Anti-drug antibodies in patients with multiple sclerosis

Multiple sclerosis (MS) is an inflammatory disease affecting the brain and spinal cord and it is the main cause of neurological disability among young adults. Recombinant interferon beta (IFNβ) and natalizumab are commonly used disease-modifying drugs that reduce disease severity. Even though these treatments show beneficial clinical effects they are associated with the development of anti-drug antibodies (ADAs), which at high titer levels reduce drug efficacy. Although ADAs are known to adversely affect the clinical effect of the treatment on a group level, the treatment response in individual patients is less characterized. In addition, it is unknown why only a subgroup of treated MS patients develops ADAs. The objective of this thesis was to identify biologically relevant ADA titer cut-points that can be used to predict treatment response and persistence of ADAs in individual patients, and to investigate if genetic and immunological factors influence the development of ADAs in MS patients. MS patients analyzed for the presence of ADAs against IFNβ or natalizumab in the routine NAb laboratory at Karolinska Institutet were included in this project. In Sweden, NAb monitoring became clinical practice in 2003 and during 2003-2004 the overall seroprevalence of neutralizing antibodies (NAbs) against IFNβ was 32%. When the NAb seroprevalence was analyzed five years later, in 2009-2010, the overall frequency of NAb-positive patients had decreased significantly to 19%. Importantly, the greatest reduction was observed in patients with high NAb titers (study I). By correlating the in vivo IFNβ bioactivity with patients’ NAb titers we identified that a NAb titer of 150 TRU/ml is a biologically functional cut-point for treatment response, since titers above 150 TRU/ml completely block IFNβ bioactivity (study II). Furthermore, characterization of ADA responses in natalizumab-treated patients revealed that the level of total anti-natalizumab antibodies in a first positive sample can be used to predict patients at risk of becoming persistently antibody positive (study V). It is known that factors such as protein modifications and/or impurities impact the immunogenicity of IFNβ, which can explain the variation in NAb positivity between IFNβ preparations. In addition, since only a subgroup of IFNβ-treated patients develops NAbs, patient-related factors are likely to influence the immunogenicity of IFNβ. In study III, we hypothesized that MS patients with and without intrathecal production of oligoclonal IgG bands (OCB) have different propensities to induce humoral immune responses. The presence of OCB was found to be associated with NAb development, and this risk was confined to NAbs against IFNβ-1a. From these results we proposed that MS patients with and without OCB differ immunologically, potentially influenced by distinct human leukocyte antigen (HLA) alleles. The role of HLA in the immunogenicity of IFNβ was further investigated in study IV, in which we found that HLA-DRB1*15 carriage was associated with increased risk of developing NAbs. Stratification on type of IFNβ preparation showed that HLA-DRB1*15 increased the risk of NAbs against IFNβ-1a, while HLA-DRB1*04 increased the risk of NAbs against IFNβ-1b, indicating that there is an IFNβ preparation-specific genetically determined risk to develop NAbs. Overall, these results can be used to assist when making decisions about whether treatment should be discontinued or not. In addition, the identification of factors contributing to the immunogenicity of protein therapeutics can increase our understanding of the immunological mechanisms leading to ADA responses, possibly resulting in less immunogenic drugs in the future

Swedish employment policy after EU-membership

'Dieser Artikel argumentiert, dass die Koordinierte Strategie nationaler Beschäftigungspolitiken in der EU trotz ihres pragmatischen neo-liberalen Charakters Schweden nicht hindert, seine traditionelle selektive Arbeitsmarktpolitik fortzusetzen. Andere Aspekte der europäischen Integration, und hier insbesondere die makroökonomische Konvergenz im Rahmen der Europäischen Währungsunion, haben sich allerdings deutlich auf die schwedische Beschäftigungspolitik ausgewirkt. Es ist zu dramatischen Veränderungen des schwedischen post-industriellen Wachstumspfades sowie des wohlfahrtsstaatlichen Regimes gekommen. Allerdings bleiben wichtige Elemente des alten schwedischen Modells erhalten, und dieser Artikel schließt mit einer Vorschau über seine Überlebenschancen in der Zukunft.' (Autorenreferat)'The article argues that whilst the Coordinated Strategy of National Employment Policies of the EU (CSNEP) is primarily informed by a pragmatic neo-liberalism, it does not as such prevent Sweden from pursuing its traditional selective labour market policy. However, other aspects of European integration, especially macroeconomic convergence towards the EMS and the EMU have had profound effects on Swedish employment policy, and it has led to a dramatic shift in Sweden's post-industrial growth trajectory and welfare policy regime. Nevertheless, significant elements of the old Swedish model remain, and the article concludes by discussing future prospects of these.' (author's abstract

