Analysis of differentiation trees using transcriptome data : application to hematopoiesis

Cellular differentiation is a complicated and highly important system in all multicellular organisms. The remarkable aspect about differentiation is that the multitude of different and highly specialised cell types are all descendant from one cell, the zygote. Not surprisingly differentiation is a highly regulated process. A complicated interplay of environmental signals and intracellular regulation defines the ultimate mature state of all cell types. In this work a method was developed that can analyse differentiation trees computationally. The development of the method was guided by three questions. Do microarrays contain enough information to retrace steps in differentiation? Can this information be used to validate proposed differentiation paths? Can this information be used to compare differentiation in different contexts? The method starts from microarray data and uses a combination of methods to identify the most likely differentiation tree out of all possibilities. The method has two components, one component identifies the most likely conformation using a scoring system. The other component identifies the most likely root node using a comparison system. The conformation scoring system relies on transcriptional changes in previously defined subnetworks, all possible differentiation conformations are tested in a manner similar to maximum parsimony. Maximum parsimony is used in molecular phylogeny to score possible evolutionary trees, a problem similar to the one tackled in this work. Root node identification is done using a value calculated based on within cell type gene expression correlations, high values indicate the cell is less mature. The method was tested on microarray data from the myeloid lineage of hematopoiesis. The datasets are comprised of expression data taken from four different cell types: Hematopoietic Stem Cells, Common Myeloid Progenitors, Granulocyte Monocyte Progenitors and Megakaryocyte Erythrocyte Progenitors. Data was gathered from healthy donors and patients suffering Chronic Myeloid Leukemia and Multiple Myeloma respectively. The method performed well, in most cases the correct differentiation tree could be identified. This indicates that there is indeed enough information present in microarray data to retrace differentiation. Interesting results where seen for the root node identification component. When analysing the dataset taken from patients with CML, the method predicted known differences in stemness in that particular cancer

Implementing preoperative Botulinum toxin A and progressive pneumoperitoneum through the use of an algorithm in giant ventral hernia repair

Background Repair of large ventral hernias with loss of domain can be facilitated by preoperative Botulinum toxin A (BTA) injections and preoperative progressive pneumoperitoneum (PPP). The aim of this study is to evaluate the outcomes of ventral hernioplasty using a standardized algorithm, including component separation techniques, preoperative BTA and PPP. Methods All patients between June 2014 and August 2018 with giant hernias (either primary or incisional) of more than 12 cm width were treated according to a previously developed standardized algorithm. Retrospective data analysis from a prospectively collected dataset was performed. The primary outcome was closure of the anterior fascia. Secondary outcomes included complications related to the preoperative treatment, postoperative complications, and recurrences. Results Twenty-three patients were included. Median age was 65 years (range 28-77) and median BMI was 31.4 (range 22.7-38.0 kg/m(2)). The median loss of domain was 29% (range 12-226%). For the primary and secondary endpoints, 22 patients were analyzed. Primary closure of the anterior fascia was possible in 82% of all patients. After a median follow-up of 19.5 months (range 10-60 months), 3 patients (14%) developed a hernia recurrence and 16 patients (73%) developed 23 surgical site occurrences, most of which were surgical site infections (54.5%). Conclusion Our algorithm using both anterior or posterior component separation, together with preoperative BTA injections and PPP, achieved an acceptable fascial closure rate. Further studies are needed to explore the individual potential of BTA injections and PPP, and to research whether these methods can prevent the need for component separation, as postoperative wound morbidity remains high in our study

On-line estimation of O2 production, CO2 uptake, and growth kinetics of microalgal cultures in a gas-tight photobioreactor

