Revised simulation model does not predict rebound in gonorrhoea prevalence where core groups are treated in the presence of antimicrobial resistance.

OBJECTIVES: To determine the effects of using discrete versus continuous quantities of people in a compartmental model examining the contribution of antimicrobial resistance (AMR) to rebound in the prevalence of gonorrhoea. METHODS: A previously published transmission model was reconfigured to represent the occurrence of gonorrhoea in discrete persons, rather than allowing fractions of infected individuals during simulations. RESULTS: In the revised model, prevalence only rebounded under scenarios reproduced from the original paper when AMR occurrence was increased by 10(5) times. In such situations, treatment of high-risk individuals yielded outcomes very similar to those resulting from treatment of low-risk and intermediate-risk individuals. Otherwise, in contrast with the original model, prevalence was the lowest when the high-risk group was treated, supporting the current policy of targeting treatment to high-risk groups. CONCLUSIONS: Simulation models can be highly sensitive to structural features. Small differences in structure and parameters can substantially influence predicted outcomes and policy prescriptions, and must be carefully considered.

Defining the specificity of cotranslationally acting chaperones by systematic analysis of mRNAs associated with ribosome-nascent chain complexes.

Polypeptides exiting the ribosome must fold and assemble in the crowded environment of the cell. Chaperones and other protein homeostasis factors interact with newly translated polypeptides to facilitate their folding and correct localization. Despite the extensive efforts, little is known about the specificity of the chaperones and other factors that bind nascent polypeptides. To address this question we present an approach that systematically identifies cotranslational chaperone substrates through the mRNAs associated with ribosome-nascent chain-chaperone complexes. We here focused on two Saccharomyces cerevisiae chaperones: the Signal Recognition Particle (SRP), which acts cotranslationally to target proteins to the ER, and the Nascent chain Associated Complex (NAC), whose function has been elusive. Our results provide new insights into SRP selectivity and reveal that NAC is a general cotranslational chaperone. We found surprising differential substrate specificity for the three subunits of NAC, which appear to recognize distinct features within nascent chains. Our results also revealed a partial overlap between the sets of nascent polypeptides that interact with NAC and SRP, respectively, and showed that NAC modulates SRP specificity and fidelity in vivo. These findings give us new insight into the dynamic interplay of chaperones acting on nascent chains. The strategy we used should be generally applicable to mapping the specificity, interplay, and dynamics of the cotranslational protein homeostasis network.

Necrobiotic xanthogranuloma without a monoclonal gammopathy.

Necrobiotic xanthogranuloma (NXG) is an indolent non-Langerhans cell histiocytosis characterized by yellow xanthomatous plaques that tend to ulcerate. Necrobiotic xanthogranulomas have a predilection for the bilateral periorbital region and often present with consequential ophthalmic findings. Histopathology usually reveals a distinctive pattern of histiocytic xanthogranuloma with hyaline necrobiosis. Necrobiotic xanthogranuloma has been documented to have a close association with paraproteinemia. We report the case of a 76-year-old man with periorbital NXG without development of a monoclonal gammopathy. Clinically, the patient presented with dry eyes and substantial periorbital edema with multiple yellow indurated plaques. He developed the condition 30 years prior to presentation at which time it was initially diagnosed as xanthelasma. He underwent surgical excision of the lesions 10 years prior to the current presentation and biopsy results revealed a diagnosis of NXG. The periorbital lesions recurred several years prior to presentation, prompting annual computed tomography scans to rule out ocular invasion. Periorbital edema and plaques improved during a 6-month regimen of acitretin but returned to baseline just months after discontinuation.

The safety of immunosuppressants in the treatment of psoriasis patients: is there concern regarding those with familial lymphoproliferative disease?

