The Immunopeptidomics Ontology (ImPO).

The adaptive immune response plays a vital role in eliminating infected and aberrant cells from the body. This process hinges on the presentation of short peptides by major histocompatibility complex Class I molecules on the cell surface. Immunopeptidomics, the study of peptides displayed on cells, delves into the wide variety of these peptides. Understanding the mechanisms behind antigen processing and presentation is crucial for effectively evaluating cancer immunotherapies. As an emerging domain, immunopeptidomics currently lacks standardization-there is neither an established terminology nor formally defined semantics-a critical concern considering the complexity, heterogeneity, and growing volume of data involved in immunopeptidomics studies. Additionally, there is a disconnection between how the proteomics community delivers the information about antigen presentation and its uptake by the clinical genomics community. Considering the significant relevance of immunopeptidomics in cancer, this shortcoming must be addressed to bridge the gap between research and clinical practice. In this work, we detail the development of the ImmunoPeptidomics Ontology, ImPO, the first effort at standardizing the terminology and semantics in the domain. ImPO aims to encapsulate and systematize data generated by immunopeptidomics experimental processes and bioinformatics analysis. ImPO establishes cross-references to 24 relevant ontologies, including the National Cancer Institute Thesaurus, Mondo Disease Ontology, Logical Observation Identifier Names and Codes and Experimental Factor Ontology. Although ImPO was developed using expert knowledge to characterize a large and representative data collection, it may be readily used to encode other datasets within the domain. Ultimately, ImPO facilitates data integration and analysis, enabling querying, inference and knowledge generation and importantly bridging the gap between the clinical proteomics and genomics communities. As the field of immunogenomics uses protein-level immunopeptidomics data, we expect ImPO to play a key role in supporting a rich and standardized description of the large-scale data that emerging high-throughput technologies are expected to bring in the near future. Ontology URL: https://zenodo.org/record/10237571 Project GitHub: https://github.com/liseda-lab/ImPO/blob/main/ImPO.owl.

Somatic mutational profiling and clinical impact of driver genes in Latin-Iberian medulloblastomas: Towards precision medicine.

Medulloblastoma (MB) is the most prevalent malignant brain tumor in children, known for its heterogeneity and treatment-associated toxicity, and there is a critical need for new therapeutic targets. We analyzed the somatic mutation profile of 15 driver genes in 69 Latin-Iberian molecularly characterized medulloblastomas using the Illumina TruSight Tumor 15 panel. We classified the variants based on their clinical impact and oncogenicity. Among the patients, 66.7% were MBSHH, 13.0% MBWNT, 7.3% MBGrp3, and 13.0% MBGrp4. Among the 63 variants found, 54% were classified as Tier I/II and 31.7% as oncogenic/likely oncogenic. We observed 33.3% of cases harboring at least one mutation. TP53 (23.2%, 16/69) was the most mutated gene, followed by PIK3CA (5.8%, 4/69), KIT (4.3%, 3/69), PDGFRA (2.9%, 2/69), EGFR (1.4%, 1/69), ERBB2 (1.4%, 1/69), and NRAS (1.4%, 1/69). Approximately 41% of MBSHH tumors exhibited mutations, TP53 (32.6%) being the most frequently mutated gene. Tier I/II and oncogenic/likely oncogenic TP53 variants were associated with relapse, progression, and lower survival rates. Potentially actionable variants in the PIK3CA and KIT genes were identified. Latin-Iberian medulloblastomas, particularly the MBSHH, exhibit higher mutation frequencies than other populations. We corroborate the TP53 mutation status as an important prognostic factor, while PIK3CA and KIT are potential therapeutic targets.

High frequency of WNT-activated medulloblastomas with CTNNB1 wild type suggests a higher proportion of hereditary cases in a Latin-Iberian population.

