Risk factors for surgery in stricturing small bowel Crohn's disease: A retrospective cohort study from the GETAID pédiatrique

OBJECTIVES

Previous studies have shown rates of surgical resection of up to 41% in stricturing pediatric Crohn's disease. In this retrospective multicenter study, our aims were to identify clinical risk factors and magnetic resonance enterography (MRE) features of small bowel strictures associated with surgery.

METHODS

Pediatric patients with symptomatic stricturing small bowel CD (defined as obstructive symptoms or proximal dilatation on MRE) confirmed by MRE between 2010 and 2020 were recruited from 12 French tertiary hospitals. Patient characteristics were compared by surgical outcome multivariable Cox regression.

RESULTS

Fifty-six patients (61% boys) aged 12.2 ± 2.7 years at diagnosis of CD were included. Median duration of CD before diagnosis of stricture was 11.7 months (interquartile range [IQR]: 25-75: 1.2-29.9). Nineteen (34%) patients had stricturing phenotype (B2) at baseline. Treatments received  before stricture diagnosis included MODULEN-IBD (n = 31), corticosteroids (n = 35), antibiotics (n = 10), anti-TNF (n = 27), immunosuppressants (n = 28). Thirty-six patients (64%) required surgery, within 4.8 months (IQR: 25-75: 1.8-17.3) after stricture diagnosis. Parameters associated with surgical resection were antibiotic exposure before stricture diagnosis (adjusted odds ratio [aOR]: 15.62 [3.35-72.73], p = 0.0005), Crohn's disease obstructive symptoms score (CDOS) > 4 (aOR: 3.04 [1.15-8.03], p = 0.02) and dilation proximal to stricture >28 mm (aOR: 3.62 [1.17-11.20], p = 0.03).

CONCLUSION

In this study, antibiotic treatment before stricture diagnosis, intensity of obstructive symptoms, and diameter of dilation proximal to small bowel stricture on MRE were associated with risk for surgical resection.

Feeding disorders in children with oesophageal atresia: a cross-sectional study

INTRODUCTION

With advances in surgical and neonatal care, the survival of patients with oesophageal atresia (OA) has improved over time. Whereas a number of OA-related conditions (delayed primary anastomosis, anastomotic stricture and oesophageal dysmotility) may have an impact on feeding development and although children with OA experience several oral aversive events, paediatric feeding disorders (PFD) remain poorly described in this population. The primary aim of our study was to describe PFD in children born with OA, using a standardised scale. The secondary aim was to determine conditions associated with PFD.

METHODS

The Feeding Disorders in Children with Oesophageal Atresia Study is a national cohort study based on the OA registry from the French National Network. Parents of children born with OA between 2013 and 2016 in one of the 22 participating centres were asked to complete the French version of the Montreal Children's Hospital Feeding Scale.

RESULTS

Of the 248 eligible children, 145 children, with a median age of 2.3 years (Q1-Q3 1.8-2.9, min-max 1.1-4.0 years), were included. Sixty-one children (42%) developed PFD; 13% were tube-fed (n=19). Almost 40% of children with PFD failed to thrive (n=23). The presence of chronic respiratory symptoms was associated with the development of PFD. Ten children with PFD (16%) had no other condition or OA-related complication.

CONCLUSION

PFD are common in children with OA, and there is no typical profile of patients at risk of PFD. Therefore, all children with OA require a systematic screening for PFD that could improve the care and outcomes of patients, especially in terms of growth.

Preexisting autoantibodies to type I IFNs underlie critical COVID-19 pneumonia in patients with APS-1

Patients with biallelic loss-of-function variants of AIRE suffer from autoimmune polyendocrine syndrome type-1 (APS-1) and produce a broad range of autoantibodies (auto-Abs), including circulating auto-Abs neutralizing most type I interferons (IFNs). These auto-Abs were recently reported to account for at least 10% of cases of life-threatening COVID-19 pneumonia in the general population. We report 22 APS-1 patients from 21 kindreds in seven countries, aged between 8 and 48 yr and infected with SARS-CoV-2 since February 2020. The 21 patients tested had auto-Abs neutralizing IFN-α subtypes and/or IFN-ω; one had anti-IFN-β and another anti-IFN-ε, but none had anti-IFN-κ. Strikingly, 19 patients (86%) were hospitalized for COVID-19 pneumonia, including 15 (68%) admitted to an intensive care unit, 11 (50%) who required mechanical ventilation, and four (18%) who died. Ambulatory disease in three patients (14%) was possibly accounted for by prior or early specific interventions. Preexisting auto-Abs neutralizing type I IFNs in APS-1 patients confer a very high risk of life-threatening COVID-19 pneumonia at any age.

Safety of endoscopic retrograde cholangiopancreatography in the pediatric population: a multicenter study

INTRODUCTION

The aims of this retrospective multicenter study were to assess the technical success and adverse events of endoscopic retrograde cholangiopancreatography (ERCP) procedures in children in French and Belgian centers.

