-hairpin.
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| 4. |
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| 5. |
- Bill-Axelson, Anna, et al.
(author)
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Radical Prostatectomy or Watchful Waiting in Early Prostate Cancer
- 2014
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In: New England Journal of Medicine. - Waltham : Massachusetts Medical Society. - 0028-4793 .- 1533-4406. ; 370:10, s. 932-942
-
Journal article (peer-reviewed)abstract
- BackgroundRadical prostatectomy reduces mortality among men with localized prostate cancer; however, important questions regarding long-term benefit remain. MethodsBetween 1989 and 1999, we randomly assigned 695 men with early prostate cancer to watchful waiting or radical prostatectomy and followed them through the end of 2012. The primary end points in the Scandinavian Prostate Cancer Group Study Number 4 (SPCG-4) were death from any cause, death from prostate cancer, and the risk of metastases. Secondary end points included the initiation of androgen-deprivation therapy. ResultsDuring 23.2 years of follow-up, 200 of 347 men in the surgery group and 247 of the 348 men in the watchful-waiting group died. Of the deaths, 63 in the surgery group and 99 in the watchful-waiting group were due to prostate cancer; the relative risk was 0.56 (95% confidence interval [CI], 0.41 to 0.77; P=0.001), and the absolute difference was 11.0 percentage points (95% CI, 4.5 to 17.5). The number needed to treat to prevent one death was 8. One man died after surgery in the radical-prostatectomy group. Androgen-deprivation therapy was used in fewer patients who underwent prostatectomy (a difference of 25.0 percentage points; 95% CI, 17.7 to 32.3). The benefit of surgery with respect to death from prostate cancer was largest in men younger than 65 years of age (relative risk, 0.45) and in those with intermediate-risk prostate cancer (relative risk, 0.38). However, radical prostatectomy was associated with a reduced risk of metastases among older men (relative risk, 0.68; P=0.04). ConclusionsExtended follow-up confirmed a substantial reduction in mortality after radical prostatectomy; the number needed to treat to prevent one death continued to decrease when the treatment was modified according to age at diagnosis and tumor risk. A large proportion of long-term survivors in the watchful-waiting group have not required any palliative treatment. (Funded by the Swedish Cancer Society and others.) The randomized Swedish trial of prostatectomy versus watchful waiting in disease detected mainly clinically (not by PSA screening) continues to show a benefit for early prostatectomy. The number of men younger than 65 needed to treat to prevent one death is now four. The Scandinavian Prostate Cancer Group Study Number 4 (SPCG-4), a randomized trial of radical prostatectomy versus watchful waiting in men with localized prostate cancer diagnosed before the era of prostate-specific antigen (PSA) testing, showed a survival benefit of radical prostatectomy as compared with observation at 15 years of follow-up.(1) By contrast, the Prostate Cancer Intervention versus Observation Trial (PIVOT), initiated in the early era of PSA testing, showed that radical prostatectomy did not significantly reduce prostate cancer-specific or overall mortality after 12 years.(2) PSA screening profoundly changes the clinical domain of study. Among other considerations, the substantial additional lead time ...
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| 6. |
- Bill-Axelson, Anna, et al.
(author)
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Radical prostatectomy versus watchful waiting in localized prostate cancer : the Scandinavian prostate cancer group-4 randomized trial
- 2008
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In: Journal of the National Cancer Institute. - : Oxford University Press. - 0027-8874 .- 1460-2105. ; 100:16, s. 1144-1154
-
Journal article (peer-reviewed)abstract
- BACKGROUND: The benefit of radical prostatectomy in patients with early prostate cancer has been assessed in only one randomized trial. In 2005, we reported that radical prostatectomy improved prostate cancer survival compared with watchful waiting after a median of 8.2 years of follow-up. We now report results after 3 more years of follow-up.METHODS: From October 1, 1989, through February 28, 1999, 695 men with clinically localized prostate cancer were randomly assigned to radical prostatectomy (n = 347) or watchful waiting (n = 348). Follow-up was complete through December 31, 2006, with histopathologic review and blinded evaluation of causes of death. Relative risks (RRs) were estimated using the Cox proportional hazards model. Statistical tests were two-sided.RESULTS: During a median of 10.8 years of follow-up (range = 3 weeks to 17.2 years), 137 men in the surgery group and 156 in the watchful waiting group died (P = .09). For 47 of the 347 men (13.5%) who were randomly assigned to surgery and 68 of the 348 men (19.5%) who were not, death was due to prostate cancer. The difference in cumulative incidence of death due to prostate cancer remained stable after about 10 years of follow-up. At 12 years, 12.5% of the surgery group and 17.9% of the watchful waiting group had died of prostate cancer (difference = 5.4%, 95% confidence interval [CI] = 0.2 to 11.1%), for a relative risk of 0.65 (95% CI = 0.45 to 0.94; P = .03). The difference in cumulative incidence of distant metastases did not increase beyond 10 years of follow-up. At 12 years, 19.3% of men in the surgery group and 26% of men in the watchful waiting group had been diagnosed with distant metastases (difference = 6.7%, 95% CI = 0.2 to 13.2%), for a relative risk of 0.65 (95% CI = 0.47 to 0.88; P = .006). Among men who underwent radical prostatectomy, those with extracapsular tumor growth had 14 times the risk of prostate cancer death as those without it (RR = 14.2, 95% CI = 3.3 to 61.8; P < .001).CONCLUSION: Radical prostatectomy reduces prostate cancer mortality and risk of metastases with little or no further increase in benefit 10 or more years after surgery.
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| 7. |
- Dalin, Frida, 1984-, et al.
