A universal tool for predicting differentially active features in single-cell and spatial genomics data.

With the growing complexity of single-cell and spatial genomics data, there is an increasing importance of unbiased and efficient exploratory data analysis tools. One common exploratory data analysis step is the prediction of genes with different levels of activity in a subset of cells or locations inside a tissue. We previously developed singleCellHaystack, a method for predicting differentially expressed genes from single-cell transcriptome data, without relying on comparisons between clusters of cells. Here we present an update to singleCellHaystack, which is now a universally applicable method for predicting differentially active features: (1) singleCellHaystack now accepts continuous features that can be RNA or protein expression, chromatin accessibility or module scores from single-cell, spatial and even bulk genomics data, and (2) it can handle 1D trajectories, 2-3D spatial coordinates, as well as higher-dimensional latent spaces as input coordinates. Performance has been drastically improved, with up to ten times reduction in computational time and scalability to millions of cells, making singleCellHaystack a suitable tool for exploratory analysis of atlas level datasets. singleCellHaystack is available as packages in both R and Python.

Intercellular crosstalk in adult dental pulp is mediated by heparin-binding growth factors Pleiotrophin and Midkine.

BACKGROUND: In-depth knowledge of the cellular and molecular composition of dental pulp (DP) and the crosstalk between DP cells that drive tissue homeostasis are not well understood. To address these questions, we performed a comparative analysis of publicly available single-cell transcriptomes of healthy adult human DP to 5 other reference tissues: peripheral blood mononuclear cells, bone marrow, adipose tissue, lung, and skin. RESULTS: Our analysis revealed that DP resident cells have a unique gene expression profile when compared to the reference tissues, and that DP fibroblasts are the main cell type contributing to this expression profile. Genes coding for pleiotrophin (PTN) and midkine (MDK), homologous heparin-binding growth-factors, possessed the highest differential expression levels in DP fibroblasts. In addition, we identified extensive crosstalk between DP fibroblasts and several other DP resident cells, including Schwann cells, mesenchymal stem cells and odontoblasts, mediated by PTN and MDK. CONCLUSIONS: DP fibroblasts emerge as unappreciated players in DP homeostasis, mainly through their crosstalk with glial cells. These findings suggest that fibroblast-derived growth factors possess major regulatory functions and thus have a potential role as dental therapeutic targets.

Thyroid hormone regulators in human cerebral cortex development.

Brain development is critically dependent on the timely supply of thyroid hormones. The thyroid hormone transporters are central to the action of thyroid hormones in the brain, facilitating their passage through the blood-brain barrier. Mutations of the monocarboxylate transporter 8 (MCT8) cause the Allan-Herndon-Dudley syndrome, with altered thyroid hormone concentrations in the blood and profound neurological impairment and intellectual deficit. Mouse disease models have revealed interplay between transport, deiodination, and availability of T3 to receptors in specific cells. However, the mouse models are not satisfactory, given the fundamental differences between the mouse and human brains. The goal of the present work is to review human neocortex development in the context of thyroid pathophysiology. Recent developments in single-cell transcriptomic approaches aimed at the human brain make it possible to profile the expression of thyroid hormone regulators in single-cell RNA-Seq datasets of the developing human neocortex. The data provide novel insights into the specific cellular expression of thyroid hormone transporters, deiodinases, and receptors.

Dual Mobility Cups as the Routine Choice in Total Hip Arthroplasty.

Background and Objectives: Total hip arthroplasty (THA) is considered the most successful surgical procedure in orthopedics. However, dislocation remains the main indication for surgical revision. New designs of dual mobility cups (DMC) have lowered the classical complications and have extended the indications of DMC in elective surgeries. Our aim is to assess the trend of DMC indications in THA as well as the incidence of their dislocation. Materials and Methods: We retrospectively reviewed all patients undergoing THA with DMC during the years 2015 and 2021. The original indication for DMC included patients sustaining neck of femur fractures (NOF#) and associated risk factors for dislocations. Five years later, DMC was considered our standard of care in total hip arthroplasty. The approach (anterolateral or posterolateral) was chosen by the surgeon according to his/her preferences, as was the implant. Data collected included patients' demographics, diagnosis, admission time, surgical approach, cup models, and inclination and complications. Patients sustaining a hip dislocation were prospectively reviewed and assessed for treatment received, new dislocations, and need for surgical revision. Two groups were created for the analysis according to the presence or absence of dislocation during follow-up. Results: In the analysis, 531 arthroplasties were included (mean age 72.2 years) with a mean follow-up of 2.86 years. The trend of indications for DMC increased from 16% of THA in 2015 to 78% of THA in 2021. We found a total of 8 dislocations (1.5%), none of them associated with elective surgery. Closed reduction was unsatisfactory in four cases (50%). There was one case of intraprosthetic dislocation. Dislocations were associated to smaller heads (22 mm) (1.5% vs. 25%, p = 0.008) and cups (51.2 mm vs. 48.7 mm, p = 0.038) and posterior approach (62.5% vs. 37.5%, p = 0.011). Conclusion: Dual mobility cups are a great option to reduce the risk of dislocation after a THA both in the neck of femur fractures and elective cases. The use of an anterolateral approach in THA after a neck or femur fracture might considerably decrease the risk of dislocation.

