The role of Alu elements in the cis-regulation of RNA processing

The human genome is under constant invasion by retrotransposable elements. The most successful of these are the Alu elements; with a copy number of over a million, they occupy about 10 % of the entire genome. Interestingly, the vast majority of these Alu insertions are located in gene-rich regions, and one-third of all human genes contains an Alu insertion. Alu sequences are often embedded in gene sequence encoding pre-mRNAs and mature mRNAs, usually as part of their intron or UTRs. Once transcribed, they can regulate gene expression as well as increase the number of RNA isoforms expressed in a tissue or a species. They also regulate the function of other RNAs, like microRNAs, circular RNAs, and potentially long non-coding RNAs. Mechanistically, Alu elements exert their effects by influencing diverse processes, such as RNA editing, exonization, and RNA processing. In so doing, they have undoubtedly had a profound effect on human evolution.

The measurement invariance of schizotypy in Europe

The short version of the Oxford-Liverpool Inventory of Feelings and Experiences (sO-LIFE) is a widely used measure assessing schizotypy. There is limited information, however, on how sO-LIFE scores compare across different countries. The main goal of the present study is to test the measurement invariance of the sO-LIFE scores in a large sample of non-clinical adolescents and young adults from four European countries (UK, Switzerland, Italy, and Spain). The scores were obtained from validated versions of the sO-LIFE in their respective languages. The sample comprised 4190 participants (M=20.87 years; SD=3.71 years). The study of the internal structure, using confirmatory factor analysis, revealed that both three (i.e., positive schizotypy, cognitive disorganisation, and introvertive anhedonia) and four-factor (i.e., positive schizotypy, cognitive disorganisation, introvertive anhedonia, and impulsive nonconformity) models fitted the data moderately well. Multi-group confirmatory factor analysis showed that the three-factor model had partial strong measurement invariance across countries. Eight items were non-invariant across samples. Significant statistical differences in the mean scores of the s-OLIFE were found by country. Reliability scores, estimated with Ordinal alpha ranged from 0.75 to 0.87. Using the Item Response Theory framework, the sO-LIFE provides more accuracy information at the medium and high end of the latent trait. The current results show further evidence in support of the psychometric proprieties of the sO-LIFE, provide new information about the cross-cultural equivalence of schizotypy and support the use of this measure to screen for psychotic-like features and liability to psychosis in general population samples from different European countries.

Information Technology for Clinical, Translational and Comparative Effectiveness Research. Findings from the Yearbook 2015 Section on Clinical Research Informatics

OBJECTIVES

To summarize excellent current research in the field of Bioinformatics and Translational Informatics with application in the health domain and clinical care.

METHOD

We provide a synopsis of the articles selected for the IMIA Yearbook 2015, from which we attempt to derive a synthetic overview of current and future activities in the field. As last year, a first step of selection was performed by querying MEDLINE with a list of MeSH descriptors completed by a list of terms adapted to the section. Each section editor has evaluated separately the set of 1,594 articles and the evaluation results were merged for retaining 15 articles for peer-review.

RESULTS

The selection and evaluation process of this Yearbook's section on Bioinformatics and Translational Informatics yielded four excellent articles regarding data management and genome medicine that are mainly tool-based papers. In the first article, the authors present PPISURV a tool for uncovering the role of specific genes in cancer survival outcome. The second article describes the classifier PredictSNP which combines six performing tools for predicting disease-related mutations. In the third article, by presenting a high-coverage map of the human proteome using high resolution mass spectrometry, the authors highlight the need for using mass spectrometry to complement genome annotation. The fourth article is also related to patient survival and decision support. The authors present datamining methods of large-scale datasets of past transplants. The objective is to identify chances of survival.

CONCLUSIONS

The current research activities still attest the continuous convergence of Bioinformatics and Medical Informatics, with a focus this year on dedicated tools and methods to advance clinical care. Indeed, there is a need for powerful tools for managing and interpreting complex, large-scale genomic and biological datasets, but also a need for user-friendly tools developed for the clinicians in their daily practice. All the recent research and development efforts contribute to the challenge of impacting clinically the obtained results towards a personalized medicine.

