ColocZStats: a z-stack signal colocalization extension tool for 3D slicer.

Confocal microscopy has evolved to be a widely adopted imaging technique in molecular biology and is frequently utilized to achieve accurate subcellular localization of proteins. Applying colocalization analysis on image z-stacks obtained from confocal fluorescence microscopes is a dependable method of revealing the relationship between different molecules. In addition, despite the established advantages and growing adoption of 3D visualization software in various microscopy research domains, there have been few systems that can support colocalization analysis within a user-specified region of interest (ROI). In this context, several broadly employed biological image visualization platforms are meticulously explored in this study to understand the current landscape. It has been observed that while these applications can generate three-dimensional (3D) reconstructions for z-stacks, and in some cases transfer them into an immersive virtual reality (VR) scene, there is still little support for performing quantitative colocalization analysis on such images based on a user-defined ROI and thresholding levels. To address these issues, an extension called ColocZStats (pronounced Coloc-Zee-Stats) has been developed for 3D Slicer, a widely used free and open-source software package for image analysis and scientific visualization. With a custom-designed user-friendly interface, ColocZStats allows investigators to conduct intensity thresholding and ROI selection on imported 3D image stacks. It can deliver several essential colocalization metrics for structures of interest and produce reports in the form of diagrams and spreadsheets.

SmartVR Pointer: Using Smartphones and Gaze Orientation for Selection and Navigation in Virtual Reality.

Some of the barriers preventing virtual reality (VR) from being widely adopted are the cost and unfamiliarity of VR systems. Here, we propose that in many cases, the specialized controllers shipped with most VR head-mounted displays can be replaced by a regular smartphone, cutting the cost of the system, and allowing users to interact in VR using a device they are already familiar with. To achieve this, we developed SmartVR Pointer, an approach that uses smartphones to replace the specialized controllers for two essential operations in VR: selection and navigation by teleporting. In SmartVR Pointer, a camera mounted on the head-mounted display (HMD) is tilted downwards so that it points to where the user will naturally be holding their phone in front of them. SmartVR Pointer supports three selection modalities: tracker based, gaze based, and combined/hybrid. In the tracker-based SmartVR Pointer selection, we use image-based tracking to track a QR code displayed on the phone screen and then map the phone's position to a pointer shown within the field of view of the camera in the virtual environment. In the gaze-based selection modality, the user controls the pointer using their gaze and taps on the phone for selection. The combined technique is a hybrid between gaze-based interaction in VR and tracker-based Augmented Reality. It allows the user to control a VR pointer that looks and behaves like a mouse pointer by moving their smartphone to select objects within the virtual environment, and to interact with the selected objects using the smartphone's touch screen. The touchscreen is used for selection and dragging. The SmartVR Pointer is simple and requires no calibration and no complex hardware assembly or disassembly. We demonstrate successful interactive applications of SmartVR Pointer in a VR environment with a demo where the user navigates in the virtual environment using teleportation points on the floor and then solves a Tetris-style key-and-lock challenge.

CardioHotspots: a database of mutational hotspots for cardiac disorders.

Mutational hotspots are DNA regions with an abnormally high frequency of genetic variants. Identifying whether a variant is located in a mutational hotspot is critical for determining the variant's role in disorder predisposition, development, and treatment response. Despite their significance, current databases on mutational hotspots are limited to the oncology domain. However, identifying mutational hotspots is critical for any disorder in which genetics plays a role. This is true for the world's leading cause of death: cardiac disorders. In this work, we present CardioHotspots, a literature-based database of manually curated hotspots for cardiac diseases. This is the only database we know of that provides high-quality and easily accessible information about hotspots associated with cardiac disorders. CardioHotspots is publicly accessible via a web-based platform (https://genomics-hub.pros.dsic.upv.es:3099/). Database URL: https://genomics-hub.pros.dsic.upv.es:3099/.

The Delfos Platform: A Conceptual Model-Based Solution for the Enhancement of Precision Medicine.

