Non-coding RNAs in saliva: emerging biomarkers for molecular diagnostics.

Saliva is a complex body fluid that comprises secretions from the major and minor salivary glands, which are extensively supplied by blood. Therefore, molecules such as proteins, DNA, RNA, etc., present in plasma could be also present in saliva. Many studies have reported that saliva body fluid can be useful for discriminating several oral diseases, but also systemic diseases including cancer. Most of these studies revealed messenger RNA (mRNA) and proteomic biomarker signatures rather than specific non-coding RNA (ncRNA) profiles. NcRNAs are emerging as new regulators of diverse biological functions, playing an important role in oncogenesis and tumor progression. Indeed, the small size of these molecules makes them very stable in different body fluids and not as susceptible as mRNAs to degradation by ribonucleases (RNases). Therefore, the development of a non-invasive salivary test, based on ncRNAs profiles, could have a significant applicability to clinical practice, not only by reducing the cost of the health system, but also by benefitting the patient. Here, we summarize the current status and clinical implications of the ncRNAs present in human saliva as a source of biological information

Guia clínica per a la prevenció de l'ictus

Les persones que es troben en situació de risc vascular elevat són més propenses a patir un ictus, la qual cosa pot provocar una discapacitat permanent o, fins i tot, la mort. Poder incidir en la prevenció precoç en aquelles persones que no l'han patit, i actuar de manera intensa en les que ja han sofert un ictus, és un dels objectius estratègics del Ministeri de Sanitat i Política Social en redactar una guia per a la promoció de la salut i la prevenció de malalties prevalents. Investigadors de la Universitat Autònoma de Barcelona han participat en la elaboració d'una versió breu sobre aquesta guia, publicada a Medicina Clínica.Las personas que se encuentran en situación de riesgo vascular elevado son más propensas a sufrir un ictus, lo cual puede provocar una discapacidad permanente o, incluso, la muerte. Poder incidir en la prevención precoz en aquellas personas que no lo han sufrido, y actuar de manera intensa en las que ya han sufrido un ictus, es uno de los objetivos estratégicos del Ministerio de Sanidad y Política Social al redactar una guía para la promoción de la salud y la prevención de enfermedades prevalentes. Investigadores de la Universitat Autònoma de Barcelona han participado en la elaboración de una versión breve sobre esta guía, publicada en Medicina Clínica

Interferon-gamma release assays for the diagnosis of tuberculosis and tuberculosis infection in HIV-infected adults: a systematic review and meta-analysis.

Background: Despite the widespread use of interferon-gamma release assays (IGRAs), their role in diagnosing tuberculosis and targeting preventive therapy in HIV-infected patients remains unclear. We conducted a comprehensive systematic review to contribute to the evidence-based practice in HIV-infected people. Methodology/Principal Findings: We searched MEDLINE, Cochrane, and Biomedicine databases to identify articles published between January 2005 and July 2011 that assessed QuantiFERON H -TB Gold In-Tube (QFT-GIT) and T-SPOT H .TB (T-SPOT.TB) in HIV-infected adults. We assessed their accuracy for the diagnosis of tuberculosis and incident active tuberculosis, and the proportion of indeterminate results. The search identified 38 evaluable studies covering a total of 6514 HIV-infected participants. The pooled sensitivity and specificity for tuberculosis were 61% and 72% for QFT-GIT, and 65% and 70% for T-SPOT.TB. The cumulative incidence of subsequent active tuberculosis was 8.3% for QFT-GIT and 10% for T-SPOT.TB in patients tested positive (one study each), and 0% for QFT-GIT (two studies) and T-SPOT.TB (one study) respectively in those tested negative. Pooled indeterminate rates were 8.2% for QFT-GIT and 5.9% for T-SPOT.TB. Rates were higher in high burden settings (12.0% for QFT-GIT and 7.7% for T-SPOT.TB) than in low-intermediate burden settings (3.9% for QFT-GIT and 4.3% for T-SPOT.TB). They were also higher in patients with CD4 + T-cell count, 200 (11.6% for QFT-GIT and 11.4% for T-SPOT.TB) than in those with CD4 + T-cell count $ 200 (3.1% for QFT-GIT and 7.9% for T-SPOT.TB). Conclusions/Significance: IGRAs have suboptimal accuracy for confirming or ruling out active tuberculosis disease in HIV-infected adults. While their predictive value for incident active tuberculosis is modest, a negative QFT-GIT implies a very low short- to medium-term risk. Identifying the factors associated with indeterminate results will help to optimize the use of IGRAs in clinical practice, particularly in resource-limited countries with a high prevalence of HIV-coinfection