Immunosuppressant drugs may increase the risk of lymphoproliferative disease (LPD) states, and additionally, the diagnosis of psoriasis may predispose to lymphoma. It is important to educate patients regarding the side effects of any treatment regimen. A positive family history of LPD disease may increase the risk of personal acquisition of LPD disease in those patients with psoriasis additionally making use of immunosuppressant therapy, such as the biologics. It is currently recommended to employ caution in those being treated with biologics who carry a high risk of developing malignancy. Those with a positive family history may fit into this category.

Concordant regulation of translation and mRNA abundance for hundreds of targets of a human microRNA.

MicroRNAs (miRNAs) regulate gene expression posttranscriptionally by interfering with a target mRNA's translation, stability, or both. We sought to dissect the respective contributions of translational inhibition and mRNA decay to microRNA regulation. We identified direct targets of a specific miRNA, miR-124, by virtue of their association with Argonaute proteins, core components of miRNA effector complexes, in response to miR-124 transfection in human tissue culture cells. In parallel, we assessed mRNA levels and obtained translation profiles using a novel global approach to analyze polysomes separated on sucrose gradients. Analysis of translation profiles for approximately 8,000 genes in these proliferative human cells revealed that basic features of translation are similar to those previously observed in rapidly growing Saccharomyces cerevisiae. For approximately 600 mRNAs specifically recruited to Argonaute proteins by miR-124, we found reductions in both the mRNA abundance and inferred translation rate spanning a large dynamic range. The changes in mRNA levels of these miR-124 targets were larger than the changes in translation, with average decreases of 35% and 12%, respectively. Further, there was no identifiable subgroup of mRNA targets for which the translational response was dominant. Both ribosome occupancy (the fraction of a given gene's transcripts associated with ribosomes) and ribosome density (the average number of ribosomes bound per unit length of coding sequence) were selectively reduced for hundreds of miR-124 targets by the presence of miR-124. Changes in protein abundance inferred from the observed changes in mRNA abundance and translation profiles closely matched changes directly determined by Western analysis for 11 of 12 proteins, suggesting that our assays captured most of miR-124-mediated regulation. These results suggest that miRNAs inhibit translation initiation or stimulate ribosome drop-off preferentially near the start site and are not consistent with inhibition of polypeptide elongation, or nascent polypeptide degradation contributing significantly to miRNA-mediated regulation in proliferating HEK293T cells. The observation of concordant changes in mRNA abundance and translational rate for hundreds of miR-124 targets is consistent with a functional link between these two regulatory outcomes of miRNA targeting, and the well-documented interrelationship between translation and mRNA decay.

Cost, utilization, and patterns of medication use associated with chronic idiopathic urticaria.

BACKGROUND: The literature on chronic idiopathic urticaria (CIU) lacks large-scale population-based studies. OBJECTIVE: To characterize an insured population with CIU, including their demographic characteristics and comorbidities. METHODS: We conducted a cross-sectional analysis using insurance claims. We included patients with 1 outpatient claim with an International Classification of Diseases, 9(th)Edition, Clinical Modification (ICD-9-CM) code for idiopathic, other specified, or unspecified urticaria (ICD-9-CM 708.1, 708.8, or 708.9) and either (1) another of these claims 6 or more weeks later; (2) a claim for angioedema (ICD-9-CM 995.1) 6 or more weeks from the urticaria diagnosis; or (3) overlapping claims for 2 prescription medications commonly used for CIU. RESULTS: We identified 6,019 patients who had claims consistent with CIU. The mean age was 36 years. Fifty-six percent of patients had primary care physicians as their usual source of care, 14% had allergists, and 5% had dermatologists. Allergic rhinitis was diagnosed in 48%, asthma in 21%, other allergy in 19%, and atopic dermatitis in 8%. Sixty-seven percent of patients used prescription antihistamines, 54% used oral corticosteroids (OCSs), 24% used montelukast, and 9% used oral doxepin. Antihistamine users received a mean of 152 days of prescription antihistamines, OCS users 30 days of OCSs, montelukast users 190 days of montelukast, and oral doxepin users 94 days of doxepin. CONCLUSIONS: Primary care physicians managed most patients with CIU. Antihistamines were the most common treatment for CIU, although OCSs were frequently prescribed. Thirty days of OCS supply among users may represent multiple steroid bursts each year. Given the known risks of OCSs, identifying other CIU treatments with more favorable safety profiles may be beneficial.

