Characterization of a novel Ser/Thr kinase/phosphatase pair in Escherichia coli

Regulatory protein phosphorylation is a well conserved mechanism of signal transduction in all biological systems. In bacteria, signal transduction by phosphorylation is thought to occur primarily on His and Asp residues. However, phosphoproteomic surveys in phylogenetically diverse bacteria over the past decade have identified numerous proteins that are phosphorylated on serine (Ser) and/or threonine (Thr) residues. Consistently, genes encoding Ser/Thr kinases are present in many bacterial genomes such as E. coli, which encodes at least three Ser/Thr kinases. Since Ser/Thr phosphorylation is a stable modification, a dedicated phosphatase is necessary to allow reversible regulation. Bacterial Ser/Thr phosphatases which have extensive sequence and structural homology to eukaryotic Ser/Thr PP2C-type phosphatases are referred to as eukaryotic-like Ser/Thr phosphatases (eSTPs). eSTPs have been identified in a number of bacteria, but none have been reported in E. coli. The work presented in this thesis was aimed at identifying and biochemically characterizing a eukaryotic-like Ser/Thr phosphatase and its partner Ser/Thr kinase in E.coli. Chapter 3 describes the identification of a novel PP2C-like Ser/Thr phosphatase PphC encoded by an E. coli ORF, yegK, and characterization of its biochemical properties including kinetics, substrate specificity and sensitivity to known phosphatase inhibitors. I investigated differences in the activity of this protein in closely related E. coli strains. Finally, I demonstrated that this eSTP acts to dephosphorylate a novel Ser/Thr kinase which is encoded in the same operon suggesting that they most likely function as a pair in regulating Ser/Thr phosphorylation. Chapter 4 describes the biochemical characterization of a Ser/Thr kinase YegI in E. coli. I show that YegI is an active kinase with significant structural homology to eukaryotic Ser/Thr kinases. The YegI kinase domain is tethered to a cytoplasmic C-terminal domain containing two non-specific DNA binding Helix-hairpin helix motifs. I have identified enolase and elongation factor-Tu (EF-Tu) as potential physiological substrates of YegI and have demonstrated that phosphorylation of EF-Tu by YegI inhibits protein translation in vitro

Development and validation of the impact of dry eye on everyday life (IDEEL) questionnaire, a patient-reported outcomes (PRO) measure for the assessment of the burden of dry eye on patients

<p>Abstract</p> <p>Objective</p> <p>To develop and validate a comprehensive patient-reported outcomes instrument focusing on the impact of dry eye on everyday life (IDEEL).</p> <p>Methods</p> <p>Development and validation of the IDEEL occurred in four phases: 1) focus groups with 45 dry eye patients to develop a draft instrument, 2) item generation, 3) pilot study to assess content validity in 16 patients and 4) psychometric validation in 210 subjects: 130 with non-Sjögren's keratoconjunctivitis sicca, 32 with Sjögren's syndrome and 48 controls, and subsequent item reduction.</p> <p>Results</p> <p>Focus groups identified symptoms and the associated bother, the impact of dry eye on daily life and the patients' satisfaction with their treatment as the central concepts in patients' experience of dry eye. Qualitative analysis indicated that saturation was achieved for these concepts and yielded an initial 112-item draft instrument. Patients understood the questionnaire and found the items to be relevant indicating content validity. Patient input, item descriptive statistics and factor analysis identified 55 items that could be deleted. The final 57-item IDEEL assesses dry eye impact constituting 3 modules: dry eye symptom-bother, dry eye impact on daily life comprising impact on daily activities, emotional impact, impact on work, and dry eye treatment satisfaction comprising satisfaction with treatment effectiveness and treatment-related bother/inconvenience. The psychometric analysis results indicated that the IDEEL met the criteria for item discriminant validity, internal consistency reliability, test-retest reliability and floor/ceiling effects. As expected, the correlations between IDEEL and the Dry Eye Questionnaire (a habitual symptom questionnaire) were higher than between IDEEL and Short-Form-36 and EuroQoL-5D, indicating concurrent validity.</p> <p>Conclusion</p> <p>The IDEEL is a reliable, valid and comprehensive questionnaire relevant to issues that are specific to dry eye patients, and meets current FDA patient-reported outcomes guidelines. The use of this questionnaire will provide assessment of the impact of dry eye on patient dry eye-related quality of life, impact of treatment on patient outcomes in clinical trials, and may aid in treatment effectiveness evaluation.</p