RNA editing of non-coding RNA and its role in gene regulation

It has for a long time been known that repetitive elements, particularly Alu sequences in human, are edited by the adenosine deaminases acting on RNA, ADAR, family. The functional interpretation of these events has been even more difficult than that of editing events in coding sequences, but today there is an emerging understanding of their downstream effects. A surprisingly large fraction of the human transcriptome contains inverted Alu repeats, often forming long double stranded structures in RNA transcripts, typically occurring in introns and UTRs of protein coding genes. Alu repeats are also common in other primates, and similar inverted repeats can frequently be found in non-primates, although the latter are less prone to duplex formation. In human, as many as 700,000 Alu elements have been identified as substrates for RNA editing, of which many are edited at several sites. In fact, recent advancements in transcriptome sequencing techniques and bioinformatics have revealed that the human editome comprises at least a hundred million adenosine to inosine (A-to-I) editing sites in Alu sequences. Although substantial additional efforts are required in order to map the editome, already present knowledge provides an excellent starting point for studying cis-regulation of editing. In this review, we will focus on editing of long stem loop structures in the human transcriptome and how it can effect gene expression.

Bridging data models and terminologies to support adverse drug event reporting using EHR data

INTRODUCTION

This article is part of the Focus Theme of METHODs of Information in Medicine on "Managing Interoperability and Complexity in Health Systems".

BACKGROUND

SALUS project aims at building an interoperability platform and a dedicated toolkit to enable secondary use of electronic health records (EHR) data for post marketing drug surveillance. An important component of this toolkit is a drug-related adverse events (AE) reporting system designed to facilitate and accelerate the reporting process using automatic prepopulation mechanisms.

OBJECTIVE

To demonstrate SALUS approach for establishing syntactic and semantic interoperability for AE reporting.

METHOD

Standard (e.g. HL7 CDA-CCD) and proprietary EHR data models are mapped to the E2B(R2) data model via SALUS Common Information Model. Terminology mapping and terminology reasoning services are designed to ensure the automatic conversion of source EHR terminologies (e.g. ICD-9-CM, ICD-10, LOINC or SNOMED-CT) to the target terminology MedDRA which is expected in AE reporting forms. A validated set of terminology mappings is used to ensure the reliability of the reasoning mechanisms.

RESULTS

The percentage of data elements of a standard E2B report that can be completed automatically has been estimated for two pilot sites. In the best scenario (i.e. the available fields in the EHR have actually been filled), only 36% (pilot site 1) and 38% (pilot site 2) of E2B data elements remain to be filled manually. In addition, most of these data elements shall not be filled in each report.

CONCLUSION

SALUS platform's interoperability solutions enable partial automation of the AE reporting process, which could contribute to improve current spontaneous reporting practices and reduce under-reporting, which is currently one major obstacle in the process of acquisition of pharmacovigilance data.

Information technology for clinical, translational and comparative effectiveness research. Findings from the section clinical research informatics

OBJECTIVE

To select and summarize key contributions to current research in the field of Clinical Research Informatics (CRI).

METHOD

A bibliographic search using a combination of MeSH and free terms search over PubMed was performed followed by a blinded review.

RESULTS

The review process resulted in the selection of four papers illustrating various aspects of current research efforts in the area of CRI. The first paper tackles the challenge of extracting accurate phenotypes from Electronic Healthcare Records (EHRs). Privacy protection within shared de-identified, patient-level research databases is the focus of the second selected paper. Two other papers exemplify the growing role of formal representation of clinical data - in metadata repositories - and knowledge - in ontologies - for supporting the process of reusing data for clinical research.

CONCLUSIONS

The selected articles demonstrate how concrete platforms are currently achieving interoperability across clinical research and care domains and have reached the evaluation phase. When EHRs linked to genetic data have the potential to shift the research focus from research driven patient recruitment to phenotyping in large population, a key issue is to lower patient re-identification risks for biomedical research databases. Current research illustrates the potential of knowledge engineering to support, in the coming years, the scientific lifecycle of clinical research.

Piloting the EHR4CR feasibility platform across Europe

BACKGROUND

Pharmaceutical clinical trials are primarily conducted across many countries, yet recruitment numbers are frequently not met in time. Electronic health records store large amounts of potentially useful data that could aid in this process. The EHR4CR project aims at re-using EHR data for clinical research purposes.

OBJECTIVE

To evaluate whether the protocol feasibility platform produced by the Electronic Health Records for Clinical Research (EHR4CR) project can be installed and set up in accordance with local technical and governance requirements to execute protocol feasibility queries uniformly across national borders.