METHODS

All children aged 1 day to 17 years who underwent ERCP between January 2008 and March 2019 in 15 tertiary care hospitals were retrospectively included.

RESULTS

271 children underwent 470 ERCP procedures. Clinical long-term follow-up was available for 72 % of our patients (340/470 procedures). The median age at intervention was 10.9 years. ERCP was therapeutic in 90 % (423/470) and diagnostic in cases of neonatal cholestasis in 10 % of the patients. The most common biliary indication was choledocholithiasis; the most common pancreatic indication was chronic pancreatitis. Biliary cannulation was successful in 92 % of cases (270/294); pancreatic cannulation in 96 % of cases (169/176); and planned therapeutic procedures in 92 % of cases (388/423). The overall complication rate was 19 % (65/340). The most common complication was post-ERCP pancreatitis (PEP) in 12 % of cases (40/340) and sepsis in 5 % (18/340). On univariate analyses, pancreatic stent removal was protective against PEP (odds ratio [OR] 0.1, 95 % confidence interval [CI] 0.01 - 0.75; P = 0.03), and sepsis was associated with history of liver transplantation (OR 7.27, 95 %CI 1.7 - 31.05; P = 0.01). Five patients had post-ERCP hemorrhage and two had intestinal perforation. All complications were managed with supportive medical care. There was no procedure-related mortality.

CONCLUSION

Our cohort demonstrates that ERCP can be performed safely with high success rates in many pancreaticobiliary diseases of children. The rate of adverse events was similar to that in previous reports.

Molecular features of untreated breast cancer and initial metastatic event inform clinical decision-making and predict outcome: long-term results of ESOPE, a single-arm prospective multicenter study

Background

Prognosis evaluation of advanced breast cancer and therapeutic strategy are mostly based on clinical features of advanced disease and molecular profiling of the primary tumor. Very few studies have evaluated the impact of metastatic subtyping during the initial metastatic event in a prospective study. The genomic landscape of metastatic breast cancer has mostly been described in very advanced, pretreated disease, limiting the findings transferability to clinical use.

Methods

We developed a multicenter, single-arm, prospective clinical trial in order to address these issues. Between November 2010 and September 2013, 123 eligible patients were included. Patients at the first, untreated metastatic event were eligible. All matched primary tumors and metastatic samples were centrally reviewed for pathological typing. Targeted and whole-exome sequencing was applied to matched pairs of frozen tissue. A multivariate overall survival analysis was performed (median follow-up 64 months).

Results

Per central review in 84 patients (out of 130), we show that luminal A breast tumors are more prone to subtype switching. By combining targeted sequencing of a 91 gene panel (n = 67) and whole-exome sequencing (n = 30), a slight excess of mutations is observed in the metastases. Luminal A breast cancer has the most heterogeneous mutational profile and the highest number of mutational signatures, when comparing primary tumor and the matched metastatic tissue. Tumors with a subtype change have more mutations that are private. The metastasis-specific mutation load is significantly higher in late than in de novo metastases. The most frequently mutated genes were TP53 and PIK3CA. The most frequent metastasis-specific druggable genes were PIK3CA, PTEN, KDR, ALK, CDKN2A, NOTCH4, POLE, SETD2, SF3B1, and TSC2. Long-term outcome is driven by a combination of tumor load and metastasis biology.

Conclusions

Profiling of the first, untreated, metastatic event of breast cancer reveals a profound heterogeneity mostly in luminal A tumors and in late metastases. Based on this profiling, we can derive information relevant to prognosis and therapeutic intervention, which support current guidelines recommending a biopsy at the first metastatic relapse.

Trial registration

The trial was registered at ClinicalTrials.gov (NCT01956552).

Supplementary Information

The online version contains supplementary material available at 10.1186/s13073-021-00862-6.

The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals

Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced by integrating multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). It is based exclusively on curated healthy wild-type expression data (e.g., no gene knock-out, no treatment, no disease), to provide a comparable reference of normal gene expression. Curation includes very large datasets such as GTEx (re-annotation of samples as ‘healthy’ or not) as well as many small ones. Data are integrated and made comparable between species thanks to consistent data annotation and processing, and to calls of presence/absence of expression, along with expression scores. As a result, Bgee is capable of detecting the conditions of expression of any single gene, accommodating any data type and species. Bgee provides several tools for analyses, allowing, e.g., automated comparisons of gene expression patterns within and between species, retrieval of the prefered conditions of expression of any gene, or enrichment analyses of conditions with expression of sets of genes. Bgee release 14.1 includes 29 animal species, and is available at https://bgee.org/ and through its Bioconductor R package BgeeDB.

