Logic programming to infer complex RNA expression patterns from RNA-seq data.

To meet the increasing demand in the field, numerous long noncoding RNA (lncRNA) databases are available. Given many lncRNAs are specifically expressed in certain cell types and/or time-dependent manners, most lncRNA databases fall short of providing such profiles. We developed a strategy using logic programming to handle the complex organization of organs, their tissues and cell types as well as gender and developmental time points. To showcase this strategy, we introduce 'RenalDB' (http://renaldb.uni-frankfurt.de), a database providing expression profiles of RNAs in major organs focusing on kidney tissues and cells. RenalDB uses logic programming to describe complex anatomy, sample metadata and logical relationships defining expression, enrichment or specificity. We validated the content of RenalDB with biological experiments and functionally characterized two long intergenic noncoding RNAs: LOC440173 is important for cell growth or cell survival, whereas PAXIP1-AS1 is a regulator of cell death. We anticipate RenalDB will be used as a first step toward functional studies of lncRNAs in the kidney.

Airn Regulates Igf2bp2 Translation in Cardiomyocytes.

RATIONALE: Increasing evidence indicates the presence of lncRNAs in various cell types. Airn is an imprinting gene transcribed from the paternal chromosome. It is in antisense orientation to the imprinted, but maternally derived, Igf2r gene, on which Airn exerts its regulation in cis. Although Airn is highly expressed in the heart, functions aside from imprinting remain unknown. OBJECTIVE: Here, we studied the functions of Airn in the heart, especially cardiomyocytes. METHODS AND RESULTS: Silencing of Airn via siRNAs augmented cell death, vulnerability to cellular stress, and reduced cell migration. To find the cause of such phenotypes, the potential binding partners of Airn were identified via RNA pull-down followed by mass spectrometry, which indicated Igf2bp2 (insulin-like growth factor 2 mRNA-binding protein 2) and Rpa1 (replication protein A1) as potential binding partners. Further experiments showed that Airn binds to Igf2bp2 to control the translation of several genes. Moreover, silencing of Airn caused less binding of Igf2bp2 to other mRNAs and reduced translation of Igf2bp2 protein. CONCLUSIONS: Our study uncovers a new function of Airn and demonstrates that Airn is important for the physiology of cardiomyocytes.

Screening and validation of lncRNAs and circRNAs as miRNA sponges.

Intensive research in past two decades has uncovered the presence and importance of noncoding RNAs (ncRNAs), which includes microRNAs (miRs) and long ncRNAs (lncRNAs). These two classes of ncRNAs interact to a certain extent, as some lncRNAs bind to miRs to sequester them. Such lncRNAs are collectively called 'competing endogenous RNAs' or 'miRNA sponges'. In this study, we screened for lncRNAs that may act as miRNA sponges using the publicly available data sets and databases. To uncover the roles of miRNA sponges, loss-of-function experiments were conducted, which revealed the biological roles as miRNA sponges. LINC00324 is important for the cell survival by binding to miR-615-5p leading to the de-repression of its target BTG2. LOC400043 controls several biological functions via sequestering miR-28-3p and miR-96-5p, thereby changing the expressions of transcriptional regulators. Finally, we also screened for circular RNAs (circRNAs) that may function as miRNA sponges. The results were negative at least for the selected circRNAs in this study. In conclusion, miRNA sponges can be identified by applying a series of bioinformatics techniques and validated with biological experiments.

E2f1 deletion attenuates infarct-induced ventricular remodeling without affecting O-GlcNAcylation.