Purpose: Medulloblastomas are the most common primary malignant brain tumors in children. They are divided into molecular subgroups: WNT-activated, SHH-Activated, TP53 mutant or wild type, and non-WNT/non-SHH (Groups 3 and 4). WNT-activated medulloblastomas are usually caused by mutations in the CTNNB1 gene (85%-90%), and most remaining cases of CTNNB1 wild type are thought to be caused by germline mutations in APC. So far, the frequencies of CTNNB1 have been reported mainly in North American and European populations. The aim of this study was to report the frequency of CTNNB1 mutations in WNT-activated medulloblastomas in a Latin-Iberian population and correlate with their clinicopathological characteristics. Methods: A total of 266 medulloblastomas from seven different institutions from Brazil (n=211), Portugal (n=38), and Argentina (n=17) were evaluated. Following RNA and DNA isolation from formalin-fixed, paraffin-embedded (FFPE) tumor tissues, the molecular classification and CTNNB1 mutation analysis were performed by nCounter and Sanger sequencing, respectively. Results: WNT-activated medulloblastomas accounted for 15% (40/266) of the series. We observed that 73% of WNT-activated medulloblastomas harbored CTNNB1 mutations. CTNNB1 wild-type cases (27%) were more prevalent in female individuals and suggested to be associated with a worse outcome. Among the CTNNB1 wild-type cases, the available analysis of family history revealed two cases with familiar adenomatous polyposis, harboring APC germline variants. Conclusion: We observed a lower incidence of CTNNB1 mutations in WNT-activated medulloblastomas in our Latin-Iberian cohort compared to frequencies previously described in other populations. Considering that CTNNB1 wild-type cases may exhibit APC germline mutations, our study suggests a higher incidence (~30%) of hereditary WNT-activated medulloblastomas in the Latin-Iberian population.

Multi-domain knowledge graph embeddings for gene-disease association prediction.

BACKGROUND: Predicting gene-disease associations typically requires exploring diverse sources of information as well as sophisticated computational approaches. Knowledge graph embeddings can help tackle these challenges by creating representations of genes and diseases based on the scientific knowledge described in ontologies, which can then be explored by machine learning algorithms. However, state-of-the-art knowledge graph embeddings are produced over a single ontology or multiple but disconnected ones, ignoring the impact that considering multiple interconnected domains can have on complex tasks such as gene-disease association prediction. RESULTS: We propose a novel approach to predict gene-disease associations using rich semantic representations based on knowledge graph embeddings over multiple ontologies linked by logical definitions and compound ontology mappings. The experiments showed that considering richer knowledge graphs significantly improves gene-disease prediction and that different knowledge graph embeddings methods benefit more from distinct types of semantic richness. CONCLUSIONS: This work demonstrated the potential for knowledge graph embeddings across multiple and interconnected biomedical ontologies to support gene-disease prediction. It also paved the way for considering other ontologies or tackling other tasks where multiple perspectives over the data can be beneficial. All software and data are freely available.

Single nCounter assay for prediction of MYCN amplification and molecular classification of medulloblastomas: a multicentric study.

PURPOSE: Medulloblastoma is the most frequent pediatric malignant brain tumor, and is divided into four main subgroups: WNT, SHH, group 3, and group 4. MYCN amplification is an important medulloblastoma prognostic biomarker. We aimed to molecular classify and predict MYCN amplification in a single assay. METHODS: It was included 209 medulloblastomas from 205 patients (Brazil, Argentina, and Portugal), divided into training (n = 50) and validation (n = 159) sets. A nCounter assay was carried out using a custom panel for molecular classification, with additional genes, including MYCN. nSolver 4.0 software and the R environment were used for profiling and MYCN mRNA analysis. MYCN amplification by FISH was performed in 64 cases. RESULTS: The 205 medulloblastomas were classified in SHH (44.9%), WNT (15.6%), group 3 (18.1%) and group 4 (21.4%). In the training set, MYCN amplification was detected in three SHH medulloblastomas by FISH, which showed significantly higher MYCN mRNA counts than non-FISH amplified cases, and a cutoff for MYCN amplification was established ([Formula: see text] + 4σ = 11,124.3). Applying this threshold value in the validation set, we identified MYCN mRNA counts above the cutoff in three cases, which were FISH validated. CONCLUSION: We successfully stratified medulloblastoma molecular subgroups and predicted MYCN amplification using a single nCounter assay without the requirement of additional biological tissue, costs, or bench time.