Transgenerational effects of inter-ploidy cross direction on reproduction and F2 seed development of Arabidopsis thaliana F1 hybrid triploids

Reproduction in triploid plants is important for understanding polyploid population dynamics. We show that genetically identical reciprocal F1 hybrid triploids can display transgenerational epigenetic effects on viable F2 seed development. The success or failure of reproductive outcomes from intra-species crosses between plants of different ploidy levels is an important factor in flowering plant evolution and crop breeding. However, the effects of inter-ploidy cross directions on F1 hybrid offspring fitness are poorly understood. In Arabidopsis thaliana, hybridization between diploid and tetraploid plants can produce viable F1 triploid plants. When selfed, such F1 triploid plants act as aneuploid gamete production "machines" where the vast majority of gametes generated are aneuploid which, following sexual reproduction, can generate aneuploid swarms of F2 progeny (Henry et al. 2009). There is potential for some aneuploids to cause gametophyte abortion and/or F2 seed abortion (Henry et al. 2009). In this study, we analyse the reproductive success of 178 self-fertilized inter-accession F1 hybrid triploids and demonstrate that the proportions of aborted or normally developed F2 seeds from the selfed F1 triploids depend upon a combination of natural variation and cross direction, with strong interaction between these factors. Single-seed ploidy analysis indicates that the embryonic DNA content of phenotypically normal F2 seeds is highly variable and that these DNA content distributions are also affected by genotype and cross direction. Notably, genetically identical reciprocal F1 hybrid triploids display grandparent-of-origin effects on F2 seed set, and hence on the ability to tolerate aneuploidy in F2 seed. There are differences between reciprocal F1 hybrid triploids regarding the proportions of normal and aborted F2 seeds generated, and also for the DNA content averages and distributions of the F2 seeds. To identify genetic variation for tolerance of aneuploidy in F2 seeds, we carried out a GWAS which identified two SNPs, termed MOT and POT, which represent candidate loci for genetic control of the proportion of normal F2 seeds obtained from selfed F1 triploids. Parental and grandparental effects on F2 seeds obtained from selfed F1 triploids can have transgenerational consequences for asymmetric gene flow, emergence of novel genotypes in polyploid populations, and for control of F2 seed set in triploid crops.

6E11, a highly selective inhibitor of Receptor-Interacting Protein Kinase 1, protects cells against cold hypoxia-reoxygenation injury

Necroptosis is a programmed cell death pathway that has been shown to be of central pathophysiological relevance in multiple disorders (hepatitis, brain and cardiac ischemia, pancreatitis, viral infection and inflammatory diseases). Necroptosis is driven by two serine threonine kinases, RIPK1 (Receptor Interacting Protein Kinase 1) and RIPK3, and a pseudo-kinase MLKL (Mixed Lineage Kinase domain-Like) associated in a multi-protein complex called necrosome. In order to find new inhibitors for use in human therapy, a chemical library containing highly diverse chemical structures was screened using a cell-based assay. The compound 6E11, a natural product derivative, was characterized as a positive hit. Interestingly, this flavanone compound: inhibits necroptosis induced by death receptors ligands TNF-α (Tumor Necrosis Factor) or TRAIL (TNF-Related Apoptosis-Inducing Ligand); is an extremely selective inhibitor, among kinases, of human RIPK1 enzymatic activity with a nM Kd; has a non-ATP competitive mode of action and a novel putative binding site; is weakly cytotoxic towards human primary blood leukocytes or retinal pigment epithelial cells at effective concentrations; protects human aortic endothelial cells (HAEC) from cold hypoxia/reoxygenation injury more effectively than necrostatin-1 (Nec-1) and Nec-1s. Altogether, these data demonstrate that 6E11 is a novel potent small molecular inhibitor of RIPK1-driven necroptosis.

Abstract PD1-06: Comparison of mutational landscapes of primary breast cancer and first metastatic relapse: Results from the ESOPE study

Background

Genomic profile of breast cancer metastases (M) may differ from that of the primary tumor (PT). In a multicenter prospective study (ESOPE, NCT 01956552) including 130 patients with biopsies of the first metastatic deposit, we have shown that luminal breast cancers are the most prone to phenotypical subtype changes (Comte et al, ASCO 2016#550). We report here the first results of a comparative PT/M targeted next generation sequencing (NGS) mutational analysis.

Methods

Of 130 patients, 117 paired PT/M samples obtained before any treatment were available for analysis. Targeted Sequencing was done using Illumina Hiseq2500 technology with a custom made 95 breast cancer associated genes panel. Sequence data were aligned to the human reference genome (hg19) using Bowtie2 algorithm. Median depth was 607X and 87% of targets achieved 100X depth. SNVs and indels were called using GATK UnifiedGenotyper. We retained COSMIC confirmed non synonymous, exonic/splice variants and observed at a frequency lower than 0,1% in population. Further confirmation of detected variants was performed with comparison to public databases (cbioportal, tumorportal), and potential pathogenicity was evaluated with 4 different public algorithms. We present here the results obtained from the first 35 matched PT/M samples (liver mets 68%), focusing analysis on 40 genes including PIK3CA (20 genes), ER (6 genes) and MAPK (11 genes) pathways, RUNX1, CDH1 and TP53 genes.