Phototoxic and photoallergic potential of tazarotene foam 0.1% in 2 phase 1 patch studies.

Two phase 1 patch studies were conducted to evaluate tazarotene foam 0.1% for phototoxic (study A) and photoallergic (study B) potential. In study A, 38 participants were exposed to patches containing tazarotene foam 0.1%, vehicle foam, or no foam (blank patch) over 24 hours. One set each was exposed to UV irradiation, UV and visible (VIS) light, and no irradiation. In study B, 59 participants received patches containing tazarotene foam 0.1% and vehicle foam; sites were exposed to UVB irradiation and VIS light after each application during the induction phase. After 10 to 17 days, participants received both UVA and UVA/UVB irradiation, UVA/UVB plus VIS irradiation, or no irradiation during the challenge phase. Erythema grades and local skin reactions did not differ systematically by study product or across patch sites, and no pattern of increased reactivity at tazarotene foam 0.1% sites was observed. None of the participants demonstrated conclusive photoallergic reactions. Findings suggest that tazarotene foam 0.1% is not a major photoirritant and has a low potential for phototoxic or photoallergic reactions.

Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system.

RNA-binding proteins (RBPs) have roles in the regulation of many post-transcriptional steps in gene expression, but relatively few RBPs have been systematically studied. We searched for the RNA targets of 40 proteins in the yeast Saccharomyces cerevisiae: a selective sample of the approximately 600 annotated and predicted RBPs, as well as several proteins not annotated as RBPs. At least 33 of these 40 proteins, including three of the four proteins that were not previously known or predicted to be RBPs, were reproducibly associated with specific sets of a few to several hundred RNAs. Remarkably, many of the RBPs we studied bound mRNAs whose protein products share identifiable functional or cytotopic features. We identified specific sequences or predicted structures significantly enriched in target mRNAs of 16 RBPs. These potential RNA-recognition elements were diverse in sequence, structure, and location: some were found predominantly in 3'-untranslated regions, others in 5'-untranslated regions, some in coding sequences, and many in two or more of these features. Although this study only examined a small fraction of the universe of yeast RBPs, 70% of the mRNA transcriptome had significant associations with at least one of these RBPs, and on average, each distinct yeast mRNA interacted with three of the RBPs, suggesting the potential for a rich, multidimensional network of regulation. These results strongly suggest that combinatorial binding of RBPs to specific recognition elements in mRNAs is a pervasive mechanism for multi-dimensional regulation of their post-transcriptional fate.

Gene Set Analysis: Challenges, Opportunities, and Future Research.

Gene set analysis methods are widely used to provide insight into high-throughput gene expression data. There are many gene set analysis methods available. These methods rely on various assumptions and have different requirements, strengths and weaknesses. In this paper, we classify gene set analysis methods based on their components, describe the underlying requirements and assumptions for each class, and provide directions for future research in developing and evaluating gene set analysis methods.

Molecular and Immunologic Signatures are Related to Clinical Benefit from Treatment with Vocimagene Amiretrorepvec (Toca 511) and 5-Fluorocytosine (Toca FC) in Patients with Glioma.