Globally solving the Gromov-Wasserstein problem for point clouds in low dimensional Euclidean spaces

This paper presents a framework for computing the Gromov-Wasserstein problem between two sets of points in low dimensional spaces, where the discrepancy is the squared Euclidean norm. The Gromov-Wasserstein problem is a generalization of the optimal transport problem that finds the assignment between two sets preserving pairwise distances as much as possible. This can be used to quantify the similarity between two formations or shapes, a common problem in AI and machine learning. The problem can be formulated as a Quadratic Assignment Problem (QAP), which is in general computationally intractable even for small problems. Our framework addresses this challenge by reformulating the QAP as an optimization problem with a low-dimensional domain, leveraging the fact that the problem can be expressed as a concave quadratic optimization problem with low rank. The method scales well with the number of points, and it can be used to find the global solution for large-scale problems with thousands of points. We compare the computational complexity of our approach with state-of-the-art methods on synthetic problems and apply it to a near-symmetrical problem which is of particular interest in computational biology.Comment: 20 pages, 5 figure

Identification and classification of human cytomegalovirus capsids in textured electron micrographs using deformed template matching

BACKGROUND: Characterization of the structural morphology of virus particles in electron micrographs is a complex task, but desirable in connection with investigation of the maturation process and detection of changes in viral particle morphology in response to the effect of a mutation or antiviral drugs being applied. Therefore, we have here developed a procedure for describing and classifying virus particle forms in electron micrographs, based on determination of the invariant characteristics of the projection of a given virus structure. The template for the virus particle is created on the basis of information obtained from a small training set of electron micrographs and is then employed to classify and quantify similar structures of interest in an unlimited number of electron micrographs by a process of correlation. RESULTS: Practical application of the method is demonstrated by the ability to locate three diverse classes of virus particles in transmission electron micrographs of fibroblasts infected with human cytomegalovirus. These results show that fast screening of the total number of viral structures at different stages of maturation in a large set of electron micrographs, a task that is otherwise both time-consuming and tedious for the expert, can be accomplished rapidly and reliably with our automated procedure. Using linear deformation analysis, this novel algorithm described here can handle capsid variations such as ellipticity and furthermore allows evaluation of properties such as the size and orientation of a virus particle. CONCLUSION: Our methodological procedure represents a promising objective tool for comparative studies of the intracellular assembly processes of virus particles using electron microscopy in combination with our digitized image analysis tool. An automated method for sorting and classifying virus particles at different stages of maturation will enable us to quantify virus production in all stages of the virus maturation process, not only count the number of infectious particles released from un infected cell

Clinical practice of analysis of anti-drug antibodies against interferon beta and natalizumab in multiple sclerosis patients in Europe: A descriptive study of test results