Electroconvulsive Therapy in Refractory Obsessive-Compulsive Disorder: A Case Report.

ABSTRACT: Electroconvulsive therapy (ECT) is a treatment of undisputed efficacy for severe and treatment-resistant psychiatric disorders. Notwithstanding extensive data on efficacy and safety, it is significantly underused, corresponding to one of the most stigmatized approaches in psychiatry. The list of problems for which ECT is potentially effective does not include obsessive-compulsive disorder (OCD), resulting in only a few available case reports in the literature in which OCD is the target of this specific therapeutic strategy. The authors describe a patient with refractory OCD for whom ECT was prescribed, with remarkable clinical response and functional improvement. The existence of a clear response to ECT in reported cases of OCD, albeit in a globally small number of patients, should make it essential to identify predictors of ECT response that could assist clinicians in assessing and guiding such cases, particularly those labeled as refractory to treatment.

TAMOXIFEN-INDUCED CHORIORETINAL CHANGES: An Optical Coherence Tomography and Optical Coherence Tomography Angiography Study.

PURPOSE: To study structural chorioretinal changes in tamoxifen-treated patients. METHODS: Cross-sectional case-control study comparing structural chorioretinal aspects in tamoxifen-treated patients and healthy controls. Enhanced depth spectral domain optic coherence tomography with choroidal binarization and optic coherence tomography angiography were performed. Individual retinal layer thickness and chorioretinal vascular components were compared. Subgroup analysis regarding history of chemotherapy was performed. RESULTS: Two hundred eyes of 100 TAM-treated patients (Group 1) and 80 eyes of 40 healthy controls (Group 2) were included. Of the 200 spectral domain optic coherence tomography scans from patients, 2 showed structural changes attributable to tamoxifen. Group 1 showed significantly lower values in choroidal parameters and in total retinal, ganglion cell layer, inner plexiform layer, outer nuclear layer, and retinal pigment epithelial thicknesses as well as an increased thickness in the outer plexiform layer. The subgroup not submitted to chemotherapy maintained significant reductions in total retinal thickness, ganglion cell layer, retinal pigment epithelium, outer nuclear layer, outer retinal layer, choroidal parameters, as well as an increased thickness in the outer plexiform layer, in comparison with Group 2. CONCLUSION: Subclinical structural retinal changes could indicate early retinal pigment epithelial and photoreceptor damage. The new finding of choroidal thinning could point toward another important pathophysiologic process in tamoxifen-induced toxicity.

Antibacterial activity of propolis extracts from the south of Portugal.

To examine the antibacterial activity of diverse extracts of propolis harvested at winter and spring from several locations of Algarve, Portugal, against Gram-negative and Gram-positive bacteria was the main goal of the present work. For such, the antibacterial activity was determined by agar diffusion. The results showed that all tested bacterial strains showed susceptibility to diluted propolis extracts and in a dose-dependent manner. Two propolis samples collected at springtime showed higher antibacterial activity, in comparison with samples harvested at wintertime. Ethanolic and methanolic extracts have a very similar activity (P<0.05). Helicobacter pylori strains J99 and 26695 were the most susceptible strains to the tested extracts (33.67±2.52 mm and 35.67±0.58mm, respectively). This study constitutes the first approach of the biological activities of Portuguese propolis from the Algarve region and evidences its potential use to combat bacterial infections, in particular against the gastric pathogen H. pylori.

Targeted high-throughput sequencing for genetic diagnostics of hemophagocytic lymphohistiocytosis.

