Single-cell and spatial transcriptomics analysis of non-small cell lung cancer

Lung cancer is the second most frequently diagnosed cancer and the leading cause of cancer-related mortality worldwide. Tumour ecosystems feature diverse immune cell types. Myeloid cells, in particular, are prevalent and have a well-established role in promoting the disease. In our study, we profile approximately 900,000 cells from 25 treatment-naive patients with adenocarcinoma and squamous-cell carcinoma by single-cell and spatial transcriptomics. We note an inverse relationship between anti-inflammatory macrophages and NK cells/T cells, and with reduced NK cell cytotoxicity within the tumour. While we observe a similar cell type composition in both adenocarcinoma and squamous-cell carcinoma, we detect significant differences in the co-expression of various immune checkpoint inhibitors. Moreover, we reveal evidence of a transcriptional "reprogramming" of macrophages in tumours, shifting them towards cholesterol export and adopting a foetal-like transcriptional signature which promotes iron efflux. Our multi-omic resource offers a high-resolution molecular map of tumour-associated macrophages, enhancing our understanding of their role within the tumour microenvironment.

Abstract 3367: Tumor-derived Extracellular Vesicles as a potential PD biomarker for TEAD central pocket binder activity in liquid biopsy

We assessed the utility of mRNAs in extracellular vesicles as biomarkers for inhibition of YAP1/TEAD signaling by the TEAD central pocket inhibitor. The field of liquid biopsies is of enormous interest for noninvasive monitoring of cancer progression and response to treatment. Extracellular Vesicles (EVs) such as exosomes, microvesicles, and apoptotic bodies, are nanoparticles found in all biological fluids. These cell-derived, small secreted vesicles convey biological information, either by surface-to-surface interaction or by shuttling bioactive molecules to a recipient cell’s cytoplasm. Because EVs harbor the cargos of their original cells, their contents may be useful as biomarkers to follow drug activity. (F. Urabi et al., 2020). We compared the effects of YAP1/TEAD inhibitor treatment on intracellular and EV-encapsulated mRNAs in three compound-sensitive tumor cell lines (and one insensitive cell line) based on TEAD inhibitor IC50 assay profiles. Cell lines were treated at four doses of YAP1/TEAD inhibitor (0.0 µM, 0.3 µM, 1.0 µM & 3.0 µM) for 24h. EVs and intracellular RNAs were isolated and profiled by RNAseq. To estimate YAP1/TEAD pathway activity, we used a transcriptomic signature identified previously by our group (L. Calvet et al., 2022) and we showed that the effects of YAP1/TEAD inhibitor treatment on the YAP1/TEAD score in intracellular mRNAs corresponded to a decrease of the score in EV-secreted RNAs. In addition, we ran an unbiased analysis to identify single transcripts in the EVs that were modulated by YAP1/TEAD inhibitor. One of the best markers identified by regression analysis was CYR61, that is part of the signature and is a well-established downstream target of YAP/TEAD pathway. In conclusion, these results suggest that the YAP1/TEAD signature in EV mRNAs represents a relevant PD biomarker to monitor YAP1/TEAD inhibitor activity and could potentially serve as a noninvasive liquid biopsy-based biomarker detection in the clinic.

Citation Format: Manoel Nunes, Emmanuel Spanakis, Wilson Dos-Santos-Bele, Emilia Rabia, Stephane Soubigou, Gaelle Muzard, Odette Dos-Santos, Jack Pollard, Angela Hadjipanayis, Fabien Delahaye, Olivier Venier, Laurent Debussche, Don Jackson, Colette Dib, Iris Valtingojer, Matteo Cesaroni. Tumor-derived Extracellular Vesicles as a potential PD biomarker for TEAD central pocket binder activity in liquid biopsy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3367.