Unbiased integration of single cell transcriptome replicates.

Single cell transcriptomic approaches are becoming mainstream, with replicate experiments commonly performed with the same single cell technology. Methods that enable integration of these datasets by removing batch effects while preserving biological information are required for unbiased data interpretation. Here, we introduce Canek for this purpose. Canek leverages information from mutual nearest neighbor to combine local linear corrections with cell-specific non-linear corrections within a fuzzy logic framework. Using a combination of real and synthetic datasets, we show that Canek corrects batch effects while introducing the least amount of bias compared with competing methods. Canek is computationally efficient and can easily integrate thousands of single-cell transcriptomes from replicated experiments.

Single-Cell Transcriptome Profiling of Thyroid Hormone Effectors in the Human Fetal Neocortex: Expression of SLCO1C1, DIO2, and THRB in Specific Cell Types.

Background: Thyroid hormones are crucial for brain development, acting through the thyroid hormone nuclear receptors (TR)α1 and ß to control gene expression. Triiodothyronine (T3), the receptor-ligand, is transported into the brain from the blood by the monocarboxylate transporter 8 (MCT8). Another source of brain T3 is from the local deiodination of thyroxine (T4) by type 2 deiodinase (DIO2). While these mechanisms are very similar in mice and humans, important species-specific differences confound our understanding of disease using mouse models. To fill this knowledge gap on thyroid hormone action in the human fetal brain, we analyzed the expression of transporters, DIO2, and TRs, which we call thyroid hormone effectors, at single-cell resolution. Methods: We analyzed publicly available single-cell transcriptome data sets of isolated cerebral cortex neural cells from three different studies, with expression data from 393 to almost 40,000 cells. We generated Uniform Manifold Approximation and Projection scatterplots and cell clusters to identify differentially expressed genes between clusters, and correlated their gene signatures with the expression of thyroid effectors. Results: The radial glia, mainly the outer radial glia, and astrocytes coexpress SLCO1C1 and DIO2, indicating close cooperation between the T4 transporter OATP1C1 and DIO2 in local T3 formation. Strikingly, THRB was mainly present in two classes of interneurons: a majority expressing CALB2/calretinin, from the caudal ganglionic eminence, and in somatostatin-expressing interneurons from the medial ganglionic eminence. By contrast, many cell types express SLC16A2 and THRA. Conclusions:SLCO1C1 and DIO2 coexpression in the outer radial glia, the universal stem cell of the cerebral cortex, highlights the likely importance of brain-generated T3 in neurogenesis. The unique expression of THRB in discrete subsets of interneurons is a novel finding whose pathophysiological meaning deserves further investigation.

A clustering-independent method for finding differentially expressed genes in single-cell transcriptome data.

A common analysis of single-cell sequencing data includes clustering of cells and identifying differentially expressed genes (DEGs). How cell clusters are defined has important consequences for downstream analyses and the interpretation of results, but is often not straightforward. To address this difficulty, we present singleCellHaystack, a method that enables the prediction of DEGs without relying on explicit clustering of cells. Our method uses Kullback-Leibler divergence to find genes that are expressed in subsets of cells that are non-randomly positioned in a multidimensional space. Comparisons with existing DEG prediction approaches on artificial datasets show that singleCellHaystack has higher accuracy. We illustrate the usage of singleCellHaystack through applications on 136 real transcriptome datasets and a spatial transcriptomics dataset. We demonstrate that our method is a fast and accurate approach for DEG prediction in single-cell data. singleCellHaystack is implemented as an R package and is available from CRAN and GitHub.

Methods for sequence and structural analysis of B and T cell receptor repertoires.