The use in the clinical practice of the vast amount of genomic data generated by current sequencing technologies constitutes a bottleneck for the progress of Precision Medicine (PM). Various problems inherent to the genomics domain (i.e., dispersion, heterogeneity, discrepancies, lack of standardization, and data quality issues) remain unsolved. In this paper, we present the Delfos platform, a conceptual model-based solution developed following a rigorous methodological and ontological background, whose main aim is to minimize the impact of these problems when transferring the research results to clinical practice. This paper presents the SILE method that provides methodological support for the Delfos platform, the Conceptual Schema of the Genome that provides a shared understanding of the domain, and the technological architecture behind the implementation of the platform. This paper also exemplifies the use of the Delfos platform through two use cases that involve the study of the DNA variants associated with the risk of developing Dilated Cardiomyopathies and Neuroblastoma.

Intravenous Ascorbic Acid for the Prevention of Postreperfusion Syndrome in Orthotopic Liver Transplantation: Protocol for a Randomized Controlled Trial.

BACKGROUND: Liver transplantation is the last therapeutic option for patients with end-stage liver disease. Postreperfusion syndrome (PRS), defined as a fall in mean arterial pressure of more than 30% within the first 5 minutes after reperfusion of at least 1 minute, can occur in liver transplantation as a deep hemodynamic instability with associated hyperfibrinolysis immediately after reperfusion of the new graft. Its incidence has remained unchanged since it was first described in 1987. PRS is related to ischemia-reperfusion (I/R) injury, whose pathophysiology involves the release of several mediators from both the donor and the recipient. The antioxidant effect of ascorbic acid has been studied in resuscitating patients with septic shock and burns. Even today, there are publications with conflicting results, and there is a need for further studies to confirm or rule out the usefulness of this drug in this group of patients. The addition of ascorbic acid to preservation solutions used in solid organ transplantation is under investigation to harness its antioxidant effect and mitigate I/R injury. Since PRS could be considered a manifestation of I/R injury, we believe that the possible beneficial effect of ascorbic acid on the occurrence of PRS should be investigated. OBJECTIVE: The aim of this randomized controlled trial is to assess the benefits of ascorbic acid over saline in the development of PRS in adult liver transplantation. METHODS: We plan to conduct a single-center randomized controlled trial at the Hospital Universitario Ramón y Cajal in Spain. A total of 70 participants aged 18 years or older undergoing liver transplantation will be randomized to receive either ascorbic acid or saline. The primary outcome will be the difference between groups in the incidence of PRS. The randomized controlled trial will be conducted under conditions of respect for fundamental human rights and ethical principles governing biomedical research involving human participants and in accordance with the international recommendations contained in the Declaration of Helsinki and its subsequent revisions. RESULTS: The enrollment process began in 2020. A total of 35 patients have been recruited so far. Data cleaning and analysis are expected to occur in the first months of 2024. Results are expected around the middle of 2024. CONCLUSIONS: We believe that this study could be particularly relevant because it will be the first to analyze the clinical effect of ascorbic acid in liver transplantation. Moreover, we believe that this study fills an important gap in the knowledge of the potential benefits of ascorbic acid in the field of liver transplantation, particularly in relation to PRS. TRIAL REGISTRATION: European Union Drug Regulating Authorities Clinical Trials Database 2020-000123-39; https://tinyurl.com/2cfzddw8; ClinicalTrials.gov NCT05754242; https://tinyurl.com/346vw7sm. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/50091.

The consequences of data dispersion in genomics: a comparative analysis of data sources for precision medicine.

BACKGROUND: Genomics-based clinical diagnosis has emerged as a novel medical approach to improve diagnosis and treatment. However, advances in sequencing techniques have increased the generation of genomics data dramatically. This has led to several data management problems, one of which is data dispersion (i.e., genomics data is scattered across hundreds of data repositories). In this context, geneticists try to remediate the above-mentioned problem by limiting the scope of their work to a single data source they know and trust. This work has studied the consequences of focusing on a single data source rather than considering the many different existing genomics data sources. METHODS: The analysis is based on the data associated with two groups of disorders (i.e., oncology and cardiology) accessible from six well-known genomic data sources (i.e., ClinVar, Ensembl, GWAS Catalog, LOVD, CIViC, and CardioDB). Two dimensions have been considered in this analysis, namely, completeness and concordance. Completeness has been evaluated at two levels. First, by analyzing the information provided by each data source with regard to a conceptual schema data model (i.e., the schema level). Second, by analyzing the DNA variations provided by each data source as related to any of the disorders selected (i.e., the data level). Concordance has been evaluated by comparing the consensus among the data sources regarding the clinical relevance of each variation and disorder. RESULTS: The data sources with the highest completeness at the schema level are ClinVar, Ensembl, and CIViC. ClinVar has the highest completeness at the data level data source for the oncology and cardiology disorders. However, there are clinically relevant variations that are exclusive to other data sources, and they must be considered in order to provide the best clinical diagnosis. Although the information available in the data sources is predominantly concordant, discordance among the analyzed data exist. This can lead to inaccurate diagnoses. CONCLUSION: Precision medicine analyses using a single genomics data source leads to incomplete results. Also, there are concordance problems that threaten the correctness of the genomics-based diagnosis results.