METHODS

We installed specifically engineered software and warehouses at local sites. Approvals for data access and usage of the platform were acquired and terminology mapping of local site codes to central platform codes were performed. A test data set, or real EHR data where approvals were in place, were loaded into data warehouses. Test feasibility queries were created on a central component of the platform and sent to the local components at eleven university hospitals.

RESULTS

To use real, de-identified EHR data we obtained permissions and approvals from 'data controllers' and ethics committees. Through the platform we were able to create feasibility queries, distribute them to eleven university hospitals and retrieve aggregated patient counts of both test data and de-identified EHR data.

CONCLUSION

It is possible to install a uniform piece of software in different university hospitals in five European countries and configure it to the requirements of the local networks, while complying with local data protection regulations. We were also able set up ETL processes and data warehouses, to re-use EHR data for feasibility queries distributed over the EHR4CR platform.

Alu elements shape the primate transcriptome by cis-regulation of RNA editing

Background

RNA editing by adenosine to inosine deamination is a widespread phenomenon, particularly frequent in the human transcriptome, largely due to the presence of inverted Alu repeats and their ability to form double-stranded structures – a requisite for ADAR editing. While several hundred thousand editing sites have been identified within these primate-specific repeats, the function of Alu-editing has yet to be elucidated.

Results

We show that inverted Alu repeats, expressed in the primate brain, can induce site-selective editing in cis on sites located several hundred nucleotides from the Alu elements. Furthermore, a computational analysis, based on available RNA-seq data, finds that site-selective editing occurs significantly closer to edited Alu elements than expected. These targets are poorly edited upon deletion of the editing inducers, as well as in homologous transcripts from organisms lacking Alus. Sequences surrounding sites near edited Alus in UTRs, have been subjected to a lesser extent of evolutionary selection than those far from edited Alus, indicating that their editing generally depends on cis-acting Alus. Interestingly, we find an enrichment of primate-specific editing within encoded sequence or the UTRs of zinc finger-containing transcription factors.

Conclusions

We propose a model whereby primate-specific editing is induced by adjacent Alu elements that function as recruitment elements for the ADAR editing enzymes. The enrichment of site-selective editing with potentially functional consequences on the expression of transcription factors indicates that editing contributes more profoundly to the transcriptomic regulation and repertoire in primates than previously thought.

Abstract P3-15-06: Results of the MARS study on the management of antiangiogenics’ renovascular safety in breast cancer

Background:

Anti-VEGF drugs (AVD) are widely used in cancer patients (pts). Hypertension (HTN) and proteinuria (Pu) are class-side-effects of AVD, related to the inhibition of the VEGF pathway. The MARS study has been conducted to assess the renovascular tolerance of these drugs in the clinical setting.

Methods:

This multicentric, prospective, observational study evaluated the renovascular safety of AVD in pts naive from any AVD, conducted in 7 centres in France, from 2009 to 2012, with a follow-up (f/u) of 1 year. Data collected included: gender, age, serum creatinine (SCr), diabetes, HTN, hematuria (Hu) and dipstick Pu, at baseline and at each visit.

Results:

1124 cancer pts were included; 402 breast cancer (BC) pts received bevacizumab (1st line: 14.4%; median durations of treatment: months)). Median age at inclusion was 55 years (19-65). Visceral, bone and cerebral metastasis frequencies were 74.7, 5.1 and 2.5%, respectively. HTN prevalences: 12.4%. Baseline renal assessment retrieved: Pu 23.9%, Hu 16.2%, mean aMDRD 96.4 ml/min/1.73m2 and 14 pts with aMDRD<60. The incidence of de novo Pu and HTN during f/u was 61.7 and 16.8% (Table). 69.7% of pts with Pu at inclusion improved or remained stable. Among pts with de novo Pu, 75.7% afterwards improved/normalized. No grade 4 Pu has been reported. Renal function remained stable with a mean aMDRD of 96.2 at the end of f/u. 7.4% had grade 2-3 SCr increase (no grade 3-4). No thrombotic micro-angiopathy (TMA) was reported.