B cell receptors (BCRs) and T cell receptors (TCRs) make up an essential network of defense molecules that, collectively, can distinguish self from non-self and facilitate destruction of antigen-bearing cells such as pathogens or tumors. The analysis of BCR and TCR repertoires plays an important role in both basic immunology as well as in biotechnology. Because the repertoires are highly diverse, specialized software methods are needed to extract meaningful information from BCR and TCR sequence data. Here, we review recent developments in bioinformatics tools for analysis of BCR and TCR repertoires, with an emphasis on those that incorporate structural features. After describing the recent sequencing technologies for immune receptor repertoires, we survey structural modeling methods for BCR and TCRs, along with methods for clustering such models. We review downstream analyses, including BCR and TCR epitope prediction, antibody-antigen docking and TCR-peptide-MHC Modeling. We also briefly discuss molecular dynamics in this context.

Analysis of early failure of Biotronik Linox Smart implantable cardioverter-defibrillator leads: A comparative study of three defibrillator leads.

BACKGROUND AND OBJECTIVES: Early failure of Biotronik Linox and Linox Smart leads (Biotronik, Berlin, Germany) has been reported in numerous recent publications. The aim of this study was to assess the performance of this lead compared with that of two other contemporary leads. METHODS: We conducted an ambispective study of all consecutive first implantations of defibrillator leads carried out in our center: Endotak (model 148, 158, Boston Scientific, Marlborough, MA, USA) (n = 173), Sprint Quattro (model 6644, 6947, Medtronic, Dublin, Ireland) (n = 145), and Linox Smart (Biotronik, model SD 65/16) (n = 120). RESULTS: During a median follow-up of 4.6 ± 2.1 years, failure occurred in nine Linox Smart (7.5%), one Endotak Reliance (0.6%), and no Sprint Quattro leads. The survival probability of the Linox Smart group was significantly lower than that of the Endotak and Sprint Quattro groups measured by the log-rank test (Linox vs Endotak; P < 0.001 and Linox vs Sprint Quattro; P < 0.001). Nonphysiological signals not due to external interference were observed in all Linox Smart leads, with normal parameters and without visible anomalies on chest x-ray. CONCLUSIONS: In this single-center experience, the survival rate of Linox Smart leads was 88% at 5 years of follow-up, which was significantly lower than that of the other leads. Comprehensive vigilance of Linox Smart leads, including home monitoring, may be advisable to facilitate early detection of lead failure and avoid inappropriate shocks.

Mapping circulating serum miRNAs to their immune-related target mRNAs.

PURPOSE: Evidence suggests that circulating serum microRNAs (miRNAs) might preferentially target immune-related mRNAs. If this were the case, we hypothesized that immune-related mRNAs would have more predicted serum miRNA binding sites than other mRNAs and, reciprocally, that serum miRNAs would have more immune-related mRNA targets than non-serum miRNAs. MATERIALS AND METHODS: We developed a consensus target predictor using the random forest framework and calculated the number of predicted miRNA-mRNA interactions in various subsets of miRNAs (serum, non-serum) and mRNAs (immune related, nonimmune related). RESULTS: Immune-related mRNAs were predicted to be targeted by serum miRNA more than other mRNAs. Moreover, serum miRNAs were predicted to target many more immune-related mRNA targets than non-serum miRNAs; however, these two biases in immune-related mRNAs and serum miRNAs appear to be completely independent. CONCLUSION: Immune-related mRNAs have more miRNA binding sites in general, not just for serum miRNAs; likewise, serum miRNAs target many more mRNAs than non-serum miRNAs overall, regardless of whether they are immune related or not. Nevertheless, these two independent phenomena result in a significantly larger number of predicted serum miRNA-immune mRNA interactions than would be expected by chance.

Aleteo auricular atípico y ablación de la conducción transauricular receptor-donante tras trasplante cardiaco ortotópico / Atypical atrial flutter and ablation of recipient-to-donor atrioatrial conduction after orthotopic heart transplant

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Exploring the interactions of the RAS family in the human protein network and their potential implications in RAS-directed therapies.

RAS proteins are the founding members of the RAS superfamily of GTPases. They are involved in key signaling pathways regulating essential cellular functions such as cell growth and differentiation. As a result, their deregulation by inactivating mutations often results in aberrant cell proliferation and cancer. With the exception of the relatively well-known KRAS, HRAS and NRAS proteins, little is known about how the interactions of the other RAS human paralogs affect cancer evolution and response to treatment. In this study we performed a comprehensive analysis of the relationship between the phylogeny of RAS proteins and their location in the protein interaction network. This analysis was integrated with the structural analysis of conserved positions in available 3D structures of RAS complexes. Our results show that many RAS proteins with divergent sequences are found close together in the human interactome. We found specific conserved amino acid positions in this group that map to the binding sites of RAS with many of their signaling effectors, suggesting that these pairs could share interacting partners. These results underscore the potential relevance of cross-talking in the RAS signaling network, which should be taken into account when considering the inhibitory activity of drugs targeting specific RAS oncoproteins. This study broadens our understanding of the human RAS signaling network and stresses the importance of considering its potential cross-talk in future therapies.