(author)
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Clinical and immunological characteristics of Autoimmune Addison's disease : a nationwide Swedish multicenter study
- 2017
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In: Journal of Clinical Endocrinology and Metabolism. - : Oxford University Press. - 0021-972X .- 1945-7197. ; 102:2, s. 379-389
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Journal article (peer-reviewed)abstract
- CONTEXT: Studies on clinical and immunological features of Autoimmune Addison's disease (AAD) are needed to understand the disease burden and increased mortality.OBJECTIVE: To provide upgraded data on autoimmune comorbidities, replacement therapy, autoantibody profiles and cardiovascular risk factors.DESIGN, SETTING AND PARTICIPANTS: Cross sectional, population-based study. 660 AAD patients were included utilizing the Swedish Addison Registry (SAR) 2008-2014. When analyzing cardiovascular risk factors, 3,594 individuals from the population-based survey in Northern Sweden, MONICA (MONItoring of Trends and Determinants of CArdiovascular Disease), served as controls.MAIN OUTCOME MEASURE: Prevalence of autoimmune comorbidities and cardiovascular risk factors. Autoantibodies against 13 autoantigens were determined.RESULTS: Sixty percent of the SAR cohort consisted of females. Mean age at diagnosis was significantly higher for females than for males (36.8 vs. 31.1 years). The proportion of 21-hydroxylase autoantibody positive patients was 83% and 62% of patients had one or more associated autoimmune diseases, more frequently coexisting in females (p<0.0001). AAD patients had lower BMI (p<0.0001) and prevalence of hypertension (p=0.027) compared with controls. Conventional hydrocortisone tablets were used by 89% of patients; with the mean dose 28.1±8.5 mg/day. The mean hydrocortisone equivalent dose normalized to body surface was 14.8±4.4 mg/m(2)/day. Higher hydrocortisone equivalent dose was associated with higher incidence of hypertension (p=0.046).CONCLUSIONS: Careful monitoring of AAD patients is warranted to detect associated autoimmune diseases. Contemporary Swedish AAD patients do not have increased prevalence of overweight, hypertension, T2DM or hyperlipidemia. However, high glucocorticoid replacement doses may be a risk factor for hypertension.
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| 8. |
- Forsman, Huamei, et al.
(author)
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Stable formyl peptide receptor agonists that activate the neutrophil NADPH-oxidase identified through screening of a compound library.
- 2011
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In: Biochemical pharmacology. - : Elsevier BV. - 1873-2968 .- 0006-2952. ; 81:3, s. 402-411
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Journal article (peer-reviewed)abstract
- The neutrophil formyl peptide receptors (FPR1 and FPR2) are G-protein coupled receptors that can induce pro-inflammatory as well as anti-inflammatory activities when activated. Accordingly, these receptors may become therapeutic targets for the development of novel drugs to be used for reducing the inflammation induced injuries in asthma, rheumatoid arthritis, Alzheimer's disease, cardiovascular diseases and traumatic shock. We screened a library of more then 50K small compounds for an ability of the compounds to induce a transient rise in intracellular Ca(2+) in cells transfected to express FPR2 (earlier called FPRL1 or the lipoxin A(4) receptor). Ten agonist hits were selected for further analysis representing different chemical series and five new together with five earlier described molecules were further profiled. Compounds 1-10 gave rise to a calcium response in the FPR2 transfectants with EC(50) values ranging from 4×10(-9)M to 2×10(-7)M. All 10 compounds activated human neutrophils to release superoxide, and based on the potency of their activity, the three most potent activators of the neutrophil NADPH-oxidase were further characterized. These three agonists were largely resistant to inactivation by neutrophil produced reactive oxygen species and shown to trigger the same functional repertoire in neutrophils as earlier described peptide agonists. Accordingly they induced chemotaxis, granule mobilization and secretion of superoxide. Interestingly, the oxidase activity was largely inhibited by cyclosporine H, an FPR1 selective antagonist, but not by PBP10, an FPR2 selective inhibitor, suggesting that FPR1 is the preferred receptor in neutrophils for all three agonists.
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| 9. |
- Hendrikse, Natalie, et al.
(author)
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Ancestral diterpene cyclases show increased thermostability and substrate acceptance
- 2018
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In: The FEBS Journal. - : Wiley-VCH Verlagsgesellschaft. - 1742-464X .- 1742-4658. ; 285:24, s. 4660-4673
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Journal article (peer-reviewed)abstract
- Bacterial diterpene cyclases are receiving increasing attention in biocatalysis and synthetic biology for the sustainable generation of complex multicyclic building blocks. Herein, we explore the potential of ancestral sequence reconstruction (ASR) to generate remodeled cyclases with enhanced stability, activity, and promiscuity. Putative ancestors of spiroviolene synthase, a bacterial class I diterpene cyclase, display an increased yield of soluble protein of up to fourfold upon expression in the model organism Escherichia coli. Two of the resurrected enzymes, with an estimated age of approximately 1.7 million years, display an upward shift in thermostability of 7-13 degrees C. Ancestral spiroviolene synthases catalyze cyclization of the natural C-20-substrate geranylgeranyl diphosphate (GGPP) and also accept C-15 farnesyl diphosphate (FPP), which is not converted by the extant enzyme. In contrast, the consensus sequence generated from the corresponding multiple sequence alignment was found to be inactive toward both substrates. Mutation of a nonconserved position within the aspartate-rich motif of the reconstructed ancestral cyclases was associated with modest effects on activity and relative substrate specificity (i.e., k(cat)/K-M for GGPP over k(cat)/K-M for FPP). Kinetic analyses performed at different temperatures reveal a loss of substrate saturation, when going from the ancestor with highest thermostability to the modern enzyme. The kinetics data also illustrate how an increase in temperature optimum of biocatalysis is reflected in altered entropy and enthalpy of activation. Our findings further highlight the potential and limitations of applying ASR to biosynthetic machineries in secondary metabolism.
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| 10. |
- Hendrikse, Natalie, et al.
(author)
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Ancestral lysosomal enzymes with increased activity harbor therapeutic potential for treatment of Hunter syndrome
- 2021
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In: ISCIENCE. - : Elsevier BV. - 2589-0042. ; 24:3
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Journal article (peer-reviewed)abstract
- We show the successful application of ancestral sequence reconstruction to enhance the activity of iduronate-2-sulfatase (IDS), thereby increasing its therapeutic potential for the treatment of Hunter syndrome-a lysosomal storage disease caused by impaired function of IDS. Current treatment, enzyme replacement therapy with recombinant human IDS, does not alleviate all symptoms, and an unmet medical need remains. We reconstructed putative ancestral sequences of mammalian IDS and compared them with extant IDS. Some ancestral variants displayed up to 2-fold higher activity than human IDS in in vitro assays and cleared more substrate in ex vivo experiments in patient fibroblasts. This could potentially allow for lower dosage or enhanced therapeutic effect in enzyme replacement therapy, thereby improving treatment outcomes and cost efficiency, as well as reducing treatment burden. In summary, we showed that ancestral sequence reconstruction can be applied to lysosomal enzymes that function in concert with modern enzymes and receptors in cells.
