An integrated biological effects assessment of the discharge water into the Sunndalsfjord from an aluminium smelter

An integrated biological effects study using field transplanted mussels was applied to determine the potential biological effects of an effluent discharge from an aluminium smelter into a Norwegian fjord. Chemical body burden and biological effects were measured in mussels positioned downstream (1, 2, 5, 10 and 20 km) from the aluminium smelters discharge for a period of 6 weeks. A suite of biomarkers, from whole organism to subcellular responses were measured. Chemical concentrations in mussel tissues were low; however, a change in the PAC (polyaromatic compound) profile from high to low pyrogenic influence provided evidence of exposure to the smelter's effluent. Overall, the biological responses observed where greater in the mussels positioned closest to the smelter (1-5 km). Lowest chemical accumulation and biomarker responses were observed in mussels positioned 10 km from the smelter and were considered as the reference field population. Mussels located furthest from the smelter (20 km) exhibited significant biomarker responses and suggested a different contaminant source within the fjord. The integrated biological response index (IBR) was applied and reflected the expected level of exposure to the smelters discharge, with highest IBR calculated in mussels positioned closest to the discharge (1-5 km). Principal component analysis (PCA) also differentiated among mussel groups, with the most impacted located closest to the smelter. Not one chemical factor could explain the biological responses observed in mussels, but the presence of PAH16, PAH41 and metals Mn, Ni and Cr were the main contributors measured to the higher stress seen in the mussels from the 1 and 5 km groups.

Transcriptome-wide analyses of early immune responses in lumpfish leukocytes upon stimulation with poly(I:C)

Background

Both bacterial and viral diseases are a major threat to farmed fish. As the antiviral immune mechanisms in lumpfish (Cyclopterus lumpus L.) are poorly understood, lumpfish leukocytes were stimulated with poly(I:C), a synthetic analog of double stranded RNA, which mimic viral infections, and RNA sequencing was performed.

Methods

To address this gap, we stimulated lumpfish leukocytes with poly(I:C) for 6 and 24 hours and did RNA sequencing with three parallels per timepoint. Genome guided mapping was performed to define differentially expressed genes (DEGs).

Results

Immune genes were identified, and transcriptome-wide analyses of early immune responses showed that 376 and 2372 transcripts were significantly differentially expressed 6 and 24 hours post exposure (hpe) to poly(I:C), respectively. The most enriched GO terms when time had been accounted for, were immune system processes (GO:0002376) and immune response (GO:0006955). Analysis of DEGs showed that among the most highly upregulated genes were TLRs and genes belonging to the RIG-I signaling pathway, including LGP2, STING and MX, as well as IRF3 and IL12A. RIG-I was not identified, but in silico analyses showed that genes encoding proteins involved in pathogen recognition, cell signaling, and cytokines of the TLR and RIG-I signaling pathway are mostly conserved in lumpfish when compared to mammals and other teleost species.

Conclusions

Our analyses unravel the innate immune pathways playing a major role in antiviral defense in lumpfish. The information gathered can be used in comparative studies and lay the groundwork for future functional analyses of immune and pathogenicity mechanisms. Such knowledge is also necessary for the development of immunoprophylactic measures for lumpfish, which is extensively cultivated for use as cleaner fish in the aquaculture for removal of sea lice from Atlantic salmon (Salmo salar L.).

O-283 Evidence based management of endometriosis – what has changed since 2013?

In 2005, under the auspices of ESHRE, a group of international experts evaluated the existing best evidence and published the first European guideline on the management of endometriosis. This highly successful project was the first guideline by ESHRE and was adopted by many counties as their national standard. A second, fully-updated edition was presented in 2013.

For the new ESHRE Endometriosis Guideline, published in February 2022, all available evidence for twelve chosen topics was gathered by a senior research specialist. Subgroups comprised of patient representatives and experts in healthcare, reproductive science and epidemiology evaluated the data according to GRADE criteria. Each subgroup wrote a chapter and formulated their recommendations which were then presented by a representative to the core group. There, a provisional document was generated and made available for stakeholder review. The resulting comments were taken into account and where relevant incorporated into the final guideline document for which approval was sought and gained from the ESHRE Executive Committee.

35 PICO (Patients, Interventions, Comparison, Outcome) and seven narrative questions were addressed resulting in 78 Research Recommendations were formulated. Where sufficient scientific evidence was lacking and the Guideline Development Group (GDG) was of the opinion that an important topic needed to be highlighted Good Clinical Practice Points where created based on experts’ experience.

During the process of reviewing the literature it became apparent that large knowledge gaps of the best clinical approach to endometriosis exist. As a result, 30 research recommendations were also produced.

One of the main differences to the 2013 version of the ESHRE guidelines is that laparoscopy is no longer the gold standard for endometriosis per se as there exist sufficient data to support the use of transvaginal ultrasound performed by an experienced operator or MRI can equally identify or rule out ovarian and most of deep endometriosis. However, it is recognised by the GDG that the required imaging standards are not ubiquitously available and for peritoneal disease both sensitivity and specificity using either imaging modalities are still poor. As opposed to the 2013 recommendation, the GDG does not anymore recommend an ultralong protocol for the women with rASRM stage III/IV endometriosis to improve IVF success rates. Furthermore, gonadotropin releasing hormone antagonists seem to be effective in the treatment of endometriosis-associate pain and, where available, could be considered as second-line treatment.

Other changes were specific chapters on endometriosis in adolescents and in menopausal women as the GDG strongly felt that these groups are concerningly underrepresented in clinical care and research. Finally, a chapter focussing on the association of endometriosis with certain forms of cancer namely subgroups of ovarian cancer, breast and thyroid cancer was added to give both patients and clinicians a better insight into the current evidence of this complex topic.

The GDG hope that the new ESHRE Endometriosis Guideline will improve the clinical management of a highly prevalent and heterogenous disease and that the freely-available patient-friendly version of the guideline empowers symptomatic and asymptomatic women to seek the best available advice, support and treatment.

Developmental stage and morphology of the competent blastocyst are associated with sex of the child but not with other obstetric outcomes: a multicenter cohort study

STUDY QUESTION

Are transfer day, developmental stage and morphology of the competent blastocyst in pregnancies leading to live birth associated with preterm birth, birthweight, length at birth and sex of the child?

SUMMARY ANSWER

A high score in blastocyst developmental stage and in trophectoderm (TE) showed a significant association with the sex of the child, while no other associations with obstetric outcomes were observed.

WHAT IS KNOWN ALREADY

The association between blastocyst assessment scores and obstetric outcomes have been reported in small single-center studies and the results are conflicting.

STUDY DESIGN, SIZE, DURATION

Multicenter historical cohort study based on exposure data (transfer day (blastocyst developmental stage reached by Day 5 or Day 6)) blastocyst developmental stage (1-6) and morphology (TE and inner cell mass (ICM): A, B, C)) and outcome data (preterm birth, birthweight, length at birth, and sex of the child) from women undergoing single blastocyst transfer resulting in a singleton pregnancy and live birth.