Several post-translational modifications figure prominently in ventricular remodeling. The beta-O-linkage of N-acetylglucosamine (O-GlcNAc) to proteins has emerged as an important signal in the cardiovascular system. Although there are limited insights about the regulation of the biosynthetic pathway that gives rise to the O-GlcNAc post-translational modification, much remains to be elucidated regarding the enzymes, such as O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA), which regulate the presence/absence of O-GlcNAcylation. Recently, we showed that the transcription factor, E2F1, could negatively regulate OGT and OGA expression in vitro. The present study sought to determine whether E2f1 deletion would improve post-infarct ventricular function by de-repressing expression of OGT and OGA. Male and female mice were subjected to non-reperfused myocardial infarction (MI) and followed for 1 or 4 week. MI significantly increased E2F1 expression. Deletion of E2f1 alone was not sufficient to alter OGT or OGA expression in a naïve setting. Cardiac dysfunction was significantly attenuated at 1-week post-MI in E2f1-ablated mice. During chronic heart failure, E2f1 deletion also attenuated cardiac dysfunction. Despite the improvement in function, OGT and OGA expression was not normalized and protein O-GlcNAcyltion was not changed at 1-week post-MI. OGA expression was significantly upregulated at 4-week post-MI but overall protein O-GlcNAcylation was not changed. As an alternative explanation, we also performed guided transcriptional profiling of predicted targets of E2F1, which indicated potential differences in cardiac metabolism, angiogenesis, and apoptosis. E2f1 ablation increased heart size and preserved remote zone capillary density at 1-week post-MI. During chronic heart failure, cardiomyocytes in the remote zone of E2f1-deleted hearts were larger than wildtype. These data indicate that, overall, E2f1 exerts a deleterious effect on ventricular remodeling. Thus, E2f1 deletion improves ventricular remodeling with limited impact on enzymes regulating O-GlcNAcylation.

The identification and characterization of novel transcripts from RNA-seq data.

Owing greatly to the advancement of next-generation sequencing (NGS), the amount of NGS data is increasing rapidly. Although there are many NGS applications, one of the most commonly used techniques 'RNA sequencing (RNA-seq)' is rapidly replacing microarray-based techniques in laboratories around the world. As more and more of such techniques are standardized, allowing technicians to perform these experiments with minimal hands-on time and reduced experimental/operator-dependent biases, the bottleneck of such techniques is clearly visible; that is, data analysis. Further complicating the matter, increasing evidence suggests most of the genome is transcribed into RNA; however, the majority of these RNAs are not translated into proteins. These RNAs that do not become proteins are called 'noncoding RNAs (ncRNAs)'. Although some time has passed since the discovery of ncRNAs, their annotations remain poor, making analysis of RNA-seq data challenging. Here, we examine the current limitations of RNA-seq analysis using case studies focused on the detection of novel transcripts and examination of their characteristics. Finally, we validate the presence of novel transcripts using biological experiments, showing novel transcripts can be accurately identified when a series of filters is applied. In conclusion, novel transcripts that are identified from RNA-seq must be examined carefully before proceeding to biological experiments.

Familial hypercholesterolemia class II low-density lipoprotein receptor response to statin treatment.

Low-density lipoprotein (LDL) receptor (LDLR) mutations are the primary cause of familial hypercholesterolemia (FH). Class II LDLR mutations result in a misfolded LDLR retained in the endoplasmic reticulum (ER). We have developed a model of FH class II and CRISPR-corrected induced pluripotent stem cells (iPSC) capable of replicating mutant and repaired LDLR functions. We show here that iPSC and derived hepatocyte-like cells (HLC) replicate misfolded LDLR accumulation and restoration of LDLR function in CRISPR-corrected cells. It was reported that model cells overexpressing class II LDLR mutants result in endoplasmic reticulum (ER) accumulation of immature LDLR and activation of the unfolded protein response (UPR). We show here that statins induce a similar accumulation of immature LDLR that is resolved with class II correction. We also demonstrate that, although capable of UPR induction with tunicamycin treatment, unlike overexpression models, statin-treated class II iPSC and derived HLC do not induce the common UPR markers Grp78 (also known as HSPA5) or spliced XBP1 [XBP1 (S)]. Because statins are reported to inhibit UPR, we utilized lipoprotein-deficient serum (LPDS) medium, but still did not detect UPR induction at the Grp78 and XBP1 (S) levels. Our study demonstrates the recapitulation of mutant and corrected class II LDLR function and suggests that overexpression models may not accurately predict statin-mediated class II protein biology.