Plasma Fatty Acid Composition, Oxidative and Inflammatory Status, and Adherence to the Mediterranean Diet of Patients with Non-Alcoholic Fatty Liver Disease.

Non-alcoholic fatty liver disease (NAFLD) is a complex and increasingly prevalent cardiometabolic disorder worldwide. As of today, NAFLD is a pathology without specific pharmacological treatment, with the Mediterranean diet (MedDiet) being the most widely used approach for its management. The objective of this study is to assess the effects of adherence to the Mediterranean diet on fatty acid plasma levels, as well as on the oxidative and inflammatory status of NAFLD patients. A total of 100 adult patients (40-60 years old) diagnosed with NAFLD and from the Balearic Islands, Spain, were classified into three groups according to their adherence to the MedDiet. Consumption was assessed using a validated 143-item semiquantitative Food Frequency Questionnaire. Food items (g/day) were categorised according to their processing using the NOVA system. Anthropometrics, blood pressure, aminotransferases, Dietary Inflammatory Index (DII), inflammatory biomarkers, and fatty acid levels were measured in the plasma of NAFLD patients. High adherence to the MedDiet is associated to a highly plant-based diet, low ultra-processed food (UPF) consumption, low intake of dietary lipids, low intake of animal fats, high intake of monounsaturated fatty acid (MUFA; mainly palmitoleic acid), low intake of saturated fatty acids (SFAs; practically all dietary SFAs), low intake of trans-fatty acids, high intake of omega-3 fatty acids (mainly eicosapentaenoic acid), a higher n-6:n-3 in ratio, low intake of omega-6 fatty acids, and a low level of interleukin-6 (IL-6). High adherence to the MedDiet is related to a better fatty acid profile in the plasma, fewer SFAs and more MUFA and polyunsaturated fatty acids (PUFAs), a plasma biochemical profile, better proinflammatory status, and decreased ultra-processed food consumption of NAFLD patients.

Conceptual modelling for life sciences based on systemist foundations.

BACKGROUND: All aspects of our society, including the life sciences, need a mechanism for people working within them to represent the concepts they employ to carry out their research. For the information systems being designed and developed to support researchers and scientists in conducting their work, conceptual models of the relevant domains are usually designed as both blueprints for a system being developed and as a means of communication between the designer and developer. Most conceptual modelling concepts are generic in the sense that they are applied with the same understanding across many applications. Problems in the life sciences, however, are especially complex and important, because they deal with humans, their well-being, and their interactions with the environment as well as other organisms. RESULTS: This work proposes a "systemist" perspective for creating a conceptual model of a life scientist's problem. We introduce the notion of a system and then show how it can be applied to the development of an information system for handling genomic-related information. We extend our discussion to show how the proposed systemist perspective can support the modelling of precision medicine. CONCLUSION: This research recognizes challenges in life sciences research of how to model problems to better represent the connections between physical and digital worlds. We propose a new notation that explicitly incorporates systemist thinking, as well as the components of systems based on recent ontological foundations. The new notation captures important semantics in the domain of life sciences. It may be used to facilitate understanding, communication and problem-solving more broadly. We also provide a precise, sound, ontologically supported characterization of the term "system," as a basic construct for conceptual modelling in life sciences.

Including business strategy in model-driven methods: an experiment.