Non-coding Rnas In Saliva: Emerging Biomarkers For Molecular Diagnostics

Saliva is a complex body fluid that comprises secretions from the major and minor salivary glands, which are extensively supplied by blood. Therefore, molecules such as proteins, DNA, RNA, etc., present in plasma could be also present in saliva. Many studies have reported that saliva body fluid can be useful for discriminating several oral diseases, but also systemic diseases including cancer. Most of these studies revealed messenger RNA (mRNA) and proteomic biomarker signatures rather than specific non-coding RNA (ncRNA) profiles. NcRNAs are emerging as new regulators of diverse biological functions, playing an important role in oncogenesis and tumor progression. Indeed, the small size of these molecules makes them very stable in different body fluids and not as susceptible as mRNAs to degradation by ribonucleases (RNases). Therefore, the development of a non-invasive salivary test, based on ncRNAs profiles, could have a significant applicability to clinical practice, not only by reducing the cost of the health system, but also by benefitting the patient. Here, we summarize the current status and clinical implications of the ncRNAs present in human saliva as a source of biological information

Loose ends: almost one in five human genes still have unresolved coding status

Seventeen years after the sequencing of the human genome, the human proteome is still under revision. One in eight of the 22 210 coding genes listed by the Ensembl/GENCODE, RefSeq and UniProtKB reference databases are annotated differently across the three sets. We have carried out an in-depth investigation on the 2764 genes classified as coding by one or more sets of manual curators and not coding by others. Data from large-scale genetic variation analyses suggests that most are not under protein-like purifying selection and so are unlikely to code for functional proteins. A further 1470 genes annotated as coding in all three reference sets have characteristics that are typical of non-coding genes or pseudogenes. These potential non-coding genes also appear to be undergoing neutral evolution and have considerably less supporting transcript and protein evidence than other coding genes. We believe that the three reference databases currently overestimate the number of human coding genes by at least 2000, complicating and adding noise to large-scale biomedical experiments. Determining which potential non-coding genes do not code for proteins is a difficult but vitally important task since the human reference proteome is a fundamental pillar of most basic research and supports almost all large-scale biomedical projects.National Institutes of Health [2 U41 HG007234 to I.J., L.M., J.M.R. and M.L.T., R01 HG004037 to I.J.]. Funding for open access charge: NIH [2 U41 HG007234].S

Quality Assessment of Clinical Practice Guidelines for the Prescription of Antidepressant Drugs During Pregnancy

Antidepressant use during the gestational period remains a controversial issue. The objective of this study was to appraise the quality of the available clinical practice guidelines (CPGs) that includes recommendations for antidepressant use during pregnancy. We systematically searched for documents published between January 2000 and September 2010 in MEDLINE / TRIP database and on clearinghouses and main scientific societies websites. Four appraisers evaluated each guideline using the Appraisal of Guidelines for Research and Evaluation tool (AGREE II). Intra-class correlation coefficients (ICC) with 95% confidence intervals (CI) were calculated as an overall indicator of agreement. Twelve CPGs were included from a total of 539 references. Only two guidelines were specifically addressed to pregnant women. The overall agreement among reviewers was high (ICC: 0.94, 95% CI: 0.86-0.98). The mean scores and standard deviation (SD) for each of the AGREE II domains were: scope and purpose: 84.4% (12); stakeholder involvement: 67.4% (29.8); rigor of development: 68.6% (19.8); clarity and presentation: 83.4% (17.4); applicability: 44% (37.3); and editorial independence: 62.1% (30.4). After standardizing the scores of the 12 guidelines, 5 were considered as being “recommended”, 5 as “recommended with modifications, and 2 as “not recommended”. Among the five recommended guidelines, two were specifically conceived to the gestational period. CPGs containing recommendations for antidepressant use during pregnancy were of moderate to high quality. Future guidelines should take into account the observed drawbacks in some domains, and specifically focus a more in depth approach of depression during pregnanc