DUX4 expression activates JNK and p38 MAP kinases in myoblasts

Facioscapulohumeral muscular dystrophy (FSHD) is caused by misexpression of the DUX4 transcription factor in skeletal muscle that results in transcriptional alterations, abnormal phenotypes and cell death. To gain insight into the kinetics of DUX4-induced stresses, we activated DUX4 expression in myoblasts and performed longitudinal RNA sequencing paired with proteomics and phosphoproteomics. This analysis revealed changes in cellular physiology upon DUX4 activation, including DNA damage and altered mRNA splicing. Phosphoproteomic analysis uncovered rapid widespread changes in protein phosphorylation following DUX4 induction, indicating that alterations in kinase signaling might play a role in DUX4-mediated stress and cell death. Indeed, we demonstrate that two stress-responsive MAP kinase pathways, JNK and p38, are activated in response to DUX4 expression. Inhibition of each of these pathways ameliorated DUX4-mediated cell death in myoblasts. These findings uncover that the JNK pathway is involved in DUX4-mediated cell death and provide additional insights into the role of the p38 pathway, a clinical target for the treatment of FSHD.

BDK inhibition acts as a catabolic switch to mimic fasting and improve metabolism in mice

OBJECTIVE

Branched chain amino acid (BCAA) catabolic defects are implicated to be causal determinates of multiple diseases. This work aimed to better understand how enhancing BCAA catabolism affected metabolic homeostasis as well as the mechanisms underlying these improvements.

METHODS

The rate limiting step of BCAA catabolism is the irreversible decarboxylation by the branched chain ketoacid dehydrogenase (BCKDH) enzyme complex, which is post-translationally controlled through phosphorylation by BCKDH kinase (BDK). This study utilized BT2, a small molecule allosteric inhibitor of BDK, in multiple mouse models of metabolic dysfunction and NAFLD including the high fat diet (HFD) model with acute and chronic treatment paradigms, the choline deficient and methionine minimal high fat diet (CDAHFD) model, and the low-density lipoprotein receptor null mouse model (Ldlr^-/-). shRNA was additionally used to knock down BDK in liver to elucidate liver-specific effects of BDK inhibition in HFD-fed mice.

RESULTS

A rapid improvement in insulin sensitivity was observed in HFD-fed and lean mice after BT2 treatment. Resistance to steatosis was assessed in HFD-fed mice, CDAHFD-fed mice, and Ldlr^-/- mice. In all cases, BT2 treatment reduced steatosis and/or inflammation. Fasting and refeeding demonstrated a lack of response to feeding-induced changes in plasma metabolites including insulin and beta-hydroxybutyrate and hepatic gene changes in BT2-treated mice. Mechanistically, BT2 treatment acutely altered the expression of genes involved in fatty acid oxidation and lipogenesis in liver, and upstream regulator analysis suggested that BT2 treatment activated PPARα. However, BT2 did not directly activate PPARα in vitro. Conversely, shRNA-AAV-mediated knockdown of BDK specifically in liver in vivo did not demonstrate any effects on glycemia, steatosis, or PPARα-mediated gene expression in mice.

CONCLUSIONS

These data suggest that BT2 treatment acutely improves metabolism and liver steatosis in multiple mouse models. While many molecular changes occur in liver in BT2-treated mice, these changes were not observed in mice with AAV-mediated shRNA knockdown of BDK. All together, these data suggest that systemic BDK inhibition is required to improve metabolism and steatosis by prolonging a fasting signature in a paracrine manner. Therefore, BCAA may act as a "fed signal" to promote nutrient storage and reduced systemic BCAA levels as shown in this study via BDK inhibition may act as a "fasting signal" to prolong the catabolic state.

Ageing and interferon gamma response drive the phenotype of neutrophils in the inflamed joint

OBJECTIVE

Neutrophils are typically the most abundant leucocyte in arthritic synovial fluid. We sought to understand changes that occur in neutrophils as they migrate from blood to joint.

METHODS

We performed RNA sequencing of neutrophils from healthy human blood, arthritic blood and arthritic synovial fluid, comparing transcriptional signatures with those from murine K/BxN serum transfer arthritis. We employed mass cytometry to quantify protein expression and sought to reproduce the synovial fluid phenotype ex vivo in cultured healthy blood neutrophils.

RESULTS

Blood neutrophils from healthy donors and patients with active arthritis showed largely similar transcriptional signatures. By contrast, synovial fluid neutrophils exhibited more than 1600 differentially expressed genes. Gene signatures identified a prominent response to interferon gamma (IFN-γ), as well as to tumour necrosis factor, interleukin-6 and hypoxia, in both humans and mice. Mass cytometry confirmed that healthy and arthritic donor blood neutrophils are largely indistinguishable but revealed a range of neutrophil phenotypes in synovial fluid defined by downregulation of CXCR1 and upregulation of FcγRI, HLA-DR, PD-L1, ICAM-1 and CXCR4. Reproduction of key elements of this signature in cultured blood neutrophils required both IFN-γ and prolonged culture.