Results

Patients characteristics are representative of patients with first line metastatic breast cancer (Comte et al, ASCO 2016#550). Among the 40 genes analyzed in the 70 samples, we detected 134 somatic mutations (70 in PT and 64 in M) including 15 indels and 119 SNV. Among these 134 mutations there were 74 different mutations (66SNV and 8 indels) classified pathogenic for 26 and of unknown pathogenicity for 48 of them. We detected at least 1 mutation in 31 PT and in 28 M. Median numbers of mutations were 1 in PT (range 1-9) and 1 in M (range1-22) samples (p=0.295, Wilcoxon rank sum test). Top ten mutated genes in PT included PIK3CA, TP53, NCOR1, NF1, GATA3, CDH1, ERBB3, PTEN, HRAS, INPP4B. In M samples, the 10 top genes were PIK3CA, TP53, ERBB3, AKT3, CDH1, ERBB4, GATA3, INPP4B, MET, MTOR. Only 3 ESR1 mutations were detected, including 1 PT/M pair and 1 M. Beyond highly shared PIK3CA and TP53 mutations, overall crude PT/M discordance rate was 31%. Analysis by histological subtypes showed PT and M specific mutational profiles, suggesting a role in ERB gene family (notably ERBB3) and MAPK driven pathways in early metastatic progression. Specific metastatic site analysis suggested enrichment in MAPK pathway mutations in liver metastases when compared to other sites. Variant allelic fractions were globally not significantly different between PT and M samples.

Conclusion

In this prospective multicenter series of systematic biopsies of first metastases, we report a targeted mutational analysis of matched PT and M samples not modified by previous therapy exposure. Early analyses suggest specific genotypical changes according to tumor subtype and/or metastatic site. Extended and updated results will be reported at the meeting.

Citation Format: Cottu PH, Boulai A, Callens C, Baulande S, Legoix-Ne P, Bernard V, Vincent-Salomon A, Benhamo V, Brain EGC, Chemlali W, Campone M, Bachelot TD, Giacchetti S, Bonneterre J, Bidard F-C, Servois V, Comte A, Belin L, Sigal B, Bièche I. Comparison of mutational landscapes of primary breast cancer and first metastatic relapse: Results from the ESOPE study [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr PD1-06.

Abstract P2-05-06: Clinical utility of systematic biopsy of first metastatic event in breast cancer: Results from a prospective multicenter trial

BACKGROUND: Cumulative evidence for phenotypic and molecular heterogeneity between primary breast cancer (BC) site and matched metastasis (mets) has been obtained in retrospective studies. Current expert consensus suggests performing biopsies of mets, but clinical utility and cost are unknown. The primary objective of the ESOPE study (NCT01956552) was to compare the phenotype and genotype of the primary tumor (PT) with those of matched mets at time of first distant relapse, before the start of any treatment, in order to optimize the treatment of mets

PATIENTS and METHODS: Between Nov. 2010 and Sept. 2013, we conducted a prospective multicenter study on BC patients (pts) with diagnosis of first mets. All pts were to have available Formalin-Fixed Paraffin-Embedded (FFPE) PT sample and mets accessible to either percutaneous or surgical sampling. All tissue samples were centrally analyzed with immunohistochemistry (ER, PgR, HER2, and Ki67) and FISH when indicated. Frozen samples were stored for further analyses. We recorded intended therapeutic decision before and after biopsy.

RESULTS: Of 93 pts included, 89 were eligible for biopsy. Median age was 57 years (28-81); median interval between PT and mets was 42 months (0-211), including 14 pts with novo metastatic breast cancer. Mets biopsy was performed in 85 pts (96%, refusal n=2, not feasible n=2). Toxicity was limited to only 1 grade 1 hemorrhage. Sampled sites were liver (44%), lung (16%), bone (13%), lymph node (13%), skin/muscle/chest wall (9%), ovary/peritoneum (4%), and adrenal gland (1%). PT was not available in 4 pts; mets biopsy was non contributive in 6 pts but led to a diagnosis of second primary cancer in 3 pts.

In 72 pts with matched PT and mets, PT were luminal A (n=11), luminal B (n=33), triple negative (n=13), HER2 (n=13), non-evaluable (n=2). Mets were luminal A (n=6), luminal B (n=30), triple negative (n=16), HER2 (n=14), non-evaluable (n=6). Discrepancy rates were: ER 18% [kappa for concordance =0.6, CI 95 % (0.42-0.77)], PgR: 39% [kappa=0.19, CI 95% (0.01-0.39)], Her2: 4% [kappa=0.86, CI 95% (0.7-1)], Ki67: 25% [kappa=0.19, CI 95% (-0.09; 0.49)].