BACKGROUND: Hemophagocytic lymphohistiocytosis (HLH) is a rapid-onset, potentially fatal hyperinflammatory syndrome. A prompt molecular diagnosis is crucial for appropriate clinical management. Here, we validated and prospectively evaluated a targeted high-throughput sequencing approach for HLH diagnostics. METHODS: A high-throughput sequencing strategy of 12 genes linked to HLH was validated in 13 patients with previously identified HLH-associated mutations and prospectively evaluated in 58 HLH patients. Moreover, 2504 healthy individuals from the 1000 Genomes project were analyzed in silico for variants in the same genes. RESULTS: Analyses revealed a mutation detection sensitivity of 97.3%, an average coverage per gene of 98.0%, and adequate coverage over 98.6% of sites previously reported as mutated in these genes. In the prospective cohort, we achieved a diagnosis in 22 out of 58 patients (38%). Genetically undiagnosed HLH patients had a later age at onset and manifested higher frequencies of known secondary HLH triggers. Rare, putatively pathogenic monoallelic variants were identified in nine patients. However, such monoallelic variants were not enriched compared with healthy individuals. CONCLUSIONS: We have established a comprehensive high-throughput platform for genetic screening of patients with HLH. Almost all cases with reduced natural killer cell function received a diagnosis, but the majority of the prospective cases remain genetically unexplained, highlighting genetic heterogeneity and environmental impact within HLH. Moreover, in silico analyses of the genetic variation affecting HLH-related genes in the general population suggest caution with respect to interpreting causality between monoallelic mutations and HLH. A complete understanding of the genetic susceptibility to HLH thus requires further in-depth investigations, including genome sequencing and detailed immunological characterization.

Cyanobacteria toxicity: potential public health impact in South Portugal populations.

Cyanobacteria are prokaryotic, plantlike organisms present in lakes, recreational waters, and reservoirs, and often dominate phytoplankton communities in warm, nutrient-enriched hard waters. A stable water column rich in certain nutrients, especially nitrogen and phosphorus, is associated with favorable environmental conditions that support development of cyanobacterial population maxima or "blooms." Under specific conditions, cyanobacteria produce toxins that are responsible for acute poisoning and death of animals and humans. The main aim of this study was to correlate the presence of cyanobacteria blooms with potential toxicity to humans as a public health issue. In Portugal, seven reservoirs located in the southern region were selected and studied between 2000 and 2008. Reservoirs were characterized by physical and chemical aspects, and identification of phytoplankton communities. In the case of cyanobacterial blooms, toxins that affected the liver, nervous system, and skin were detected, namely, Microcystis aeruginosa, Aphanizomenon spp., and Oscillatoria. These findings suggest the presence of a potential risk for public health, and indicate the need to implement mitigation measures in all studied reservoirs. These measures may involve (1) water eutrophication control to avoid blooms, (2) appropriate treatment of water for human consumption, and (3) public warnings or information to those individuals that use these reservoirs for several recreational activities.

Propolis volatiles characterisation from acaricide-treated and -untreated beehives maintained at Algarve (Portugal).

The variability of the volatile profile of 70 propolis samples from acaricide-treated and -untreated beehives maintained at Algarve (Portugal) was evaluated. Propolis samples were collected in three regions of Algarve at three different periods. Cluster analysis based on the propolis volatiles' chemical composition defined two main clusters, not related to the time of year, collection site, altitude, temperature or humidity ranges, and was based mainly on the relative amounts of viridiflorol, n-tricosane and n-nonadecane for cluster I. Cluster II was mainly characterised by the high thymol content, followed by viridiflorol, n-tricosane and n-nonadecane. The presence of higher thymol levels in propolis samples from cluster II may reflect the long use of an acaricide with thymol as main active ingredient. All samples showed an intense rock-rose aroma supported by the presence of characteristic Cistus and labdanum oil volatile components. Given the nowadays frequent propolis household use, volatiles thorough characterisation may assist in its quality assessment.

Local fetal lung renin-angiotensin system as a target to treat congenital diaphragmatic hernia.