CONCLUSIONS

Circulating neutrophils from patients with arthritis resemble those from healthy controls, but joint fluid cells exhibit a network of changes, conserved across species, that implicate IFN-γ response and ageing as complementary drivers of the synovial fluid neutrophil phenotype.

A functional genomic approach to actionable gene fusions for precision oncology

Fusion genes represent a class of attractive therapeutic targets. Thousands of fusion genes have been identified in patients with cancer, but the functional consequences and therapeutic implications of most of these remain largely unknown. Here, we develop a functional genomic approach that consists of efficient fusion reconstruction and sensitive cell viability and drug response assays. Applying this approach, we characterize ~100 fusion genes detected in patient samples of The Cancer Genome Atlas, revealing a notable fraction of low-frequency fusions with activating effects on tumor growth. Focusing on those in the RTK-RAS pathway, we identify a number of activating fusions that can markedly affect sensitivity to relevant drugs. Last, we propose an integrated, level-of-evidence classification system to prioritize gene fusions systematically. Our study reiterates the urgent clinical need to incorporate similar functional genomic approaches to characterize gene fusions, thereby maximizing the utility of gene fusions for precision oncology.

Repercussions of the COVID-19 pandemic on child and adolescent mental health: A matter of concern-A joint statement from EAP and ECPCP

COVID-19 pandemic and the consequent rigid social distancing measures implemented, including school closures, have heavily impacted children's and adolescents' psychosocial wellbeing, and their mental health problems significantly increased. However, child and adolescent mental health were already a serious problem before the Pandemic all over the world. COVID-19 is not just a pandemic, it is a syndemic and mentally or socially disadvantaged children and adolescents are the most affected. Non-Communicable Diseases (NCDs) and previous mental health issues are an additional worsening condition. Even though many countries have responded with decisive efforts to scale-up mental health services, a more integrated and community-based approach to mental health is required. EAP and ECPCP makes recommendations to all the stakeholders to take action to promote, protect and care for the mental health of a generation.

Correction to: Vilnius Declaration on chronic respiratory diseases: multisectoral care pathways embedding guided self-management, mHealth and air pollution in chronic respiratory diseases

An amendment to this paper has been published and can be accessed via the original article.

Metformin and 2-Deoxyglucose Collaboratively Suppress Human CD4+ T Cell Effector Functions and Activation-Induced Metabolic Reprogramming

Metabolic reprogramming plays a central role in T cell activation and differentiation, and the inhibition of key metabolic pathways in activated T cells represents a logical approach for the development of new therapeutic agents for treating autoimmune diseases. The widely prescribed antidiabetic drug metformin and the glycolytic inhibitor 2-deoxyglucose (2-DG) have been used to study the inhibition of oxidative phosphorylation and glycolysis, respectively, in murine immune cells. Published studies have demonstrated that combination treatment with metformin and 2-DG was efficacious in dampening mouse T cell activation-induced effector processes, relative to treatments with either metformin or 2-DG alone. In this study, we report that metformin + 2-DG treatment more potently suppressed IFN-γ production and cell proliferation in activated primary human CD4⁺ T cells than either metformin or 2-DG treatment alone. The effects of metformin + 2-DG on human T cells were accompanied by significant remodeling of activation-induced metabolic transcriptional programs, in part because of suppression of key transcriptional regulators MYC and HIF-1A. Accordingly, metformin + 2-DG treatment significantly suppressed MYC-dependent metabolic genes and processes, but this effect was found to be independent of mTORC1 signaling. These findings reveal significant insights into the effects of metabolic inhibition by metformin + 2-DG treatment on primary human T cells and provide a basis for future work aimed at developing new combination therapy regimens that target multiple pathways within the metabolic networks of activated human T cells.