The most frequent discrepancy rate was observed in pts with lum A PT, as only 3/10 developed Lum A mets. HER2 and triple negative were the most stable subtypes (12/13 and 12/12 respectively). Most importantly, mets biopsy led to a change in therapeutic decision in 25 pts (independent evaluation by 2 oncologists). Additional comparative targeted NGS analyses are ongoing on a first subset of 54 FFPE paired samples, and parallel whole exome sequencing is planned on 38 paired samples with available constitutional DNA.

CONCLUSION: Comparative analysis of breast cancer PT and first mets is routinely feasible, with very low morbidity and a significant impact for patients' management: 29% had a second cancer diagnosis or were proposed a therapeutic change. Furthermore, this study will provide additional data on quality and quantity of tissue available for molecular analysis, and ultimately in terms of cost-efficacy.

Citation Format: Comte A, Sigal-Zafrani B, Belin L, Bièche I, Callens C, Diéras V, Bidard F-C, Mariani O, Servois V, Szwarc D, Vincent-Salomon A, Brain ECG, Cottu PH. Clinical utility of systematic biopsy of first metastatic event in breast cancer: Results from a prospective multicenter trial. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P2-05-06.

Uncovering hidden duplicated content in public transcriptomics data

As part of the development of the database Bgee (a dataBase for Gene Expression Evolution), we annotate and analyse expression data from different types and different sources, notably Affymetrix data from GEO and ArrayExpress, and RNA-Seq data from SRA. During our quality control procedure, we have identified duplicated content in GEO and ArrayExpress, affecting ∼14% of our data: fully or partially duplicated experiments from independent data submissions, Affymetrix chips reused in several experiments, or reused within an experiment. We present here the procedure that we have established to filter such duplicates from Affymetrix data, and our procedure to identify future potential duplicates in RNA-Seq data.

Database URL:http://bgee.unil.ch/

vHOG, a multispecies vertebrate ontology of homologous organs groups

MOTIVATION

Most anatomical ontologies are species-specific, whereas a framework for comparative studies is needed. We describe the vertebrate Homologous Organs Groups ontology, vHOG, used to compare expression patterns between species.

RESULTS

vHOG is a multispecies anatomical ontology for the vertebrate lineage. It is based on the HOGs used in the Bgee database of gene expression evolution. vHOG version 1.4 includes 1184 terms, follows OBO principles and is based on the Common Anatomy Reference Ontology (CARO). vHOG only describes structures with historical homology relations between model vertebrate species. The mapping to species-specific anatomical ontologies is provided as a separate file, so that no homology hypothesis is stated within the ontology itself. Each mapping has been manually reviewed, and we provide support codes and references when available.

AVAILABILITY AND IMPLEMENTATION

vHOG is available from the Bgee download site (http://bgee.unil.ch/), as well as from the OBO Foundry and the NCBO Bioportal websites.

CONTACT

bgee@isb-sib.ch; frederic.bastian@unil.ch.

PHLDA2 is an imprinted gene in cattle

Genomic imprinting is an epigenetic non-Mendelian phenomenon found predominantly in placental mammals. Imprinted genes display differential expression in the offspring depending on whether the gene is maternally or paternally inherited. Currently, some 100 imprinted genes have been reported in mammals, and while some of these genes are imprinted across most mammalian species, others have been shown to be imprinted in only a few species. The PHLDA2 gene that codes for a pleckstrin homology-like domain, family A (member 2), protein has to date been shown to be a maternally expressed imprinted gene in humans, mice and pigs. Genes subject to imprinting can have major effects on mammalian growth, development and disease. For instance, disruption of imprinted genes can lead to aberrant growth syndromes in cloned domestic mammals, and it has been demonstrated that PHLDA2 mRNA expression levels are aberrant in the placenta of somatic clones of cattle. In this study, we demonstrate that PHLDA2 is expressed across a range of cattle foetal tissues and stages and provide the first evidence that PHLDA2 is a monoallelically expressed imprinted gene in cattle foetal tissues, and also in the bovine placenta.

Identification of imprinted genes subject to parent-of-origin specific expression in Arabidopsis thaliana seeds

BACKGROUND

Epigenetic regulation of gene dosage by genomic imprinting of some autosomal genes facilitates normal reproductive development in both mammals and flowering plants. While many imprinted genes have been identified and intensively studied in mammals, smaller numbers have been characterized in flowering plants, mostly in Arabidopsis thaliana. Identification of additional imprinted loci in flowering plants by genome-wide screening for parent-of-origin specific uniparental expression in seed tissues will facilitate our understanding of the origins and functions of imprinted genes in flowering plants.