APPRAISE-RS: Automated, updated, participatory, and personalized treatment recommender systems based on GRADE methodology

Attention deficit hyperactivity disorder; Evidence-based medicine; Meta-analysisTrastorn per dèficit d'atenció amb hiperactivitat; Medicina basada en l'evidència; MetaanàlisiTrastorno por déficit de atención con hiperactividad; Medicina basada en la evidencia; MetanálisisPurpose: Clinical practice guidelines (CPGs) have become fundamental tools for evidence-based medicine (EBM). However, CPG suffer from several limitations, including obsolescence, lack of applicability to many patients, and limited patient participation. This paper presents APPRAISE-RS, which is a methodology that we developed to overcome these limitations by automating, extending, and iterating the methodology that is most commonly used for building CPGs: the GRADE methodology.Method: APPRAISE-RS relies on updated information from clinical studies and adapts and automates the GRADE methodology to generate treatment recommendations. APPRAISE-RS provides personalized recommendations because they are based on the patient's individual characteristics. Moreover, both patients and clinicians express their personal preferences for treatment outcomes which are considered when making the recommendation (participatory). Rule-based system approaches are used to manage heuristic knowledge.Results: APPRAISE-RS has been implemented for attention deficit hyperactivity disorder (ADHD) and tested experimentally on 28 simulated patients. The resulting recommender system (APPRAISE-RS/TDApp) shows a higher degree of treatment personalization and patient participation than CPGs, while recommending the most frequent interventions in the largest body of evidence in the literature (EBM). Moreover, a comparison of the results with four blinded psychiatrist prescriptions supports the validation of the proposal.Conclusions: APPRAISE-RS is a valid methodology to build recommender systems that manage updated, personalized and participatory recommendations, which, in the case of ADHD includes at least one intervention that is identical or very similar to other drugs prescribed by psychiatrists.This work was supported by European Regional Development Fund (ERDF), the Spanish Ministry of the Economy, Industry and Competitiveness (MINECO) and the Carlos III Research Institute [PI19/00375], Fundació Pascual i Prats & Campus Salut, UdG [AIN2018E], Generalitat de Catalunya [2017 SGR 1551]

Characteristics and impact of interventions to support healthcare providers’ compliance with guideline recommendations for breast cancer: a systematic literature review

BackgroundBreast cancer clinical practice guidelines (CPGs) offer evidence-based recommendations to improve quality of healthcare for patients. Suboptimal compliance with breast cancer guideline recommendations remains frequent, and has been associated with a decreased survival. The aim of this systematic review was to characterize and determine the impact of available interventions to support healthcare providers' compliance with CPGs recommendations in breast cancer healthcare.MethodsWe searched for systematic reviews and primary studies in PubMed and Embase (from inception to May 2021). We included experimental and observational studies reporting on the use of interventions to support compliance with breast cancer CPGs. Eligibility assessment, data extraction and critical appraisal was conducted by one reviewer, and cross-checked by a second reviewer. Using the same approach, we synthesized the characteristics and the effects of the interventions by type of intervention (according to the EPOC taxonomy), and applied the GRADE framework to assess the certainty of evidence.ResultsWe identified 35 primary studies reporting on 24 different interventions. Most frequently described interventions consisted in computerized decision support systems (12 studies); educational interventions (seven), audit and feedback (two), and multifaceted interventions (nine). There is low quality evidence that educational interventions targeted to healthcare professionals may improve compliance with recommendations concerning breast cancer screening, diagnosis and treatment. There is moderate quality evidence that reminder systems for healthcare professionals improve compliance with recommendations concerning breast cancer screening. There is low quality evidence that multifaceted interventions may improve compliance with recommendations concerning breast cancer screening. The effectiveness of the remaining types of interventions identified have not been evaluated with appropriate study designs for such purpose. There is very limited data on the costs of implementing these interventions.ConclusionsDifferent types of interventions to support compliance with breast cancer CPGs recommendations are available, and most of them show positive effects. More robust trials are needed to strengthen the available evidence base concerning their efficacy. Gathering data on the costs of implementing the proposed interventions is needed to inform decisions about their widespread implementation