Global impact of somatic structural variation on the DNA methylome of human cancers

Background

Genomic rearrangements exert a heavy influence on the molecular landscape of cancer. New analytical approaches integrating somatic structural variants (SSVs) with altered gene features represent a framework by which we can assign global significance to a core set of genes, analogous to established methods that identify genes non-randomly targeted by somatic mutation or copy number alteration. While recent studies have defined broad patterns of association involving gene transcription and nearby SSV breakpoints, global alterations in DNA methylation in the context of SSVs remain largely unexplored.

Results

By data integration of whole genome sequencing, RNA sequencing, and DNA methylation arrays from more than 1400 human cancers, we identify hundreds of genes and associated CpG islands (CGIs) for which the nearby presence of a somatic structural variant (SSV) breakpoint is recurrently associated with altered expression or DNA methylation, respectively, independently of copy number alterations. CGIs with SSV-associated increased methylation are predominantly promoter-associated, while CGIs with SSV-associated decreased methylation are enriched for gene body CGIs. Rearrangement of genomic regions normally having higher or lower methylation is often involved in SSV-associated CGI methylation alterations. Across cancers, the overall structural variation burden is associated with a global decrease in methylation, increased expression in methyltransferase genes and DNA damage response genes, and decreased immune cell infiltration.

Conclusion

Genomic rearrangement appears to have a major role in shaping the cancer DNA methylome, to be considered alongside commonly accepted mechanisms including histone modifications and disruption of DNA methyltransferases.

Abstract 566: Branched Chain Ketoacid Dehydrogenase Kinase Inhibition Alters Substrate Utilization and Gene Expression in Myocytes

Circulating increases in branched chain amino acid (BCAA) levels have long been associated with type II diabetes and metabolic syndrome. Emerging data also suggest that impaired BCAA catabolism may play a role in heart failure progression. BCAA are catabolized via the branched chain ketoacid (BCKA) dehydrogenase enzyme complex (BCKDH). BCKD kinase (BCKDK) is a negative regulator of BCAA catabolism through its inhibitory phosphorylation of the BCKDHE1a subunit, and the phosphatase PPM1k dephosphorylates this same site to activate BCAA catabolism. Using an inhibitor of BCKDK (BT2), BCAA catabolism is increased in vivo. Here, we utilized metabolomics to evaluate the contribution of BCAA catabolism to substrate preference in heart and skeletal muscle. Surprisingly, BCKDK inhibition with BT2 had no effect on incorporation of glucose into TCA cycle intermediates in heart or skeletal muscle. Because others have recently shown that the primary site of BCAA catabolism is skeletal muscle, we knocked down BCKDK and PPM1k in human skeletal myocytes to further investigate how BCKDK loss or inhibition affects substrate utilization. Similar to our in vivo observations, knockdown of BCKDK and PPM1k had no effect on glucose and pyruvate utilization in a mitochondrial function assay. However, an increase in maximal respiration was observed after BCKDK knockdown when fatty acids were used. To evaluate the mechanisms underlying this increase we then performed RNAseq in these cells after BCKDK and PPM1K knockdown and observed changes in a number of genes that may explain these alterations in substrate utilization. Finally, we performed C13 BCAA metabolomics in human skeletal myocytes after BT2 treatment or knockdown of BCKDK and PPM1k. Using BT2, we observed a dose-responsive reduction in BCKA production from C13 BCAA by the muscle cells as expected; however, though BCKA production was increased after PPM1k was knocked down, we surprisingly did not observe a decrease in BCKA production after BCKDK knockdown. Collectively these data suggest that BCKDK inhibition may improve metabolism and cardiac function by altering substrate preference in skeletal myocytes.

Vilnius Declaration on chronic respiratory diseases: multisectoral care pathways embedding guided self-management, mHealth and air pollution in chronic respiratory diseases

Background

Over 1 billion people suffer from chronic respiratory diseases such as asthma, COPD, rhinitis and rhinosinusitis. They cause an enormous burden and are considered as major non-communicable diseases. Many patients are still uncontrolled and the cost of inaction is unacceptable. A meeting was held in Vilnius, Lithuania (March 23, 2018) under the patronage of the Ministry of Health and several scientific societies to propose multisectoral care pathways embedding guided self-management, mHealth and air pollution in selected chronic respiratory diseases (rhinitis, chronic rhinosinusitis, asthma and COPD). The meeting resulted in the Vilnius Declaration that was developed by the participants of the EU Summit on chronic respiratory diseases under the leadership of Euforea.