Software-centric organisations design a loosely coupled organisation structure around strategic objectives, replicating this design to their business processes and information systems. Nowadays, dealing with business strategy in a model-driven development context is a challenge since key concepts such as the organisation's structure and strategic ends and means have been mostly addressed at the enterprise architecture level for the strategic alignment of the whole organisation, and have not been included into MDD methods as a requirements source. To overcome this issue, researchers have designed the LiteStrat, a business strategy modelling method compliant with MDD for developing information systems. This article presents an empirical comparison of LiteStrat and with i*, one of the most used models for strategic alignment in an MDD context. The article contributes with a literature review on the experimental comparison of modelling languages, the design of a study for measuring and comparing the semantic quality of modelling languages, and empirical evidence of the LiteStrat and i* differences. The evaluation consists of a 2 × 2 factorial experiment recruiting 28 undergraduate subjects. Significant differences favouring LiteStrat were found for models' accuracy and completeness, while no differences in modeller's efficiency and satisfaction were detected. These results yield evidence of the suitability of LiteStrat for business strategy modelling in a model-driven context.

"MiR-7 controls cholesterol biosynthesis through posttranscriptional regulation of DHCR24 expression".

Dysregulation of cholesterol homeostasis is associated with several pathologies including cardiovascular diseases and neurological disorders such as Alzheimer's disease (AD). MicroRNAs (miRNAs) have emerged as key post-transcriptional regulators of cholesterol metabolism. We previously established the role of miR-7 in regulating insulin resistance and amyloidosis, which represents a common pathological feature between type 2 diabetes and AD. We show here an additional metabolic function of miR-7 in cholesterol biosynthesis. We found that miR-7 blocks the last steps of the cholesterol biosynthetic pathway in vitro by targeting relevant genes including DHCR24 and SC5D posttranscriptionally. Intracranial infusion of miR-7 on an adeno-associated viral vector reduced the expression of DHCR24 in the brain of wild-type mice, supporting in vivo miR-7 targeting. We also found that cholesterol regulates endogenous levels of miR-7 in vitro, correlating with transcriptional regulation through SREBP2 binding to its promoter region. In parallel to SREBP2 inhibition, the levels of miR-7 and hnRNPK (the host gene of miR-7) were concomitantly reduced in brain in a mouse model of Niemann Pick type C1 disease and in murine fatty liver, which are both characterized by intracellular cholesterol accumulation. Taken together, the results establish a novel regulatory feedback loop by which miR-7 modulates cholesterol homeostasis at the posttranscriptional level, an effect that could be exploited for therapeutic interventions against prevalent human diseases.

Ellagic acid and its metabolites urolithins A/B ameliorate most common disease phenotypes in cellular and mouse models for lysosomal storage disorders by enhancing extracellular vesicle secretion.

Niemann Pick diseases types A (NPDA) and C (NPDC) are lysosomal storage disorders (LSDs) leading to cognitive impairment, neurodegeneration, and early death. NPDA and NPDC have different genetic origins, being caused by mutations in the acid sphingomyelinase (ASM) or the cholesterol transport protein NPC1, respectively. However, they share a common pathological hallmark in the accumulation of lipids in the endolysosomal compartment. Here, we tested the hypothesis that polyphenols reduce lipid overload in NPD cells by enhancing the secretion of extracellular vesicles (ECVs). We show that among the polyphenols tested, the ellagic acid metabolites, urolithin A and B, were the safest and most efficient in increasing ECV secretion. They reduced levels of accumulating lipids and lysosomal size and permeabilization in cultured bone marrow-derived macrophages and neurons from ASMko and NPC1 mutant mice, which mimic NPDA and NPDC, respectively. Moreover, oral treatment with ellagic acid reduced lipid levels, ameliorated lysosomal alterations, and diminished microglia activation in the brain of NPD mice. These results support the therapeutic value of ECV secretion and polyphenols for NPDs, which may also help treat other LSDs characterized by intracellular lipid overload.

Dihydrosphingolipids are associated with steatosis and increased fibrosis damage in non-alcoholic fatty liver disease.