PARTICIPANTS/MATERIALS, SETTING, METHODS

Data from 16 private and university-based facilities for clinical services and research were used. A total of 7246 women, who in 2014-2018 underwent fresh-embryo transfer with a single blastocyst or frozen-thawed embryo transfer (FET) with a single blastocyst resulting in a singleton pregnancy were identified. Linking to the Danish Medical Birth Registry resulted in a total of 4842 women with a live birth being included. Cycles with pre-implantation genetic testing and donated gametes were excluded. The analyses were adjusted for female age (n = 4842), female BMI (n = 4302), female smoking (n = 4290), parity (n = 4365), infertility diagnosis (n = 4765), type of treatment (n = 4842) and center (n = 4842); some analyses additionally included gestational age (n = 4368) and sex of the child (n = 4833).

MAIN RESULTS AND THE ROLE OF CHANCE

No statistically significant associations between blastocyst assessment scores (transfer day, developmental stage, TE, ICM) and preterm birth (8.3%) or birthweight (mean 3461.7 g) were found. The adjusted association between blastocysts with a TE score of C and a TE score of A and length at birth (mean 51.6 cm) were statistically significant (adjusted mean difference 0.4 cm (95% CI: 0.02; 0.77)). Blastocysts transferred with developmental stage score 5 compared to blastocysts transferred with score 3 had a 34% increased probability of being a boy (odds ratio (OR) 1.34 (95% CI: 1.09; 1.64). Further, TE score B blastocysts compared to TE score A blastocysts had a 31% reduced probability of being a boy (OR 0.69 (95% CI: 0.60; 0.80)).

LIMITATIONS, REASONS FOR CAUTION

It is possible that some residual confounding remains.

WIDER IMPLICATIONS OF THE FINDINGS

Blastocyst selection during ART does not appear to introduce any negative effects on obstetric outcome. Therefore, clinicians and patients can be reassured that the assessment scores of the selected blastocyst will not in themselves pose a risk of preterm birth or affect birthweight and the length at birth.

STUDY FUNDING/COMPETING INTEREST(S)

Unrestricted grant from Gedeon Richter Nordics AB, Sweden. None of the authors have any competing interest to declare.

TRIAL REGISTRATION NUMBER

N/A.

P–741 Fetal exposure to maternal perceived stress and male reproductive function in a cohort of young adults

Study question

Is exposure to maternal perceived stress during pregnancy associated with reproductive function in adult male offspring?

Summary answer

While maternal perceived stress was prevalent in the first trimesters of pregnancy, our preliminary findings indicate little association with reproductive function in young men.

What is known already

Though studies in animals point to a connection between prenatal exposure to maternal stress and reproductive function in offspring, the underlying biological mechanisms generating a deficit remain largely unclear. In humans, the few available studies focus on exposure to bereavement or other relatively strong objective stressful life events. Our individual perception of stress is, however, more likely the sum of a complex process involving both the actual input, previous experiences, coping strategies and support from our surroundings.

Study design, size, duration

Young men and their mothers were identified through records from the Danish National Birth Cohort (DNBC). Information on exposure, i.e. maternal perceived life and emotional stress, was available from telephone interviews conducted at approximately 30 weeks of gestation (1996 to 2001). Recruitment of the young men lasted from 2017 to 2019 with 1058 participants enrolled in the final FEPOS cohort.

Participants/materials, setting, methods

Each of the 1058 men in the FEPOS cohort completed an online questionnaire and clinical examinations and provided a blood and semen sample. Information on potential pre- and postnatal confounders was retrieved from the DNBC, the Danish National Patient Register and the Danish Medical Birth Register. We applied negative binomial regression models to examine associations between maternal perceived life and emotional stress scores and semen quality, testicular size and reproductive hormones among the young men.

Main results and the role of chance

Among the 1052 young men included in preliminary analyses, the majority was exposed to maternal perceived life and/or emotional stress (76% and 83%, respectively) during the first trimesters. Life stress was predominantly related to the actual pregnancy (48%), maternal disease (19%) or occupational conditions (33%). Emotional stress included especially being touchy (58%), sad (38%) or tense (36%), covering aspects of both stress, depression and anxiety. Overall, results indicate little association between maternal stress scores and measures of semen quality and testicular size. Our study involves a large cohort with prospectively collected exposure data and direct measures of several male reproductive outcomes. We applied inverse probability weighting to account for selection into the FEPOS cohort and included a range of a priori selected maternal confounders in our models.

Limitations, reasons for caution

The male fetus may be particularly sensitive to exposure during the differentiation of reproductive tissues (8–14 weeks of gestation). Our self-reported measures of exposure cover the first 30 weeks of gestation. Absence of association may, thus, be due to a lack of specific information on timing of symptoms.

Wider implications of the findings: While our preliminary findings may appear reassuring, further efforts to improve our understanding of maternal stress in relation to fetal health and potential consequences later in life are needed.

Trial registration number

Not applicable

Necessary duration of follow-up to assess complications of mesh in hernia surgery: a time-lapse study based on 460 explants

PURPOSE

Risk of complications following hernia repair is the key parameter to assess risk/benefit ratio of a technique. As mesh devices are permanent, their risks are life-long. Too many reports in the past assessed mesh safety prematurely after short follow-ups. We aimed to explore what length of follow up would reveal the full extent of complications.

METHODS

Time lapses between implantation and excision were analyzed in 460 cases of meshes excised for complications after hernia repair. Patterns of percentage growth and time lapses at 50th and 95th percentiles were used to compare groups of different hernia type, age, gender and reason for excision.

RESULTS

The 50th and 95th case percentiles in the dataset were at 3.75 and 15.0 years between mesh implantation and excision. For hernia types, the longest time lapses were for groin hernias (4.0 and 16.11 years at 50th and 95th percentiles). The shortest were for umbilical hernias (2.16 and 9.68 years). Males had later excisions than females (4.11 and 16.1 vs. 2.47 and 9.79 years). Younger patients (< 45 y.o.) had later excisions than older patients (4.12 and 17.68 vs. 3.37 and 10.0 years). Out of all subgroups, the longest time lapses were for groin hernias in younger males (4.77 and 18.89 years) and for mesh erosion into organs (4.67 and 17.0 years).

CONCLUSIONS

Follow-up of more than 15 years is needed to fully assess complications after mesh hernia repair. Especially longer periods are needed to detect mesh erosion into organs and complications in younger males. Presently, short observations and lack of reporting standard in the literature prohibit accurate assessment of complication risks. We propose to use cumulative incidence for standardized risk reporting (y% risk at x years). This will show time-dependent patterns and allow comparisons between different techniques and studies of variable duration. Standardization will also help to predict long-term risks beyond shorter (practical) follow-ups and facilitate real-time monitoring during surveillance.

