Psoriasis Symptom Inventory (PSI) as a patient-reported outcome in mild psoriasis: Real life data from a large psoriatic arthritis registry

Objective: Our aim is to test the validity of the Psoriasis Symptom Inventory (PSI), a patient-reported outcome, to assess the psoriasis severity within the scope of rheumatology. Methods: Within the PsA international database (PSART-ID), 571 patients had PSI, while 322 of these also showed body surface area (BSA). Correlations between PSI, BSA, and other patient- and physician-reported outcomes were investigated. Results: There was a good correlation between PSI and BSA (r=0.546, p<0.001), which was even higher for mild psoriasis (BSA<3 (n=164): T-0.608, p<0.001). PSI significantly correlated with fatigue, pain, and patient and physician global parameters (p<0.001). Conclusion: PSI has a good correlation with other patient- and physician-reported outcomes, and our findings support its use in rheumatology practice

Sensitive detection of glucagon aggregation using amyloid fibril‐specific antibodies

Sensitive detection of protein aggregates is important for evaluating the quality of biopharmaceuticals and detecting misfolded proteins in several neurodegenerative diseases. However, it is challenging to detect extremely low concentrations (20 times more sensitive than detection using a conventional, amyloid‐specific fluorescent dye (Thioflavin T). We expect that this type of sensitive immunoassay can be readily integrated into the drug development process to improve the generation of safe and potent peptide therapeutics.Sensitive detection of protein aggregates is important for evaluating the quality of biopharmaceuticals and detecting misfolded proteins in several neurodegenerative diseases. However, it is challenging to detect extremely low concentrations (20 times more sensitive than conventional methods for detecting glucagon fibrils.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/150615/1/bit26994_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/150615/2/bit26994.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/150615/3/bit26994-sup-0001-Supporting_Information__submission_.pd

Prevalence and risk factors of allergies in turkey (PARFAIT): Results of a multicentre cross-sectional study in adults

The Prevalence and Risk Factors of Allergies in Turkey (PARFAIT) study was planned to evaluate the prevalence of and risk factors for asthma and allergic diseases in Turkey. The present analysis used data from 25,843 parents of primary school children, obtained from a cross-sectional questionnaire-based study. A total of 25,843 questionnaires from 14 centres were evaluated. In rural areas, the prevalences asthma, wheezing, allergic rhinitis and eczema in males were: 8.5% (95% confidence interval (CI) 7.9-9.1%), 13.5% (95% CI 12.8-14.2%), 17.5% (95% CI 16.7-18.2%) and 10.8% (95% CI 10.211.4%), respectively; and in females were: 11.2% (95% CI 10.9-11.8%), 14.7% (95% CI 14.315.1%), 21.2% (95% CI 20.4-22.0%) and 13.1% (95% CI 2.4-13.8%), respectively. In urban areas, the corresponding prevalences in males were: 6.2% (95% CI 5.8-6.6%), 10.8% (95% CI 10.311.3%), 11.7% (95% CI 11.4-12.0%) and 6.6% (95% CI 6.2-7.0%), respectively; and in females were: 7.5 % (95% CI 7.9-7.1%), 12.0% (95% CI 11.7-12.3%), 17.0% (95% CI 16.4-17.6%) and 7.3% (95% CI 6.9-7.7%), respectively. Having an atopic first-degree relative or any other atopic diseases had significant effects on the prevalence of allergic diseases. Housing conditions, such as living in a shanty-type house, visible moulds at home and use of wood or biomass as heating or cooking material were associated with one or more allergic diseases. Although genetic susceptibility is strongly associated, country-and population-based environmental factors may contribute to increased prevalence rates of allergic diseases. Copyright © ERS Journals Ltd 2009

Structural and functional characterization of an intramembrane peptidase and a non-peptidase homolog

