PhenoLinker: Phenotype-Gene Link Prediction and Explanation using Heterogeneous Graph Neural Networks

The association of a given human phenotype to a genetic variant remains a critical challenge for biology. We present a novel system called PhenoLinker capable of associating a score to a phenotype-gene relationship by using heterogeneous information networks and a convolutional neural network-based model for graphs, which can provide an explanation for the predictions. This system can aid in the discovery of new associations and in the understanding of the consequences of human genetic variation.Comment: 22 pages, 6 figure

Inferior fronto-occipital fascicle displacement in temporoinsular gliomas using diffusion tensor imaging

Background and purpose: Brain tumors can result in displacement or destruction of important white matter tracts such as the inferior fronto-occipital fascicle (IFOF). Diffusion tensor imaging (DTI) can assess the extent of this effect and potentially provide neurosurgeons with an accurate map to guide tumor resection; analyze IFOF displacement patterns in temporoinsular gliomas based on tumor grading and topography in the temporal lobe; and assess whether these patterns follow a predictable pattern, to assist in maximal tumor resection while preserving IFOF function. Methods: Thirty-four patients with temporal gliomas and available presurgical MRI were recruited. Twenty-two had insula infiltration. DTI deterministic region of interest (ROI)-based tractography was performed using commercial software. Tumor topographic imaging characteristics analyzed were as follows: location in the temporal lobe and extent of extratemporal involvement. Qualitative tractographic data obtained from directional DTI color maps included type of involvement (displaced/edematous-infiltrated/destroyed) and displacement direction. Quantitative tractographic data of ipsi- and contralateral IFOF included whole tract volume, fractional anisotropy, and fractional anisotropy of a 2-dimensional coronal ROI on the tract at the point of maximum tumor involvement. Results: The most common tract involvement pattern was edematous/infiltrative displacement. Displacement patterns depended on main tumor location in the temporal lobe and presence of insular involvement. All tumors showed superior displacement pattern. In lateral tumors, displacement tendency was medial. In medial tumors, displacement tendency was lateral. When we add insular involvement, the tendency was more medial displacement. A qualitative and quantitative assessment supported these results. Conclusions: IFOF displacement patterns are reproducible and suitable for temporoinsular gliomas presurgical planning

Categorization of Mining Materials for Restoration Projects by Means of Pollution Indices and Bioassays

Sulfide mining wastes may lead to severe environmental and human health risks. This study aims to use geochemical and ecotoxicological indicators for the assessment of the ecological risks of potentially toxic elements (PTEs) in the San Quintín mining group to categorize wastes prior to mining restoration. Ecotoxicity was evaluated using crustacean (Dahpnia magna, Thamnocephalus platyurus) and algae (Raphidocelis subcapitata) bioassays. The geochemical and mineralogical results suggested that the mining residues underwent intense weathering processes, with active processes of acidity generation and metal mobility. Total PTEs concentrations indicated that the mining materials were extremely polluted, with Pb, Zn and Cd geoaccumulation index (Igeo) values higher than 5 in more than 90% of the samples. The pollution load index (PLI) showed average values of 18.1, which classifies them as very highly polluted. The toxicity tests showed a higher toxicity for plants than crustaceans, being the highest values of toxicity related to toxic elements (Pb, Cd and Zn), electrical conductivity and to pH. This paper presents for the first time the combination of indices in the categorization of mining waste prior to its restoration. The combination of them has made it possible to categorize the waste and adapt the restoration and remediation procedures.Depto. de Mineralogía y PetrologíaFac. de Ciencias GeológicasTRUEMinisterio de Ciencia e Innovaciónpu

Molecular recognition of a membrane-anchored HIV-1 pan-neutralizing epitope.

Antibodies against the carboxy-terminal section of the membrane-proximal external region (C-MPER) of the HIV-1 envelope glycoprotein (Env) are considered as nearly pan-neutralizing. Development of vaccines capable of producing analogous broadly neutralizing antibodies requires deep understanding of the mechanism that underlies C-MPER recognition in membranes. Here, we use the archetypic 10E8 antibody and a variety of biophysical techniques including single-molecule approaches to study the molecular recognition of C-MPER in membrane mimetics. In contrast to the assumption that an interfacial MPER helix embodies the entire C-MPER epitope recognized by 10E8, our data indicate that transmembrane domain (TMD) residues contribute to binding affinity and specificity. Moreover, anchoring to membrane the helical C-MPER epitope through the TMD augments antibody binding affinity and relieves the effects exerted by the interfacial MPER helix on the mechanical stability of the lipid bilayer. These observations support that addition of TMD residues may result in more efficient and stable anti-MPER vaccines.This study was supported by MCIN/AEI/10.13039/501100011033 - “ERDF A way of making Europe” (Grant PID2021-126014OB-I00 to J.L.N. and B.A.), MCIN/AEI/10.13039/501100011033 (Grant PID2020-112821GB-I00 to M.A.J.), Basque Government (Grant: IT1449-22 to J.L.N. and B.A.) and Kiban-B grant 20H03228 from JSPS to J.M.M.C. L.R.-M. acknowledges funding from the Agence National de la Recherche (ANR), as part of the ‘Investments d′Avenir’ Program (I-SITE ULNE/ANR-16-IDEX-0004 ULNE). This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No. 895819 (to C.V.). Work at Pompeu Fabra University was supported by the María de Maeztu network of Units of Excellence of the Spanish Ministry of Science and Innovation. Technical assistance from Miguel García-Porras is greatly acknowledged. The NMR experiments were performed in the “Manuel Rico” NMR laboratory, LMR, CSIC, a node of the Spanish Large-Scale National Facility ICTS R-LRB