Common gene expression signatures in Parkinson's disease are driven by changes in cell composition

The etiology of Parkinson’s disease is largely unknown. Genome-wide transcriptomic studies in bulk brain tissue have identified several molecular signatures associated with the disease. While these studies have the potential to shed light into the pathogenesis of Parkinson’s disease, they are also limited by two major confounders: RNA post-mortem degradation and heterogeneous cell type composition of bulk tissue samples. We performed RNA sequencing following ribosomal RNA depletion in the prefrontal cortex of 49 individuals from two independent case-control cohorts. Using cell type specific markers, we estimated the cell type composition for each sample and included this in our analysis models to compensate for the variation in cell type proportions. Ribosomal RNA depletion followed by capture by random primers resulted in substantially more even transcript coverage, compared to poly(A) capture, in post-mortem tissue. Moreover, we show that cell type composition is a major confounder of differential gene expression analysis in the Parkinson’s disease brain. Accounting for cell type proportions attenuated numerous transcriptomic signatures that have been previously associated with Parkinson’s disease, including vesicle trafficking, synaptic transmission, immune and mitochondrial function. Conversely, pathways related to endoplasmic reticulum, lipid oxidation and unfolded protein response were strengthened and surface as the top differential gene expression signatures in the Parkinson’s disease prefrontal cortex. Our results indicate that differential gene expression signatures in Parkinson’s disease bulk brain tissue are significantly confounded by underlying differences in cell type composition. Modeling cell type heterogeneity is crucial in order to unveil transcriptomic signatures that represent regulatory changes in the Parkinson’s disease brain and are, therefore, more likely to be associated with underlying disease mechanisms.

Inhibition of mitochondrial respiration prevents BRAF-mutant melanoma brain metastasis

Melanoma patients carry a high risk of developing brain metastases, and improvements in survival are still measured in weeks or months. Durable disease control within the brain is impeded by poor drug penetration across the blood-brain barrier, as well as intrinsic and acquired drug resistance. Augmented mitochondrial respiration is a key resistance mechanism in BRAF-mutant melanomas but, as we show in this study, this dependence on mitochondrial respiration may also be exploited therapeutically. We first used high-throughput pharmacogenomic profiling to identify potentially repurposable compounds against BRAF-mutant melanoma brain metastases. One of the compounds identified was β-sitosterol, a well-tolerated and brain-penetrable phytosterol. Here we show that β-sitosterol attenuates melanoma cell growth in vitro and also inhibits brain metastasis formation in vivo. Functional analyses indicated that the therapeutic potential of β-sitosterol was linked to mitochondrial interference. Mechanistically, β-sitosterol effectively reduced mitochondrial respiratory capacity, mediated by an inhibition of mitochondrial complex I. The net result of this action was increased oxidative stress that led to apoptosis. This effect was only seen in tumor cells, and not in normal cells. Large-scale analyses of human melanoma brain metastases indicated a significant role of mitochondrial complex I compared to brain metastases from other cancers. Finally, we observed completely abrogated BRAF inhibitor resistance when vemurafenib was combined with either β-sitosterol or a functional knockdown of mitochondrial complex I. In conclusion, based on its favorable tolerability, excellent brain bioavailability, and capacity to inhibit mitochondrial respiration, β-sitosterol represents a promising adjuvant to BRAF inhibitor therapy in patients with, or at risk for, melanoma brain metastases.

Identification of highly connected and differentially expressed gene subnetworks in metastasizing endometrial cancer

We have identified nine highly connected and differentially expressed gene subnetworks between aggressive primary tumors and metastatic lesions in endometrial carcinomas. We implemented a novel pipeline combining gene set and network approaches, which here allows integration of protein-protein interactions and gene expression data. The resulting subnetworks are significantly associated with disease progression across tumor stages from complex atypical hyperplasia, primary tumors to metastatic lesions. The nine subnetworks include genes related to metastasizing features such as epithelial-mesenchymal transition (EMT), hypoxia and cell proliferation. TCF4 and TWIST2 were found as central genes in the subnetwork related to EMT. Two of the identified subnetworks display statistically significant association to patient survival, which were further supported by an independent validation in the data from The Cancer Genome Atlas data collection. The first subnetwork contains genes related to cell proliferation and cell cycle, while the second contains genes involved in hypoxia such as HIF1A and EGLN3. Our findings provide a promising context to elucidate the biological mechanisms of metastasis, suggest potential prognostic markers and further identify therapeutic targets. The pipeline R source code is freely available, including permutation tests to assess statistical significance of the identified subnetworks.

Norwegian e-Infrastructure for Life Sciences (NeLS)

The Norwegian e-Infrastructure for Life Sciences (NeLS) has been developed by ELIXIR Norway to provide its users with a system enabling data storage, sharing, and analysis in a project-oriented fashion. The system is available through easy-to-use web interfaces, including the Galaxy workbench for data analysis and workflow execution. Users confident with a command-line interface and programming may also access it through Secure Shell (SSH) and application programming interfaces (APIs).  NeLS has been in production since 2015, with training and support provided by the help desk of ELIXIR Norway. Through collaboration with NorSeq, the national consortium for high-throughput sequencing, an integrated service is offered so that sequencing data generated in a research project is provided to the involved researchers through NeLS. Sensitive data, such as individual genomic sequencing data, are handled using the TSD (Services for Sensitive Data) platform provided by Sigma2 and the University of Oslo. NeLS integrates national e-infrastructure storage and computing resources, and is also integrated with the SEEK platform in order to store large data files produced by experiments described in SEEK.   In this article, we outline the architecture of NeLS and discuss possible directions for further development.

Transcriptome-wide mapping of signaling pathways and early immune responses in lumpfish leukocytes upon in vitro bacterial exposure

We performed RNA sequencing, identified components of the immune system and mapped early immune responses of lumpfish (Cyclopterus lumpus) leukocytes following in vitro exposure to the pathogenic bacterium Vibrio anguillarum O1. This is the first characterization of immune molecules in lumpfish at the gene level. In silico analyses revealed that genes encoding proteins involved in pathogen recognition, cell signaling and cytokines in mammals and teleosts are conserved in lumpfish. Unique molecules were also identified. Pathogen recognition components include 13 TLRs, several NLRs and complement factors. Transcriptome-wide analyses of immune responses 6 and 24 hours post bacterial exposure revealed differential expression of 9033 and 15225 genes, respectively. These included TLR5S, IL-1β, IL-8, IL-6, TNFα, IL-17A/F3, IL-17C and several components of the complement system. The data generated will be valuable for comparative studies and make an important basis for further functional analyses of immune and pathogenicity mechanisms. Such knowledge is also important for design of immunoprophylactic measures in lumpfish, a species of fish now farmed intensively for use as cleaner-fish in Atlantic salmon (Salmo salar) aquaculture.

Tumour-associated glial host cells display a stem-like phenotype with a distinct gene expression profile and promote growth of GBM xenografts

BACKGROUND

Little is known about the role of glial host cells in brain tumours. However, supporting stromal cells have been shown to foster tumour growth in other cancers.

METHODS

We isolated stromal cells from patient-derived glioblastoma (GBM) xenografts established in GFP-NOD/scid mice. With simultaneous removal of CD11b⁺ immune and CD31⁺ endothelial cells by fluorescence activated cell sorting (FACS), we obtained a population of tumour-associated glial cells, TAGs, expressing markers of terminally differentiaed glial cell types or glial progenitors. This cell population was subsequently characterised using gene expression analyses and immunocytochemistry. Furthermore, sphere formation was assessed in vitro and their glioma growth-promoting ability was examined in vivo. Finally, the expression of TAG related markers was validated in human GBMs.