PURPOSE: High-grade gliomas (HGGs) are central nervous system tumors with poor prognoses and limited treatment options. Vocimagene amiretrorepvec (Toca 511) is a retroviral replicating vector encoding cytosine deaminase, which converts extended release 5-fluorocytosine (Toca FC) into the anticancer agent, 5-fluorouracil. According to preclinical studies, this therapy kills cancer cells and immunosuppressive myeloid cells in the tumor microenvironment, leading to T-cell-mediated antitumor immune activity. Therefore, we sought to elucidate this immune-related mechanism of action in humans, and to investigate potential molecular and immunologic indicators of clinical benefit from therapy. PATIENTS AND METHODS: In a phase I clinical trial (NCT01470794), patients with recurrent HGG treated with Toca 511 and Toca FC showed improved survival relative to historical controls, and some had durable complete responses to therapy. As a part of this trial, we performed whole-exome DNA sequencing, RNA-sequencing, and multiplex digital ELISA measurements on tumor and blood samples. RESULTS: Genetic analyses suggest mutations, copy-number variations, and neoantigens are linked to survival. Quantities of tumor immune infiltrates estimated by transcript abundance may potentially predict clinical outcomes. Peak values of cytokines in peripheral blood samples collected during and after therapy could indicate response. CONCLUSIONS: These results support an immune-related mechanism of action for Toca 511 and Toca FC, and suggest that molecular and immunologic signatures are related to clinical benefit from treatment.

Measuring consistency among gene set analysis methods: A systematic study.

Gene set analysis is a quantitative approach for generating biological insight from gene expression datasets. The abundance of gene set analysis methods speaks to their popularity, but raises the question of the extent to which results are affected by the choice of method. Our systematic analysis of 13 popular methods using 6 different datasets, from both DNA microarray and RNA-Seq origin, shows that this choice matters a great deal. We observed that the overall number of gene sets reported by each method differed by up to 2 orders of magnitude, and there was a bias toward reporting large gene sets with some methods. Furthermore, there was substantial disagreement between the 20 most statistically significant gene sets reported by the methods. This was also observed when expanding to the 100 most statistically significant reported gene sets. For different datasets of the same phenotype/condition, the top 20 and top 100 most significant results also showed little to no agreement even when using the same method. GAGE, PAGE, and ORA were the only methods able to achieve relatively high reproducibility when comparing the 20 and 100 most statistically significant gene sets. Biological validation on a juvenile idiopathic arthritis (JIA) dataset showed wide variation in terms of the relevance of the top 20 and top 100 most significant gene sets to known biology of the disease, where GAGE predicted the most relevant gene sets, followed by GSEA, ORA, and PAGE.

Hydrocortisone butyrate 0.1% lotion in the treatment of atopic dermatitis in pediatric subjects.

BACKGROUND: Hydrocortisone butyrate (HCB) is currently marketed as a cream, ointment, and solution. A new lotion formulation of hydrocortisone butyrate 0.1% (Locoid lotion) has been developed and evaluated. OBJECTIVE: The objective of this study was to evaluate the efficacy and safety of HCB 0.1% lotion compared to the vehicle in subjects aged 3 months to less than 18 years with mild to moderate atopic dermatitis (AD). METHODS: In this multicenter double-blind study, 284 subjects with mild to moderate AD were randomized 1:1 to receive HCB 0.1% lotion or the vehicle for a duration of 4 weeks. "Treatment success" was defined as those subjects with a final Physician Global Assessment (PGA) score of 0 or 1 that had at least a 2-point reduction in the PGA score from baseline to day 29. Safety was assessed by monitoring adverse events. RESULTS: Analyses of the final PGA score showed a significant treatment effect (P <.001) in favor of the HCB 0.1% lotion group. The safety profile of the HCB 0.1% lotion was also favorable. LIMITATIONS: The study did not assess the durability of the treatment effects (ie, safety and efficacy) after completion of the 4-week treatment period nor the potential need for longer term therapy given the chronic nature of AD. CONCLUSION: Results demonstrate the safety and efficacy of HCB 0.1% lotion in the treatment of mild to moderate AD in children 3 months to 18 years of age.

Imiquimod-induced hypopigmentation following treatment of periungual verruca vulgaris.