High-Sensitivity Troponin T and Soluble Form of AXL as Long-Term Prognostic Biomarkers after Heart Transplantation

Cardiac allograft vasculopathy (CAV) is a frequent complication limiting the long-term (>1 year) survival after heart transplantation (HTx). CAV is initiated by endothelial dysfunction and can lead to severe cardiovascular (CV) complications. Since CAV is often clinically silent, biomarkers could help identifying HTx patients at risk of CAV and their severe complications. Evaluate the clinical yield of high-sensitivity cardiac troponin T (hs-cTnT), marker of cardiomyocyte damage, and the soluble form of AXL (sAXL), biomarker of endothelial dysfunction, to assess the prognosis of long-term cardiovascular (CV) events occurring after HTx. 96 patients were evaluated at least > 1 year after HTx. CAV was evaluated by coronary angiography or multisliced tomography, and hs-cTnT and sAXL measured 6 months before or after CAV evaluation. Patients were followed during 42 ± 15 months for a combined end point including cardiac death, angina or acute myocardial infarction, left ventricular ejection fraction 21 ng/L (p<0.001). Hs-cTnT, but not sAXL, measured during the long-term follow-up of HTx patients appears as a helpful biomarker to identify patients at low risk of adverse CV outcomes

A genome-wide association study follow-up suggests a possible role for PPARG in systemic sclerosis susceptibility

Introduction: A recent genome-wide association study (GWAS) comprising a French cohort of systemic sclerosis (SSc) reported several non-HLA single-nucleotide polymorphisms (SNPs) showing a nominal association in the discovery phase. We aimed to identify previously overlooked susceptibility variants by using a follow-up strategy.&lt;p&gt;&lt;/p&gt; Methods: Sixty-six non-HLA SNPs showing a P value &#60;10-4 in the discovery phase of the French SSc GWAS were analyzed in the first step of this study, performing a meta-analysis that combined data from the two published SSc GWASs. A total of 2,921 SSc patients and 6,963 healthy controls were included in this first phase. Two SNPs, PPARG rs310746 and CHRNA9 rs6832151, were selected for genotyping in the replication cohort (1,068 SSc patients and 6,762 healthy controls) based on the results of the first step. Genotyping was performed by using TaqMan SNP genotyping assays. Results: We observed nominal associations for both PPARG rs310746 (PMH = 1.90 × 10-6, OR, 1.28) and CHRNA9 rs6832151 (PMH = 4.30 × 10-6, OR, 1.17) genetic variants with SSc in the first step of our study. In the replication phase, we observed a trend of association for PPARG rs310746 (P value = 0.066; OR, 1.17). The combined overall Mantel-Haenszel meta-analysis of all the cohorts included in the present study revealed that PPARG rs310746 remained associated with SSc with a nominal non-genome-wide significant P value (PMH = 5.00 × 10-7; OR, 1.25). No evidence of association was observed for CHRNA9 rs6832151 either in the replication phase or in the overall pooled analysis.&lt;p&gt;&lt;/p&gt; Conclusion: Our results suggest a role of PPARG gene in the development of SSc

Factors associated with severe dry eye in primary Sjögren´s syndrome diagnosed patients