Peptidases play fundamental roles in all living organisms and their dysfunction is associated with a variety of diseases. Although sequences of peptidases encoded in genomes throughout life have become readily available via high throughput sequencing technologies, research on their structural and functional characterizations lags behind due to challenges related to their crystallization and time-intensive biochemical/biophysical studies. Signal Peptide Peptidase (SPP) is an intramembrane aspartyl peptidase that cleaves signal peptides within the hydrophobic region of cellular membrane. SPP plays important roles in cellular functions such as immune system regulation. Structural characterization of membrane proteins including SPP is challenging due to their hydrophobic content which prevents crystallization. Structures of membrane proteins are severely underrepresented: number of unique membrane protein structures is still less than 1% in Protein Data Bank. Here, a new generalizable method was introduced to overcome crystallization challenge of membrane proteins. A toolbox of single chain antibody fragments (scFvs) specific to the EYMPME peptide (EE) epitope was developed for use as co-crystallization chaperones. Structures of all designed scFvs were solved and their crystallization propensities were systematically explored to improve their chaperone abilities. Tight complexation of anti-EE scFvs with EE-tagged SPP and another test membrane protein was demonstrated. Important lessons learned during crystallization and co-crystallization trials of scFvs and SPP are discussed in this dissertation. To understand peptidases at a mechanistic level requires both high resolution structures and extensive structure-function studies in which residues are systematically altered and differences in functionality of the peptidase are measured. Although a low resolution structure of inactive SPP became available during my PhD studies, details on how SPP recognizes and catalyzes its substrate are still not known. Here, preliminary data for a structure-function study to understand substrate gating mechanism of SPP are presented. Finally, structure-function studies of 5-nitroanthralinic acid aminohydrolase (5NAA-A), a metallo-peptidase family member that catalyzes a deamination reaction on a natural, toxic nitroaromatic compound, are presented. 5NAA-A has evolved a function other than peptide hydrolysis but is structurally and evolutionary related to peptidases and is thus classified as a non-peptidase homolog. We characterized 5NAA-A biochemically and biophysically, and obtained snapshots of its mechanism by solving its crystal structures in various states. The 5NAA-A structure and its nucleophilic aromatic substitution mechanism expand our understanding of the great diversity of enzymes capable of transforming natural organic compounds in our ecosystem.Ph.D

Protein engineering approaches for antibody fragments: directed evolution and rational design approaches

The number of therapeutic antibodies in preclinical, clinical, or approved phases has been increasing exponentially, mostly due to their known successes. Development of antibody engineering methods has substantially hastened the development of therapeutic antibodies. A variety of protein engineering techniques can be applied to antibodies to improve their affinity and/or biophysical properties such as solubility and stability. Antibody fragments (where all or some parts of constant regions are eliminated while the essential antigen binding region is preserved) are more suitable for protein engineering techniques because there are many in vitro screening technologies available for antibody fragments but not full-length antibodies. Improvement of biophysical characteristics is important in the early development phase because most antibodies fail at the later stage of development and this leads to loss of resources and time. Here, we review directed evolution and rational design methods to improve antibody properties. Recent developments in rational design approaches and antibody display technologies, and especially phage display, which was recently awarded the 2018 Nobel Prize, are discussed to be used in antibody research and development

Conformational changes in a Vernier zone region: Implications for antibody dual specificity

Understanding the determinants of antibody specificity is one of the challenging tasks in antibody development. Monospecific antibodies are still dominant in approved antibody therapeutics but there is a significant body of work to show that multispecific antibodies can increase the overall therapeutic effect. Dual-specific or "Two-in-One" antibodies can bind to two different antigens separately with the same antigen-binding site as opposed to bispecifics, which simultaneously bind to two different antigens through separate antigen-binding units. These nonstandard dual-specific antibodies were recently shown to be promising for new antibody-based therapeutics. Here, we physicochemically and structurally analyzed six different antibodies of which two are monospecific and four are dual-specific antibodies derived from monospecific templates to gain insight about dual-specificity determinants. These dual-specific antibodies can target both human epidermal growth factor receptor 2 and vascular endothelial growth factor at different binding affinities. We showed that a particular region of clustered Vernier zone residues might play key roles in gaining dual specificity. While there are minimal intramolecular interactions between a certain Vernier zone region, namely LV4 and LCDR1 of monospecific template, there is a significant structural change and consequently close contact formation between LV4-LCDR1 loops of derived dual-specific antibodies. Although Vernier zone residues were previously shown to be important for humanization applications, they are mostly underestimated in the literature. Here, we also aim to resurrect Vernier zone residues for antibody engineering efforts

Phage display derived therapeutic antibodies have enriched aliphatic content: Insights for developability issues

Phage display is one of the most widely used technology for antibody discovery and engineering. Number of therapeutic antibodies derived from phage display increases rapidly due to its ease of use and ability to control antibody sequence information. Although there are numerous antibody candidates as promising therapeutics, most of them fail at later stages of development due to undesired biophysical properties. Antibody candidates with poor properties should be prevented or improved in early development phases to minimize enormous loss of time and resources. In this study, we showed that phage display derived therapeutic antibodies show higher self-interaction and polyspecificity compared to non-phage display derived ones. To identify molecular determinants behind this, physicochemical properties of CDR regions of 137 therapeutic antibodies were analyzed. We found multiple significant differences in both heavy and light chain CDR regions. Most profoundly, aliphatic content of HCDR3, HCDR2, and LCDR3 regions were enriched in phage display derived antibodies compared to non-phage display derived ones. Physicochemical determinants documented here seem to play important roles in polyspecific and aggregation-prone natures of antibodies which should be avoided in early development phases