Imiquimod is a topical immunomodulating medication approved by the US Food and Drug Administration for the treatment of condyloma acuminata, actinic keratoses (AKs), and superficial basal cell carcinoma (BCC). Imiquimod commonly is used off label for its antiviral and antitumoral effects. We present a case of a 51-year-old man with vitiligolike depigmentation following treatment of periungual verruca vulgaris with imiquimod therapy.

Basaloid Follicular Hamartoma: A Case Report and a Novel Cosmetic Treatment.

Introduction: Basaloid follicular hamartoma (BFH) is a rare, benign neoplasm of the hair follicle, characterized by multiple brown papules involving the face, scalp, and trunk. It is described by multiple clinical forms, and can present as localized or generalized. Diagnosis is made histologically via biopsy, which is important in order to distinguish BFH from basal cell carcinoma (BCC) or other malignant epithelial neoplasms. Correct diagnosis allows for the avoidance of unnecessary surgeries to remove benign lesions. While benign, lesions can be cosmetically unacceptable. Case Report: A 68-year-old man with a two-year history of brown, homogenous papules on his face presented to discuss treatment options. A physical examination revealed hundreds of dark brown, 1- to 3mm verrucous papules distributed throughout the face. Two punch biopsies revealed histologic features consistent with BFH. Discussion: BFHs classically present with multiple 1- to 2mm tan-to-brown-colored papules distributed on the face, scalp, neck, axilla, trunk, and pubic area. Differential diagnoses can include nevus sebaceous, lichen striatus, linear epidermal nevus, and basal cell nevus. BFH arises from a mutation in the patch gene, the same gene thought to cause nevoid BCC syndrome. Histologic examination of BFH lesions is essential to diagnosis. No standard of care exists for BFH; treatment options remain limited. This patient was treated with three rounds of pulsed dye laser (PDL) therapy and showed marked improvement in the treated areas. The authors propose PDL to be a safe, effective, and novel cosmetic treatment for BFH and potentially other adnexal tumors.

Determination of the presence of 5-methylcytosine in Paramecium tetraurelia.

5-methylcytosine DNA methylation regulates gene expression and developmental programming in a broad range of eukaryotes. However, its presence and potential roles in ciliates, complex single-celled eukaryotes with germline-somatic genome specialization via nuclear dimorphism, are largely uncharted. While canonical cytosine methyltransferases have not been discovered in published ciliate genomes, recent studies performed in the stichotrichous ciliate Oxytricha trifallax suggest de novo cytosine methylation during macronuclear development. In this study, we applied bisulfite genome sequencing, DNA mass spectrometry and antibody-based fluorescence detection to investigate the presence of DNA methylation in Paramecium tetraurelia. While the antibody-based methods suggest cytosine methylation, DNA mass spectrometry and bisulfite sequencing reveal that levels are actually below the limit of detection. Our results suggest that Paramecium does not utilize 5-methylcytosine DNA methylation as an integral part of its epigenetic arsenal.

Correction: Determination of the presence of 5-methylcytosine in Paramecium tetraurelia.

[This corrects the article DOI: 10.1371/journal.pone.0206667.].

Molecular Analyses Support the Safety and Activity of Retroviral Replicating Vector Toca 511 in Patients.