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| 11. |
- Hendrikse, Natalie
(author)
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Engineering enzymes towards biotherapeutic applications using ancestral sequence reconstruction
- 2020
-
Doctoral thesis (other academic/artistic)abstract
- Enzymes are versatile biocatalysts that fulfill essential functions in all forms of life and, therefore, play an important role in health and disease. One specific application of enzymes in life science is their use as biopharmaceuticals, which typically benefits from high catalytic activity and stability. Increased stability and activity are both desirable properties for biopharmaceuticals as they are directly related to dosage, which in turn affects administration time, cost of production and potency of a drug. The aim of the work presented in this thesis is to enhance the therapeutic potential of enzymes by means of enzyme engineering, in particular using ancestral sequence reconstruction. In Paper I, we established the utility of this method in a model system and obtained ancestral terpene cyclases with increased activity, stability and substrate scope. In Paper II, we described the successful crystallization of the most stable ancestral terpene cyclase, which allowed for rational design of substrate specificity. Finally, we applied the method to two therapeutically relevant enzyme families associated with rare metabolic disorders. We obtained ancestral phenylalanine/tyrosine ammonia-lyases with substantially enhanced thermostability and long-term stability in Paper III and ancestral iduronate-2-sulfatases with increased activity in Paper IV. In summary, the results presented herein highlight the potential of ancestral sequence reconstruction as a method to obtain stable enzyme scaffolds for further engineering and to enhance therapeutic properties of enzymes.
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| 12. |
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| 13. |
- Herzog, Erik, et al.
(author)
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Experience from Introducing Systems Engineering in an Academic Environment Using an Industry Training Course
- 2018
-
Conference paper (peer-reviewed)abstract
- Training and educating Systems Engineers is a key activity for any organization developing complex heterogeneous systems. Ideally, the regional/national academic community will providecourses and education programs facilitating for the needs of industry and society. However, Systems Engineering is not a traditional academic subject and despite the growing academic interest in the subject there are many regions with no dedicated academic courses and programs in the subject.This paper presents experience from introducing Systems Engineering via a capstone project course in a mechatronics master’s program at the Royal Institute of Technology (KTH) in Sweden. Systemengineers from industry give an industry-developed Systems Engineering course, as part of a capstone course. We believe that the approach is novel and can serve as a mechanism for introducing Systems Engineering to both students and lecturers in the academic world, who have no previous exposure to the subject. Moreover, student feedback indicate that having lecturers with industrial experience was highly appreciated, making the activity a worthwhile branding investment for industry as well.
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| 14. |
- Holmberg, Lars, et al.
(author)
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A randomized trial comparing radical prostatectomy with watchful waiting in early prostate cancer
- 2002
-
In: New England Journal of Medicine. - 0028-4793 .- 1533-4406. ; 347:11, s. 781-789
-
Journal article (peer-reviewed)abstract
- BACKGROUND: Radical prostatectomy is widely used in the treatment of early prostate cancer. The possible survival benefit of this treatment, however, is unclear. We conducted a randomized trial to address this question. METHODS: From October 1989 through February 1999, 695 men with newly diagnosed prostate cancer in International Union against Cancer clinical stage T1b, T1c, or T2 were randomly assigned to watchful waiting or radical prostatectomy. We achieved complete follow-up through the year 2000 with blinded evaluation of causes of death. The primary end point was death due to prostate cancer, and the secondary end points were overall mortality, metastasis-free survival, and local progression. RESULTS: During a median of 6.2 years of follow-up, 62 men in the watchful-waiting group and 53 in the radical-prostatectomy group died (P=0.31). Death due to prostate cancer occurred in 31 of 348 of those assigned to watchful waiting (8.9 percent) and in 16 of 347 of those assigned to radical prostatectomy (4.6 percent) (relative hazard, 0.50; 95 percent confidence interval, 0.27 to 0.91; P=0.02). Death due to other causes occurred in 31 of 348 men in the watchful-waiting group (8.9 percent) and in 37 of 347 men in the radical-prostatectomy group (10.6 percent). The men assigned to surgery had a lower relative risk of distant metastases than the men assigned to watchful waiting (relative hazard, 0.63; 95 percent confidence interval, 0.41 to 0.96). CONCLUSIONS: In this randomized trial, radical prostatectomy significantly reduced disease-specific mortality, but there was no significant difference between surgery and watchful waiting in terms of overall survival.
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| 15. |
- Jörnsten, Rebecka, 1971, et al.
(author)
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Network modeling of the transcriptional effects of copy number aberrations in glioblastoma
- 2011
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In: Molecular Systems Biology. - : EMBO. - 1744-4292. ; 7
-
Journal article (peer-reviewed)abstract
- DNA copy number aberrations (CNAs) are a hallmark of cancer genomes. However, little is known about how such changes affect global gene expression. We develop a modeling framework, EPoC (Endogenous Perturbation analysis of Cancer), to (1) detect disease-driving CNAs and their effect on target mRNA expression, and to (2) stratify cancer patients into long- and short-term survivors. Our method constructs causal network models of gene expression by combining genome-wide DNA- and RNA-level data. Prognostic scores are obtained from a singular value decomposition of the networks. By applying EPoC to glioblastoma data from The Cancer Genome Atlas consortium, we demonstrate that the resulting network models contain known disease-relevant hub genes, reveal interesting candidate hubs, and uncover predictors of patient survival. Targeted validations in four glioblastoma cell lines support selected predictions, and implicate the p53-interacting protein Necdin in suppressing glioblastoma cell growth. We conclude that large-scale network modeling of the effects of CNAs on gene expression may provide insights into the biology of human cancer. Free software in MATLAB and R is provided.