Dihydrosphingolipids are lipids biosynthetically related to ceramides. An increase in ceramides is associated with enhanced fat storage in the liver, and inhibition of their synthesis is reported to prevent the appearance of steatosis in animal models. However, the precise association of dihydrosphingolipids with non-alcoholic fatty liver disease (NAFLD) is yet to be established. We employed a diet induced NAFLD mouse model to study the association between this class of compounds and disease progression. Mice fed a high-fat diet were sacrificed at 22, 30 and 40 weeks to reproduce the full spectrum of histological damage found in human disease, steatosis (NAFL) and steatohepatitis (NASH) with and without significant fibrosis. Blood and liver tissue samples were obtained from patients whose NAFLD severity was assessed histologically. To demonstrate the effect of dihydroceramides over NAFLD progression we treated mice with fenretinide an inhibitor of dihydroceramide desaturase-1 (DEGS1). Lipidomic analyses were performed using liquid chromatography-tandem mass spectrometry. Triglycerides, cholesteryl esters and dihydrosphingolipids were increased in the liver of model mice in association with the degree of steatosis and fibrosis. Dihydroceramides increased with the histological severity observed in liver samples of mice (0.024 ± 0.003 nmol/mg vs 0.049 ± 0.005 nmol/mg, non-NAFLD vs NASH-fibrosis, p < 0.0001) and patients (0.105 ± 0.011 nmol/mg vs 0.165 ± 0.021 nmol/mg, p = 0.0221). Inhibition of DEGS1 induce a four-fold increase in dihydroceramides improving steatosis but increasing the inflammatory activity and fibrosis. In conclusion, the degree of histological damage in NAFLD correlate with dihydroceramide and dihydrosphingolipid accumulation. LAY SUMMARY: Accumulation of triglyceride and cholesteryl ester lipids is the hallmark of non-alcoholic fatty liver disease. Using lipidomics, we examined the role of dihydrosphingolipids in NAFLD progression. Our results demonstrate that de novo dihydrosphingolipid synthesis is an early event in NAFLD and the concentrations of these lipids are correlated with histological severity in both mouse and human disease.

Use of Extended Reality in Medical Education: An Integrative Review.

Extended reality (XR) has emerged as an innovative simulation-based learning modality. An integrative review was undertaken to explore the nature of evidence, usage, and effectiveness of XR modalities in medical education. One hundred and thirty-three (N = 133) studies and articles were reviewed. XR technologies are commonly reported in surgical and anatomical education, and the evidence suggests XR may be as effective as traditional medical education teaching methods and, potentially, a more cost-effective means of curriculum delivery. Further research to compare different variations of XR technologies and best applications in medical education and training are required to advance the field. Supplementary Information: The online version contains supplementary material available at 10.1007/s40670-022-01698-4.

The challenge of managing the evolution of genomics data over time: a conceptual model-based approach.

BACKGROUND: Precision medicine is a promising approach that has revolutionized disease prevention and individualized treatment. The DELFOS oracle is a model-driven genomics platform that aids clinicians in identifying relevant variations that are associated with diseases. In its previous version, the DELFOS oracle did not consider the high degree of variability of genomics data over time. However, changes in genomics data have had a profound impact on clinicians' work and pose the need for changing past, present, and future clinical actions. Therefore, our objective in this work is to consider changes in genomics data over time in the DELFOS oracle. METHODS: Our objective has been achieved through three steps. First, we studied the characteristics of each database from which the DELFOS oracle extracts data. Second, we characterized which genomics concepts of the conceptual schema that supports the DELFOS oracle change over time. Third, we updated the DELFOS Oracle so that it can manage the temporal dimension. To validate our approach, we carried out a use case to illustrate how the new version of the DELFOS oracle handles the temporal dimension. RESULTS: Three events can change genomics data, namely, the addition of a new variation, the addition of a new link between a variation and a phenotype, and the update of a link between a variation and a phenotype. These events have been linked to the entities of the conceptual model that are affected by them. Finally, a new version of the DELFOS oracle that can deal with the temporal dimension has been implemented. CONCLUSION: Huge amounts of genomics data that is associated with diseases change over time, impacting patients' diagnosis and treatment. Including this information in the DELFOS oracle added an extra layer of complexity, but using a model-driven based approach mitigated the cost of implementing the needed changes. The new version handles the temporal dimension appropriately and eases clinicians' work.

Semantic interoperability: ontological unpacking of a viral conceptual model.