RESULTS

TAGs were highly enriched for the expression of glial cell proteins including GFAP and myelin basic protein (MBP), and immature markers such as Nestin and O4. A fraction of TAGs displayed sphere formation in stem cell medium. Moreover, TAGs promoted brain tumour growth in vivo when co-implanted with glioma cells, compared to implanting only glioma cells, or glioma cells and unconditioned glial cells from mice without tumours. Genome-wide microarray analysis of TAGs showed an expression profile distinct from glial cells from healthy mice brains. Notably, TAGs upregulated genes associated with immature cell types and self-renewal, including Pou3f2 and Sox2. In addition, TAGs from highly angiogenic tumours showed upregulation of angiogenic factors, including Vegf and Angiopoietin 2. Immunohistochemistry of three GBMs, two patient biopsies and one GBM xenograft, confirmed that the expression of these genes was mainly confined to TAGs in the tumour bed. Furthermore, their expression profiles displayed a significant overlap with gene clusters defining prognostic subclasses of human GBMs.

CONCLUSIONS

Our data demonstrate that glial host cells in brain tumours are functionally distinct from glial cells of healthy mice brains. Furthermore, TAGs display a gene expression profile with enrichment for genes related to stem cells, immature cell types and developmental processes. Future studies are needed to delineate the biological mechanisms regulating the brain tumour-host interplay.

EPHB4 kinase-inactivating mutations cause autosomal dominant lymphatic-related hydrops fetalis

Hydrops fetalis describes fluid accumulation in at least 2 fetal compartments, including abdominal cavities, pleura, and pericardium, or in body tissue. The majority of hydrops fetalis cases are nonimmune conditions that present with generalized edema of the fetus, and approximately 15% of these nonimmune cases result from a lymphatic abnormality. Here, we have identified an autosomal dominant, inherited form of lymphatic-related (nonimmune) hydrops fetalis (LRHF). Independent exome sequencing projects on 2 families with a history of in utero and neonatal deaths associated with nonimmune hydrops fetalis uncovered 2 heterozygous missense variants in the gene encoding Eph receptor B4 (EPHB4). Biochemical analysis determined that the mutant EPHB4 proteins are devoid of tyrosine kinase activity, indicating that loss of EPHB4 signaling contributes to LRHF pathogenesis. Further, inactivation of Ephb4 in lymphatic endothelial cells of developing mouse embryos led to defective lymphovenous valve formation and consequent subcutaneous edema. Together, these findings identify EPHB4 as a critical regulator of early lymphatic vascular development and demonstrate that mutations in the gene can cause an autosomal dominant form of LRHF that is associated with a high mortality rate.

Regulatory T cell frequencies are increased in preterm infants with clinical early-onset sepsis

The predisposition of preterm neonates to invasive infection is, as yet, incompletely understood. Regulatory T cells (Tregs ) are potential candidates for the ontogenetic control of immune activation and tissue damage in preterm infants. It was the aim of our study to characterize lymphocyte subsets and in particular CD4(+) CD25(+) forkhead box protein 3 (FoxP3)(+) Tregs in peripheral blood of well-phenotyped preterm infants (n = 117; 23 + 0 - 36 + 6 weeks of gestational age) in the first 3 days of life in comparison to term infants and adults. We demonstrated a negative correlation of Treg frequencies and gestational age. Tregs were increased in blood samples of preterm infants compared to term infants and adults. Notably, we found an increased Treg frequency in preterm infants with clinical early-onset sepsis while cause of preterm delivery, e.g. chorioamnionitis, did not affect Treg frequencies. Our data suggest that Tregs apparently play an important role in maintaining maternal-fetal tolerance, which turns into an increased sepsis risk after preterm delivery. Functional analyses are needed in order to elucidate whether Tregs have potential as future target for diagnostics and therapeutics.

RareVariantVis: new tool for visualization of causative variants in rare monogenic disorders using whole genome sequencing data

MOTIVATION

The search for causative genetic variants in rare diseases of presumed monogenic inheritance has been boosted by the implementation of whole exome (WES) and whole genome (WGS) sequencing. In many cases, WGS seems to be superior to WES, but the analysis and visualization of the vast amounts of data is demanding.

RESULTS

To aid this challenge, we have developed a new tool-RareVariantVis-for analysis of genome sequence data (including non-coding regions) for both germ line and somatic variants. It visualizes variants along their respective chromosomes, providing information about exact chromosomal position, zygosity and frequency, with point-and-click information regarding dbSNP IDs, gene association and variant inheritance. Rare variants as well as de novo variants can be flagged in different colors. We show the performance of the RareVariantVis tool in the Genome in a Bottle WGS data set.

AVAILABILITY AND IMPLEMENTATION

https://www.bioconductor.org/packages/3.3/bioc/html/RareVariantVis.html

CONTACT

tomasz.stokowy@k2.uib.no

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

[Methodology of the S3 guidelines on alcohol and tobacco-related disorders]

BACKGROUND

From 2010 until 2015 two interdisciplinary evidence-based guidelines were developed to summarize the current knowledge regarding screening, diagnostics and treatment of alcohol and tobacco-related disorders.

METHODS

Both guidelines were prepared under the auspices of the German Society for Psychiatry, Psychotherapy and Psychosomatics (Deutsche Gesellschaft für Psychiatrie, Psychotherapie, Psychosomatik und Nervenheilkunde, DGPPN) and the German Society for Addiction Research and Therapy (Deutsche Gesellschaft für Suchtforschung und -therapie, DG-Sucht). To meet the methodological criteria for the highest quality guidelines (S3 criteria) as defined by the Association of the Scientific Medical Societies in Germany (Arbeitsgemeinschaft der Wissenschaftlichen Medizinischen Fachgesellschaften, AWMF) the following criteria were realized: (1) a systematic search, selection and appraisal of the international literature, (2) a structured process to reach consensus and (3) inclusion of all relevant representatives of future guideline users.

RESULTS

More than 60 clinical experts and researchers analyzed the scientific literature. In total 41 international and national guidelines (23 for alcohol and 18 for tobacco) were used. Moreover, 83 systematic Cochrane reviews (alcohol 28, tobacco 55) and 5863 articles (alcohol 2213, tobacco 3650) were analyzed. A total of 7 expert groups formulated 174 recommendations for the screening, diagnosis and treatment of alcohol-related disorders. Six expert groups created 81 recommendations for the screening, diagnosis and treatment of tobacco-related disorders. Approximately 50 scientific associations, professional organizations, patient and family initiatives, as well as representatives of the healthcare system formed a consensus group. In seven 1 and 2-day conferences, all clinical recommendations were discussed and approved by this group. Both guidelines will be revised on a regular basis to guarantee that the clinical recommendations are kept up to date.

CONCLUSIONS

Both systematically developed, evidence-based treatment guidelines are comprehensive instruments to provide orientation and assist the decision-making process for physicians, psychologists and other therapists as well as patients and their families in the diagnosis and treatment of alcohol and tobacco use related disorders.