Purpose: Toca 511 is a gammaretroviral replicating vector encoding cytosine deaminase that selectively infects tumor cells and converts the antifungal drug 5-fluorocytosine into the antineoplastic drug 5-fluorouracil, which directly kills tumor cells and stimulates antitumor immune responses. As part of clinical monitoring of phase I clinical trials in recurrent high-grade glioma, we have performed extensive molecular analyses of patient specimens to track vector fate.Patients and Methods: Toca 511 and Toca FC (extended-release 5-fluorocytosine) have been administered to 127 high-grade glioma patients across three phase I studies. We measured Toca 511 RNA and DNA levels in available body fluids and tumor samples from patients to assess tumor specificity. We mapped Toca 511 integration sites and sequenced integrated Toca 511 genomes from patient samples with detectable virus. We measured Toca 511 levels in a diverse set of tissue samples from one patient.Results: Integrated Toca 511 is commonly detected in tumor samples and is only transiently detected in blood in a small fraction of patients. There was no believable evidence for clonal expansion of cells with integrated Toca 511 DNA, or preferential retrieval of integration sites near oncogenes. Toca 511 sequence profiles suggest most mutations are caused by APOBEC cytidine deaminases acting during reverse transcription. Tissue samples from a single whole-body autopsy affirm Toca 511 tumor selectivity.Conclusions: Toca 511 and Toca FC treatment was not associated with inappropriate integration sites and clonal expansion. The vector is tumor-selective and persistent in patients who received Toca 511 injections. Clin Cancer Res; 24(19); 4680-93. ©2018 AACR.

Durable complete responses in some recurrent high-grade glioma patients treated with Toca 511 + Toca FC.

Background: Vocimagene amiretrorepvec (Toca 511) is an investigational gamma-retroviral replicating vector encoding cytosine deaminase that, when used in combination with extended-release 5-fluorocytosine (Toca FC), results preclinically in local production of 5-fluorouracil, depletion of immune-suppressive myeloid cells, and subsequent induction of antitumor immunity. Recurrent high-grade glioma (rHGG) patients have a high unmet need for effective therapies that produce durable responses lasting more than 6 months. In this setting, relapse is nearly universal and most responses are transient. Methods: In this Toca 511 ascending-dose phase I trial (NCT01470794), HGG patients who recurred after standard of care underwent surgical resection and received Toca 511 injected into the resection cavity wall, followed by orally administered cycles of Toca FC. Results: Among 56 patients, durable complete responses were observed. A subgroup was identified based on Toca 511 dose and entry requirements for the follow-up phase III study. In this subgroup, which included both isocitrate dehydrogenase 1 (IDH1) mutant and wild-type tumors, the durable response rate is 21.7%. Median duration of follow-up for responders is 35.7+ months. As of August 25, 2017, all responders remain in response and are alive 33.9+ to 52.2+ months after Toca 511 administration, suggesting a positive association of durable response with overall survival. Conclusions: Multiyear durable responses have been observed in rHGG patients treated with Toca 511 + Toca FC in a phase I trial, and the treatment will be further evaluated in a randomized phase III trial. Among IDH1 mutant patients treated at first recurrence, there may be an enrichment of complete responders.

Preferential expression of scores of functionally and evolutionarily diverse DNA and RNA-binding proteins during Oxytricha trifallax macronuclear development.

During its sexual reproduction, the stichotrichous ciliate Oxytricha trifallax orchestrates a remarkable transformation of one of the newly formed germline micronuclear genomes. Hundreds of thousands of gene pieces are stitched together, excised from chromosomes, and replicated dozens of times to yield a functional somatic macronuclear genome composed of ~16,000 distinct DNA molecules that typically encode a single gene. Little is known about the proteins that carry out this process. We profiled mRNA expression as a function of macronuclear development and identified hundreds of mRNAs preferentially expressed at specific times during the program. We find that a disproportionate number of these mRNAs encode proteins that are involved in DNA and RNA functions. Many mRNAs preferentially expressed during macronuclear development have paralogs that are either expressed constitutively or are expressed at different times during macronuclear development, including many components of the RNA polymerase II machinery and homologous recombination complexes. Hundreds of macronuclear development-specific genes encode proteins that are well-conserved among multicellular eukaryotes, including many with links to germline functions or development. Our work implicates dozens of DNA and RNA-binding proteins with diverse evolutionary trajectories in macronuclear development in O. trifallax. It suggests functional connections between the process of macronuclear development in unicellular ciliates and germline specialization and differentiation in multicellular organisms, and argues that gene duplication is a key source of evolutionary innovation in this process.