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| 16. |
- Kronqvist, Nina, et al.
(author)
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Sequential pH-driven dimerization and stabilization of the N-terminal domain enables rapid spider silk formation
- 2014
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In: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 5:1, s. 3254-
-
Journal article (peer-reviewed)abstract
- The mechanisms controlling the conversion of spider silk proteins into insoluble fibres, which happens in a fraction of a second and in a defined region of the silk glands, are still unresolved. The N-terminal domain changes conformation and forms a homodimer when pH is lowered from 7 to 6; however, the molecular details still remain to be determined. Here we investigate site-directed mutants of the N-terminal domain from Euprosthenops australis major ampullate spidroin 1 and find that the charged residues D40, R60 and K65 mediate intersubunit electrostatic interactions. Protonation of E79 and E119 is required for structural conversions of the subunits into a dimer conformation, and subsequent protonation of E84 around pH 5.7 leads to the formation of a fully stable dimer. These residues are highly conserved, indicating that the now proposed three-step mechanism prevents premature aggregation of spidroins and enables fast formation of spider silk fibres in general.
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| 17. |
- Morgan, Daniel, 1988-, et al.
(author)
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A generalized framework for controlling FDR in gene regulatory network inference
- 2019
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In: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 35:6, s. 1026-1032
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Journal article (peer-reviewed)abstract
- Motivation: Inference of gene regulatory networks (GRNs) from perturbation data can give detailed mechanistic insights of a biological system. Many inference methods exist, but the resulting GRN is generally sensitive to the choice of method-specific parameters. Even though the inferred GRN is optimal given the parameters, many links may be wrong or missing if the data is not informative. To make GRN inference reliable, a method is needed to estimate the support of each predicted link as the method parameters are varied.Results: To achieve this we have developed a method called nested bootstrapping, which applies a bootstrapping protocol to GRN inference, and by repeated bootstrap runs assesses the stability of the estimated support values. To translate bootstrap support values to false discovery rates we run the same pipeline with shuffled data as input. This provides a general method to control the false discovery rate of GRN inference that can be applied to any setting of inference parameters, noise level, or data properties. We evaluated nested bootstrapping on a simulated dataset spanning a range of such properties, using the LASSO, Least Squares, RNI, GENIE3 and CLR inference methods. An improved inference accuracy was observed in almost all situations. Nested bootstrapping was incorporated into the GeneSPIDER package, which was also used for generating the simulated networks and data, as well as running and analyzing the inferences.
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| 18. |
- Morgan, Daniel, et al.
(author)
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Perturbation-based gene regulatory network inference to unravel oncogenic mechanisms
-
Other publication (other academic/artistic)abstract
- Motivation: Cancer is known to stem from multiple, independent mutations, the effects of which aggregate to drive the cell into a cancerous state. To understand the complex interplay between affected genes, their gene regulatory network (GRN) needs to be uncovered, to revealing detailed insights of regulatory mechanisms. We therefore decided to infer a reliable GRN from perturbation responses of 40 genes known or suspected to have a role in human cancers yet whose regulatory interactions are poorly known.Results: siRNA knockdown experiments of each gene were done in a human squamous carcinoma cell line, after which the transcriptomic response was measured. From these data GRNs were inferred using several methods, and the false discovery rate was controlled by the NestBoot framework. The best GRN was shown to be significantly more predictive than the null model, both in crossvalidated benchmarks and for an independent dataset of the same genes but subjected to double perturbations. It agrees with many known links in addition to predicting a large number of novel interactions, a subset of which were experimentally validated. The inferred GRN captures regulatory interactions central to cancer-relevant processes and thus provides mechanistic insights that are useful for future cancer research.
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| 19. |
- Morgan, Daniel, et al.
(author)
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Perturbation-based gene regulatory network inference to unravel oncogenic mechanisms
- 2020
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In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 10:1
-
Journal article (peer-reviewed)abstract
- The gene regulatory network (GRN) of human cells encodes mechanisms to ensure proper functioning. However, if this GRN is dysregulated, the cell may enter into a disease state such as cancer. Understanding the GRN as a system can therefore help identify novel mechanisms underlying disease, which can lead to new therapies. To deduce regulatory interactions relevant to cancer, we applied a recent computational inference framework to data from perturbation experiments in squamous carcinoma cell line A431. GRNs were inferred using several methods, and the false discovery rate was controlled by the NestBoot framework. We developed a novel approach to assess the predictiveness of inferred GRNs against validation data, despite the lack of a gold standard. The best GRN was significantly more predictive than the null model, both in cross-validated benchmarks and for an independent dataset of the same genes under a different perturbation design. The inferred GRN captures many known regulatory interactions central to cancer-relevant processes in addition to predicting many novel interactions, some of which were experimentally validated, thus providing mechanistic insights that are useful for future cancer research.