Intrinsically disordered proteins and conformational noise: Implications in cancer

Intrinsically disordered proteins, IDPs, are proteins that lack a rigid 3D structure under physiological conditions, at least in vitro. Despite the lack of structure, IDPs play important roles in biological processes and transition from disorder to order upon binding to their targets. With multiple conformational states and rapid conformational dynamics, they engage in myriad and often “promiscuous” interactions. These stochastic interactions between IDPs and their partners, defined here as conformational noise, is an inherent characteristic of IDP interactions. The collective effect of conformational noise is an ensemble of protein network configurations, from which the most suitable can be explored in response to perturbations, conferring protein networks with remarkable flexibility and resilience. Moreover, the ubiquitous presence of IDPs as transcriptional factors and, more generally, as hubs in protein networks, is indicative of their role in propagation of transcriptional (genetic) noise. As effectors of transcriptional and conformational noise, IDPs rewire protein networks and unmask latent interactions in response to perturbations. Thus, noise-driven activation of latent pathways could underlie state-switching events such as cellular transformation in cancer. To test this hypothesis, we created a model of a protein network with the topological characteristics of a cancer protein network and tested its response to a perturbation in presence of IDP hubs and conformational noise. Because numerous IDPs are found to be epigenetic modifiers and chromatin remodelers, we hypothesize that they could further channel noise into stable, heritable genotypic changes

CETN1 is a cancer testis antigen with expression in prostate and pancreatic cancers

Background: The Cancer Testis Antigens (CTAs) are a group of genes that are highly expressed in the normal testis and several types of cancer. Due to their restricted expression in normal adult tissues, CTAs have been attractive targets for immunotherapy and biomarker development. In this work, we discovered that Centrin 1 (CETN1) which is found in the centrosome of all eukaryotes, may be a member of this group and is highly expressed in prostate and pancreatic cancer. Three members of the centrin family of calcium binding proteins (CETN) are localized to the centrosome in all eukaryotes with CDC31 being the sole yeast homolog. CETN1 is a retrogene that probably arose from a retrotransposition of CETN2, an X-linked gene. A previous mouse study shows that CETN1 is expressed solely in the testis, while CETN2 is expressed in all organs. Results: In this work, we show that CETN1 is a new member of the growing group of CTAs. Through the mining of publicly available microarray data, we discovered that human CETN1 expression but not CETN2 or CETN3 is restricted to the testis. In fact, CETN1 is actually down-regulated in testicular malignancies compared to normal testis. Using q-PCR, CETN1 expression is shown to be highly up-regulated in cancer of the prostate and in pancreatic xenografts. Unexpectedly however, CETN1 expression was virtually absent in various cell lines until they were treated with the DNA demethylation agent 5’AZA-2’Deoxycytidine (AZA) but showed no increased expression upon incubation with Histone deacetylase inhibitor Trichostatin-A (TSA) alone. Additionally, like most CTAs, CETN1 appears to be an intrinsically disordered protein which implies that it may occupy a hub position in key protein interaction networks in cancer. Neither CETN1 nor CETN2 could compensate for loss of CDC31 expression in yeast which is analogous to published data for CETN3. Conclusions: This work suggests that CETN1 is a novel CTA with expression in cancer of the prostate and pancreas. In cell lines, the expression is probably regulated by promoter methylation, while the method of regulation in normal adult tissues remains unknown

Comparative Outcomes of Commonly Used Off-Label Atypical Antipsychotics in the Treatment of Dementia-Related Psychosis: A Network Meta-Analysis