Conclusion

The Vilnius Declaration represents an important step for the fight against air pollution in chronic respiratory diseases globally and has a clear strategic relevance with regard to the EU Health Strategy as it will bring added value to the existing public health knowledge.

A Pan-Cancer Compendium of Genes Deregulated by Somatic Genomic Rearrangement across More Than 1,400 Cases

A systematic cataloging of genes affected by genomic rearrangement, using multiple patient cohorts and cancer types, can provide insight into cancer-relevant alterations outside of exomes. By integrative analysis of whole-genome sequencing (predominantly low pass) and gene expression data from 1,448 cancers involving 18 histopathological types in The Cancer Genome Atlas, we identified hundreds of genes for which the nearby presence (within 100 kb) of a somatic structural variant (SV) breakpoint is associated with altered expression. While genomic rearrangements are associated with widespread copy-number alteration (CNA) patterns, approximately 1,100 genes-including overexpressed cancer driver genes (e.g., TERT, ERBB2, CDK12, CDK4) and underexpressed tumor suppressors (e.g., TP53, RB1, PTEN, STK11)-show SV-associated deregulation independent of CNA. SVs associated with the disruption of topologically associated domains, enhancer hijacking, or fusion transcripts are implicated in gene upregulation. For cancer-relevant pathways, SVs considerably expand our understanding of how genes are affected beyond point mutation or CNA.

Migrant children's health problems, care needs, and inequalities: European primary care paediatricians' perspective

BACKGROUND

Primary care paediatricians' perception of migrant children's health in Europe has not been explored before. Our aim was to examine European paediatricians' knowledge on migrant children's health problems, needs, inequalities, and barriers to access health care.

METHODS

European primary care paediatricians were invited by the European Academy of Paediatrics Research in Ambulatory Setting Network country coordinators to complete a web-based survey concerning health care of migrant children. A descriptive analysis of all variables was performed.

RESULTS

The survey was completed by 492 paediatricians. Sixty-three per cent of the respondents reported that the general health of migrant children is worse than that of nonmigrants, chronic diseases cited by 66% of the respondents as the most frequent health problem. Sixty-six per cent of the paediatricians reported that migrant children have different health needs compared to nonmigrant children, proper oral health care mentioned by 86% of the respondents. Cultural/linguistic factors have been reported as the most frequent barrier (90%).to access health care. However, only 37% of providers have access to professional interpreters and cultural mediators. Fifty-two per cent and 32% do not know whether one or more of the family members are undocumented and whether they are refugees/asylum seekers, respectively. Updated guidelines for care of migrant children are available for only 35% of respondents, and 80% of them have not received specific training on migrant children's care.

CONCLUSIONS

European primary care paediatricians recognize migrant children as a population at risk with more frequent and specific health problems and needs, but they are often unaware of their legal state. Lack of interpreters augments the existing language barriers to access proper care and should be solved. Widespread lack of guidelines and specific providers' training should be addressed to optimize health care delivery to migrant children.

A Pan-Cancer Proteogenomic Atlas of PI3K/AKT/mTOR Pathway Alterations

Molecular alterations involving the PI3K/AKT/mTOR pathway (including mutation, copy number, protein, or RNA) were examined across 11,219 human cancers representing 32 major types. Within specific mutated genes, frequency, mutation hotspot residues, in silico predictions, and functional assays were all informative in distinguishing the subset of genetic variants more likely to have functional relevance. Multiple oncogenic pathways including PI3K/AKT/mTOR converged on similar sets of downstream transcriptional targets. In addition to mutation, structural variations and partial copy losses involving PTEN and STK11 showed evidence for having functional relevance. A substantial fraction of cancers showed high mTOR pathway activity without an associated canonical genetic or genomic alteration, including cancers harboring IDH1 or VHL mutations, suggesting multiple mechanisms for pathway activation.

Use of electronic health records by child primary healthcare providers in Europe

BACKGROUND

There is limited data on the use and functionality level of electronic health records (EHRs) supporting primary child health care in Europe. Our objective was to determine European primary child healthcare providers' use of EHRs, and functionality level of the systems used.