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| 20. |
- Nordling, Erik
(author)
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Biocomputational studies on protein structures
- 2002
-
Doctoral thesis (other academic/artistic)abstract
- Biology in the post-genomic era produces large amount of data. This, in combination with the need for efficient algorithms to find genes in the genomic material, has brought a renaissance into the field of computational biology. Methods now range from lead discovery in the drug discovery process, by virtual ligand screening, through sequence comparisons and homology searches, to micro array data analysis and visualisation. This thesis primarily deals with sequence analysis, different aspects of protein structure prediction and ligand--enzyme complex characterisation, I have applied bioinformatic techniques on the enzyme families of medium-chain dehydrogenases/reductases (MDR), short-chain dehydrogenases/reductases (SDR) and biologically active peptides. Sequence analysis of the MDR superfamily extends the evolutionary context of this superfamily, as MDR enzymes were collected from completely sequenced genomes. The analysis reveals the presence of eight families whereof several were previously uncharacterised. Three families are formed by dimeric alcohol dehydrogenases (ADH), cinnamyl alcohol dehydrogenases (CAD) and tetrameric alcohol dehydrogenases (YADH). Three further families are centred on forms initially detected as mitochondrial respiratory function proteins (MRF), acetyl-CoA reductases of fatty acid synthases (ACR), and leukotriene B4 dehydrogenases (LTD). The two remaining families, with polyol dehydrogenases (PDH) and quinone reductases (QOR), are also distinct but with variable sequences. The analysis also suggests that new functions have evolved in this superfamily in higher organisms. Factors that govern the substrate specificity of gammagammaADH were investigated with docking calculations and can be traced to active site characteristics, most notably the Ser48/thr48 replacement between gammagammaADH and betabetaADH, which allow the oxidation of 3beta-hydroxy bile acids, such as isoUDCA, in gammagammaADH, while both enzymes are inactive versus 3alpha-hydroxy bile acids. A homology model of type 10 17beta-hydroxysteroid dehydrogenase was constructed from 7alpha-hydroxysteroid dehydrogenase. The validity of the model was investigated by its ability to distinguish between active and inactive using docking calculations. Substrates tested ranged from steroids and bile acids to L- and D-hydroxyacyl CoA. Ligands with 17P or 3alpha hydroxy groups and L-hydroxyacyl CoA could achieve interactions favourable for catalysis at the active site. A crystallographically determined structure published after the submission of our paper verified large portions of our model. The role of a conserved asparagine in the short-chain dehydrogenase/reductase (SDR) fold is investigated through structural comparisons of 21 members with experimentally verified structures. An extensive hydrogen-bonding network including parts of the active site is revealed in 16 out of 21 SDR forms. Molecular dynamics simulations were employed to study the effect of deleterious mutants and replacements, known to diminish fibrillation, to the stability of the helical region of the amyloidogenic peptides amyloid beta-peptide (AP) and surfactant protein-C (SP-C). The effects in SP-C are quantitatively distinguishable, while the noise ratio in the AP simulations makes valid predictions somewhat difficult. Sequence comparisons of the C-peptide of proinsulin displays a sequence variability that is 1 to 2 orders of magnitude greater than that of insulin, but in the same order of magnitude as the well established peptide hormones relaxin and parathormone, which in conjunction with functional reports may indicate a hormonal function for the C-peptide.
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| 21. |
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| 22. |
- Nordling, Mikael, et al.
(author)
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Mixed-state non-Abelian holonomy for subsystems
- 2005
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In: Physical Review A. Atomic, Molecular, and Optical Physics. - 1050-2947 .- 1094-1622. ; 71:1, s. 012110-
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Journal article (peer-reviewed)abstract
- Non-Abelian holonomy in dynamical systems may arise in adiabatic transport of energetically degenerate sets of states. We examine such a holonomy structure for mixtures of energetically degenerate quantal states. We demonstrate that this structure has a natural interpretation in terms of the standard Wilczek-Zee holonomy associated with a certain class of Hamiltonians that couple the system to an ancilla. The mixed state holonomy is analyzed for holonomic quantum computation using ion traps.
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| 23. |
- Rehfisch, Pia, et al.
(author)
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Lung Function and Respiratory Symptoms in Hard Metal Workers Exposed to Cobalt
- 2012
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In: Journal of Occupational and Environmental Medicine. - Philadelphia, USA : Lippincott Williams & Wilkins. - 1076-2752 .- 1536-5948. ; 54:4, s. 409-413
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Journal article (peer-reviewed)abstract
- Objective: To follow-up lung function and airway symptoms in workers exposed to cobalt dust at a hard metal plant. Methods: A total of 582 employees underwent spirometry and completed a questionnaire. A historical exposure matrix was created, assigning figures for historical and recent work-related exposure. Results: At the time of employment, 5% reported symptoms from respiratory tract. At follow-up, 5% suffered from persistent coughing and 7% reported asthma; 20% were daily smokers. Among nonsmokers without asthma, an evident, statistically nonsignificant, dose-response effect was seen between increasing cobalt exposure and decline in FEV1 (forced expiratory volume in the first second). In all exposure categories, the FEV1 in smokers declined 10 mL more per year than for nonsmokers. Conclusions: Even low levels of cobalt exposure seem to hamper lung function both in smokers and nonsmokers. This impact is considered low in relation to the effect of aging.
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| 24. |
- Rising, Anna, et al.
(author)
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Systemic AA amyloidosis in the red fox (Vulpes vulpes)
- 2017
-
In: Protein Science. - : WILEY. - 0961-8368 .- 1469-896X. ; 26:11, s. 2312-2318
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Journal article (peer-reviewed)abstract
- Amyloid A (AA) amyloidosis occurs spontaneously in many mammals and birds, but the prevalence varies considerably among different species, and even among subgroups of the same species. The Blue fox and the Gray fox seem to be resistant to the development of AA amyloidosis, while Island foxes have a high prevalence of the disease. Herein, we report on the identification of AA amyloidosis in the Red fox (Vulpes vulpes). Edman degradation and tandem MS analysis of proteolyzed amyloid protein revealed that the amyloid partly was composed of full-length SAA. Its amino acid sequence was determined and found to consist of 111 amino acid residues. Based on inter-species sequence comparisons we found four residue exchanges (Ser31, Lys63, Leu71, Lys72) between the Red and Blue fox SAAs. Lys63 seems unique to the Red fox SAA. We found no obvious explanation to how these exchanges might correlate with the reported differences in SAA amyloidogenicity. Furthermore, in contrast to fibrils from many other mammalian species, the isolated amyloid fibrils from Red fox did not seed AA amyloidosis in a mouse model.
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| 25. |
- Secilmis, Deniz, et al.
(author)
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A Subset Selection Method for Accurate Gene Regulatory Network Inference of Uninformative Datasets
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Other publication (other academic/artistic)abstract
- Motivation: The interactions among the components of a living cell that constitute the gene regulatory network (GRN) can be inferred from perturbation-based gene expression data. Such networks are useful for providing mechanistic insights of a biological system. In order to explore the feasibility and quality of GRN inference at a large scale, we used the L1000 data where approximately 1000 genes have been perturbed and their expression levels have been quantified in 9 cancer cell lines. First we identified key properties of the datasets, i.e., signal-to-noise ratio (SNR) and condition number which we have shown to affect the performance of various inference methods.Results: We found that all L1000 datasets have a very low SNR level causing them to be highly uninformative not suitable to infer accurate GRNs. Therefore, we have developed a gene reduction pipeline in which we eliminate the uninformative genes from the system using a selection criteria based on SNR until reaching an informative subset. The results show that our pipeline can identify an informative subset in an uninformative dataset, improving the accuracy of the GRN inference significantly.