RESULTS

cDNA-AFLP can detect allele-specific expression that is parent-of-origin dependent for expressed genes in which restriction site polymorphisms exist in the transcripts derived from each allele. Using a genome-wide cDNA-AFLP screen surveying allele-specific expression of 4500 transcript-derived fragments, we report the identification of 52 maternally expressed genes (MEGs) displaying parent-of-origin dependent expression patterns in Arabidopsis siliques containing F1 hybrid seeds (3, 4 and 5 days after pollination). We identified these MEGs by developing a bioinformatics tool (GenFrag) which can directly determine the identities of transcript-derived fragments from (i) their size and (ii) which selective nucleotides were added to the primers used to generate them. Hence, GenFrag facilitates increased throughput for genome-wide cDNA-AFLP fragment analyses. The 52 MEGs we identified were further filtered for high expression levels in the endosperm relative to the seed coat to identify the candidate genes most likely representing novel imprinted genes expressed in the endosperm of Arabidopsis thaliana. Expression in seed tissues of the three top-ranked candidate genes, ATCDC48, PDE120 and MS5-like, was confirmed by Laser-Capture Microdissection and qRT-PCR analysis. Maternal-specific expression of these genes in Arabidopsis thaliana F1 seeds was confirmed via allele-specific transcript analysis across a range of different accessions. Differentially methylated regions were identified adjacent to ATCDC48 and PDE120, which may represent candidate imprinting control regions. Finally, we demonstrate that expression levels of these three genes in vegetative tissues are MET1-dependent, while their uniparental maternal expression in the seed is not dependent on MET1.

CONCLUSIONS

Using a cDNA-AFLP transcriptome profiling approach, we have identified three genes, ATCDC48, PDE120 and MS5-like which represent novel maternally expressed imprinted genes in the Arabidopsis thaliana seed. The extent of overlap between our cDNA-AFLP screen for maternally expressed imprinted genes, and other screens for imprinted and endosperm-expressed genes is discussed.

Time course of odorant- and trigeminal-induced activation in the human brain: an event-related functional magnetic resonance imaging study

It is well known that most odorants stimulate the trigeminal system but the time course of the brain regions activated by these chemical stimulations remains poorly documented, especially regarding the trigeminal system. This functional magnetic resonance imaging (fMRI) study compares brain activations resulting from the contrast between two odorant conditions (one bimodal odor and one relatively pure olfactory stimulant) according to the duration of the stimulation (i.e. one inhalation, or three or six successive inhalations). The results show striking differences in the main brain regions activated according to these durations. The caudate nucleus and the orbitofrontal cortex are only involved in short-duration stimulations, and the posterior insular cortex and post-central gyrus (SI) are only activated by long duration stimulations. Different regions of the frontal, temporal and occipital lobe are activated depending on the duration but mainly during medium-duration stimulations. These results expand on the findings of previous studies and contribute to the description of temporal networks in trigeminal perception.

Molecular signaling in zebrafish development and the vertebrate phylotypic period

During development vertebrate embryos pass through a stage where their morphology is most conserved between species, the phylotypic period (approximately the pharyngula). To explain the resistance to evolutionary changes of this period, one hypothesis suggests that it is characterized by a high level of interactions. Based on this hypothesis, we examined protein–protein interactions, signal transduction cascades and miRNAs over the course of zebrafish development, and the conservation of expression of these genes in mouse development. We also investigated the characteristics of genes highly expressed before or during the presumed phylotypic period. We show that while there is a high diversity of interactions during the phylotypic period (protein–DNA, RNA–RNA, cell–cell, and between tissues), which is well conserved with mouse, there is no clear difference with later, more morphologically divergent, stages. We propose that the phylotypic period may rather be the expression at the morphological level of strong conservation of molecular processes earlier in development.

Plutonium in the environment: key factors related to impact assessment in case of an accidental atmospheric release

This paper deals with plutonium and key factors related to impact assessment. It is based on recent work performed by CEA which summarize the main features of plutonium behaviour from sources inside installations to the environment and man, and to report current knowledge on the different parameters used in models for environmental and radiological impact assessment. These key factors are illustrated through a case study based on an accidental atmospheric release of Pu in a nuclear facility.

Development of a database: DACTARI for a radiotoxic element ranking methodology

Dosimetric impact studies aim at evaluating potential radiological effects of chronic or acute releases from nuclear facilities. A methodology for ranking radionuclides (RN) in terms of their health-related impact on the human population was first developed at CEA with specific criteria for each RN that could be applied to a variety of situations. It is based, in particular, on applying physico-chemical criteria to the complete RN inventory (present in the release or in the source term) and on applying norms related to radiation protection and chemical toxicology. The initial step consisted in identifying and collecting data necessary to apply the methodology, with reference to a previous database of long-lived radionuclides (LLRN, with half-lives ranging from 30 to 10(14) y) containing 95 radionuclides. The initial results have allowed us to identify missing data and revealed the need to complete the study for both toxic and radiotoxic aspects. This led us to the next step, developing a specific database, DAtabase for Chemical Toxicity and Radiotoxicity Assessment of RadIonuclides (DACTARI), to collect data on chemical toxicity and radiotoxicity, including acute or chronic toxicity, the chemical form of the compounds, the contamination route (ingestion, inhalation), lethal doses, target organs, intestinal and maternal-foetal transfer, drinking water guidelines and the mutagenic and carcinogenic properties.