Investigation of RNA Editing Sites within Bound Regions of RNA-Binding Proteins.

Studies in epitranscriptomics indicate that RNA is modified by a variety of enzymes. Among these RNA modifications, adenosine to inosine (A-to-I) RNA editing occurs frequently in the mammalian transcriptome. These RNA editing sites can be detected directly from RNA sequencing (RNA-seq) data by examining nucleotide changes from adenosine (A) to guanine (G), which substitutes for inosine (I). However, a careful investigation of such nucleotide changes must be conducted to distinguish sequencing errors and genomic mutations from the genuine editing sites. Building upon our recent introduction of an easy-to-use bioinformatics tool, RNA Editor, to detect RNA editing events from RNA-seq data, we examined the extent by which RNA editing events affect the binding of RNA-binding proteins (RBP). Through employing bioinformatic techniques, we uncovered that RNA editing sites occur frequently in RBP-bound regions. Moreover, the presence of RNA editing sites are more frequent when RNA editing islands were examined, which are regions in which RNA editing sites are present in clusters. When the binding of one RBP, human antigen R [HuR; encoded by ELAV-like protein 1 (ELAV1)], was quantified experimentally, its binding was reduced upon silencing of the RNA editing enzyme adenosine deaminases acting on RNA (ADAR) compared to the control-suggesting that the presence of RNA editing islands influence HuR binding to its target regions. These data indicate RNA editing as an important mediator of RBP-RNA interactions-a mechanism which likely constitutes an additional mode of post-transcription gene regulation in biological systems.

Cutaneous epithelioid hemangioendothelioma.

Epithelioid hemangioendothelioma (EHE) is a rare vascular tumor of endothelial cell origin. We describe an EHE arising on the plantar surface of the foot that was treated as verruca vulgaris for several years before a biopsy showed EHE. We discuss the clinical and histopathologic differential diagnoses for these tumors and review additional cases in which EHE has been mistaken for benign entities clinically.

Videodermoscopy: a useful tool for diagnosing congenital triangular alopecia.

Congenital triangular alopecia, despite its name, usually presents in children between 3 and 6 years of age, but adult patients have been reported. It is not uncommon for triangular alopecia to be misdiagnosed as alopecia areata and treated for such. This is especially true when a lesion of triangular alopecia presents in an area of the scalp other than the typical fronto-temporal hairline or later in adulthood. Videodermoscopy may serve as a useful tool to perform the right diagnosis as it can highlight signs not seen by the unaided eye and may be able to spare the patient from a biopsy.

Long Non-coding RNAs in Endothelial Biology.

In recent years, the role of RNA has expanded to the extent that protein-coding RNAs are now the minority with a variety of non-coding RNAs (ncRNAs) now comprising the majority of RNAs in higher organisms. A major contributor to this shift in understanding is RNA sequencing (RNA-seq), which allows a largely unconstrained method for monitoring the status of RNA from whole organisms down to a single cell. This observational power presents both challenges and new opportunities, which require specialized bioinformatics tools to extract knowledge from the data and the ability to reuse data for multiple studies. In this review, we summarize the current status of long non-coding RNA (lncRNA) research in endothelial biology. Then, we will cover computational methods for identifying, annotating, and characterizing lncRNAs in the heart, especially endothelial cells.

A novel long non-coding RNA Myolinc regulates myogenesis through TDP-43 and Filip1.

