Identification of Novel Molecular and Clinical Biomarkers of Survival in Glioblastoma Multiforme Patients: A Study Based on The Cancer Genome Atlas Data.

Glioblastoma multiforme (GBM) is the most prevalent type of brain tumour; although advancements in treatment have been made, the median survival time for GBM patients has persisted at 15 months. This study is aimed at investigating the genetic alterations and clinical features of GBM patients to find predictors of survival. GBM patients' methylation and gene expression data along with clinical information from TCGA were retrieved. The most overrepresented pathways were identified independently for each omics dataset. From the genes found in at least 30% of these pathways, one gene that was identified in both sets was further examined using the Kaplan-Meier method for survival analysis. Additionally, three groups of patients who started radio and chemotherapy at different times were identified, and the influence of these variations in treatment modality on patient survival was evaluated. Four pathways that seemed to negatively impact survival and two with the opposite effect were identified. The methylation status of PRKCB was highlighted as a potential novel biomarker for patient survival. The study also found that treatment with chemotherapy prior to radiotherapy can have a significant impact on patient survival, which could lead to improvements in clinical management and therapeutic approaches for GBM patients.

Principles in the Management of Glioblastoma.

Glioblastoma, the most aggressive and common malignant primary brain tumour, is characterized by infiltrative growth, abundant vascularization, and aggressive clinical evolution. Patients with glioblastoma often face poor prognoses, with a median survival of approximately 15 months. Technological progress and the subsequent improvement in understanding the pathophysiology of these tumours have not translated into significant achievements in therapies or survival outcomes for patients. Progress in molecular profiling has yielded new omics data for a more refined classification of glioblastoma. Several typical genetic and epigenetic alterations in glioblastoma include mutations in genes regulating receptor tyrosine kinase (RTK)/rat sarcoma (RAS)/phosphoinositide 3-kinase (PI3K), p53, and retinoblastoma protein (RB) signalling, as well as mutation of isocitrate dehydrogenase (IDH), methylation of O6-methylguanine-DNA methyltransferase (MGMT), amplification of epidermal growth factor receptor vIII, and codeletion of 1p/19q. Certain microRNAs, such as miR-10b and miR-21, have also been identified as prognostic biomarkers. Effective treatment options for glioblastoma are limited. Surgery, radiotherapy, and alkylating agent chemotherapy remain the primary pillars of treatment. Only promoter methylation of the gene MGMT predicts the benefit from alkylating chemotherapy with temozolomide and it guides the choice of first-line treatment in elderly patients. Several targeted strategies based on tumour-intrinsic dominant signalling pathways and antigenic tumour profiles are under investigation in clinical trials. This review explores the potential genetic and epigenetic biomarkers that could be deployed as analytical tools in the diagnosis and prognostication of glioblastoma. Recent clinical advancements in treating glioblastoma are also discussed, along with the potential of liquid biopsies to advance personalized medicine in the field of glioblastoma, highlighting the challenges and promises for the future.

Characterization of Plastic Scintillator Detector for In Vivo Dosimetry in Gynecologic Brachytherapy.

(1) Background: High dose gradients and manual steps in brachytherapy treatment procedures can lead to dose errors which make the use of in vivo dosimetry (IVD) highly recommended for verifying brachytherapy treatments. A new procedure was presented to obtain a calibration factor which allows fast and robust calibration of plastic scintillation detector (PSD) probes for the geometry of a compact phantom using Monte Carlo simulations. Additionally, characterization of PSD energy, angular, and temperature dependences was performed. (2) Methods: PENELOPE/PenEasy code was used to obtain the calibration factor. To characterize the energy dependence of the PSD, the signal was measured at different radial and transversal distances. The sensitivity to the angular position was characterized in axial and azimuthal planes. (3) Results: The calibration factor obtained allows for an absorbed dose to water determination in full scatter conditions from ionization measured in a mini polymethylmethacrylate (PMMA) phantom. The energy dependence of the PSD along the radial distances obtained was (2.3 ± 2.1)% (k = 1). The azimuthal angular dependence measured was (2.6 ± 3.4)% (k = 1). The PSD response decreased by (0.19 ± 0.02)%/°C with increasing detector probe temperature. (4) Conclusions: The energy, angular, and temperature dependence of a PSD is compatible with IVD.

Transcriptomic remodeling of gastric cells by Helicobacter pylori outer membrane vesicles.