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| 26. |
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| 27. |
- Seçilmiş, Deniz, 1991-, et al.
(author)
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Knowledge of the perturbation design is essential for accurate gene regulatory network inference
- 2022
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In: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 12:1
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Journal article (peer-reviewed)abstract
- The gene regulatory network (GRN) of a cell executes genetic programs in response to environmental and internal cues. Two distinct classes of methods are used to infer regulatory interactions from gene expression: those that only use observed changes in gene expression, and those that use both the observed changes and the perturbation design, i.e. the targets used to cause the changes in gene expression. Considering that the GRN by definition converts input cues to changes in gene expression, it may be conjectured that the latter methods would yield more accurate inferences but this has not previously been investigated. To address this question, we evaluated a number of popular GRN inference methods that either use the perturbation design or not. For the evaluation we used targeted perturbation knockdown gene expression datasets with varying noise levels generated by two different packages, GeneNetWeaver and GeneSpider. The accuracy was evaluated on each dataset using a variety of measures. The results show that on all datasets, methods using the perturbation design matrix consistently and significantly outperform methods not using it. This was also found to be the case on a smaller experimental dataset from E. coli. Targeted gene perturbations combined with inference methods that use the perturbation design are indispensable for accurate GRN inference.
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| 28. |
- Seçilmiş, Deniz, et al.
(author)
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Uncovering cancer gene regulation by accurate regulatory network inference from uninformative data
- 2020
-
In: npj Systems Biology and Applications. - : Springer Science and Business Media LLC. - 2056-7189. ; 6:1
-
Journal article (peer-reviewed)abstract
- The interactions among the components of a living cell that constitute the gene regulatory network (GRN) can be inferred from perturbation-based gene expression data. Such networks are useful for providing mechanistic insights of a biological system. In order to explore the feasibility and quality of GRN inference at a large scale, we used the L1000 data where similar to 1000 genes have been perturbed and their expression levels have been quantified in 9 cancer cell lines. We found that these datasets have a very low signal-to-noise ratio (SNR) level causing them to be too uninformative to infer accurate GRNs. We developed a gene reduction pipeline in which we eliminate uninformative genes from the system using a selection criterion based on SNR, until reaching an informative subset. The results show that our pipeline can identify an informative subset in an overall uninformative dataset, allowing inference of accurate subset GRNs. The accurate GRNs were functionally characterized and potential novel cancer-related regulatory interactions were identified.
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| 29. |
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| 30. |
- Sedigh, Amir, et al.
(author)
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Perfusion of Porcine Kidneys With Macromolecular Heparin Reduces Early Ischemia Reperfusion Injury
- 2019
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In: Transplantation. - : LIPPINCOTT WILLIAMS & WILKINS. - 0041-1337 .- 1534-6080. ; 103:2, s. 420-427
-
Journal article (peer-reviewed)abstract
- Background: Previously, we have been able to demonstrate the possibility of coating the inner surface of the renal arteries in porcine kidneys with a heparin conjugate during hypothermic machine perfusion (HMP). The purpose of this study was to assess the efficacy of this treatment in reducing early ischemia-reperfusion injury.Method: Brain death was induced in male landrace pigs by stepwise volume expansion of an epidural balloon catheter until negative cerebral perfusion pressure (CPP) was obtained. Both kidneys (matched pairs; n = 6 + 6) were preserved for 20 hours byHMP during which 50mg heparin conjugate was added to one of the HMP systems (treated group). A customized ex vivo normothermic oxygenated perfusion (NP) system with added exogenous creatinine was used to evaluate early kidney function. Blood, urine and histological samples were collected during the subsequent 3 hours of NP.Results: Kidney weight was lower at the end of NP (P = 0.017) in the treated group compared with control kidneys. The rate of decline in creatinine level was faster (P = 0.024), total urinary volume was higher (P = 0.031), and the level of urine neutrophil gelatinase-associated lipocalin (NGAL) was lower (P = 0.031) in the treated group. Histologically, less tubular changes were seen (P = 0.046). During NP intrarenal resistance remained lower (P < 0.0001) in the treated group.Conclusions: Perfusion of porcine kidneys with heparin conjugate during HMP reduces preservation injury and improves organ function shortly after reperfusion. No increased risk of bleeding was seen in this setup. This protective strategy may potentially improve the quality of transplanted kidneys in the clinical setting.
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| 31. |
- Stenberg, Erik, 1969-, et al.
(author)
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En ny plattform för att lösa bostadsfrågan : En antologi om samverkan kring bo- och byggnadsfrågor
- 2019
-
Reports (pop. science, debate, etc.)abstract
- Bakgrund: Hur hamnade vi här (sid 16-28)av Carl-Johan Engström, Kristian Skånberg och Erik StenbergByggandet utgör en stor delav de svenska samhälleligainvesteringarna. Boendet ståri sin tur för den enskilt störstaposten i de flestas hushållsbudget.Detta gör att det sammantagethandlar om mycket stora pengaroch resursflöden kopplade tillhållbarhetsfrågor. Det rör ocksåde miljöer där de flesta människortillbringar merparten av sina liv,med alla de beröringspunkter kringsocial hållbarhet som detta för medsig. Det gör förändringar mycket angelägna.Byggandet: Kolsänka och energiproducentav Victoria Kalén och Erik Stenberg (sid 55-61)Bygg- och fastighetssektorn stårför en stor del av samhälletsutsläpp av växthusgaser. År 2015var de inhemska utsläppen avväxthusgaser ca 11,1 miljonerton koldioxidekvivalenter. Detmotsvarade 18 procent av Sverigestotala utsläpp av växthusgaser.Lägger vi till utsläppen som byggochfastighetssektorn genererarutomlands så blir totalen över 20miljoner ton koldioxidekvivalenter.Boverkets miljöindikatorer visaratt bygg- och fastighetssektornsmiljöpåverkan ökat ytterligaresedan dess. Dessutom kommervia de globala varukedjorna förbyggmaterial ytterligare uppemot 10miljoner ton koldioxidekvivalenter ini den svenska byggprocessen årligen.Ur ett konsumtionsperspektiv äralltså de byggrelaterade utsläppenännu högre.Hela rapporten:En ny plattform för att lösa bostadsfrågan är en antologi skriven av sex författare i samråd med Global Utmanings programråd för Hållbara Städer. Antologin tar avstamp i bostadsfrågan ur ett historiskt perspektiv och belyser frågan utifrån den gemensamma strategin för en hållbara omställning – Agenda 2030. Plattformen hanterar en såväl ekonomisk, som social och miljömässig omställning av ”bostadsfrågan”, det vill säga boendet, byggandet och stadsutvecklingen. Antologin innehåller dels förslaget till plattform för samverkan och dels fem bidrag som konkretiserar problem och utmaningar.