Conclusion:

These results on the renovascular safety of bevacizumab in BC pts showed that 1) TMA is rare, 2) Grade 3 Pu developed in 4.6% of pts, with no grade 4, 3) less than 17% developed HTN, and 4) aMDRD was stable. Furthermore, in case of a renovascular effect, investigators followed the recommendations from the French Society of Nephrology (Halimi JM. Nephrol Ther 2008) and no treatment withdrawal for unmanageable renovascular toxicity occurred.

Renovascular effects in MARS breast cancer patients treated with bevacizumabRenovascular effectsPrevalence at inclusionIncidence during follow-up (de novo**)Pu* (All grades)23.9%61.7%Pu* (Grade 1)22.2%47.1%Pu* (Grade 2)1.7%10.0%Pu* (Grade 3)0.0%4.6%Pu* (Grade 4)0.0%0.0%Hypertension12.4%16.8%Hu* (All Hu)16.2%42.1%Hu* (Traces/+)11.7%33.2%Hu* (++)2.6%6.3%Hu* (+++)1.9%2.6%SCr increase* (All grades)-80.0%SCr increase* (Grade 1)-68.6%SCr increase* (Grade 2)-7.1%SCr increase* (Grade 3)-0.3%*NCI-CTC v4; **de novo = patients with no event at inclusion and who presented an event during follow-up.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P3-15-06.

Electronic health records: new opportunities for clinical research

Clinical research is on the threshold of a new era in which electronic health records (EHRs) are gaining an important novel supporting role. Whilst EHRs used for routine clinical care have some limitations at present, as discussed in this review, new improved systems and emerging research infrastructures are being developed to ensure that EHRs can be used for secondary purposes such as clinical research, including the design and execution of clinical trials for new medicines. EHR systems should be able to exchange information through the use of recently published international standards for their interoperability and clinically validated information structures (such as archetypes and international health terminologies), to ensure consistent and more complete recording and sharing of data for various patient groups. Such systems will counteract the obstacles of differing clinical languages and styles of documentation as well as the recognized incompleteness of routine records. Here, we discuss some of the legal and ethical concerns of clinical research data reuse and technical security measures that can enable such research while protecting privacy. In the emerging research landscape, cooperation infrastructures are being built where research projects can utilize the availability of patient data from federated EHR systems from many different sites, as well as in international multilingual settings. Amongst several initiatives described, the EHR4CR project offers a promising method for clinical research. One of the first achievements of this project was the development of a protocol feasibility prototype which is used for finding patients eligible for clinical trials from multiple sources.

Information Technology for Clinical, Translational and Comparative Effectiveness Research

Objectives: To summarize advances of excellent current research in the new emerging field of Clinical Research Informatics.

Method: Synopsis of four key articles selected for the IMIA Yearbook 2013. The selection was performed by querying PubMed and Web of Science with predefined keywords. From the original set of 590 papers, a first subset of 461 articles which was in the scope of Clinical Research Informatics was refined into a second subset of 79 relevant articles from which 15 articles were retained for peer-review.

Results: The four selected articles exemplify current research efforts conducted in the areas of data representation and management in clinical trials, secondary use of EHR data for clinical research, information technology platforms for translational and comparative effectiveness research and implementation of privacy control.

Conclusions: The selected articles not only illustrate how innovative information technology supports classically organized randomized controlled trials but also demonstrate that the long promised benefits of electronic health care data for research are becoming a reality through concrete platforms and projects.

Antiperlecan antibodies are novel accelerators of immune-mediated vascular injury

Acute vascular rejection (AVR) is characterized by immune-mediated vascular injury and heightened endothelial cell (EC) apoptosis. We reported previously that apoptotic ECs release a bioactive C-terminal fragment of perlecan referred to as LG3. Here, we tested the possibility that LG3 behaves as a neoantigen, fuelling the production of anti-LG3 antibodies of potential importance in regulating allograft vascular injury. We performed a case-control study in which we compared anti-LG3 IgG titers in kidney transplant recipients with AVR (n=15) versus those with acute tubulo-interstitial rejection (ATIR) (n=15) or stable graft function (n=30). Patients who experienced AVR had elevated anti-LG3 titers pre and posttransplantation compared to subjects with ATIR or stable graft function (p<0.05 for both mediators). Elevated pretransplant anti-LG3 titers (OR: 4.62, 95% CI: 1.08-19.72) and pretransplant donor-specific antibodies (DSA) (OR 4.79, 95% CI: 1.03-22.19) were both independently associated with AVR. To address the functional role of anti-LG3 antibodies in AVR, we turned to passive transfer of anti-LG3 antibodies in an animal model of vascular rejection based on orthotopic aortic transplantation between fully MHC-mismatched mice. Neointima formation, C4d deposition and allograft inflammation were significantly increased in recipients of an ischemic aortic allograft passively transferred with anti-LG3 antibodies. Collectively, these data identify anti-LG3 antibodies as novel accelerators of immune-mediated vascular injury and obliterative remodeling.