BACKGROUND: Outer membrane vesicles (OMVs) are spontaneously released by Gram-negative bacteria and influence bacteria-host interactions by acting as a delivery system for bacterial components and by interacting directly with host cells. Helicobacter pylori, a pathogenic bacterium that chronically colonizes the human stomach, also sheds OMVs, and their impact on bacterial-mediated diseases is still being elucidated. MATERIALS AND METHODS: Transcriptomic profiling of the human gastric cell line MKN74 upon challenge with H. pylori OMVs compared to control and infected cells was performed using the Ion AmpliSeq™ Transcriptome Human Gene Expression Panel to understand the gene expression changes that human gastric epithelial cells might undergo when exposed to H. pylori OMVs. RESULTS: H. pylori OMVs per se modify the gene expression profile of gastric epithelial cells, adding another layer of (gene) regulation to the already complex host-bacteria interaction. The most enriched pathways include those related to amino acid metabolism, mitogen-activated protein kinase signaling, autophagy, and ferroptosis, whereas the cell cycle, DNA replication, and DNA repair were the most downregulated. The transcriptomic changes induced by OMVs were mostly similar to those induced by the parental bacteria, likely amplifying the effects of the bacterium itself. CONCLUSIONS: Our data provide a valuable portrayal of the transcriptomic remodeling of gastric cells induced by H. pylori OMVs. It demonstrates the breadth of cellular pathways and genes affected by OMVs, most previously unreported, which can be further dissected for the underlying molecular mediators and explored to understand the pathobiology of the full spectrum of H. pylori-mediated diseases.

Mind the gap: reconciling tropical forest carbon flux estimates from earth observation and national reporting requires transparency.

BACKGROUND: The application of different approaches calculating the anthropogenic carbon net flux from land, leads to estimates that vary considerably. One reason for these variations is the extent to which approaches consider forest land to be "managed" by humans, and thus contributing to the net anthropogenic flux. Global Earth Observation (EO) datasets characterising spatio-temporal changes in land cover and carbon stocks provide an independent and consistent approach to estimate forest carbon fluxes. These can be compared against results reported in National Greenhouse Gas Inventories (NGHGIs) to support accurate and timely measuring, reporting and verification (MRV). Using Brazil as a primary case study, with additional analysis in Indonesia and Malaysia, we compare a Global EO-based dataset of forest carbon fluxes to results reported in NGHGIs. RESULTS: Between 2001 and 2020, the EO-derived estimates of all forest-related emissions and removals indicate that Brazil was a net sink of carbon (- 0.2 GtCO2yr-1), while Brazil's NGHGI reported a net carbon source (+ 0.8 GtCO2yr-1). After adjusting the EO estimate to use the Brazilian NGHGI definition of managed forest and other assumptions used in the inventory's methodology, the EO net flux became a source of + 0.6 GtCO2yr-1, comparable to the NGHGI. Remaining discrepancies are due largely to differing carbon removal factors and forest types applied in the two datasets. In Indonesia, the EO and NGHGI net flux estimates were similar (+ 0.6 GtCO2 yr-1), but in Malaysia, they differed in both magnitude and sign (NGHGI: -0.2 GtCO2 yr-1; Global EO: + 0.2 GtCO2 yr-1). Spatially explicit datasets on forest types were not publicly available for analysis from either NGHGI, limiting the possibility of detailed adjustments. CONCLUSIONS: By adjusting the EO dataset to improve comparability with carbon fluxes estimated for managed forests in the Brazilian NGHGI, initially diverging estimates were largely reconciled and remaining differences can be explained. Despite limited spatial data available for Indonesia and Malaysia, our comparison indicated specific aspects where differing approaches may explain divergence, including uncertainties and inaccuracies. Our study highlights the importance of enhanced transparency, as set out by the Paris Agreement, to enable alignment between different approaches for independent measuring and verification.

Exosomes modified with anti-MEK1 siRNA lead to an effective silencing of triple negative breast cancer cells.

Triple negative breast cancer (TNBC) is a highly heterogenous disease not sensitive to endocrine or HER2 therapy and standardized treatment regimens are still missing. Therefore, development of novel TNBC treatment approaches is of utmost relevance. Herein, the potential of MAPK/ERK downregulation by RNAi-based therapeutics in a panel of mesenchymal stem-like TNBC cell lines was uncovered. Our data revealed that suppression of one of the central nodes of this signaling pathway, MEK1, affects proliferation, migration, and invasion of TNBC cells, that may be explained by the reversion of the epithelial-mesenchymal transition phenotype, which is facilitated by the MMP-2/MMP-9 downregulation. Moreover, an exosome-based system was successfully generated for the siRNA loading (iExoMEK1). Our data suggested absence of modification of the physical properties and general integrity of the iExoMEK1 comparatively to the unmodified counterparts. Such exosome-mediated downregulation of MEK1 led to a tumor regression accompanied by a decrease of angiogenesis using the chick chorioallantoic-membrane model. Our results highlight the potential of the targeting of MAPK/ERK cascade as a promising therapeutic approach against TNBC.