Endometrial Status in Queens Evaluated by Histopathology Findings and Two Cytological Techniques : low-volume uterine lavage and uterine swabbing

Endometritis is associated with fertility problems in many species, with endometrial biopsy being the main diagnostic tool. In feline queens, the reduced size of the uterus may make it difficult to obtain representative diagnostic samples. Endometrial cytology may represent a valuable diagnostic tool for evaluating the health status of the endometrium in queens. Fifty domestic shorthair queens were included and divided into two cytological diagnostic technique groups, the uterine lavage (UL; n = 28) and uterine swabbing (US; n = 22) groups. Cytological results were compared with histopathological and bacteriological information. Changes in the histopathological patterns were also evaluated and compared with progesterone levels to confirm previous published data. Furthermore, the results from both cytological sampling methods were compared to evaluate the utility of each method. Endometritis was ruled out in all queens by means of histology and microbiology. Leukocyte counts and red blood cell/endometrial cell ratios were significantly higher in US than UL samples. Additionally, UL sampling is less affected by blood contamination and cells are better preserved. The combination of endometrial cytology and uterine culture might be useful for evaluating the endometrial characteristics in queens. The UL evaluation method is more representative of the actual endometrial status than the US technique

3D chromatin connectivity underlies replication origin efficiency in mouse embryonic stem cells

In mammalian cells, chromosomal replication starts at thousands of origins at which replisomes are assembled. Replicative stress triggers additional initiation events from 'dormant' origins whose genomic distribution and regulation are not well understood. In this study, we have analyzed origin activity in mouse embryonic stem cells in the absence or presence of mild replicative stress induced by aphidicolin, a DNA polymerase inhibitor, or by deregulation of origin licensing factor CDC6. In both cases, we observe that the majority of stress-responsive origins are also active in a small fraction of the cell population in a normal S phase, and stress increases their frequency of activation. In a search for the molecular determinants of origin efficiency, we compared the genetic and epigenetic features of origins displaying different levels of activation, and integrated their genomic positions in three-dimensional chromatin interaction networks derived from high-depth Hi-C and promoter-capture Hi-C data. We report that origin efficiency is directly proportional to the proximity to transcriptional start sites and to the number of contacts established between origin-containing chromatin fragments, supporting the organization of origins in higher-level DNA replication factories.MCIN/AEI/10.13039/501100011033 [BFU2016-80402-R and PID2019-106707RB-100 to JM; BFU2016-78849-P and PID2019-105949GB-I00 to MG]; ‘ERDF A way of making Europe’; ‘CNIO Friends’ postdoctoral fellowship (to V.P.); Fondation Toulouse Cancer Santé and the Pierre Fabre Research Institute as part of the Chair of Bioinformatics in Oncology of the CRCT; CNIO-La Caixa predoctoral fellowships (to K.J., M.R.); Portuguese Foundation for Science and Technology [FCT-SFRH/BD/81027/2011 to R.A.]; Spanish Ministry of Science and Innovation [BES-2014–070050 to J.M.F.-J.]; Foundation for Polish Science co-financed by the European Union ERFD funds [TEAM/2016–3/30 to K.J.]; Polish National Science Centre [2020/37/B/NZ2/03757 to K.J.). Funding for open access charge: Spanish Ministry of Science and Innovation (PID2019-106707RB-100)