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| 32. |
- Studham, Matthew E., et al.
(author)
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Functional association networks as priors for gene regulatory network inference
- 2014
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In: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 30:12, s. 130-138
-
Journal article (peer-reviewed)abstract
- Motivation: Gene regulatory network (GRN) inference reveals the influences genes have on one another in cellular regulatory systems. If the experimental data are inadequate for reliable inference of the network, informative priors have been shown to improve the accuracy of inferences. Results: This study explores the potential of undirected, confidence-weighted networks, such as those in functional association databases, as a prior source for GRN inference. Such networks often erroneously indicate symmetric interaction between genes and may contain mostly correlation-based interaction information. Despite these drawbacks, our testing on synthetic datasets indicates that even noisy priors reflect some causal information that can improve GRN inference accuracy. Our analysis on yeast data indicates that using the functional association databases FunCoup and STRING as priors can give a small improvement in GRN inference accuracy with biological data.
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| 33. |
- Thalén, Niklas, 1985-, et al.
(author)
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Systems biology greatly improve activity of secreted therapeutic sulfatase in CHO bioprocess
-
Other publication (other academic/artistic)abstract
- Rare diseases are, despite their name, collectively common and millions of people are affected daily of conditions where treatment often is unavailable. Sulfatases are a large family of activating enzymes related to several of these diseases. Heritable genetic variations in sulfatases may lead to impaired activity and a reduced macromolecular breakdown within the lysosome, with several severe and lethal conditions as a consequence. While therapeutic options are scarce, treatment for some sulfatase deficiencies by recombinant enzyme replacement are available. However, such recombinant production of sulfatases suffers greatly from low product activity and yield, further limiting accessibility for patient groups. Here, we have addressed this problem by defining key-proteins necessary for active sulfatase secretion by comparison of CHO clones with different levels of production of active sulfatase. Quantitative transcriptomic analysis highlighted 14 key genes associated with sulfatase production, and experimental validation by co-expression improved the sulfatase enzyme activity by up to 150-fold. Furthermore, a correlation between product mRNA levels and sulfatase activity were observed and expression with lower activity promoters showed an increased in sulfatase activity. The workflow devised is general and we propose it to be useful for resolving bottlenecks in cellular machineries for improvement of cell factories for other biologics as well.
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| 34. |
- Thalén, Niklas, et al.
(author)
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Tuning of CHO secretional machinery improve activity of secreted therapeutic sulfatase 150-fold
- 2024
-
In: Metabolic engineering. - : Elsevier BV. - 1096-7176 .- 1096-7184. ; 81, s. 157-166
-
Journal article (peer-reviewed)abstract
- Rare diseases are, despite their name, collectively common and millions of people are affected daily of conditions where treatment often is unavailable. Sulfatases are a large family of activating enzymes related to several of these diseases. Heritable genetic variations in sulfatases may lead to impaired activity and a reduced macromolecular breakdown within the lysosome, with several severe and lethal conditions as a consequence. While therapeutic options are scarce, treatment for some sulfatase deficiencies by recombinant enzyme replacement are available. The recombinant production of such sulfatases suffers greatly from both low product activity and yield, further limiting accessibility for patient groups. To mitigate the low product activity, we have investigated cellular properties through computational evaluation of cultures with varying media conditions and comparison of two CHO clones with different levels of one active sulfatase variant. Transcriptome analysis identified 18 genes in secretory pathways correlating with increased sulfatase production. Experimental validation by upregulation of a set of three key genes improved the specific enzymatic activity at varying degree up to 150-fold in another sulfatase variant, broadcasting general production benefits. We also identified a correlation between product mRNA levels and sulfatase activity that generated an increase in sulfatase activity when expressed with a weaker promoter. Furthermore, we suggest that our proposed workflow for resolving bottlenecks in cellular machineries, to be useful for improvements of cell factories for other biologics as well.
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| 35. |
- Tjärnberg, Andreas, et al.
(author)
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Avoiding pitfalls in L-1-regularised inference of gene networks
- 2015
-
In: Molecular Biosystems. - : Royal Society of Chemistry (RSC). - 1742-206X .- 1742-2051. ; 11:1, s. 287-296
-
Journal article (peer-reviewed)abstract
- Statistical regularisation methods such as LASSO and related L-1 regularised regression methods are commonly used to construct models of gene regulatory networks. Although they can theoretically infer the correct network structure, they have been shown in practice to make errors, i.e. leave out existing links and include non-existing links. We show that L-1 regularisation methods typically produce a poor network model when the analysed data are ill-conditioned, i.e. the gene expression data matrix has a high condition number, even if it contains enough information for correct network inference. However, the correct structure of network models can be obtained for informative data, data with such a signal to noise ratio that existing links can be proven to exist, when these methods fail, by using least-squares regression and setting small parameters to zero, or by using robust network inference, a recent method taking the intersection of all non-rejectable models. Since available experimental data sets are generally ill-conditioned, we recommend to check the condition number of the data matrix to avoid this pitfall of L-1 regularised inference, and to also consider alternative methods.
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| 36. |
- Tjärnberg, Andreas, et al.