From Dizziness and Hearing Loss to Coma: A Case of Basilar Artery Occlusion.

Basilar artery (BA) occlusion is a rare and devastating cause of ischemic stroke. Presenting symptoms are frequently non-specific and include dizziness, vertigo, nausea, vomiting, headache, and, rarely, hypoacusis. Clinical history and appropriate neurological evaluation are essential for diagnosis. We present the case of a 65-year-old female with dizziness, vomiting, dysarthria, and hearing loss, progressing to right-side hemiparesis and decreased level of consciousness culminating in a coma in just a few hours. She had an atherothrombotic BA occlusion and was submitted to mechanical thrombectomy with full artery recanalization, resulting in rapid neurological improvement in the first days after treatment and almost full recovery during the following months. Early suspicion of posterior circulation stroke from non-specific symptoms is paramount for correct diagnosis and timely treatment, which has an important impact on disability and mortality. Early and complete BA recanalization can result in a positive outcome in a disease that would otherwise be extremely severe. All physicians should be aware of a possible posterior circulation stroke in patients presenting with dizziness, vertigo, vomiting, or sudden hypoacusis and should meticulously search for specific signs or symptoms of neurological dysfunction such as nystagmus, gaze palsies, dysarthria, hemiparesis, or a decreased level of consciousness.

Interaction between genetics and the adherence to the Mediterranean diet: the risk for age-related macular degeneration. Coimbra Eye Study Report 8.

BACKGROUND: Age-related macular degeneration (AMD) is a multifactorial degenerative disease of the macula. Different factors, environmental, genetic and lifestyle, contribute to its onset and progression. However, how they interconnect to promote the disease, or its progression, is still unclear. With this work, we aim to assess the interaction of the genetic risk for AMD and the adherence to the Mediterranean diet in the Coimbra Eye Study. METHODS: Enrolled subjects (n = 612) underwent ophthalmological exams and answered a food questionnaire. Adherence to the Mediterranean diet was assessed with mediSCORE. An overall value was calculated for each participant, ranging from 0 to 9, using the sum of 9 food groups, and a cut off value of ≥ 6 was considered high adherence. Rotterdam Classification was used for grading. Participants' genotyping was performed in collaboration with The European Eye Epidemiology Consortium. The genetic risk score (GRS) was calculated for each participant considering the number of alleles at each variant and their effect size. Interaction was assessed with additive and multiplicative models, adjusted for age, sex, physical exercise, and smoking. RESULTS: The AMD risk was reduced by 60% in subjects with high adherence to the Mediterranean diet compared to subjects with low adherence to the Mediterranean diet. Combined effects of having low adherence to the Mediterranean diet and high GRS led to almost a 5-fold increase in the risk for AMD, compared to low GRS and high adherence to the Mediterranean diet. The multiplicative scale suggested a multiplicative interaction, although not statistically significant [odds ratio (OR) = 1.111, 95% CI 0.346-3.569, P = 0.859]. The additive model showed a causal positive effect of the interaction of GRS and adherence to the Mediterranean diet: relative excess risk due to interaction (RERI) = 150.9%, (95% CI: - 0.414 to 3.432, P = 0.062), attributable proportion due to interaction (AP) = 0.326 (95% CI: - 0.074 to 0.726, P = 0.055) and synergy index (SI) = 1.713 (95% CI: 0.098-3.329, P = 0.019). High GRS people benefited from adhering to the Mediterranean diet with a 60% risk reduction. For low-GRS subjects, a risk reduction was also seen, but not significantly. CONCLUSIONS: Genetics and Mediterranean diet interact to protect against AMD, proving there is an interplay between genetics and environmental factors. TRIAL REGISTRATION: The AMD Incidence (NCT02748824) and Lifestyle and Food Habits Questionnaire in the Portuguese Population Aged 55 or More (NCT01715870) studies are registered at www. CLINICALTRIALS: gov . Five-year Incidence of Age-related Macular Degeneration in the Central Region of Portugal (AMD IncidencePT); NCT02748824: date of registration: 22/04/16. Lifestyle and Food Habits Questionnaire in the Portuguese Population Aged 55 or More; NCT01715870: date of registration: 29/10/12.

Characterization of the functional and transcriptomic effects of pro-inflammatory cytokines on human EndoC-ßH5 beta cells.