A mechanism of mesh-related post-herniorrhaphy neuralgia

PURPOSE

The objective is to compare nerve densities in explanted polypropylene meshes in patients with or without chronic pain. Pain has supplanted recurrences as a complication of hernia surgery. The increased incidence of pain mirrors a parallel increase in the use of polypropylene meshes. Neither triple neurectomy nor careful nerve preservation has brought relief. Perhaps because we have forgotten that nerves, in response to some evolutionary mechanism, tend to regenerate, undergo changes imposed by prosthetic elements and architecture, mimicking entrapment and compartment syndromes.

METHODS

A total of 33 hernia meshes have been analyzed: 17 excised due to severe pain, two for combined pain and recurrence, 14 sampled during revision for recurrence without pain. Each mesh had standardized sampling for histology and the nerves were highlighted by S100 stain. Nerve densities were assessed within the mesh spaces and in tissue outside the mesh.

RESULTS

The density of nerves present in the standardized mesh samples of patients complaining of pain was much more elevated than in the mesh of those patients who had a recurrence but no pain. The difference was statistically significant (p < 0.001). Excluding two patients who had both pain and recurrence, the difference was even more marked (p < 0.0001).

CONCLUSIONS

Re-innervation and neo-innervation are known to take place following hernia repairs in indigenous tissue as well as through polypropylene meshes. However, when pain is an overriding issue dictating mesh explant, the degree of mesh innervation is significantly higher when compared to mesh excised for recurrence. That increase has been confirmed statistically.

Cerebral Venous Thromboses in a Child with Nephrotic Syndrome

Nephrotic syndrome is associated with several complications among which are thrombo embolic phenomena. These are uncommon in children. This report describes an 8 year old male child with relapse of steroid resistant minimal change nephrotic syndrome who developed cerebral sagittal and transverse sinus thromboses. He presented with headaches, vomiting and photophobia; and developed VI cranial nerve palsy during the course of the illness. Diagnosis was made by Computed Tomographic Scan and Magnetic Resonance Angiography of the brain. He was treated with low molecular weight heparin initially and then, oral warfarin with close monitoring of the INR and anti-Factor Xa. He recovered without neurological deficits from the venous thromboses, and with marked improvements in his radiological features.

Abstract 4036: Drug repurposing to treat melanoma brain metastases

Despite recent therapeutic advances in the management of patients with metastatic melanoma, brain metastases remain an intractable problem. It has proven difficult to identify and target single genes or pathways critical to brain metastasis formation. In this work we set out to explore a more global and preventive treatment approach to melanoma brain metastases within an established xenograft model of human melanoma. Mice were injected intracardially under ultrasound guidance and followed for six weeks with whole-body BLI and brain MRI. Tumor-bearing brains, adrenals, ovaries, and femurs were harvested and enzymatically dissociated before three tumor cell samples from each organ were flow-sorted and subjected to RNA sequencing. We developed a combined workflow of several independent computational and statistical analyses based on differential expression, and defined a brain metastasis gene signature of 54 upregulated and 54 downregulated genes. We then queried the Connectivity Map database using our 108-gene signature for candidate drugs, i.e. drugs that induce an opposite gene expression profile in various cancer cell lines. Three of the top ten drugs, already in use for other clinical conditions, showed significant efficacy in monolayer proliferation assays and colony forming assays with two brain-tropic melanoma cell lines and one brain-tropic lung cancer cell line. To examine these results in vivo, we used a highly standardized and predictive model system with automated MRI-based quantification of nanoparticle-labeled cells in the mouse brain following intracardiac injection of human melanoma cells. Treatment was started shortly after verification of comparable tumor cell exposure in the mouse brains and animals were monitored with whole-body BLI and brain MRI. Preliminary results showed promising therapeutic effects with respect to brain metastatic burden and survival, as well as acceptable toxicity profiles. We are currently validating these results on a larger scale in vivo, in other models, as well as applying systems biology and network modeling approaches to explore the fundamental mechanisms of action. Together, our results demonstrate a previously unrecognized potential for drug repurposing in the treatment of patients at risk of developing melanoma brain metastases or with clinically occult micrometastatic disease. Finding new uses for old drugs can greatly expedite translation to clinical practice; thus, further investigations are warranted to determine the safety, tolerability, and efficacy of these therapies.

Citation Format: Terje Sundstrøm, Jobin K. Varughese, Francisco Azuaje, Kjell Petersen, Clifford G. Tepper, Elizabeth Ingham, Lisa Even, Sarah Tam, Kai Ove Skaftnesmo, Morten Lund-Johansen, Rolf Bjerkvig, Katherine W. Ferrara, Frits A. Thorsen. Drug repurposing to treat melanoma brain metastases. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4036. doi:10.1158/1538-7445.AM2014-4036

Endometrial Carcinoma Recurrence Score (ECARS) validates to identify aggressive disease and associates with markers of epithelial-mesenchymal transition and PI3K alterations

PURPOSE

Our previously reported 29-gene expression signature identified an aggressive subgroup of endometrial cancer patients with PI3K activation. We here wanted to validate these findings by independent patient series.

PATIENTS AND METHODS

The 29-gene expression signature was assessed in fresh frozen tumor tissue from 280 primary endometrial carcinomas (three independent cohorts), 19 metastatic lesions and in 333 primary endometrial carcinomas using TCGA data, and expression was related to clinico-pathologic features and survival. The 29-gene signature was assessed by real-time quantitative PCR, DNA oligonucleotide microarrays, or RNA sequencing. PI3K alterations were assessed by immunohistochemistry, DNA microarrays, DNA sequencing, SNP arrays or fluorescence in situ hybridization. A panel of markers of epithelial-mesenchymal transition (EMT) was also correlated to the 29-gene signature score.

RESULTS

High 29-gene Endometrial Carcinoma Recurrence Score (ECARS) values consistently validated to identify patients with aggressive clinico-pathologic phenotype and reduced survival. Within the presumed favorable subgroups of low grade, endometrioid tumors confined to the uterus, high ECARS still predicted a poor prognosis. The score was higher in metastatic compared to primary lesions (P<0.001) and was significantly associated with potential measures of PI3K activation, markers of EMT and vascular invasion as an indicator of metastatic spread (all P<0.001).

CONCLUSIONS

ECARS validates to identify aggressive endometrial carcinomas in multiple, independent patients cohorts. The higher signature score in metastatic compared to primary lesions, and the potential link to PI3K activation and EMT, support further studies of ECARS in relation to response to PI3K and EMT inhibitors in clinical trials of metastatic endometrial carcinoma.

Dip in the gene pool: metagenomic survey of natural coccolithovirus communities

Despite the global oceanic distribution and recognised biogeochemical impact of coccolithoviruses (EhV), their diversity remains poorly understood. Here we employed a metagenomic approach to study the occurrence and progression of natural EhV community genomic variability. Analysis of EhV metagenomes from the early and late stages of an induced bloom led to three main discoveries. First, we observed resilient and specific genomic signatures in the EhV community associated with the Norwegian coast, which reinforce the existence of limitations to the capacity of dispersal and genomic exchange among EhV populations. Second, we identified a hyper-variable region (approximately 21kbp long) in the coccolithovirus genome. Third, we observed a clear trend for EhV relative amino-acid diversity to reduce from early to late stages of the bloom. This study validated two new methodological combinations, and proved very useful in the discovery of new genomic features associated with coccolithovirus natural communities.