Antenatal stimulation of lung growth is a reasonable approach to treat congenital diaphragmatic hernia (CDH), a disease characterized by pulmonary hypoplasia and hypertension. Several evidences from the literature demonstrated a possible involvement of renin-angiotensin system (RAS) during fetal lung development. Thus, the expression pattern of renin, angiotensin-converting enzyme, angiotensinogen, type 1 (AT1) and type 2 (AT2) receptors of angiotensin II (ANGII) was assessed by immunohisto-chemistry throughout gestation, whereas the function of RAS in the fetal lung was evaluated using fetal rat lung explants. These were morphometrically analyzed and intracellular pathway alterations assessed by Western blot. In nitrofen-induced CDH model, pregnant rats were treated with saline or PD-123319. In pups, lung growth, protein/DNA ratio, radial saccular count, epithelial differentiation and lung maturation, vascular morphometry, right ventricular hypertrophy and overload molecular markers, gasometry and survival time were evaluated. Results demonstrated that all RAS components were constitutively expressed in the lung during gestation and that ANGII had a stimulatory effect on lung branching, mediated by AT1 receptor, through p44/42 and Akt phosphorylation. This stimulatory effect on lung growth was mimicked by AT2-antagonist (PD-123319) treatment. In vivo antenatal PD-123319 treatment increased lung growth, ameliorated indirect parameters of pulmonary hypertension, improved lung function and survival time in nonventilated CDH pups, without maternal or fetal deleterious effects. Therefore, this study demonstrated a local and physiologically active RAS during lung morphogenesis. Moreover, selective inhibition of AT2 receptor is presented as a putative antenatal therapy for CDH.

Phenols and antioxidant activity of hydro-alcoholic extracts of propolis from Algarve, South of Portugal.

Propolis is a natural honeybee product known to be beneficial for human health, with a complex chemical composition, highly dependent on the collection site. The objective of the present research was to evaluate phenols and antioxidant activity of propolis samples collected in three main areas of Algarve, South of Portugal. Water revealed to be less effective for extracting phenolic compounds from propolis than the methanol and water/ethanol. The last two were good extraction solvents of phenols. Nevertheless water/ethanol was the solvent chosen because it was able to extract phenols in considerable amounts being less toxic than methanol. In spring, higher amounts of phenols (total phenols, flavones, flavonols, flavanones and dihydroflavonols) were detected in hydro-alcoholic extracts of propolis than in winter. Among the three main areas of Algarve where samples were collected, those from Barrocal had the highest levels of polyphenols, independent on the season (winter or spring). Within each area, the levels of phenols changed according to the zone. Concerning antioxidant activity, samples from Barrocal presented better radical scavenging abilities than those from the remaining areas, independent on the antioxidant method and collection season. Such results correlated closely with the levels of total phenols, flavones and flavonols in samples.

Ghrelin and obestatin: different role in fetal lung development?

Ghrelin and obestatin are two proteins that originate from post-translational processing of the preproghrelin peptide. Various authors claim an opposed role of ghrelin and obestatin in several systems. Preproghrelin mRNA is significantly expressed in airway epithelium throughout lung development, predominantly during the earliest stages. The aim of this study was to evaluate the role of ghrelin and obestatin in fetal lung development in vitro. Immunohistochemistry studies were performed at different gestational ages in order to clarify the expression pattern of ghrelin, GHS-R1a, obestatin and GPR39 during fetal lung development. Fetal rat lung explants were harvested at 13.5 days post-conception (dpc) and cultured during 4 days with increasing doses of total ghrelin, acylated ghrelin, desacyl-ghrelin, ghrelin antagonist (D-Lys(3)-GHRP-6) or obestatin. Immunohistochemistry studies demonstrated that ghrelin, GHS-R1a, obestatin and GPR39 proteins were expressed in primitive rat lung epithelium throughout all studied gestational ages. Total and acylated ghrelin supplementation significantly increased the total number of peripheral airway buds, whereas desacyl-ghrelin induced no effect. Moreover, GHS-R1a antagonist significantly decreased lung branching. Finally, obestatin supplementation induced no significant effect in the measured parameters. The present study showed that ghrelin has a positive effect in fetal lung development through its GHS-R1a receptor, whereas obestatin has no effect on lung branching.