Objective: EndoC-ßH5 is a newly established human beta-cell model which may be superior to previous model systems. Exposure of beta cells to pro-inflammatory cytokines is widely used when studying immune-mediated beta-cell failure in type 1 diabetes. We therefore performed an in-depth characterization of the effects of cytokines on EndoC-ßH5 cells. Methods: The sensitivity profile of EndoC-ßH5 cells to the toxic effects of interleukin-1ß (IL-1ß), interferon γ (IFNγ) and tumor necrosis factor-α (TNFα) was examined in titration and time-course experiments. Cell death was evaluated by caspase-3/7 activity, cytotoxicity, viability, TUNEL assay and immunoblotting. Activation of signaling pathways and major histocompatibility complex (MHC)-I expression were examined by immunoblotting, immunofluorescence, and real-time quantitative PCR (qPCR). Insulin and chemokine secretion were measured by ELISA and Meso Scale Discovery multiplexing electrochemiluminescence, respectively. Mitochondrial function was evaluated by extracellular flux technology. Global gene expression was characterized by stranded RNA sequencing. Results: Cytokines increased caspase-3/7 activity and cytotoxicity in EndoC-ßH5 cells in a time- and dose-dependent manner. The proapoptotic effect of cytokines was primarily driven by IFNγ signal transduction. Cytokine exposure induced MHC-I expression and chemokine production and secretion. Further, cytokines caused impaired mitochondrial function and diminished glucose-stimulated insulin secretion. Finally, we report significant changes to the EndoC-ßH5 transcriptome including upregulation of the human leukocyte antigen (HLA) genes, endoplasmic reticulum stress markers, and non-coding RNAs, in response to cytokines. Among the differentially expressed genes were several type 1 diabetes risk genes. Conclusion: Our study provides detailed insight into the functional and transcriptomic effects of cytokines on EndoC-ßH5 cells. This information should be useful for future studies using this novel beta-cell model.

Toward a roadmap for space-based observations of the land sector for the UNFCCC global stocktake.

Space-based remote sensing can make an important contribution toward monitoring greenhouse gas emissions and removals from the agriculture, forestry, and other land use (AFOLU) sector, and to understanding and addressing human-caused climate change through the UNFCCC Paris Agreement. Space agencies have begun to coordinate their efforts to identify needs, collect and harmonize available data and efforts, and plan and maintain a long-term roadmap for observations. International cooperation is crucial in developing and realizing the roadmap, and the Committee on Earth Observation Satellites (CEOS) is a key coordinating driver of this effort. Here, we first identify the data and information that will be useful to support the global stocktake (GST) of the Paris Agreement. Then, the paper explains how existing and planned space-based capabilities and products can be used and combined, particularly in the land use sector, and provides a workflow for their harmonization and contribution to greenhouse gas inventories and assessments at the national and global level.

Alvespimycin Inhibits Heat Shock Protein 90 and Overcomes Imatinib Resistance in Chronic Myeloid Leukemia Cell Lines.

Heat shock protein 90 (HSP90) facilitates folding and stability and prevents the degradation of multiple client proteins. One of these HSP90 clients is BCR-ABL, the oncoprotein characteristic of chronic myeloid leukemia (CML) and the target of tyrosine kinase inhibitors, such as imatinib. Alvespimycin is an HSP90 inhibitor with better pharmacokinetic properties and fewer side effects than other similar drugs, but its role in overcoming imatinib resistance is not yet clarified. This work studied the therapeutic potential of alvespimycin in imatinib-sensitive (K562) and imatinib-resistant (K562-RC and K562-RD) CML cell lines. Metabolic activity was determined by the resazurin assay. Cell death, caspase activity, mitochondrial membrane potential, and cell cycle were evaluated by means of flow cytometry. Cell death was also analyzed by optical microscopy. HSPs expression levels were assessed by western blotting. Alvespimycin reduced metabolic activity in a time-, dose-, and cell line-dependent manner. Resistant cells were more sensitive to alvespimycin with an IC50 of 31 nM for K562-RC and 44 nM for K562-RD, compared to 50 nM for K562. This drug induced apoptosis via the mitochondrial pathway. In K562 cells, alvespimycin induced cell cycle arrest in G0/G1. As a marker of HSP90 inhibition, a significant increase in HSP70 expression was observed. Our results suggest that alvespimycin might be a new therapeutic approach to CML treatment, even in cases of resistance to imatinib.

Aerobic exercise improves central blood pressure and blood pressure variability among patients with resistant hypertension: results of the EnRicH trial.