Left ventricular ejection fraction calculation from automatically selected and processed diastolic and systolic frames in short-axis cine-MRI

The calculation of the left ventricular ejection fraction (LVEF) is dependent upon the accurate measurement of diastolic and systolic left ventricular volumes. Although breath-hold cine magnetic resonance imaging (MRI) allows coverage of the whole cardiac cycle with an excellent time resolution, many authors rely on the visual selection of diastolic and the systolic short-axis slices in order to reduce the postprocessing time. An automatic method was developed to detect the endocardial contour on each image, allowing an automatic selection of the systolic frame. The calculated ejection fraction was compared with radionuclide ventriculography (RNV). Sixty-five patients were examined using an electrocardiogram (ECG)-gated gradient echo sequence. Among these examinations, manual and automatic processing with MRI were compared when the time of the systolic frame concorded. Good correlations have been found between the automatic MRI approach and RNV, and between manual and automatic processing on MRI alone. The results show that the automatic determination of the ejection fraction is feasible, and should constitute an important step toward a larger acceptance of MRI as a routine tool in heart disease imaging. One major benefit of using automatic postprocessing is that it may eliminate the visual choice of the systolic frame, inaccurate in more than 50% of the studied patients.

[Role of visual analysis of first-pass contrast-enhanced MRI in reperfused myocardial infarction]

The aim of this work is to evaluate the relationship between improvement of regional myocardial function and visual analysis of contrast-enhanced (CE) MRI in patients after acute myocardial infarction. MRI was performed on 19 patients 1 and 11 weeks after a reperfused acute myocardial infarction. Perfusion data (first-pass images [FPI] and delayed CE images) were acquired after an intravenous bolus of gadolinium-DTPA and visually analyzed using a 17 segment model. Each segment was then classified in 3 groups, according to the presence or absence of FPI and CE patterns at baseline study: group 0: normal-appearing segments; group 1: segments with delayed hyper-enhancement but no early hypo-enhancement; group 2: segments with early hypoenhancement. Relative Wall thickening (RWT) was analyzed in each segment and its improvement evaluated in each group. Between first MRI and follow-up study, a significant improvement of RWT occurred in group 1 (mean +/- SD) [from 43.43 +/- 26.59% to 76.71 +/- 47.38%; p = 0.001] but not in group 2 (from 32.73 +/- 25.58% to 39.57 +/- 30.57%; p = NS). In group 0, RWT despite normal value at baseline study exhibited a significant improvement at follow-up (from 65.23 +/- 46.52% to 79.73 +/- 48.46%; p = 0.0015). In conclusion, the combined analysis of early and delayed perfusion abnormalities in MRI in the week following myocardial infarction can predict myocardial viability and allows in the future an evaluation of the efficacy of perfusion therapy.

[Magnetic resonance imaging early after acute myocardial infarction. A visual analysis of myocardial perfusion based on a 17 segment model]

Magnetic resonance imaging allows an accurate calculation of the left ventricular ejection fraction and left ventricular volumes. Additionally, it makes possible to assess myocardial perfusion after gadolinium chelate injection. Late after the injection, the presence of a myocardial hyper-enhancement can be visualized. The present study has used the 17 segment standardized nomenclature for tomographic imaging of the heart as recommended for all cardiac imaging modalities. Sixty nine patients were studied after a revascularised myocardial infarction. All patients had Timi grade 3 flow in the infarct-related artery after therapy. Regional and global function was studied using cine MR short axis slices. The gadolinium chelate first pass was scored using a 5 level scale reflecting the transmural extent of the segmental myocardial enhancement. The delayed enhancement due to gadolinium accumulation in the myocardium 10 min post injection was scored in the same manner. Left ventricular ejection fraction was 51 +/- 13%. Segmental thickening parameters (systolic thickness, absolute thickening and relative thickening) appeared statistically related to the hypoperfusion and delayed enhancement scores. Absolute myocardial thickening varied from 4.8 +/- 2.7 mm in the myocardial segments free of any delayed enhancement to 2.4 +/- 2.1 mm in segments presenting with a transmural extent of the delayed hyper-enhancement. Scores obtained after gadolinium injection were also well correlated with the global left ventricular function (r = 0.65, p < 0.01 for late enhancement). Magnetic resonance imaging of the heart allows a precise characterisation of revascularised myocardium which makes this technique very attractive for evaluating the treatments designed to improve myocardial microperfusion.