Information technology for clinical, translational and comparative effectiveness research. Findings from the section clinical research informatics

OBJECTIVES

To summarize advances of excellent current research in the new emerging field of Clinical Research Informatics.

METHOD

Synopsis of four key articles selected for the IMIA Yearbook 2013. The selection was performed by querying PubMed and Web of Science with predefined keywords. From the original set of 590 papers, a first subset of 461 articles which was in the scope of Clinical Research Informatics was refined into a second subset of 79 relevant articles from which 15 articles were retained for peer-review.

RESULTS

The four selected articles exemplify current research efforts conducted in the areas of data representation and management in clinical trials, secondary use of EHR data for clinical research, information technology platforms for translational and comparative effectiveness research and implementation of privacy control.

CONCLUSIONS

The selected articles not only illustrate how innovative information technology supports classically organized randomized controlled trials but also demonstrate that the long promised benefits of electronic health care data for research are becoming a reality through concrete platforms and projects.

Abstract P5-17-04: Management of Antiangiogenics' Renovascular Safety in breast cancer. Subgroup and intermediate results of the MARS Study

Background: Hypertension (HTN) and proteinuria (Pu) are class-side-effects of anti-VEGF drugs (AVD), related to the inhibition of the VEGF pathway. The MARS study has been conducted to assess the renovascular tolerance of these drugs in the clinical setting.

Methods: The MARS study is a multicentric prospective observational study of the renovascular safety of AVD in AVD-naive patients. in 7 centres from 2009 to 2011. There was no intervention on the choice of the AVD. Data collected included: gender, age, serum creatinine (SCr), diabetes, HTN, hematuria (Hu) and dipstick Pu. This sub-group analysis presents the intermediate results for the first 184 patients with breast cancer (BC) receiving bevacizumab who completed the 1-year follow-up (f/u) (out of 337 BC patients in total).

Results: All these 184 patients received bevacizumab (mean and median durations of treatment: 7.8 and 8 months, respectively). Median age at inclusion was 60 years. Bone, visceral and cerebral metastasis frequencies were 75.0, 52.2 and 7.1%, respectively. Diabetes and HTN prevalences were 4.3% and 10.3%, respectively. Baseline renal assessment retrieved: Pu 13.0%, Hu 8.2%, mean aMDRD 98.8 ml/min/1.73m2 and 1.1% had aMDRD&lt;60. The incidence of de novo Pu during f/u was 16.3% (Table). 58.3% of patients with Pu at inclusion improved. Among patients with de novo Pu, 42.3% afterwards improved/normalized. No grade 3/4 Pu has been reported and no hematuria. 12.7% developed HTN. In addition, renal function decreased by −3.4 ml/min/1.73m2/year and 4 patients had aMDRD&lt;60 at the end of f/u. 33.2% increased their SCr: 27.7% grade 1, 4.9% grade 2, and 0.5% grade 3. All patients with grade 2–3 returned to normal or grade 1 during f/u. No thrombotic micro-angiopathy has been reported.

Conclusion: These results show that 1) No thrombotic micro-angiopathy remains rare, 2) Pu developed in 16.3% of patients, with no grade 3/4, 3) less than 13% developed HTN, and 4) renal function was only slightly impaired with transient elevations in SCr. Furthermore, in case of a renovascular effect, investigators followed the recommendations from the French Society of Nephrology (Halimi JM et Al. Nephrol Ther 2008) and no treatment withdrawal for unmanageable renovascular toxicity occurred.