Central blood pressure (BP) and BP variability are associated with cardiovascular disease risk. However, the influence of exercise on these hemodynamic parameters is unknown among patients with resistant hypertension. The EnRicH (The Exercise Training in the Treatment of Resistant Hypertension) was a prospective, single-blinded randomized clinical trial (NCT03090529). Sixty patients were randomized to a 12-week aerobic exercise program or usual care. The outcome measures include central BP, BP variability, heart rate variability, carotid-femoral pulse wave velocity, and circulating cardiovascular disease risk biomarkers including high-sensitivity C-reactive protein, angiotensin II, superoxide dismutase, interferon gamma, nitric oxide, and endothelial progenitor cells. Central systolic BP decreased by 12.22 mm Hg (95% CI, -1.88 to -22.57, P = 0.022) as did BP variability by 2.85 mm Hg (95% CI, -4.91 to -0.78, P = 0.008), in the exercise (n = 26) compared to the control group (n = 27). Interferon gamma -4.3 pg/mL (95%CI, -7.1 to -1.5, P = 0.003), angiotensin II -157.0 pg/mL (95%CI, -288.1 to -25.9, P = 0.020), and superoxide dismutase 0.4 pg/mL (95%CI, 0.1-0.6, P = 0.009) improved in the exercise compared to the control group. Carotid-femoral pulse wave velocity, heart rate variability, high-sensitivity C-reactive protein, nitric oxide, and endothelial progenitor cells were not different between groups (P > 0.05). In conclusion, a 12-week exercise training program improved central BP and BP variability, and cardiovascular disease risk biomarkers in patients with resistant hypertension. These markers are clinically relevant as they are associated with target organ damage and increased cardiovascular disease risk and mortality.

Resective Epilepsy Surgery and Respective Histopathological Diagnoses: A Retrospective Cohort Study.

INTRODUCTION: Over recent decades, brain resection for drug-resistant epilepsy has proven to be a valuable treatment option. The histopathological classification was of paramount value for patient management. The aims of this study were to characterize our resective epilepsy surgical series including the histopathological diagnoses and to understand the differences in clinical practice between two different periods of our epilepsy surgical programme. MATERIAL AND METHODS: We performed a retrospective cohort study, including patients with drug-resistant epilepsy that underwent resective surgery between 1997 and 2021 in the Coimbra University Hospital Centre. Histopathological diagnoses were classified into seven major conventional categories. For comparison purposes, the cohort was divided into two consecutive periods of 12 years. RESULTS: A total of 259 patients were included, from which 228 (88%) were adults at the time of surgery. The median disease duration prior to surgery was 14 (interquartile range 23) years. Fifty-five (21%) patients performed pre-surgical invasive work-up. The temporal lobe was the most frequently operated region (73%). Major and minor post-surgical complications were identified in 21 (8%) patients. A reduction in the number of antiepileptic drugs was possible in 96 (37%) patients after surgery. The most common histopathological diagnosis was hippocampal sclerosis, but among children it was long-term epilepsy associated tumour. Long-term epilepsy associated tumours, hippocampal sclerosis and vascular malformations had the best post-operative outcomes. Malformations of cortical development and glial scars had the worst outcomes. Regarding differences between the two periods, the absolute number of operated patients increased (119 versus 140), and the age at surgery was higher in the second period (p = 0.04). The number of malformations of cortical development increased (p = 0.01), but the number of other tumours (p = 0.01) and specimens with no lesion (p = 0.03) decreased in the same period. CONCLUSION: This study is in line with contemporaneous research, reinforcing the previous knowledge on the underlying structural aetiologies, clinical practice, and surgical outcomes over more than two decades of experience. Our data provide realistic expectations about epilepsy surgery and highlight the need for further improvements in diagnosis and treatment paradigm for people with chronic epilepsy.