METHODS

European primary care paediatricians, paediatric subspecialists and family doctors were invited by European Academy of Paediatrics Research in Ambulatory Setting Network (EAPRASnet) country coordinators to complete a web-based survey on the use of EHRs and the systems' functionalities. Binomial logistic analysis has been used to evaluate the effect of specialty and type of practice on the use of EHRs.

RESULTS

The survey was completed by 679 child primary healthcare providers (response rate 53%). Five hundred and fifty four responses coming from 10 predominant countries were taken for further analysis. EHR use by respondents varied widely between countries, all electronic type use ranging between 7% and 97%. There was no significant difference in EHR use between group practice and solo practitioners, or between family doctors and primary care paediatricians. History and physical examination can be properly recorded by respondents in most countries. However, growth chart plotting capacity in some countries ranges between 22% and 50%. Vaccination recording capacity varies between 50% and 100%, and data exchange capacity with immunization databases is mostly limited, ranging between 0% and 54%.

CONCLUSIONS

There is marked heterogeneity in the use and functionalities of EHRs used among child primary child healthcare providers in Europe. More importantly, lack of critical paediatric supportive functionalities like growth tracking and vaccination status has been documented in some countries. There is a need to explore the reasons for these findings, and to develop a cross European paediatric EHR standards.

A pilot study on the feasibility of European harmonized human biomonitoring: Strategies towards a common approach, challenges and opportunities

In 2004 the European Commission and Member States initiated activities towards a harmonized approach for Human Biomonitoring surveys throughout Europe. The main objective was to sustain environmental health policy by building a coherent and sustainable framework and by increasing the comparability of data across countries. A pilot study to test common guidelines for setting up surveys was considered a key step in this process. Through a bottom-up approach that included all stakeholders, a joint study protocol was elaborated. From September 2011 till February 2012, 17 European countries collected data from 1844 mother-child pairs in the frame of DEMOnstration of a study to COordinate and Perform Human Biomonitoring on a European Scale (DEMOCOPHES).(1) Mercury in hair and urinary cadmium and cotinine were selected as biomarkers of exposure covered by sufficient analytical experience. Phthalate metabolites and Bisphenol A in urine were added to take into account increasing public and political awareness for emerging types of contaminants and to test less advanced markers/markers covered by less analytical experience. Extensive efforts towards chemo-analytical comparability were included. The pilot study showed that common approaches can be found in a context of considerable differences with respect to experience and expertize, socio-cultural background, economic situation and national priorities. It also evidenced that comparable Human Biomonitoring results can be obtained in such context. A European network was built, exchanging information, expertize and experiences, and providing training on all aspects of a survey. A key challenge was finding the right balance between a rigid structure allowing maximal comparability and a flexible approach increasing feasibility and capacity building. Next steps in European harmonization in Human Biomonitoring surveys include the establishment of a joint process for prioritization of substances to cover and biomarkers to develop, linking biomonitoring surveys with health examination surveys and with research, and coping with the diverse implementations of EU regulations and international guidelines with respect to ethics and privacy.

Interpreting biomarker data from the COPHES/DEMOCOPHES twin projects: Using external exposure data to understand biomarker differences among countries

In 2011 and 2012, the COPHES/DEMOCOPHES twin projects performed the first ever harmonized human biomonitoring survey in 17 European countries. In more than 1800 mother-child pairs, individual lifestyle data were collected and cadmium, cotinine and certain phthalate metabolites were measured in urine. Total mercury was determined in hair samples. While the main goal of the COPHES/DEMOCOPHES twin projects was to develop and test harmonized protocols and procedures, the goal of the current paper is to investigate whether the observed differences in biomarker values among the countries implementing DEMOCOPHES can be interpreted using information from external databases on environmental quality and lifestyle. In general, 13 countries having implemented DEMOCOPHES provided high-quality data from external sources that were relevant for interpretation purposes. However, some data were not available for reporting or were not in line with predefined specifications. Therefore, only part of the external information could be included in the statistical analyses. Nonetheless, there was a highly significant correlation between national levels of fish consumption and mercury in hair, the strength of antismoking legislation was significantly related to urinary cotinine levels, and we were able to show indications that also urinary cadmium levels were associated with environmental quality and food quality. These results again show the potential of biomonitoring data to provide added value for (the evaluation of) evidence-informed policy making.