(author)
-
GeneSPIDER - gene regulatory network inference benchmarking with controlled network and data properties
- 2017
-
In: Molecular Biosystems. - : Royal Society of Chemistry (RSC). - 1742-206X .- 1742-2051. ; 13:7, s. 1304-1312
-
Journal article (peer-reviewed)abstract
- A key question in network inference, that has not been properly answered, is what accuracy can be expected for a given biological dataset and inference method. We present GeneSPIDER - a Matlab package for tuning, running, and evaluating inference algorithms that allows independent control of network and data properties to enable data-driven benchmarking. GeneSPIDER is uniquely suited to address this question by first extracting salient properties from the experimental data and then generating simulated networks and data that closely match these properties. It enables data-driven algorithm selection, estimation of inference accuracy from biological data, and a more multifaceted benchmarking. Included are generic pipelines for the design of perturbation experiments, bootstrapping, analysis of linear dependence, sample selection, scaling of SNR, and performance evaluation. With GeneSPIDER we aim to move the goal of network inference benchmarks from simple performance measurement to a deeper understanding of how the accuracy of an algorithm is determined by different combinations of network and data properties.
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| 37. |
- Tjärnberg, Andreas, et al.
(author)
-
GeneSPIDER - Generation and Simulation Package for Informative Data ExploRation
-
Other publication (other academic/artistic)abstract
- A range of tools are available to model, simulate and analyze gene regulatory networks (GRNs). However, these tools provide limited ability to control network topology, system dynamics, design of experiments, data properties, or noise characteristics. Independent control of these properties is the key to drawing conclusions on which inference method to use and what result to expect from it, as well as obtaining desired approximations of real biological systems. To draw conclusions on the relation between a network or data property and the performance of an inference method in simulations, system approximations with varying properties are needed. We present a Matlab package \gs for generation and analysis of networks and data in a dynamical systems framework with focus on the ability to vary properties. It supplies not only essential components that have been missing, but also wrappers to existing tools in common use. In particular, it contains tools for controlling and analyzing network topology (random, small-world, scale-free), stability of linear time-invariant systems, signal to noise ratio (SNR), and Interampatteness. It also contains methods for design of perturbation experiments, bootstrapping, analysis of linear dependence, sample selection, scaling of the SNR, and performance evaluation. GeneSPIDER offers control of network and data properties in simulations, together with tools to analyze these properties and draw conclusions on the quality of inferred GRNs. It can be fetched freely from the online =git= repository https://bitbucket.org/sonnhammergrni/genespider.
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| 38. |
- Tjärnberg, Andreas, et al.
(author)
-
Optimal Sparsity Criteria for Network Inference
- 2013
-
In: Journal of Computational Biology. - : Mary Ann Liebert Inc. - 1066-5277 .- 1557-8666. ; 20:5, s. 398-408
-
Journal article (peer-reviewed)abstract
- Gene regulatory network inference (that is, determination of the regulatory interactions between a set of genes) provides mechanistic insights of central importance to research in systems biology. Most contemporary network inference methods rely on a sparsity/regularization coefficient, which we call zeta (zeta), to determine the degree of sparsity of the network estimates, that is, the total number of links between the nodes. However, they offer little or no advice on how to select this sparsity coefficient, in particular, for biological data with few samples. We show that an empty network is more accurate than estimates obtained for a poor choice of zeta. In order to avoid such poor choices, we propose a method for optimization of zeta, which maximizes the accuracy of the inferred network for any sparsity-dependent inference method and data set. Our procedure is based on leave-one-out cross-optimization and selection of the zeta value that minimizes the prediction error. We also illustrate the adverse effects of noise, few samples, and uninformative experiments on network inference as well as our method for optimization of zeta. We demonstrate that our zeta optimization method for two widely used inference algorithms-Glmnet and NIR-gives accurate and informative estimates of the network structure, given that the data is informative enough.
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| 39. |
- Volk, Anna-Luisa, et al.
(author)
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Stratification of responders towards eculizumab using a structural epitope mapping strategy
- 2016
-
In: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 6
-
Journal article (peer-reviewed)abstract
- The complement component 5 (C5)-binding antibody eculizumab is used to treat patients with paroxysmal nocturnal hemoglobinuria (PNH) and atypical haemolytic uremic syndrome (aHUS). As recently reported there is a need for a precise classification of eculizumab responsive patients to allow for a safe and cost-effective treatment. To allow for such stratification, knowledge of the precise binding site of the drug on its target is crucial. Using a structural epitope mapping strategy based on bacterial surface display, flow cytometric sorting and validation via haemolytic activity testing, we identified six residues essential for binding of eculizumab to C5. This epitope co-localizes with the contact area recently identified by crystallography and includes positions in C5 mutated in non-responders. The identified epitope also includes residue W917, which is unique for human C5 and explains the observed lack of cross-reactivity for eculizumab with other primates. We could demonstrate that Ornithodorus moubata complement inhibitor (OmCI), in contrast to eculizumab, maintained anti-haemolytic function for mutations in any of the six epitope residues, thus representing a possible alternative treatment for patients non-responsive to eculizumab. The method for stratification of patients described here allows for precision medicine and should be applicable to several other diseases and therapeutics.
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| 40. |
- Willander, Hanna, et al.
(author)
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High-resolution structure of a BRICHOS domain and its implications for anti-amyloid chaperone activity on lung surfactant protein C
- 2012
-
In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 109:7, s. 2325-2329
-
Journal article (peer-reviewed)abstract
- BRICHOS domains are encoded in >30 human genes, which are associated with cancer, neurodegeneration, and interstitial lung disease (ILD). The BRICHOS domain from lung surfactant protein C proprotein (proSP-C) is required for membrane insertion of SP-C and has anti-amyloid activity in vitro. Here, we report the 2.1 angstrom crystal structure of the human proSP-C BRICHOS domain, which, together with molecular dynamics simulations and hydrogen-deuterium exchange mass spectrometry, reveals how BRICHOS domains may mediate chaperone activity. Observation of amyloid deposits composed of mature SP-C in lung tissue samples from ILD patients with mutations in the BRICHOS domain or in its peptide-binding linker region supports the in vivo relevance of the proposed mechanism. The results indicate that ILD mutations interfering with proSP-C BRICHOS activity cause amyloid disease secondary to intramolecular chaperone malfunction.
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