Introdução: Nas últimas décadas, a cirurgia ressectiva demonstrou ser uma opção valiosa no tratamento da epilepsia farmacorresistente. A classificação histopatológica foi de grande importância na orientação do doente. Os objetivos deste estudo foram caracterizar a nossa série de cirurgia de epilepsia ressectiva incluindo os diagnósticos histopatológicos, e compreender as diferenças na prática clínica entre dois períodos diferentes do programa de cirurgia da epilepsia. Material e Métodos: Realizou-se um estudo de coorte retrospetivo, incluindo doentes com epilepsia farmacorresistente submetidos a cirurgia ressectiva entre 1997 e 2021 no Centro Hospitalar e Universitário de Coimbra. Os diagnósticos histopatológicos foram classificados em sete categorias. Para análise comparativa, a coorte foi dividida em dois períodos consecutivos de 12 anos. Resultados: Um total de 259 doentes foram incluídos, sendo 228 (88%) adultos aquando da cirurgia. A mediana da duração da doença antes da cirurgia foi de 14 (amplitude interquartil 23) anos. Cinquenta e cinco (21%) doentes realizaram investigação invasiva pré-cirúrgica. O lobo temporal foi a região mais frequentemente operada (73%). Complicações pós-cirúrgicas major e minor foram identificadas em 21 (8%) doentes. Uma redução no número de antiepiléticos foi observada em 96 (37%) doentes após a cirurgia. O diagnóstico histopatológico mais comum foi a esclerose do hipocampo, mas nas crianças foi o tumor associado a epilepsia de longa duração. Tumores associados a epilepsia de longa duração, esclerose do hipocampo e malformações vasculares tiveram os melhores resultados pós-operatórios. Malformações do desenvolvimento cortical e cicatrizes gliais tiveram os piores resultados. Relativamente às diferenças entre os dois períodos, o número absoluto de doentes operados aumentou (119 versus 140), e a idade aquando da cirurgia foi maior no segundo período (p = 0,04). O número de malformações do desenvolvimento cortical aumentou (p = 0,01), mas o número de outros tumores (p = 0,01) e amostras sem lesão (p = 0,03) diminuiu no mesmo período. Conclusão: Este estudo está de acordo com a literatura atual, reforçando o conhecimento prévio sobre as etiologias estruturais, prática clínica e resultados cirúrgicos ao longo de mais de duas décadas de experiência. Os dados analisados fornecem expectativas realistas sobre a cirurgia de epilepsia e destacam a necessidade de melhorias no paradigma de diagnóstico e tratamento destes doentes.

Common and rare genetic risk variants in age-related macular degeneration and genetic risk score in the Coimbra eye study.

PURPOSE: To determine the contribution of common and rare genetic variants in age-related macular degeneration (AMD) in a Portuguese population from the Coimbra Eye Study (CES), and the genetic risk score (GRS). METHODS: Participants underwent ophthalmologic examination and imaging. A centralized reading centre performed AMD staging. Genetic sequencing was carried out with the EYE-RISK assay. Sixty-nine single nucleotide polymorphisms (SNPs) were genotyped and tested for association with AMD. Case-control and progression-to-AMD analyses were performed using logistic regression to assess allelic odds ratio (OR) at a 95% confidence interval (CI) for each variant. GRS was calculated for cases/controls and progressors/non-progressors. Cumulative impact of rare variants was compared between cases/controls using logistic regression. RESULTS: In case-control analysis (237 cases/640 controls) variants associated with risk of disease were: ARMS2 rs10490924, ARMS2_HTRA1 rs3750846, CFH rs35292876, SLC16A8 rs8135665, TGFBR1 rs1626340. Major risk variants ARMS2/HTRA1 rs3750846, CFH rs570618 and C3 rs2230199 had unexpected lower allele frequency (AF), and the highest risk-conferring variant was a rare variant, CFH rs35292876 (OR, 2.668; p-value = 0.021). In progression-to-AMD analysis (137 progressors/630 non-progressors), variants associated with risk of progression were ARMS2 rs10490924, ARMS2_HTRA1 rs3750846, CFH rs35292876. GRS of cases/controls was 1.124 ± 1.187 and 0.645 ± 1.124 (p-value < 0.001), and of progressors/non-progressors was 1.190 ± 1.178 and 0.669 ± 1.141 (p-value < 0.001). Higher proportion of pathogenic rare CFH variants was observed in cases (OR, 9.661; p-value < 0.001). CONCLUSIONS: Both common and rare variants were associated with AMD, but a CFH rare variant conferred the highest risk of disease while three major risk variants had a lower-than-expected AF in our population originary from a geographic region with lower prevalence of AMD. GRS was still significantly higher in AMD patients. Damaging CFH rare variants were cumulatively more common in AMD cases.

The Challenge of Somatic Variants in Focal Cortical Dysplasia.