Antibodies; Interferon beta; Multiple sclerosisAnticossos; Interferó beta; Esclerosi múltipleAnticuerpos; Interferón beta; Esclerosis múltipleAntibodies against biopharmaceuticals (anti-drug antibodies, ADA) have been a well-integrated part of the clinical care of multiple sclerosis (MS) in several European countries. ADA data generated in Europe during the more than 10 years of ADA monitoring in MS patients treated with interferon beta (IFNβ) and natalizumab have been pooled and characterized through collaboration within a European consortium. The aim of this study was to report on the clinical practice of ADA testing in Europe, considering the number of ADA tests performed and type of ADA assays used, and to determine the frequency of ADA testing against the different drug preparations in different countries. A common database platform (tranSMART) for querying, analyzing and storing retrospective data of MS cohorts was set up to harmonize the data and compare results of ADA tests between different countries. Retrospective data from six countries (Sweden, Austria, Spain, Switzerland, Germany and Denmark) on 20,695 patients and on 42,555 samples were loaded into tranSMART including data points of age, gender, treatment, samples, and ADA results. The previously observed immunogenic difference among the four IFNβ preparations was confirmed in this large dataset. Decreased usage of the more immunogenic preparations IFNβ-1a subcutaneous (s.c.) and IFNβ-1b s.c. in favor of the least immunogenic preparation IFNβ-1a intramuscular (i.m.) was observed. The median time from treatment start to first ADA test correlated with time to first positive test. Shorter times were observed for IFNβ-1b-Extavia s.c. (0.99 and 0.94 years) and natalizumab (0.25 and 0.23 years), which were introduced on the market when ADA testing was already available, as compared to IFNβ-1a i.m. (1.41 and 2.27 years), IFNβ-1b-Betaferon s.c. (2.51 and 1.96 years) and IFNβ-1a s.c. (2.11 and 2.09 years) which were available years before routine testing began. A higher rate of anti-IFNβ ADA was observed in test samples taken from older patients. Testing for ADA varies between different European countries and is highly dependent on the policy within each country. For drugs where routine monitoring of ADA is not in place, there is a risk that some patients remain on treatment for several years despite ADA positivity. For drugs where a strategy of ADA testing is introduced with the release of the drug, there is a reduced risk of having ADA positive patients and thus of less efficient treatment. This indicates that potential savings in health cost might be achieved by routine analysis of ADA

Structural and Functional Insights Into the Role of BamD and BamE Within the \u3cem\u3eβ\u3c/em\u3e-Barrel Assembly Machinery in \u3cem\u3eNeisseria gonorrhoeae\u3c/em\u3e

The β-barrel assembly machinery (BAM) is a conserved multicomponent protein complex responsible for the biogenesis of β-barrel outer membrane proteins (OMPs) in Gram-negative bacteria. Given its role in the production of OMPs for survival and pathogenesis, BAM represents an attractive target for the development of therapeutic interventions, including drugs and vaccines against multidrug-resistant bacteria such as Neisseria gonorrhoeae. The first structure of BamA, the central component of BAM, was from N. gonorrhoeae, the etiological agent of the sexually transmitted disease gonorrhea. To aid in pharmaceutical targeting of BAM, we expanded our studies to BamD and BamE within BAM of this clinically relevant human pathogen. We found that the presence of BamD, but not BamE, is essential for gonococcal viability. However, BamE, but not BamD, was cell-surface–displayed under native conditions; however, in the absence of BamE, BamD indeed becomes surface-exposed. Loss of BamE altered cell envelope composition, leading to slower growth and an increase in both antibiotic susceptibility and formation of membrane vesicles containing greater amounts of vaccine antigens. Both BamD and BamE are expressed in diverse gonococcal isolates, under host-relevant conditions, and throughout different phases of growth. The solved structures of Neisseria BamD and BamE share overall folds with Escherichia coli proteins but contain differences that may be important for function. Together, these studies highlight that, although BAM is conserved across Gram-negative bacteria, structural and functional differences do exist across species, which may be leveraged in the development of species-specific therapeutics in the effort to combat multidrug resistance

The splicing regulators Tra and Tra2 are unusually potent activators of pre-mRNA splicing

Sexual differentiation in Drosophila is regulated through alternative splicing of doublesex. Female-specific splicing is activated through the activity of splicing enhancer complexes assembled on multiple repeat elements. Each of these repeats serves as a binding platform for the cooperative assembly of a heterotrimeric complex consisting of the SR proteins Tra, Tra2 and 9G8. Using quantitative kinetic analyses, we demonstrate that each component of the enhancer complex is capable of recruiting the spliceosome. Surprisingly, Tra, Tra2 and 9G8 are much stronger splicing activators than other SR protein family members and their activation potential is significantly higher than expected from their serine/arginine content. 9G8 activates splicing not only through its RS domains but also through its RNA-binding domain. The RS domains of Tra and Tra2 are required but not sufficient for efficient complex assembly. Thus, the regulated assembly of the dsx enhancer complexes leads to the generation of an extended activation domain to guarantee the ‘all or none’ splicing switch that is required during Drosophila sexual differentiation