A novel affinity-based method for the isolation of highly purified extracellular vesicles.

Extracellular vesicles (EVs) such as exosomes and microvesicles serve as messengers of intercellular network, allowing exchange of cellular components between cells. EVs carry lipids, proteins, and RNAs derived from their producing cells, and have potential as biomarkers specific to cell types and even cellular states. However, conventional methods (such as ultracentrifugation or polymeric precipitation) for isolating EVs have disadvantages regarding purity and feasibility. Here, we have developed a novel method for EV purification by using Tim4 protein, which specifically binds the phosphatidylserine displayed on the surface of EVs. Because the binding is Ca2+-dependent, intact EVs can be easily released from Tim4 by adding Ca2+ chelators. Tim4 purification, which we have applied to cell conditioned media and biofluids, is capable of yielding EVs of a higher purity than those obtained using conventional methods. The lower contamination found in Tim4-purified EV preparations allows more EV-specific proteins to be detected by mass spectrometry, enabling better characterization and quantification of different EV populations' proteomes. Tim4 protein can also be used as a powerful tool for quantification of EVs in both ELISA and flow cytometry formats. Thus, the affinity of Tim4 for EVs will find abundant applications in EV studies.

Cambios durante la última década en la incidencia y las características de los pacientes politraumatizados en Navarra / Changes in the characteristics and incidence of multiple-injury accidents in the Navarre community over a 10-year period

Objetivo: Comparar las tasas de morbimortalidad, el perfil epidemiológico y la supervivencia de los pacientes politraumatizados atendidos en Navarra por el sistema de emergencias en los períodos 2002-2003 y 2010-2012. Método: Estudio observacional, analítico, de dos cohortes de pacientes accidentados con un Injury Severity Score superior a 15 puntos. Se utiliza la regresión logística para identificar las variables involucradas en la mortalidad. Resultados: Se incluyen 651 pacientes atendidos en el primer periodo y se comparan con los 626 del segundo. La tasa de incidencia descendió de 58,1 a 33,5/100.000 habitantes y año, así como la de mortalidad, que descendió de 30,3 a 15,3. La edad media de los accidentados pasó de 45 (22) a 52 (23) años y se mantuvo su distribución por sexos (75% varones). Disminuyeron los accidentados de tráfico del 44 al 24% y se incrementaron las caídas en ancianos del 9 al 26%. Conclusiones: En los últimos años se ha controlado en Navarra el problema de los jóvenes accidentados de tráfico y ha surgido el grupo de ancianos que se caen accidentalmente. Esto puede ralentizar la mejora en las tasas de mortalidad de los politraumatizados y obliga a poner en marcha medidas preventivas en relación con este mecanismo en este colectivo (AU)

Objective: To compare morbidity and mortality rates, the epidemiologic profile, and survival of patients with multiple injuries attended by the emergency services in the Navarre autonomous community in Spain in the periods of 2002–2003 and 2010–2012. Methods: Observational analysis of 2 cohorts of accident patients with Injury Severity Scores of 15 points or more. Logistic regression was used to identify variables related to mortality. Results: A total of 651 patients were attended in the first period; 626 were attended in the second. The annual multiple-injury incidence rate decreased from 58.1 per 100 000 population in the first period to 33.5 per 100 000 population in the second; mortality decreased from 30.3 to 15.3 per 100 000 population. The mean (SD) age was 45 (22) years in the first cohort and 52 (23) years in the second. The gender distribution (75% male) did not change. The percentage injured in traffic accidents decreased from 44% to 24%; the percentage of elderly patients hurt in falls increased from 9% to 26%. Conclusions: The problem of the number of young people injured in accidents in our community has been brought under control, but the proportion of older patients injured in falls has risen. This change may slow the effort to improve mortality rates in patients with multiple injuries and it obliges us to introduce measures to prevent falls in the elderly (AU)

Neuronal exosomes facilitate synaptic pruning by up-regulating complement factors in microglia.