Objective: The advent of next-generation sequencing (NGS) enabled the detection of low-level brain somatic variants in postsurgical tissue of focal cortical dysplasia (FCD). The genetic background of FCD Type I remains elusive, while the mammalian target of rapamycin (mTOR) pathway seems to have a relevant role in the pathogenesis of FCD Type II. Our goal was to uncover information on the molecular basis of FCD, performing whole genome sequencing (WGS) in postsurgical tissue to detect candidate brain-specific somatic variants, and evaluate their clinical significance. Design: WGS was performed using paired peripheral venous blood and postsurgical pathological brain deoxyribonucleic acid (DNA) samples. Libraries were prepared using the Roche KAPA HyperPrep polymerase chain reaction (PCR) free library preparation kit. Paired-end 150bp reads were generated on the Illumina NovaSeq platform. The FASTQ files were processed using the nf-core sarek pipeline (version 3.0) to call somatic variants, which were then annotated with ANNOVAR. A screening strategy was applied to obtain relevant variants. Results: Two female patients with drug-resistant epilepsy due to FCD who underwent surgical treatment were included. Regarding neuropathological diagnosis, one patient had FCD Type Ia and the other had FCD Type IIa. Five somatic nonsynonymous single nucleotide variants (SNVs) were detected using WGS, three in FCD Ia tissue (WDR24 p.Trp259Gly; MICAL1 p.Lys1036Arg; and KATNB1 p.Leu566Ile) and two in FCD IIa tissue (MATN4 p.Phe91Val and ANKRD6 p.His386Gln). All variants were predicted to be potentially pathogenic by at least two different tools. However, they were classified as variants of uncertain significance (VUS) according to the American College of Medical Genetics and Genomics (ACMG) criteria. Conclusion: Brain-specific somatic missense variants were identified by NGS in new candidate genes (WDR24, MICAL1, KATNB1, MATN4, and ANKRD6) using postsurgical FCD tissue, which may contribute to further understanding of the genetic background of FCD. All the reported genes were previously related to epilepsy and/or malformations of central nervous system (CNS) and cortical development. However, the pathogenicity assessment of these variants and, consequently, their impact on clinical practice still poses an important challenge.

Small supernumerary marker chromosomes derived from human chromosome 11.

Introduction: With only 39 reported cases in the literature, carriers of a small supernumerary marker chromosome (sSMC) derived from chromosome 11 represent an extremely rare cytogenomic condition. Methods: Herein, we present a review of reported sSMC(11), add 18 previously unpublished cases, and closely review eight cases classified as 'centromere-near partial trisomy 11' and a further four suited cases from DECIPHER. Results and discussion: Based on these data, we deduced the borders of the pericentric regions associated with clinical symptoms into a range of 2.63 and 0.96 Mb for chromosome 11 short (p) and long (q) arms, respectively. In addition, the minimal pericentric region of chromosome 11 without triplo-sensitive genes was narrowed to positions 47.68 and 60.52 Mb (GRCh37). Furthermore, there are apparent differences in the presentation of signs and symptoms in carriers of larger sSMCs derived from chromosome 11 when the partial trisomy is derived from different chromosome arms. However, the number of informative sSMC(11) cases remains low, with overlapping presentation between p- and q-arm-imbalances. In addition, uniparental disomy (UPD) of 'normal' chromosome 11 needs to be considered in the evaluation of sSMC(11) carriers, as imprinting may be an influencing factor, although no such cases have been reported. Comprehensively, prenatal sSMC(11) cases remain a diagnostic and prognostic challenge.

Dopaminergic Gene Dosage Reveals Distinct Biological Partitions between Autism and Developmental Delay as Revealed by Complex Network Analysis and Machine Learning Approaches.

The neurobiological mechanisms underlying Autism Spectrum Disorders (ASD) remains controversial. One factor contributing to this debate is the phenotypic heterogeneity observed in ASD, which suggests that multiple system disruptions may contribute to diverse patterns of impairment which have been reported between and within study samples. Here, we used SFARI data to address genetic imbalances affecting the dopaminergic system. Using complex network analysis, we investigated the relations between phenotypic profiles, gene dosage and gene ontology (GO) terms related to dopaminergic neurotransmission from a polygenic point-of-view. We observed that the degree of distribution of the networks matched a power-law distribution characterized by the presence of hubs, gene or GO nodes with a large number of interactions. Furthermore, we identified interesting patterns related to subnetworks of genes and GO terms, which suggested applicability to separation of clinical clusters (Developmental Delay (DD) versus ASD). This has the potential to improve our understanding of genetic variability issues and has implications for diagnostic categorization. In ASD, we identified the separability of four key dopaminergic mechanisms disrupted with regard to receptor binding, synaptic physiology and neural differentiation, each belonging to particular subgroups of ASD participants, whereas in DD a more unitary biological pattern was found. Finally, network analysis was fed into a machine learning binary classification framework to differentiate between the diagnosis of ASD and DD. Subsets of 1846 participants were used to train a Random Forest algorithm. Our best classifier achieved, on average, a diagnosis-predicting accuracy of 85.18% (sd 1.11%) on the test samples of 790 participants using 117 genes. The achieved accuracy surpassed results using genetic data and closely matched imaging approaches addressing binary diagnostic classification. Importantly, we observed a similar prediction accuracy when the classifier uses only 62 GO features. This result further corroborates the complex network analysis approach, suggesting that different genetic causes might converge to the dysregulation of the same set of biological mechanisms, leading to a similar disease phenotype. This new biology-driven ontological framework yields a less variable and more compact domain-related set of features with potential mechanistic generalization. The proposed network analysis, allowing for the determination of a clearcut biological distinction between ASD and DD (the latter presenting much lower modularity and heterogeneity), is amenable to machine learning approaches and provides an interesting avenue of research for the future.