A distant cis acting intronic element induces site-selective RNA editing

Transcripts have been found to be site selectively edited from adenosine-to-inosine (A-to-I) in the mammalian brain, mostly in genes involved in neurotransmission. While A-to-I editing occurs at double-stranded structures, other structural requirements are largely unknown. We have investigated the requirements for editing at the I/M site in the Gabra-3 transcript of the GABA_A receptor. We identify an evolutionarily conserved intronic duplex, 150 nt downstream of the exonic hairpin where the I/M site resides, which is required for its editing. This is the first time a distant RNA structure has been shown to be important for A-to-I editing. We demonstrate that the element also can induce editing in related but normally not edited RNA sequences. In human, thousands of genes are edited in duplexes formed by inverted repeats in non-coding regions. It is likely that numerous such duplexes can induce editing of coding regions throughout the transcriptome.

[Pneumocystis jirovecii pneumonia in non-HIV infected patients: a study of 41 cases]

BACKGROUND

The increasing use of immunosuppressive and cytotoxic therapies leads to a growing number of opportunistic infections especially Pneumocystis jirovecii pneumonia (PCP). The purpose of our study was to describe the population involved, and to assess clinical, biological, and mortality data.

METHODS

We collected retrospectively the whole medical file of all PCP cases diagnosed in non-HIV infected patients, in two French University Hospitals in the last decade (1999-2009). Diagnosis was made on standard coloration and/or immunofluorescence analysis of bronchoalveolar lavage fluid (BAL).

RESULTS

Forty-one patients were included in the study, mean age 56 (±12.5) years, sex ratio 0.71 men/woman. Underlying diseases were as follow: 12 patients (29%) were renal transplant recipients, 13 (32%) were treated for solid cancers, and 16 (39%) suffered from various diseases (three allogenic bone-marrow transplantation, 11 hematological malignancies, one pulmonary transplantation, one vasculitis). Twelve patients died (i.e. 29%). Median lymphocyte count was 542/mm(3). More than 85% patients received corticosteroids at a median cumulative 6-month dose of 2700mg. Seven patients (17%) had a PCP prophylaxis. Clinical worsening at day 5 (P<0.003), poor control of the underlying disease (P<0.015), WHO performans status superior than 2 (P<0.025), high temperature (P<0.04), and high oxygen flow (P<0.042) were linked to a poor prognosis.

DISCUSSION/CONCLUSION

The prognosis factors found are mostly linked to the patients' clinical severity. We would like to highlight: first, near to 30% mortality rate, secondly, a lack of prophylaxis in 34 patients, reflecting the difficulty to define PCP's risk in non HIV-infected patients.

Neonatal colonization of mice with Lactobacillus plantarum producing the aeroallergen Bet v 1 biases towards Th1 and T-regulatory responses upon systemic sensitization

BACKGROUND

The use of recombinant lactic acid bacteria (LAB) as vehicles for mucosal delivery of recombinant allergens is an attractive concept for antigen-defined allergy prevention/treatment. Interventions with LAB are of increasing interest early in life when immune programming is initiated. Here, we investigated the effect of neonatal colonization with a recombinant LAB producing the major birch pollen allergen Bet v 1 in a murine model of type I allergy.

METHODS

We constructed a recombinant Lactobacillus (L.) plantarum NCIMB8826 strain constitutively producing Bet v 1 to be used for natural mother-to-offspring mono-colonization of germ-free BALB/c mice. Allergen-specific immunomodulatory effects of the colonization on humoral and cellular immune responses were investigated prior and after sensitization to Bet v 1.

RESULTS

Mono-colonization with the Bet v 1 producing L. plantarum induced a Th1-biased immune response at the cellular level, evident in IFN-γ production of splenocytes upon stimulation with Bet v 1. After sensitization with Bet v 1 these mice displayed suppressed IL-4 and IL-5 production in spleen and mesenteric lymph node cell cultures as well as decreased allergen-specific antibody responses (IgG1, IgG2a, and IgE) in sera. This suppression was associated with a significant up-regulation of the regulatory marker Foxp3 at the mRNA level in the spleen cells.

CONCLUSION

Intervention at birth with a live recombinant L. plantarum producing a clinically relevant allergen reduces experimental allergy and might therefore become an effective strategy for early intervention against the onset of allergic diseases.