Myogenesis is a complex process required for skeletal muscle formation during embryonic development and for regeneration and growth of myofibers in adults. Accumulating evidence suggests that long non-coding RNAs (lncRNAs) play key roles in regulating cell fate decision and function in various tissues. However, the role of lncRNAs in the regulation of myogenesis remains poorly understood. In this study, we identified a novel muscle-enriched lncRNA called 'Myolinc (AK142388)', which we functionally characterized in the C2C12 myoblast cell line. Myolinc is predominately localized in the nucleus, and its levels increase upon induction of the differentiation. Knockdown of Myolinc impairs the expression of myogenic regulatory factors and formation of multi-nucleated myotubes in cultured myoblasts. Myolinc also regulates the expression of Filip1 in a cis-manner. Similar to Myolinc, knockdown of Filip1 inhibits myogenic differentiation. Furthermore, Myolinc binds to TAR DNA-binding protein 43 (TDP-43), a DNA/RNA-binding protein that regulates the expression of muscle genes (e.g. Acta1 and MyoD). Knockdown of TDP-43 inhibits myogenic differentiation. We also show that Myolinc-TDP-43 interaction is essential for the binding of TDP-43 to the promoter regions of muscle marker genes. Finally, we show that silencing of Myolinc inhibits skeletal muscle regeneration in adult mice. Altogether, our study identifies a novel lncRNA that controls key regulatory networks of myogenesis.

Allergic contact dermatitis caused by colophony in an epilating product.

Considering the widespread use of colophony-containing epilating products and the frequency of sensitization to colophony, it is somewhat surprising that reports of allergic contact dermatitis from these products are so infrequent. Reactions to colophony can be severe, and they may present even after initial exposure (primary sensitization). Consequently, health care practitioners should be aware of potential colophony-induced allergic contact dermatitis in patients exposed to epilating products. Patch testing with commercially available colophony unmodified rosins often fails to detect reactions to the modified-rosin derivatives found in the actual epilating products. Therefore, the evaluation of colophony allergy may require testing with the patient's own products as well as additional modified colophony rosins. We describe a case of allergic contact dermatitis caused by colophony found in an epilating product.

Etanercept for the treatment of psoriasis in the elderly.

This study's objective was to analyze the effect of etanercept on Psoriasis Area and Severity Index (PASI) 50, PASI 75, and Dermatology Life Quality Index in geriatric and nongeriatric populations. We conducted a post hoc analysis of two large phase III randomized placebo trials of etanercept. There were no statistically significant differences between the elderly and young with regard to the number of patients reaching a PASI 50 or PASI 75 at any of the 3 dosing regimens. Baseline Dermatology Life Quality Index scores were not statistically significant between both groups and both the elderly and young had similar changes in Dermatology Life Quality Index with therapy. A limitation of the study was the small number of patients in the elderly group. In conclusion, psoriasis and its treatment has a similar impact on quality of life in the elderly as it does in the young.

The utility of the TRUE test in a private practice setting.

BACKGROUND: Studies suggest that the Thin-Layer Rapid-Use Epicutaneous Test (TRUE Test) may be inadequate to completely diagnose a significant number of patients with allergic contact dermatitis (ACD). OBJECTIVE: To study the usefulness of the TRUE Test as a triage tool in a private practice setting. METHODS: A retrospective chart review of patients who were patch-tested with the TRUE Test between July 1, 2000, and June 30, 2004, in four private dermatology practices was conducted. RESULTS: Of the 183 patients evaluated, 50.8% had at least one positive reaction, 31.7% had a diagnosis of ACD, and 24.0% were suspected to have ACD from other allergens. Of the patients with positive reactions, 62.4% were determined to have reactions that were of present relevance. CONCLUSIONS: The TRUE Test allows patients with dermatitis to be triaged systematically in a private practice setting. It is important to supplement patch testing with the patients' personal products, especially in cases of facial or periorbital dermatitis, and to be aware of potential false negatives, particularly with fragrance and rubber additives.

ANGIOGENES: knowledge database for protein-coding and noncoding RNA genes in endothelial cells.