Gender differences in cadmium and cotinine levels in prepubertal children

Susceptibility to environmental stressors has been described for fetal and early childhood development. However, the possible susceptibility of the prepubertal period, characterized by the orchestration of the organism towards sexual maturation and adulthood has been poorly investigated and exposure data are scarce. In the current study levels of cadmium (Cd), cotinine and creatinine in urine were analyzed in a subsample 216 children from 12 European countries within the DEMOCOPHES project. The children were divided into six age-sex groups: boys (6-8 years, 9-10 years and 11 years old), and girls (6-7 years, 8-9 years, 10-11 years). The number of subjects per group was between 23 and 53. The cut off values were set at 0.1 µg/L for Cd, and 0.8 µg/L for cotinine defined according to the highest limit of quantification. The levels of Cd and cotinine were adjusted for creatinine level. In the total subsample group, the median level of Cd was 0.180 µg/L (range 0.10-0.69 µg/L), and for cotinine the median wet weight value was 1.50 µg/L (range 0.80-39.91 µg/L). There was no significant difference in creatinine and cotinine levels between genders and age groups. There was a significant correlation between levels of cadmium and creatinine in all children of both genders. This shows that even at such low levels the possible effect of cadmium on kidney function was present and measurable. An increase in Cd levels was evident with age. Cadmium levels were significantly different between 6-7 year old girls, 11 year old boys and 10-11 year old girls. As there was a balanced distribution in the number of subjects from countries included in the study, bias due to data clustering was not probable. The impact of low Cd levels on kidney function and gender differences in Cd levels needs further investigation.

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas

BACKGROUND

Diffuse low-grade and intermediate-grade gliomas (which together make up the lower-grade gliomas, World Health Organization grades II and III) have highly variable clinical behavior that is not adequately predicted on the basis of histologic class. Some are indolent; others quickly progress to glioblastoma. The uncertainty is compounded by interobserver variability in histologic diagnosis. Mutations in IDH, TP53, and ATRX and codeletion of chromosome arms 1p and 19q (1p/19q codeletion) have been implicated as clinically relevant markers of lower-grade gliomas.

METHODS

We performed genomewide analyses of 293 lower-grade gliomas from adults, incorporating exome sequence, DNA copy number, DNA methylation, messenger RNA expression, microRNA expression, and targeted protein expression. These data were integrated and tested for correlation with clinical outcomes.

RESULTS

Unsupervised clustering of mutations and data from RNA, DNA-copy-number, and DNA-methylation platforms uncovered concordant classification of three robust, nonoverlapping, prognostically significant subtypes of lower-grade glioma that were captured more accurately by IDH, 1p/19q, and TP53 status than by histologic class. Patients who had lower-grade gliomas with an IDH mutation and 1p/19q codeletion had the most favorable clinical outcomes. Their gliomas harbored mutations in CIC, FUBP1, NOTCH1, and the TERT promoter. Nearly all lower-grade gliomas with IDH mutations and no 1p/19q codeletion had mutations in TP53 (94%) and ATRX inactivation (86%). The large majority of lower-grade gliomas without an IDH mutation had genomic aberrations and clinical behavior strikingly similar to those found in primary glioblastoma.

CONCLUSIONS

The integration of genomewide data from multiple platforms delineated three molecular classes of lower-grade gliomas that were more concordant with IDH, 1p/19q, and TP53 status than with histologic class. Lower-grade gliomas with an IDH mutation either had 1p/19q codeletion or carried a TP53 mutation. Most lower-grade gliomas without an IDH mutation were molecularly and clinically similar to glioblastoma. (Funded by the National Institutes of Health.).