Increased A-to-I RNA editing of the transcript for GABAA receptor subunit α3 during chick retinal development

Adenosine-to-inosine (A-to-I) RNA editing is a cotranscriptional or posttranscriptional gene regulatory mechanism that increases the diversity of the proteome in the nervous system. Recently, the transcript for GABA type A receptor subunit α3 was found to be subjected to RNA editing. The aim of this study was to determine if editing of the chicken α3 subunit transcript occurs in the retina and if the editing is temporally regulated during development. We also raised the question if editing of the α3 transcript was temporally associated with the suggested developmental shift from excitation to inhibition in the GABA system. The editing frequency was studied by using Sanger and Pyrosequencing, and to monitor the temporal aspects, we studied the messenger RNA expression of the GABAA receptor subunits and chloride pumps, known to be involved in the switch. The results showed that the chick α3 subunit was subjected to RNA editing, and its expression was restricted to cells in the inner nuclear and ganglion cell layer in the retina. The extent of editing increased during development (after embryonic days 8-9) concomitantly with an increase of expression of the chloride pump KCC2. Expression of several GABAA receptor subunits known to mediate synaptic GABA actions was upregulated at this time. We conclude that editing of the chick GABAA subunit α3 transcript in chick retina gives rise to an amino acid change that may be of importance in the switch from excitatory to inhibitory receptors.

Adenosine-to-inosine RNA editing affects trafficking of the gamma-aminobutyric acid type A (GABA(A)) receptor

Recoding by adenosine-to-inosine RNA editing plays an important role in diversifying proteins involved in neurotransmission. We have previously shown that the Gabra-3 transcript, coding for the α3 subunit of the GABA(A) receptor is edited in mouse, causing an isoleucine to methionine (I/M) change. Here we show that this editing event is evolutionarily conserved from human to chicken. Analyzing recombinant GABA(A) receptor subunits expressed in HEK293 cells, our results suggest that editing at the I/M site in α3 has functional consequences on receptor expression. We demonstrate that I/M editing reduces the cell surface and the total number of α3 subunits. The reduction in cell surface levels is independent of the subunit combination as it is observed for α3 in combination with either the β2 or the β3 subunit. Further, an amino acid substitution at the corresponding I/M site in the α1 subunit has a similar effect on cell surface presentation, indicating the importance of this site for receptor trafficking. We show that the I/M editing during brain development is inversely related to the α3 protein abundance. Our results suggest that editing controls trafficking of α3-containing receptors and may therefore facilitate the switch of subunit compositions during development as well as the subcellular distribution of α subunits in the adult brain.

Recognition and coupling of A-to-I edited sites are determined by the tertiary structure of the RNA

Adenosine-to-inosine (A-to-I) editing has been shown to be an important mechanism that increases protein diversity in the brain of organisms from human to fly. The family of ADAR enzymes converts some adenosines of RNA duplexes to inosines through hydrolytic deamination. The adenosine recognition mechanism is still largely unknown. Here, to investigate it, we analyzed a set of selectively edited substrates with a cluster of edited sites. We used a large set of individual transcripts sequenced by the 454 sequencing technique. On average, we analyzed 570 single transcripts per edited region at four different developmental stages from embryogenesis to adulthood. To our knowledge, this is the first time, large-scale sequencing has been used to determine synchronous editing events. We demonstrate that edited sites are only coupled within specific distances from each other. Furthermore, our results show that the coupled sites of editing are positioned on the same side of a helix, indicating that the three-dimensional structure is key in ADAR enzyme substrate recognition. Finally, we propose that editing by the ADAR enzymes is initiated by their attraction to one principal site in the substrate.

Spin–orbit ab initio investigation of the UV photoinduced bond cleavage in iodotrimethylstannane

The photoinduced homolytic cleavage of the Sn–I bond in iodotrimethylstannane (CH3)3SnI, observed after UV irradiation, is investigated by means of spin–orbit ab initio calculations based on CASSCF (complete active space self-consistent field) and MS-CASPT2 (multi-state complete active space 2nd order perturbation theory) methods. The absorption electronic spectrum is characterized by ten low-lying 1,3A′ and 1,3A″ spin eigenstates corresponding to py(I),px(I) → σ*SnI; σSnI → σ*SnI and py(Sn), px(Sn) → σ*SnI, where σSnI and σ*SnI are the bonding and anti-bonding orbitals of the Sn–I bond along the pz axis. From the 1A′ electronic ground state and these ten spin eigenstates, 21 spin–orbit states are generated leading to various deactivation channels of (CH3)3SnI, corresponding to the formation of radicals (CH3)3Sn• and •I and to the ionic species (CH3)3Sn+ and I–. Irradiation into the upper band at 175 nm should lead to the heterolytic cleavage of the Sn–I bond to form the ionic primary products exclusively, whereas absorption into the shoulder at 250 nm induces the homolytic breaking with formation of the radical products.