Switch in FOXA1 status associates with endometrial cancer progression

BACKGROUND

The transcription factor Forkhead box A1 (FOXA1) is suggested to be important in hormone dependent cancers, although with little data for endometrial cancer. We investigated expression levels of FOXA1 in primary and metastatic endometrial cancer in relation to clinical phenotype, and transcriptional alterations related to FOXA1 status.

METHODS

Protein expression of FOXA1 was explored by immunohistochemistry in 529 primary and 199 metastatic endometrial carcinoma lesions. mRNA levels from corresponding 158 fresh frozen primary and 42 metastatic lesions were analyzed using Agilent Microarrays (44k) in parallel.

RESULTS

Low FOXA1 protein expression in primary tumors significantly correlated with low FOXA1 mRNA, high age, non-endometrioid histology, high grade, loss of ERα and PR and poor survival (all p-values <0.05). Through a Connectivity Map search, HDAC inhibitors were suggested as potential treatment for patients with low FOXA1 expression. An increase in FOXA1 expression was observed from primary to metastatic lesions and it correlated with CDKN2A expression in metastases.

CONCLUSION

Low FOXA1 is associated with poor survival and suggests a potential for HDAC inhibitors in endometrial carcinoma. A switch in FOXA1 expression from primary to metastatic lesions is observed and gene expression indicates a link between FOXA1 and CDKN2A in metastatic lesions.

Hypomethylation of the CTCFL/BORIS promoter and aberrant expression during endometrial cancer progression suggests a role as an Epi-driver gene

Cancers arise through accumulating genetic and epigenetic alterations, considered relevant for phenotype and approaches to targeting new therapies. We investigated a unique collection of endometrial cancer precursor samples and clinically annotated primary and metastatic lesions for two evolutionary and functionally related transcription factors, CCCTC-binding factor (zinc finger protein) (CTCF) and its paralogue CTCF-like factor, also denoted Brother of the Regulator of Imprinted Sites (CTCFL/BORIS). CTCF, a chromatin modeling- and transcription factor, is normally expressed in a ubiquitous fashion, while CTCFL/BORIS is restricted to the testis. In cancer, CTCF is thought to be a tumor suppressor, while CTCFL/BORIS has been suggested as an oncogene. CTCF mutations were identified in 13%, with CTCF hotspot frameshift mutations at p.T204, all observed solely in the endometrioid subtype, but with no association with outcome. Interestingly, CTCFL/BORIS was amongst the top ranked genes differentially expressed between endometrioid and non-endometrioid tumors, and increasing mRNA level of CTCFL/BORIS was highly significantly associated with poor survival. As aberrant CTCFL/BORIS expression might relate to loss of methylation, we explored methylation status in clinical samples from complex atypical hyperplasia, through primary tumors to metastatic lesions, demonstrating a pattern of DNA methylation loss during disease development and progression in line with the increase in CTCFL/BORIS mRNA expression observed. Thus, CTCF and CTCFL/BORIS are found to diverge in the different subtypes of endometrial cancer, with CTCFL/BORIS activation through demethylation from precursors to metastatic lesions. We thus propose, CTCFL/BORIS as an Epi-driver gene in endometrial cancer, suggesting a potential for future vaccine development.

Gene set based integrated data analysis reveals phenotypic differences in a brain cancer model

A key challenge in the data analysis of biological high-throughput experiments is to handle the often low number of samples in the experiments compared to the number of biomolecules that are simultaneously measured. Combining experimental data using independent technologies to illuminate the same biological trends, as well as complementing each other in a larger perspective, is one natural way to overcome this challenge. In this work we investigated if integrating proteomics and transcriptomics data from a brain cancer animal model using gene set based analysis methodology, could enhance the biological interpretation of the data relative to more traditional analysis of the two datasets individually. The brain cancer model used is based on serial passaging of transplanted human brain tumor material (glioblastoma--GBM) through several generations in rats. These serial transplantations lead over time to genotypic and phenotypic changes in the tumors and represent a medically relevant model with a rare access to samples and where consequent analyses of individual datasets have revealed relatively few significant findings on their own. We found that the integrated analysis both performed better in terms of significance measure of its findings compared to individual analyses, as well as providing independent verification of the individual results. Thus a better context for overall biological interpretation of the data can be achieved.

High-throughput mutation profiling of primary and metastatic endometrial cancers identifies KRAS, FGFR2 and PIK3CA to be frequently mutated

Background

Despite being the most common pelvic gynecologic malignancy in industrialized countries, no targeted therapies are available for patients with metastatic endometrial carcinoma. In order to improve treatment, underlying molecular characteristics of primary and metastatic disease must be explored.

Methodology/Principal Findings

We utilized the mass spectrometric-based mutation detection technology OncoMap to define the types and frequency of point somatic mutations in endometrial cancer. 67 primary tumors, 15 metastases corresponding to 7 of the included primary tumors and 11 endometrial cancer cell lines were screened for point mutations in 28 known oncogenes. We found that 27 (40.3%) of 67 primary tumors harbored one or more mutations with no increase in metastatic lesions. FGFR2, KRAS and PIK3CA were consistently the most frequently mutated genes in primary tumors, metastatic lesions and cell lines.

Conclusions/Significance

Our results emphasize the potential for targeting FGFR2, KRAS and PIK3CA mutations in endometrial cancer for development of novel therapeutic strategies.

KRAS gene amplification and overexpression but not mutation associates with aggressive and metastatic endometrial cancer

BACKGROUND

Three quarter of endometrial carcinomas are treated at early stage. Still, 15 to 20% of these patients experience recurrence, with little effect from systemic therapies. Homo sapiens v-Ki-ras2 Kirsten rat sarcoma viral oncogenes homologue (KRAS) mutations have been reported to have an important role in tumorigenesis for human cancers, but there is limited knowledge regarding clinical relevance of KRAS status in endometrial carcinomas.

METHODS

We have performed a comprehensive and integrated characterisation of genome-wide expression related to KRAS mutations and copy-number alterations in primary- and metastatic endometrial carcinoma lesions in relation to clinical and histopathological data. A primary investigation set and clinical validation set was applied, consisting of 414 primary tumours and 61 metastatic lesions totally.

RESULTS

Amplification and gain of KRAS present in 3% of the primary lesions and 18% of metastatic lesions correlated significantly with poor outcome, high International Federation of Gynaecology and Obstetrics stage, non-endometrioid subtype, high grade, aneuploidy, receptor loss and high KRAS mRNA levels, also found to be associated with aggressive phenotype. In contrast, KRAS mutations were present in 14.7% of primary lesions with no increase in metastatic lesions, and did not influence outcome, but was significantly associated with endometrioid subtype, low grade and obesity.