BACKGROUND: Genomics and virology are unquestionably important, but complex, domains being investigated by a large number of scientists. The need to facilitate and support work within these domains requires sharing of databases, although it is often difficult to do so because of the different ways in which data is represented across the databases. To foster semantic interoperability, models are needed that provide a deep understanding and interpretation of the concepts in a domain, so that the data can be consistently interpreted among researchers. RESULTS: In this research, we propose the use of conceptual models to support semantic interoperability among databases and assess their ontological clarity to support their effective use. This modeling effort is illustrated by its application to the Viral Conceptual Model (VCM) that captures and represents the sequencing of viruses, inspired by the need to understand the genomic aspects of the virus responsible for COVID-19. For achieving semantic clarity on the VCM, we leverage the "ontological unpacking" method, a process of ontological analysis that reveals the ontological foundation of the information that is represented in a conceptual model. This is accomplished by applying the stereotypes of the OntoUML ontology-driven conceptual modeling language.As a result, we propose a new OntoVCM, an ontologically grounded model, based on the initial VCM, but with guaranteed interoperability among the data sources that employ it. CONCLUSIONS: We propose and illustrate how the unpacking of the Viral Conceptual Model resolves several issues related to semantic interoperability, the importance of which is recognized by the "I" in FAIR principles. The research addresses conceptual uncertainty within the domain of SARS-CoV-2 data and knowledge.The method employed provides the basis for further analyses of complex models currently used in life science applications, but lacking ontological grounding, subsequently hindering the interoperability needed for scientists to progress their research.

Rottlerin Stimulates Exosome/Microvesicle Release Via the Increase of Ceramide Levels Mediated by Ampk in an In Vitro Model of Intracellular Lipid Accumulation.

Exosomes/microvesicles originate from multivesicular bodies that allow the secretion of endolysosome components out of the cell. In the present work, we investigated the effects of rottlerin, a polyphenol, on exosome/microvesicle secretion in a model of intracellular lipid trafficking impairment, and elucidated the mechanism of action. In a model of lipid trafficking impairment in C6 glia cells, rottlerin increased ceramide levels, while decreasing hexosylceramide content. This was accompanied by increased exosome/microvesicle secretion, thereby reducing the concentration of lipids in the endolysosomal compartment. The reduction of hexosylceramide levels by rottlerin was attributed to the increase of ß-glucosidase (glucosylceramidase) activity, and the effects of rottlerin were abrogated by ß-glucosidase inhibitors such as isofagomine D-tartrate and AMP-deoxynojirimycin. Moreover, treatment with ML-266, a potent activator of the ß-glucosidase enzyme, recapitulated the effects of rottlerin on the sphingolipid profile and exosome/microvesicle secretion. Finally, inhibition of AMPK (AMP-activated protein kinase) using compound C prevented both exosome/microvesicle secretion and the elimination of endolysosome lipids, which were promoted by rottlerin. The results showed that the decrease in intracellular lipid deposition induced by rottlerin was mediated by ß-glucosidase activation and exosome/microvesicle release via the AMPK pathway. Rottlerin consumption could represent an additional health benefit in lysosomal deposition diseases.

Novel segmentation algorithm for high-throughput analysis of spectral domain-optical coherence tomography imaging of teleost retinas.

Spectral domain-optical coherence tomography (SD-OCT) has become an essential tool for assessing ocular tissues in live subjects and conducting research on ocular development, health, and disease. The processing of SD-OCT images, particularly those from non-mammalian species, is a labor-intensive manual process due to a lack of automated analytical programs. This paper describes the development and implementation of a novel computer algorithm for the quantitative analysis of SD-OCT images of live teleost eyes. Automated segmentation processing of SD-OCT images of retinal layers was developed using a novel algorithm based on thresholding. The algorithm measures retinal thickness characteristics in a large volume of imaging data of teleost ocular structures in a short time, providing increased accuracy and repeatability of SD-OCT image analysis over manual measurements. The algorithm also generates hundreds of retinal thickness measurements per image for a large number of images for a given dataset. Meanwhile, heat mapping software that plots SD-OCT image measurements as a color gradient was also created. This software directly converts the measurements of each processed image to represent changes in thickness across the whole retinal scan. It also enables 2D and 3D visualization of retinal thickness across the scan, facilitating specimen comparison and localization of areas of interest. The study findings showed that the novel algorithm is more accurate, reliable, and repeatable than manual SD-OCT analysis. The adaptability of the algorithm makes it potentially suitable for analyzing SD-OCT scans of other non-mammalian species.