Introduction Primary Sjögren?s syndrome (pSS) is an autoimmune disease, characterized by lymphocytic infiltration of exocrine glands and other organs, resulting in dry eye, dry mouth and extraglandular systemic findings. Objective To explore the association of severe or very severe dry eye with extraocular involvement in patients diagnosed with primary Sjögren?s syndrome. Methods SJOGRENSER registry is a multicenter cross-sectional study of pSS patients. For the construction of our main variable, severe/very severe dry eye, we used those variables that represented a degree 3?4 of severity according to the 2007 Dry Eye Workshop classification. First, bivariate logistic regression models were used to identify the effect of each independent variable on severe/very severe dry eye. Secondly, multivariate analysis using regression model was used to establish the independent effect of patient characteristics. Results Four hundred and thirty-seven patients were included in SJOGRENSER registry; 94% of the patients complained of dry eye and 16% developed corneal ulcer. Schirmer?s test was pathological in 92% of the patients; 378 patients presented severe/very severe dry eye. Inflammatory articular involvement was significantly more frequent in patients with severe/very severe dry eye than in those without severe/very severe dry eye (82.5 vs 69.5%, p = 0,028). Inflammatory joint involvement was associated with severe/very severe dry eye in the multivariate analysis, OR 2.079 (95% CI 1.096?3.941). Conclusion Severe or very severe dry eye is associated with the presence of inflammatory joint involvement in patients with pSS. These results suggest that a directed anamnesis including systemic comorbidities, such as the presence of inflammatory joint involvement or dry mouth in patients with dry eye, would be useful to suspect a pSS

How does neighbourhood socio-economic status affect the interrelationships between functioning dimensions in first episode of psychosis? A network analysis approach

The links between psychosis and socio-economic disadvantage have been widely studied. No previous study has analysed the interrelationships and mutual influences between functioning dimensions in first episode of psychosis (FEP) according to their neighbourhood household income, using a multidimensional and transdiagnostic perspective. 170 patients and 129 controls, participants in an observational study (AGES-CM), comprised the study sample. The WHO Disability Assessment Schedule (WHODAS 2.0) was used to assess functioning, whereas participants' postcodes were used to obtain the average household income for each neighbourhood, collected by the Spanish National Statistics Institute (INE). Network analyses were conducted with the aim of defining the interrelationships between the different dimensions of functioning according to the neighbourhood household income. Our results show that lower neighbourhood socioeconomic level is associated with lower functioning in patients with FEP. Moreover, our findings suggest that “household responsibilities” plays a central role in the disability of patients who live in low-income neighbourhoods, whereas “dealing with strangers” is the most important node in the network of patients who live in high-income neighbourhoods. These results could help to personalize treatments, by allowing the identification of potential functioning areas to be prioritized in the treatment of FEP according to the patient's neighbourhood characteristic

Evidence for classification of c.1852_1853AA>GC in MLH1 as a neutral variant for Lynch syndrome

Background: Lynch syndrome (LS) is an autosomal dominant inherited cancer syndrome characterized by early onset cancers of the colorectum, endometrium and other tumours. A significant proportion of DNA variants in LS patients are unclassified. Reports on the pathogenicity of the c.1852_1853AA>GC (p.Lys618Ala) variant of the MLH1 gene are conflicting. In this study, we provide new evidence indicating that this variant has no significant implications for LS. Methods: The following approach was used to assess the clinical significance of the p.Lys618Ala variant: frequency in a control population, case-control comparison, co-occurrence of the p.Lys618Ala variant with a pathogenic mutation, co-segregation with the disease and microsatellite instability in tumours from carriers of the variant. We genotyped p.Lys618Ala in 1034 individuals (373 sporadic colorectal cancer [CRC] patients, 250 index subjects from families suspected of having LS [revised Bethesda guidelines] and 411 controls). Three well-characterized LS families that fulfilled the Amsterdam II Criteria and consisted of members with the p.Lys618Ala variant were included to assess co-occurrence and co-segregation. A subset of colorectal tumour DNA samples from 17 patients carrying the p.Lys618Ala variant was screened for microsatellite instability using five mononucleotide markers. Results: Twenty-seven individuals were heterozygous for the p.Lys618Ala variant; nine had sporadic CRC (2.41%), seven were suspected of having hereditary CRC (2.8%) and 11 were controls (2.68%). There were no significant associations in the case-control and case-case studies. The p.Lys618Ala variant was co-existent with pathogenic mutations in two unrelated LS families. In one family, the allele distribution of the pathogenic and unclassified variant was in trans, in the other family the pathogenic variant was detected in the MSH6 gene and only the deleterious variant co-segregated with the disease in both families. Only two positive cases of microsatellite instability (2/17, 11.8%) were detected in tumours from p.Lys618Ala carriers, indicating that this variant does not play a role in functional inactivation of MLH1 in CRC patients. Conclusions: The p.Lys618Ala variant should be considered a neutral variant for LS. These findings have implications for the clinical management of CRC probands and their relatives.Generalitat Valenciana in Spain (AP140/08) and the Biomedical Research Foundation from the Hospital of Elche, Spain (FIBElx0902). Conselleria de Educació (Generalitat Valenciana); Fundacion Juan Peran-Pikolinos; Fundacion Carolina-BBVA and Fondo Investigación Sanitaria (FI07/00303). Instituto de Salud Carlos III (INT09/208)