CONCLUSION

These results support that KRAS amplification and KRAS mRNA expression, both increasing from primary to metastatic lesions, are relevant for endometrial carcinoma disease progression.

Expression profile of heat shock proteins in acute myeloid leukaemia patients reveals a distinct signature strongly associated with FLT3 mutation status--consequences and potentials for pharmacological intervention

Heat shock proteins (HSPs) are molecular chaperones that assist proteins in their folding to native structures. HSPs are regarded as possible therapeutic targets in acute myeloid leukaemia (AML). We used bioinformatical approaches to characterize the HSP profile in AML cells from 75 consecutive patients, in addition to the effect of the HSP90 inhibitor 17-DMAG. Patients harbouring a FLT3-internal tandem duplication (FLT3-ITD) were extensively overrepresented in the cluster with high HSP levels, indicating a strong dependence of HSPs in stabilizing FLT3-ITD encoded oncoproteins. FLT3 ligation further increased the levels of HSP90 and its co-chaperone HSP70. HSP90 inhibition had a stronger pro-apoptotic effect for AML cells with FLT3-ITD than for cells with wild-type FLT3, whereas the anti-proliferative effect of HSP90 inhibition was similar for the two patient subsets. HSP90 inhibition altered the constitutive cytokine release profile in an anti-angiogenic direction independent of FLT3 mutational status: (i) pro-angiogenic CXCL8, MMP-2 and MMP-9 showed a stronger decrease than anti-angiogenic CXCL9-11, (ii) the Tie-2 agonist Ang-1 showed a stronger decrease than the potentially antagonistic Ang-2, and (iii) VEGF and HGF levels were decreased. Finally, HSP90 inhibition counteracted the leukaemia-stimulating effect of endothelial cells. Our studies demonstrate that HSP90 inhibition mediates anti-leukaemic effects through both direct and indirect activity.

Hepatic in vitro toxicity assessment of PBDE congeners BDE47, BDE153 and BDE154 in Atlantic salmon (Salmo salar L.)

The brominated flame retardant congeners BDE47, BDE153 and BDE154 are among the congeners accumulating to the highest degree in fish. In order to gain knowledge about the toxicological effects of PBDEs in fish, microarray-based transcriptomic and 2D-DIGE/MALDI-TOF/TOF proteomic approaches were used to screen for effects in primary Atlantic salmon hepatocytes exposed to these congeners alone or in combination (PBDE-MIX). A small set of stress related transcripts and proteins were differentially expressed in the PBDE exposed hepatocytes. The PBDE-MIX, and BDE153 to a lesser degree, seems to have induced metabolic disturbances by affecting several pathways related to glucose homeostasis. Further, effects on cell cycle control and proliferation signal pathways in PBDE-MIX-exposed hepatocytes clearly suggest that the PBDE exposure affected cell proliferation processes. CYP1A was 7.41- and 7.37-fold up-regulated in hepatocytes exposed to BDE47 and PBDE-MIX, respectively, and was the only biotransformation pathway affected by the PBDE exposure. The factorial design and PLS regression analyses of the effect of the PBDE-MIX indicated that BDE47 contributed the most to the observed CYP1A response, suggesting that this congener should be incorporated in the toxic equivalent (TEQ) concept in future risk assessment of dioxin-like chemicals. Additionally, a significant up-regulation of the ER-responsive genes VTG and ZP3 was observed in cells exposed to BDE47 and PBDE-MIX. Further analyses suggested that BDE47 and BDE154 have an estrogenic effect in male fish. The data also suggested an antagonistic interaction between BDE153 and BDE154. In conclusion, this study shows that PBDEs can affect several biological systems in Atlantic salmon cells, and demonstrates the need for more studies on the simultaneous exposure to chemical mixtures to identify combined effects of chemicals.

Data partitioning enables the use of standard SOAP Web Services in genome-scale workflows

Biological databases and computational biology tools are provided by research groups around the world, and made accessible on the Web. Combining these resources is a common practice in bioinformatics, but integration of heterogeneous and often distributed tools and datasets can be challenging. To date, this challenge has been commonly addressed in a pragmatic way, by tedious and error-prone scripting. Recently however a more reliable technique has been identified and proposed as the platform that would tie together bioinformatics resources, namely Web Services. In the last decade the Web Services have spread wide in bioinformatics, and earned the title of recommended technology. However, in the era of high-throughput experimentation, a major concern regarding Web Services is their ability to handle large-scale data traffic. We propose a stream-like communication pattern for standard SOAP Web Services, that enables efficient flow of large data traffic between a workflow orchestrator and Web Services. We evaluated the data-partitioning strategy by comparing it with typical communication patterns on an example pipeline for genomic sequence annotation. The results show that data-partitioning lowers resource demands of services and increases their throughput, which in consequence allows to execute in-silico experiments on genome-scale, using standard SOAP Web Services and workflows. As a proof-of-principle we annotated an RNA-seq dataset using a plain BPEL workflow engine.

Data partitioning enables the use of standard SOAP Web Services in genome-scale workflows

Biological databases and computational biology tools are provided by research groups around the world, and made accessible on the Web. Combining these resources is a common practice in bioinformatics, but integration of heterogeneous and often distributed tools and datasets can be challenging. To date, this challenge has been commonly addressed in a pragmatic way, by tedious and error-prone scripting. Recently however a more reliable technique has been identified and proposed as the platform that would tie together bioinformatics resources, namely Web Services. In the last decade the Web Services have spread wide in bioinformatics, and earned the title of recommended technology. However, in the era of high-throughput experimentation, a major concern regarding Web Services is their ability to handle large-scale data traffic. We propose a stream-like communication pattern for standard SOAP Web Services, that enables efficient flow of large data traffic between a workflow orchestrator and Web Services. We evaluated the data-partitioning strategy by comparing it with typical communication patterns on an example pipeline for genomic sequence annotation. The results show that data-partitioning lowers resource demands of services and increases their throughput, which in consequence allows to execute in-silico experiments on genome-scale, using standard SOAP Web Services and workflows. As a proof-of-principle we annotated an RNA-seq dataset using a plain BPEL workflow engine.

Effect-directed identification of naphthenic acids as important in vitro xeno-estrogens and anti-androgens in North sea offshore produced water discharges

Produced water from offshore oil production platforms represents the largest direct discharge of effluent into the offshore environment. Produced water effluents contain a complex mixture of substances which are known to bind to the estrogen receptor (ER) and antagonize the androgen receptor (AR). Short-chain petrogenic alkylphenols have been identified as responsible for around 35% of the ER agonist activity measured in vitro while the compounds responsible for antagonizing the androgen receptor are unknown. For the first time we report that petrogenic naphthenic acids are weak ER agonists that account for much of the 65% of the "unknown" ER agonist potency in North Sea produced waters while also disrupting the binding of AR agonists to the AR ligand receptor. We also report other known petrogenic components such as polycyclic aromatic hydrocarbons (PAHs) and alkylphenols as environmental AR antagonists. Our investigation shows that these petrogenic components are responsible for the majority of the ER and AR receptor mediated activity in produced waters. This hypothesis is supported by data from an effects-directed analysis of produced water using normal-phase high-performance liquid chromatography (HPLC) fractionation in combination with the yeast estrogen and androgen assays as well as androgen receptor binding assays of commercially available mixtures of naphthenic acids.