[Anatomic pathology workflow. IHE: modeling based on current developments in HL7 and DICOM]

AIMS

Consistent and complete information is essential for medical decision making. Anatomic pathology as a diagnostic discipline has a central role in the exchange of information between clinical departments throughout the diagnostic process. The IHE (Integrating the Healthcare Enterprise) has created an integration profile for information systems based on HL7 and DICOM standards.

METHODS

Created by the IHE Anatomic Pathology working group, the integration profile (so-called Technical Framework) ensures the consistent management of data and material in the pathology laboratory information system (PLIS). HL7 and DICOM standards are taken into account. Communication processes both within and outside the institute are modelled using eight actors and 13 transactions.

RESULTS

The IHE's Technical Framework covers basic business processes, provision of diagnostic services and includes requesting examinations, as well as image and report management. In particular, a consistent data model for incoming material, containers, cartridges and slides has been developed and approved by the standards committee.

Large-scale mRNA sequencing determines global regulation of RNA editing during brain development

RNA editing by adenosine deamination has been shown to generate multiple isoforms of several neural receptors, often with profound effects on receptor function. However, little is known about the regulation of editing activity during development. We have developed a large-scale RNA sequencing protocol to determine adenosine-to-inosine (A-to-I) editing frequencies in the coding region of genes in the mammalian brain. Using the 454 Life Sciences (Roche) Amplicon Sequencing technology, we were able to determine even low levels of editing with high accuracy. The efficiency of editing for 28 different sites was analyzed during the development of the mouse brain from embryogenesis to adulthood. We show that, with few exceptions, the editing efficiency is low during embryogenesis, increasing gradually at different rates up to the adult mouse. The variation in editing gave receptors like HTR2C and GABA(A) (gamma-aminobutyric acid type A) a different set of protein isoforms during development from those in the adult animal. Furthermore, we show that this regulation of editing activity cannot be explained by an altered expression of the ADAR proteins but, rather, by the presence of a regulatory network that controls the editing activity during development.

Immunomodulatory properties of Lactobacillus plantarum and its use as a recombinant vaccine against mite allergy

BACKGROUND

Selected lactic acid bacteria were reported to prevent atopic dermatitis and experimental asthma but the mechanisms of their immunomodulatory effects are not fully elucidated. In this study, the signaling pathways triggered by Lactobacillus plantarum NCIMB8826 were investigated and the potential use of this strain producing a variant of the mite allergen Der p 1 as live vaccine vehicle was evaluated.

METHODS

Mouse bone marrow-derived dendritic cells were stimulated with wild-type or a L. plantarum teichoic acid mutant to evaluate the secretion of cytokines. A recombinant L. plantarum expressing Der p 1 was engineered, its in vitro immunomodulatory properties were characterized and its prophylactic potential was evaluated in a Der p 1-sensitization murine model.

RESULTS

Mouse dendritic cells stimulated by L. plantarum triggered the release of interleukin-10 (IL-10), IL-12 p40, IL-12 p70 and tumor necrosis factor-alpha (TNF-alpha). IL-12 p40 secretion was dependent on nuclear factor-kappaB (NF-kappaB), mitogen-activated protein (MAP) kinases, Toll-like receptor 2 (TLR2), TLR9 and on the bacterial teichoic acid composition. Recombinant L. plantarum producing Der p 1 exhibited similar immunostimulatory properties as wild-type. Prophylactic intranasal pretreatment of mice with this recombinant strain prevented the development of the typical Th2-biased allergic response by a drastic reduction of specific IgE and the induction of protective allergen-specific IgG2a antibodies. Moreover, both wild-type or recombinant L. plantarum reduced airway eosinophilia following aerosolized allergen exposure and IL-5 secretion upon allergen restimulation.

CONCLUSION

By combining both Th1-type immunostimulatory properties and an efficient allergen delivery capacity, recombinant L. plantarum producing Der p 1 represents a promising vaccine against house dust mite allergy.