Harmonized European human biomonitoring in small countries: Challenges, opportunities and lessons learned in Cyprus and Luxembourg from the DEMOCOPHES study

Background: To advance human biomonitoring (HBM) for policy support in Europe, a harmonized approach was developed (COPHES project, FP7 2009- 2012) and evaluated in 17 countries (DEMOCOPHES project, Life+, 2010-2012). Cyprus (CY) and Luxembourg (LU) tested the hypothesis that the COPHES European Protocol is applicable to small countries.Materials and methods: In 2011-12, the European Protocol was adopted and tested by CY and LU for the harmonized biomonitoring of 60 children and their mothers for cadmium, phthalates and cotinine in urine and for mercury in scalp hair in two sampling areas (urban, rural). Results: Both small countries achieved the preset goals for recruitment, sample collection and analysis, which allowed for the first time the assessment of children’s and mothers’ exposures to the selected chemicals in comparison with other countries. Capacity building was accomplished and communication actions were particularly effective, with both countries taking advantage of their small size to access participants, policy makers, other stakeholders and the press. Time constrains and requirements for capacity building were limiting factors. Conclusion: The COPHES European Protocol for HBM surveys is attainable in small countries. The following elements are fundamental in the design of a harmonized European HBM program, from the perspective of small countries: (a) consultation with and active involvement of the implementing countries, (b) flexibility for national decisions, while not compromising harmonization, (c) elaboration of standardized methods, procedures and documents (d) quality assurance mechanisms, (e) means of training and support.

European Academy of Paediatrics Research in Ambulatory Setting network (EAPRASnet): a multi-national general paediatric research network for better child health

BACKGROUND

In 2008, the European Academy of Paediatrics launched a paediatric-based research network - EAPRASnet (European Academy of Paediatrics Research in Ambulatory Setting network). The network has recruited primary care and general paediatricians from European and Mediterranean countries.

METHODS

Every paediatrician joining the network has been asked to complete a recruitment survey. The aims of the survey were to characterize paediatrician's demographics, practice arrangements and patient's demographics, to define main incentives for research, and to learn what paediatricians view as unsolved issues that need to be studied.

RESULTS

A total of 156 paediatricians from 19 countries were recruited with 144 completing the questionnaire (92%). Majority of respondents (89%) were general paediatricians for more than half of their time. Practice arrangement of 47% of paediatricians was solo practice, with 40% in group practice. Electronic medical records were being used by 72% of respondents. Over 70% of the paediatricians had more than 1000 patients under their clinical care, and patients younger than 6 years old contributed nearly half of the patient population. Areas of most interest for research were: quality of care indicators, communication with parents, obesity, attention deficit hyperactivity disorder and effective well child care. Main incentives for participation in a research project were interest in the topic (81%) and effort to improve quality of care (71%). Lack of time was the leading reported obstacle for research activity (72%). EAPRASnet is growing, and the network's structure, operation and funding are described. Methods for joining the network and the process of study development are presented.

CONCLUSION

A core group of EAP general paediatricians are committed to research in their practices. The information gathered will serve for future planning of research projects in the EAPRASnet to harmonize and optimize the care given to children in the primary care setting in Europe.

Prevalence of antibodies to hepatitis A among children and adolescents in Larnaca area, Cyprus

The prevalence of antibodies to hepatitis A virus was investigated in 385 children and adolescents (52.2% males), aged 6 to 18, in the Larnaca area of Cyprus. This is the first study investigating the prevalence of hepatitis A in Cyprus for this age group. The population was stratified into two groups: 6 to 12 years old and 13 to 18 years old. None of the subjects in the first group were positive. The prevalence of hepatitis A in the age of group 13 tol8 was 1.6%. In conclusion, the low prevalence of anti-HAV demonstrates the susceptibility of young Cypriots to hepatitis A. This is a cause for concern as these unprotected young adults are frequently exposed to potentially infected individuals.

Epilepsy in patients with cerebral palsy

The incidence of epilepsy in 323 patients with cerebral palsy (CP) was 41.8%. Almost half of the patients with spastic tetraplegia and hemiplegia had epilepsy. The incidence was lower in patients with spastic diplegia. No sex differences were observed. Partial seizures were by far the most common form of epilepsy in spastic hemiplegia, while generalized tonic-clonic episodes predominated in all other forms of CP. A very high incidence of West syndrome was observed in patients with spastic tetraplegia. Most of the patients with spastic tetraplegia had their first seizure in the first year of life. In patients with spastic hemiplegia the onset of epilepsy was often delayed for several years. A high rate of polytherapy was recorded, but two-thirds of the patients remained seizure-free for long periods. In just over one-fifth of the patients successful withdrawal of medication was achieved.