Increasing evidence indicates the presence of long noncoding RNAs (lncRNAs) is specific to various cell types. Although lncRNAs are speculated to be more numerous than protein-coding genes, the annotations of lncRNAs remain primitive due to the lack of well-structured schemes for their identification and description. Here, we introduce a new knowledge database "ANGIOGENES" (http://angiogenes.uni-frankfurt.de) to allow for in silico screening of protein-coding genes and lncRNAs expressed in various types of endothelial cells, which are present in all tissues. Using the latest annotations of protein-coding genes and lncRNAs, publicly-available RNA-seq data was analyzed to identify transcripts that are expressed in endothelial cells of human, mouse and zebrafish. The analyzed data were incorporated into ANGIOGENES to provide a one-stop-shop for transcriptomics data to facilitate further biological validation. ANGIOGENES is an intuitive and easy-to-use database to allow in silico screening of expressed, enriched and/or specific endothelial transcripts under various conditions. We anticipate that ANGIOGENES serves as a starting point for functional studies to elucidate the roles of protein-coding genes and lncRNAs in angiogenesis.

The CLASI (Cutaneous Lupus Erythematosus Disease Area and Severity Index): an outcome instrument for cutaneous lupus erythematosus.

We developed and validated a measurement instrument (CLASI-Cutaneous Lupus Erythematosus Disease Area and Severity Index) for lupus erythematosus that could be used in clinical trials. The instrument has separate scores for damage and activity. A group of seven American Dermato-Rheumatologists and the "American College of Rheumatology Response Criteria Committee on SLE (systemic lupus erythematosus)" assessed content validity. After a preliminary session, we conducted standardized interviews with the raters and made slight changes to the instrument. The final instrument was evaluated by five dermatologists and six residents who scored nine patients to estimate inter- and intra-rater reliability in two sessions. Consultation with experts has established content validity of the instrument. Reliability studies demonstrated an intra-class correlation coefficient (ICC) for inter-rater reliability of 0.86 for the activity score (95% confidence interval (CI) = 0.73-0.99) and of 0.92 for the damage score (95% CI = 0.85-1.00). The Spearman's rho (Sp) for intra-rater reliability for the activity score was 0.96 (95% CI = 0.89 to 1.00) and for the damage score Sp was 0.99 (95% CI = 0.97-1.00). Clinical responsiveness needs to be evaluated in a prospective clinical trial, which is ongoing.

Lyral: a fragrance allergen.

Fragrances are a common cause of contact dermatitis and account for a large percentage of reactions to cosmetic products. Novel fragrance compounds that may not be detected by the common fragrance screening agents (including balsam of Peru and fragrance mix) are continually being produced. Lyral is one of those allergens found in many cosmetic and household products. This review will discuss the recent literature and the significance of this allergen to allergic contact dermatitis.

Neoprene.

Neoprene is a synthetic rubber with many common uses, including use in shoe insoles and adhesives, orthopedic braces, and gloves. Many cases of type IV hypersensitivity from neoprene contact have been reported. Thioureas, the most commonly used vulcanization accelerators in the manufacture of neoprene, are responsible for the majority of these cases. However, thioureas are not included in the TRUE Test whereas the North American Contact Dermatitis Group standard tray contains only mixed dialkyl thioureas. Since most data indicate that many cases will be missed when only mixed dialkyl thioureas are used for screening, a more complete thiourea panel should be used when neoprene hypersensitivity is suspected.

Allergic contact dermatitis from isocyanates among sculptors.

Allergic contact dermatitis from isocyanates is rare. We present the cases of two sculptors who developed a dermatitis from polyurethane sculpting materials. The patients reacted to diphenylmethane diisocyanate and isophorone diisocyanate. One of the patients had positive patch-test reactions to 1,6-hexamethylene diisocyanate and toluene diisocyanate as well. The patients also exhibited a sensitivity to diaminodiphenylmethane, an amine that has been reported in other cases of isocyanate sensitivity.