Integrated Multi-Omics Signature Predicts Survival in Head and Neck Cancer.

Head and Neck Cancer (HNC) is characterized by phenotypic, biological, and clinical heterogeneity. Despite treatment modalities, approximately half of all patients will die of the disease. Several molecular biomarkers have been investigated, but until now, without clinical translation. Here, we identified an integrative nine-gene multi-omics signature correlated with HNC patients' survival independently of relapses or metastasis development. This prognosis multi-omic signature comprises genes mapped in the chromosomes 1q, 3p, 8q, 17q, 19p, and 19q and encompasses alterations at copy number, gene expression, and methylation. Copy number alterations in LMCD1-A1S and GRM7, the methylation status of CEACAM19, KRT17, and ST18, and the expression profile of RPL29, UBA7, FCGR2C, and RPSAP58 can predict the HNC patients' survival. The difference higher than two years observed in the survival of HNC patients that harbor this nine-gene multi-omics signature can represent a significant step forward to improve patients' management and guide new therapeutic targets development.

Targeting endothelial cell metabolism in cancerous microenvironment: a new approach for anti-angiogenic therapy.

Anti-angiogenic therapy is a practical approach to managing diseases with increased angiogenesis, such as cancer, maculopathies, and retinopathies. Considering the fundamental gaps in the knowledge of the vital pathways involved in angiogenesis and its inhibition and the insufficient efficiency of existing angiogenesis inhibitors, there is an increasing focus on the emergence of new therapeutic strategies aimed at inhibiting pathological angiogenesis. Angiogenesis is forming a new vascular network from existing vessels; endothelial cells (ECs), vascular lining cells, are the main actors of angiogenesis in physiological or pathological conditions. Switching from a quiescent state to a highly migratory and proliferative state during new vessel formation called "angiogenic switch" is driven by a "metabolic switch" in ECs, angiogenic growth factors, and other signals. As the characteristics of ECs change by altering the surrounding environment, they appear to have a different metabolism in a tumor microenvironment (TME). Therefore, pathological angiogenesis can be inhibited by targeting metabolic pathways. In the current review, we aim to discuss the EC metabolic pathways under normal and TME conditions to verify the suitability of targeting them with novel therapies.

The landscape of common genetic drivers and DNA methylation in low-grade (epilepsy-associated) neuroepithelial tumors: A review.

Low-grade neuroepithelial tumors (LNETs) represent an important group of central nervous system neoplasms, some of which may be associated to epilepsy. The concept of long-term epilepsy-associated tumors (LEATs) includes a heterogenous group of low-grade, cortically based tumors, associated to drug-resistant epilepsy, often requiring surgical treatment. LEATs entities can sometimes be poorly discriminated by histological features, precluding a confident classification in the absence of additional diagnostic tools. This study aimed to provide an updated review on the genomic findings and DNA methylation profiling advances in LNETs, including histological entities of LEATs. A comprehensive search strategy was conducted on PubMed, Embase, and Web of Science Core Collection. High-quality peer-reviewed original manuscripts and review articles with full-text in English, published between 2003 and 2022, were included. Results were screened based on titles and abstracts to determine suitability for inclusion, and when addressed the topic of the review was screened by full-text reading. Data extraction was performed through a qualitative content analysis approach. Most LNETs appear to be driven mainly by a single genomic abnormality and respective affected signaling pathway, including BRAF p.V600E mutations in ganglioglioma, FGFR1 abnormalities in dysembryoplastic neuroepithelial tumor, MYB alterations in angiocentric glioma, BRAF fusions in pilocytic astrocytoma, PRKCA fusions in papillary glioneuronal tumor, between others. However, these molecular alterations are not exclusive, with some overlap amongst different tumor histologies. Also, clustering analysis of DNA methylation profiles allowed the identification of biologically similar molecular groups that sometimes transcend conventional histopathological classification. The exciting developments on the molecular basis of these tumors reinforce the importance of an integrative histopathological and (epi)genetic classification, which can be translated into precision medicine approaches.