Introduction Dementia-related psychosis (DRP) is characterized by hallucinations and delusions, which may increase the debilitating effects of underlying dementia. This network meta-analysis (NMA) evaluated the comparative efficacy, safety, and acceptability of atypical antipsychotics (AAPs) commonly used off label to treat DRP. Methods We included 22 eligible studies from a systematic literature review of AAPs (quetiapine, risperidone, olanzapine, aripiprazole, and brexpiprazole) used off label to treat DRP. Study outcomes were: (1) efficacy—neuropsychiatric inventory-nursing home (NPI-NH psychosis subscale), (2) safety—mortality, cerebrovascular events (CVAEs), and others (somnolence, falls, fractures, injuries, etc.), and (3) acceptability—discontinuations due to all causes, lack of efficacy, and adverse events (AEs). We used random-effects modeling to estimate pooled standardized mean differences (SMDs) for NPI-NH psychosis subscale scores and odds ratios (OR) for other dichotomous outcomes, with their respective 95% confidence intervals (CIs). Results Compared with placebo, aripiprazole (SMD − 0.12; 95% CI − 0.31, 0.06), and olanzapine (SMD − 0.17; 95% CI − 0.04; 0.02) demonstrated small, non-significant numerical improvements in NPI-NH psychosis scores (5 studies; n = 1891), while quetiapine (SMD 0.04; 95% CI − 0.23, 0.32) did not improve symptoms. The odds of mortality (15 studies, n = 4989) were higher for aripiprazole (OR 1.58; 95% CI 0.62, 4.04), brexpiprazole (OR 2.22; 95% CI 0.30, 16.56), olanzapine (OR 2.21; 95% CI 0.84, 5.85), quetiapine (OR 1.68; 95% CI 0.70, 4.03), and risperidone (OR 1.63; 95% CI 0.93, 2.85) than for placebo. Risperidone (OR 3.68; 95% CI 1.68, 8.95) and olanzapine (OR 4.47; 95% CI 1.36, 14.69) demonstrated significantly greater odds of CVAEs compared to placebo. Compared with placebo, odds of all-cause discontinuation were significantly lower for aripiprazole (OR 0.71; 95% CI 0.51, 0.98; 20 studies; 5744 patients) and higher for other AAPs. Aripiprazole (OR 0.5; 95% CI 0.31, 0.82) and olanzapine (OR 0.48; 95% CI 0.31, 0.74) had significantly lower odds of discontinuation due to lack of efficacy (OR 12 studies; n = 4382) compared to placebo, while results for quetiapine and risperidone were not significant. Compared with placebo, the odds of discontinuation due to AEs (19 studies, n = 5445) were higher for olanzapine (OR 2.62; 95% CI 1.75, 3.92), brexpiprazole (OR 1.80; 95% CI 0.80, 4.07), quetiapine (OR 1.25; 95% CI 0.82, 1.91), aripiprazole (OR 1.38; 95% CI 0.90, 2.13), and risperidone (OR 1.41; 95% CI 1.02, 1.94). Conclusions Overall results demonstrate that, compared with placebo, quetiapine is not associated with improvement in psychosis in patients with dementia, while olanzapine and aripiprazole have non-significant small numerical improvements. These off-label AAPs (quetiapine, risperidone, olanzapine, aripiprazole, and brexpiprazole) are associated with greater odds of mortality, CVAEs, and discontinuations due to AEs than placebo. These results underscore the ongoing unmet need for newer pharmacological options with a more favorable benefit-risk profile for the treatment of DRP

Cancer/testis antigens and obligate participation in multiple hallmarks of cancer: an update

The Cancer/Testis Antigens (CTAs) are a group of so-called tumor antigens that exhibit provocative expression patterns in most types of cancer. However, because most CTAs appear to be intrinsically disordered, they are recalcitrant to classical structural studies. Thus, the functions of most, if not all, CTAs have remained elusive and their potential as pharmacological targets in cancer has remained largely unexplored. In this viewpoint, we suggest that perhaps, an integrative approach applying dynamical systems theory and a system-level perspective rather a merely reductionist view, may shine new light on these enigmatic molecules