[Early study of myocardial perfusion with MRI in revascularized infarcts]

The aim of this work is to study the regional myocardial perfusion by MRI early after revascularised myocardial infarction and to compare it with regional function. This prospective work has included 15 patients with acute first myocardial infarction that was precociously revascularised. A myocardial MRI was performed between D2 and D10 after myocardial infarction. The regional myocardial thickening was evaluated from cine-MRI sequences. For the study of myocardial perfusion, the first pass of the contrast agent was analysed from curves of the signal evolution versus time. The signal enhancement on late images acquired 10 minutes after the perfusion of the contrast agent was also evaluated. Among 384 studied myocardial segments, those with a normal gadolinium first pass curve had a relative thickening of 46 +/- 38%. The segments with a severely reduced first pass kinetic have a markedly reduced relative thickening (14 +/- 20%) in relation with myocardial hypoperfusion. The myocardial enhancement is frequently seen in the infarct territory and appears related to a reduced regional contractility. The myocardium is enhanced on late images in 12% of the normally perfused segments. These segments have a mildly reduced wall thickening (3.36 +/- 2.84 mm vs 4.42 +/- 2.83 mm). The segmental contractility in a reperfused myocardial infarction appears to depend both on the myocardial perfusion which reflects the microvascularisation and on the myocardial enhancement which is linked to myocardial structural alterations. MRI appears to be an adequate method to evaluate these abnormalities and allows an easy assessment of the no-reflow phenomenon, if present.

Oxygen monitoring in supercritical carbon dioxide using a fibre optic sensor

Investigations of enzymatic reactions in supercritical CO(2) are often hindered by the high pressure involved in these processes, making reaction monitoring extremely difficult. This paper describes the implementation of a fiber optic based oxygen sensor into a high pressure reactor for supercritical carbon dioxide. The sensor is pressure resistant, working in supercritical carbon dioxide and reusable after depressurisation. The sensor signal is found to be affected by pressure changes, but stable at constant pressure. Oxygen concentration in supercritical CO(2) is monitored using the disproportionation of hydrogen peroxide as a simple oxygen producing reaction.

Modulation by external Ca2+ and nicardipine of Ca2+ influx and cytosolic concentration in human erythrocytes

Variations of Ca2+ influx (evaluated by the initial rate of 45Ca2+ uptake) and cytosolic free Ca2+ concentration ([Ca2+]i, measured with fura-2) were investigated in human erythrocytes. When external Ca2+ concentration ([Ca2+]o) rose from 1 to 2 mM, the initial rate of Ca2+ influx nearly doubled whereas [Ca2+]i increased only by 15%. Nicardipine dose-dependently decreased both initial rate of Ca2+ influx and [Ca2+]i (up to 53 and 18%. respectively at 10(-6) M). The less marked changes in [Ca2+]i than in Ca2+ influx indicate a partial adjustment of the Ca2+ extruding-pump activity to of Ca2+ influx. In vivo administration of nicardipine reduced [Ca2+]i only when its initial value exceeded 80 nM and prevented the rise in [Ca2+]i induced by the increase in [Ca2+]o. Our results indicate that nicardipine may reduce Ca2+ influx in human erythrocytes and participate in the control of [Ca2+]i when elevated.

Binding of [3H]isradipine (PN 200-110) on smooth muscle cell membranes from different bovine arteries

The binding of [3H]isradipine [( 3H]PN 200-110), a new dihydropyridine (DHP) calcium blocker on smooth muscle cell (SMC) membranes from different bovine arteries was saturable with comparable high affinities but different binding site densities (Bmax). The data were fitted to a model that provided a common estimation for the dissociation constant (Kd = 0.46 nM, SD = 0.03) but different Bmax values. Two groups of arteries could be distinguished, large-sized with high Bmax (aorta, 149 fmol/mg, SD = 4; intrapulmonary, 134 fmol/mg, SD = 4) and medium-sized with lower Bmax (mesenteric, 67 fmol/mg, SD = 2; internal carotid, 50 fmol/mg, SD = 2; renal artery, 29 fmol/mg, SD = 2). The Kd values were similar to those previously reported, but the Bmax value on aorta SMC was higher than usually reported with other DHPs, showing that isradipine was a high full antagonist of calcium channel. Our results also suggest that the increase in arterial compliance induced by DHPs will probably be more important on large-sized arteries than on medium-sized arteries because of higher DHP binding.

Binding of (+)-PN 200-110 to rat pituitaries and to normal and adenomatous human pituitaries

Endocrine cells possess voltage-sensitive Ca2+ channels involved in the modulation of hormonal secretion. Using the dihydropyridine, (+)-PN 200-110, we have investigated the binding characteristics of this ligand to pituitary membrane Ca2+ channels from normal rat, normal and adenomatous human pituitaries. [3H]PN 200-110 binds specifically to rat pituitary membranes to one class of sites (Kd = 0.41 +/- 0.10 mM; Bmax = 39 +/- 1.3 fmol/mg protein). At 37 degrees C, equilibrium is reached in 45 min and half-life of the binding is 13 min. No significant changes were observed for either the Kd or Bmax values between normal rat and human pituitaries or between the different types of adenomas (GH- and PRL-secreting and non-secreting). As the secretory activity of the pituitary adenomas, involving Ca2+ mobilization, varies from one adenoma to another, our results could indicate that, if there is a modified regulation of Ca2+ entry in the adenomas, it may not be related to a varying number of calcium channels, at least the channels labeled by the dihydropyridine (+)-PN 200-110.