Lipidomics Reveals Cisplatin-Induced Renal Lipid Alterations during Acute Kidney Injury and Their Attenuation by Cilastatin.

Nephrotoxicity is a major complication of cisplatin-based chemotherapy, leading to acute kidney injury in ca. 30% of patients, with no preventive intervention or treatment available for clinical use. Cilastatin has proved to exert a nephroprotective effect for cisplatin therapies in in vitro and in vivo models, having recently entered clinical trials. A deeper understanding at the molecular level of cisplatin-induced renal damage and the effect of potential protective agents could be key to develop successful nephroprotective therapies and to establish new biomarkers of renal damage and nephroprotection. A targeted lipidomics approach, using LC-MS/MS, was employed for the quantification of 108 lipid species (comprising phospholipids, sphingolipids, and free and esterified cholesterol) in kidney cortex and medulla extracts from rats treated with cisplatin and/or cilastatin. Up to 56 and 63 lipid species were found to be altered in the cortex and medulla, respectively, after cisplatin treatment. Co-treatment with cilastatin attenuated many of these lipid changes, either totally or partially with respect to control levels. Multivariate analysis revealed that lipid species can be used to discriminate renal damage and nephroprotection, with cholesterol esters being the most discriminating species, along with sulfatides and phospholipids. Potential diagnostic biomarkers of cisplatin-induced renal damage and cilastatin nephroprotection were also found.

The Antipsychotic Risperidone Alters Dihydroceramide and Ceramide Composition and Plasma Membrane Function in Leukocytes In Vitro and In Vivo.

Atypical or second-generation antipsychotics are used in the treatment of psychosis and behavioral problems in older persons with dementia. However, these pharmaceutical drugs are associated with an increased risk of stroke in such patients. In this study, we evaluated the effects of risperidone treatment on phospholipid and sphingolipid composition and lipid raft function in peripheral blood mononuclear cells (PBMCs) of older patients (mean age >88 years). The results showed that the levels of dihydroceramides, very-long-chain ceramides, and lysophosphatidylcholines decreased in PBMCs of the risperidone-treated group compared with untreated controls. These findings were confirmed by in vitro assays using human THP-1 monocytes. The reduction in the levels of very-long-chain ceramides and dihydroceramides could be due to the decrease in the expression of fatty acid elongase 3, as observed in THP-1 monocytes. Moreover, risperidone disrupted lipid raft domains in the plasma membrane of PBMCs. These results indicated that risperidone alters phospholipid and sphingolipid composition and lipid raft domains in PBMCs of older patients, potentially affecting multiple signaling pathways associated with these membrane domains.

A normalized signal calibration with a long-term reference improves the robustness of RPLC-MRM/MS lipidomics in plasma.

Improving the reliability of quantification in lipidomic analyses is crucial for its successful application in the discovery of new biomarkers or in clinical practice. In this study, we propose a workflow to improve the accuracy and precision of lipidomic results issued by the laboratory. Lipid species from 11 classes were analyzed by a targeted RPLC-MRM/MS method. The peak areas of species were used to estimate concentrations by an internal standard calibration approach (IS-calibration) and by an alternative normalization signal calibration schema (NS-calibration). The latter uses a long-term reference plasma material as a matrix-matched external calibrator whose accuracy was compared to the NIST SRM-1950 mean consensus values reported by the Interlaboratory Lipidomics Comparison Exercise. The bias of lipid concentrations showed a good accuracy for 69 of 89 quantified lipids. The quantitation of species by the NS-calibration schema improved the within- and between-batch reproducibility in quality control samples, in comparison to the usual IS-calibration approach. Moreover, the NS-calibration workflow improved the robustness of the lipidomics measurements reducing the between-batch variability (relative standard deviation <10% for 95% of lipid species) in real conditions tested throughout the analysis of 120 plasma samples. In addition, we provide a free access web tool to obtain the concentration of lipid species by the two previously mentioned quantitative approaches, providing an easy follow-up of quality control tasks related to lipidomics.