Selective elimination of synaptic connections is a common phenomenon which occurs during both developmental and pathological conditions. Glial cells have a central role in the pruning of synapses by specifically engulfing the degenerating neurites of inappropriate connections, but its regulatory mechanisms have been largely unknown. To identify mediators of this process, we established an in vitro cell culture assay for the synapse elimination. Neuronal differentiation and synapse formation of PC12 cells were induced by culturing the cells with nerve growth factor (NGF) in a serum-free medium. To trigger synapse elimination, the NGF-containing medium was replaced with DMEM containing 10% FBS, and the neurites of PC12 cells degenerated within two days. Co-culturing with MG6 cells, a mouse microglial cell line, accelerated the removal of degenerating neurites of PC12 cells by phagocytosis. When MG6 cells were pre-incubated with exosomes secreted from the differentiated PC12 cells after depolarization, the removal was further accelerated by increasing the expression levels of complement component 3 in the MG6 cells. These results define a role for exosomes as a regulator of synapse elimination and clarify a novel mechanism whereby active synapses promote the pruning of inactive ones by stimulating microglial phagocytosis with exosomes.

[Changes in the characteristics and incidence of multiple-injury accidents in the Navarre community over a 10-year period]. / Cambios durante la última década en la incidencia y las características de los pacientes politraumatizados en Navarra.

OBJECTIVES: To compare morbidity and mortality rates, the epidemiologic profile, and survival of patients with multiple injuries attended by the emergency services in the Navarre autonomous community in Spain in the periods of 2002-2003 and 2010-2012. MATERIAL AND METHODS: Observational analysis of 2 cohorts of accident patients with Injury Severity Scores of 15 points or more. Logistic regression was used to identify variables related to mortality. RESULTS: A total of 651 patients were attended in the first period; 626 were attended in the second. The annual multiple-injury incidence rate decreased from 58.1 per 100 000 population in the first period to 33.5 per 100 000 population in the second; mortality decreased from 30.3 to 15.3 per 100 000 population. The mean (SD) age was 45 (22) years in the first cohort and 52 (23) years in the second. The gender distribution (75% male) did not change. The percentage injured in traffic accidents decreased from 44% to 24%; the percentage of elderly patients hurt in falls increased from 9% to 26%. CONCLUSION: The problem of the number of young people injured in accidents in our community has been brought under control, but the proportion of older patients injured in falls has risen. This change may slow the effort to improve mortality rates in patients with multiple injuries and it obliges us to introduce measures to prevent falls in the elderly.

OBJETIVO: Comparar las tasas de morbimortalidad, el perfil epidemiológico y la supervivencia de los pacientes politraumatizados atendidos en Navarra por el sistema de emergencias en los períodos 2002-2003 y 2010-2012. METODO: Estudio observacional, analítico, de dos cohortes de pacientes accidentados con un Injury Severity Score superior a 15 puntos. Se utiliza la regresión logística para identificar las variables involucradas en la mortalidad. RESULTADOS: Se incluyen 651 pacientes atendidos en el primer periodo y se comparan con los 626 del segundo. La tasa de incidencia descendió de 58,1 a 33,5/100.000 habitantes y año, así como la de mortalidad, que descendió de 30,3 a 15,3. La edad media de los accidentados pasó de 45 (22) a 52 (23) años y se mantuvo su distribución por sexos (75% varones). Disminuyeron los accidentados de tráfico del 44 al 24% y se incrementaron las caídas en ancianos del 9 al 26%. CONCLUSIONES: En los últimos años se ha controlado en Navarra el problema de los jóvenes accidentados de tráfico y ha surgido el grupo de ancianos que se caen accidentalmente. Esto puede ralentizar la mejora en las tasas de mortalidad de los politraumatizados y obliga a poner en marcha medidas preventivas en relación con este mecanismo en este colectivo.

Network analysis in the investigation of chronic respiratory diseases. From basics to application.

Chronic respiratory diseases are complex multifactorial disorders whose pathogenesis depends on the interplay between host and environmental factors. To fully understand them and to identify novel treatments, a holistic approach that integrates multiple types and levels of clinical and biological data is necessary. Toward this end, the application of systems biology-based strategies, in particular, network analysis, offers great potential. These systems-based approaches rely heavily on computational methods that can be challenging for the nonspecialist. Accordingly, this Pulmonary Perspective: (1) outlines the basic concepts of networks in biology and the fundamentals of network analysis, and (2) discusses recent applications of network analysis to understand respiratory diseases. The intent of this Perspective is to provide readers with increased understanding of the strengths and weaknesses of network analysis methods as well as their usefulness in addressing research questions involving chronic respiratory diseases.