Highly infiltrative brain tumours show reduced chemosensitivity associated with a stem cell-like phenotype

AIMS

Cancer stem-like cells might have important functions in chemoresistance. We have developed a model where highly infiltrative brain tumours with a stem-like phenotype were established by orthotopic transplantation of human glioblastomas to immunodeficient rats. Serial passaging gradually transformed the tumours into a less invasive and more angiogenic phenotype (high-generation tumours). The invasive phenotype (low-generation tumours) was characterized by an increase in stem cell markers and increased phosphorylation of kinases in the phosphatidylinositol 3-kinase (PI3K)/AKT pathway. These markers were reduced in the serially passaged vascular tumours. The present study was aimed at investigating how the two phenotypes responded in vitro to doxorubicin, a clinically potent cytotoxic drug for solid tumours.

METHODS

Biopsy spheroids were implanted and passaged intracranially in nude rats. Gene expression and protein analyses were performed, and drug sensitivity was assessed.

RESULTS

Microarray analysis revealed gene ontology categories connected to developmental aspects and negative regulators of differentiation, especially in the infiltrative stem cell-like tumours. The highly invasive stem-like phenotype was chemoresistant compared with the angiogenic phenotype. By interfering with the PI3K it was possible to sensitize tumour spheroids to chemotherapy. Real-time quantitative polymerase chain reaction showed downregulation of the stem cell markers Nestin and Musashi-1 in low-generation biopsy spheroids following PI3K inhibition.

CONCLUSIONS

Highly invasive tumours with a stem-like phenotype are more chemoresistant than angiogenic tumours derived from the same patients. We suggest that treatment resistance in glioblastomas can be related to PI3K/AKT activity in stem-like tumour cells, and that targeted interference with the PI3K/AKT pathway might differentiate and sensitize this subpopulation to chemotherapy.

iTRAQ-based proteomics profiling reveals increased metabolic activity and cellular cross-talk in angiogenic compared with invasive glioblastoma phenotype

Malignant gliomas (glioblastoma multiforme) have a poor prognosis with an average patient survival under current treatment regimens ranging between 12 and 14 months. The tumors are characterized by rapid cell growth, extensive neovascularization, and diffuse cellular infiltration of normal brain structures. We have developed a human glioblastoma xenograft model in nude rats that is characterized by a highly infiltrative non-angiogenic phenotype. Upon serial transplantation this phenotype will develop into a highly angiogenic tumor. Thus, we have developed an animal model where we are able to establish two characteristic tumor phenotypes that define human glioblastoma (i.e. diffuse infiltration and high neovascularization). Here we aimed at identifying potential biomarkers expressed by the non-angiogenic and the angiogenic phenotypes and elucidating the molecular pathways involved in the switch from invasive to angiogenic growth. Focusing on membrane-associated proteins, we profiled protein expression during the progression from an invasive to an angiogenic phenotype by analyzing serially transplanted glioma xenografts in rats. Applying isobaric peptide tagging chemistry (iTRAQ) combined with two-dimensional LC and MALDI-TOF/TOF mass spectrometry, we were able to identify several thousand proteins in membrane-enriched fractions of which 1460 were extracted as quantifiable proteins (isoform- and species-specific and present in more than one sample). Known and novel candidate proteins were identified that characterize the switch from a non-angiogenic to a highly angiogenic phenotype. The robustness of the data was corroborated by extensive bioinformatics analysis and by validation of selected proteins on tissue microarrays from xenograft and clinical gliomas. The data point to enhanced intercellular cross-talk and metabolic activity adopted by tumor cells in the angiogenic compared with the non-angiogenic phenotype. In conclusion, we describe molecular profiles that reflect the change from an invasive to an angiogenic brain tumor phenotype. The identified proteins could be further exploited as biomarkers or therapeutic targets for malignant gliomas.

Genome-wide transcription analysis of histidine-related cataract in Atlantic salmon (Salmo salar L)

PURPOSE

Elevated levels of dietary histidine have previously been shown to prevent or mitigate cataract formation in farmed Atlantic salmon (Salmo salar L). The aim of this study was to shed light on the mechanisms by which histidine acts. Applying microarray analysis to the lens transcriptome, we screened for differentially expressed genes in search for a model explaining cataract development in Atlantic salmon and possible markers for early cataract diagnosis.

METHODS

Adult Atlantic salmon (1.7 kg) were fed three standard commercial salmon diets only differing in the histidine content (9, 13, and 17 g histidine/kg diet) for four months. Individual cataract scores for both eyes were assessed by slit-lamp biomicroscopy. Lens N-acetyl histidine contents were measured by high performance liquid chromatography (HPLC). Total RNA extracted from whole lenses was analyzed using the GRASP 16K salmonid microarray. The microarray data were analyzed using J-Express Pro 2.7 and validated by quantitative real-time polymerase chain reaction (qRT-PCR).

RESULTS

Fish developed cataracts with different severity in response to dietary histidine levels. Lens N-acetyl histidine contents reflected the dietary histidine levels and were negatively correlated to cataract scores. Significance analysis of microarrays (SAM) revealed 248 significantly up-regulated transcripts and 266 significantly down-regulated transcripts in fish that were fed a low level of histidine compared to fish fed a higher histidine level. Among the differentially expressed transcripts were metallothionein A and B as well as transcripts involved in lipid metabolism, carbohydrate metabolism, regulation of ion homeostasis, and protein degradation. Hierarchical clustering and correspondence analysis plot confirmed differences in gene expression between the feeding groups. The differentially expressed genes could be categorized as "early" and "late" responsive according to their expression pattern relative to progression in cataract formation.

CONCLUSIONS

Dietary histidine regimes affected cataract formation and lens gene expression in adult Atlantic salmon. Regulated transcripts selected from the results of this genome-wide transcription analysis might be used as possible biological markers for cataract development in Atlantic salmon.

Tumor endothelium is characterized by a matrix remodeling signature

Endothelial cells (EC) are attractive targets for therapeutic interference in diseases that are dependent on the formation of novel blood vessels, such as cancer. EC are readily accessible via the blood stream and are considered to be genetically stable, thus enabling efficient and effective drug delivery. However, for targeting of EC in blood vessels of the disease tissue, specific markers are needed. Though various studies have focused on the differences in gene expression in endothelial cells in different in vitro model systems, only few studies have focused on gene expression in EC derived from tumor tissues and corresponding normal tissues. Here, we review the gene expression data sets of EC isolated from tumors of the colon, breast, brain and ovaries. Gene ontology analysis reveals enrichment for genes involved in extracellular matrix turnover and adhesion. Several genes, including collagens 4A1, 4A2 and 1A1, SPARC, THY1 and MMP9 are overexpressed in the endothelium of more than one tumor type, whereas plexin domain containing 1 (PLXDC1), previously known as TEM7, is overexpressed in EC of all four tumor types.