Growth of the green algae Chlamydomonas reinhardtii and Chlorella sp. in batch cultures was investigated in a novel gas-tight photobioreactor, in which CO2, H2, and N2 were titrated into the gas phase to control medium pH, dissolved oxygen partial pressure, and headspace pressure, respectively. The exit gas from the reactor was circulated through a loop of tubing and re-introduced into the culture. CO2 uptake was estimated from the addition of CO2 as acidic titrant and O2 evolution was estimated from titration by H2, which was used to reduce O2 over a Pd catalyst. The photosynthetic quotient, PQ, was estimated as the ratio between O2 evolution and CO2 up-take rates. NH4+, NO2−, or NO3− was the final cell density limiting nutrient. Cultures of both algae were, in general, characterised by a nitrogen sufficient growth phase followed by a nitrogen depleted phase in which starch was the major product. The estimated PQ values were dependent on the level of oxidation of the nitrogen source. The PQ was 1 with NH4+ as the nitrogen source and 1.3 when NO3− was the nitrogen source. In cultures grown on all nitrogen sources, the PQ value approached 1 when the nitrogen source was depleted and starch synthesis became dominant, to further increase towards 1.3 over a period of 3–4 days. This latter increase in PQ, which was indicative of production of reduced compounds like lipids, correlated with a simultaneous increase in the degree of reduction of the biomass. When using the titrations of CO2 and H2 into the reactor headspace to estimate the up-take of CO2, the production of O2, and the PQ, the rate of biomass production could be followed, the stoichiometrical composition of the produced algal biomass could be estimated, and different growth phases could be identified

Multiple mechanisms disrupt the let-7 microRNA family in neuroblastoma

Poor prognosis in neuroblastoma is associated with genetic amplification of MYCN. MYCN is itself a target of let-7, a tumour suppressor family of microRNAs implicated in numerous cancers. LIN28B, an inhibitor of let-7 biogenesis, is overexpressed in neuroblastoma and has been reported to regulate MYCN. Here we show, however, that LIN28B is dispensable in MYCN-amplified neuroblastoma cell lines, despite de-repression of let-7. We further demonstrate that MYCN messenger RNA levels in amplified disease are exceptionally high and sufficient to sponge let-7, which reconciles the dispensability of LIN28B. We found that genetic loss of let-7 is common in neuroblastoma, inversely associated with MYCN amplification, and independently associated with poor outcomes, providing a rationale for chromosomal loss patterns in neuroblastoma. We propose that let-7 disruption by LIN28B, MYCN sponging, or genetic loss is a unifying mechanism of neuroblastoma development with broad implications for cancer pathogenesis.United States. National Institutes of Health (R01GM107536)Alex's Lemonade Stand FoundationHoward Hughes Medical InstituteBoston Children's Hospital. Manton Center for Orphan Disease ResearchNational Institute of General Medical Sciences (U.S.) (T32GM007753

Validation of nonrigid registration for multi-tracer PET-CT treatment planning in rectal cancer radiotherapy

Paper Abstract The goal of radiotherapy is to deliver maximal dose to the tumor and minimal dose to the surrounding tissue. This requires accurate target definition. In sites were the tumor is difficult to see on the CT images, such as for rectal cancer, PET-CT imaging can be used to better define the target. If the information from multiple PETCT images with different tracers needs to be combined, a nonrigid registration is indispensable to compensate for rectal tissue deformations. Such registration is complicated by the presence of different volumes of bowel gas in the images to be registered. In this paper, we evaluate the performance of different nonrigid registration approaches by looking at the overlap of manually delineated rectum contours after registration. Using a B-spline transformation model, the results for two similarity measures, sum of squared differences and mutual information, either calculated over the entire image or on a region of interest are compared. Finally, we also assess the effect of the registration direction. We show that the combination of MI with a region of interest is best able to cope with residual rectal contrast and differences in bowel filling. We also show that for optimal performance the registration direction should be chosen depending on the difference in bowel filling in the images to be registered.Slagmolen P., Roels S., Loeckx D., Haustermans K., Maes F., ''Validation of nonrigid registration for multi-tracer PET-CT treatment planning in rectal cancer radiotherapy'', SPIE medical imaging 2009 conference : image processing, vol. 7259, February 7-12, 2009, Orlando, Florida, USA.status: publishe

Nonrigid registration of multitemporal CT and MR images for radiotherapy treatment planning

External beam radiotherapy treats cancer lesions with ionizing radiation. Successful treatment requires a correct definition of the target volume. This is achieved using pre-treatment MR and CT images. However, due to changes in patient position, tumor size and organ location, adaptation of the treatment plan over the different treatment sessions might be wanted. This can be achieved with extra MR and CT images obtained during treatment. Bringing all images into a common reference frame, the initial segmentations can be propagated over time and the integrated dose can be correctly calculated. In this article, we show in two patients with rectum cancer and one with neck cancer that a significant change in tumor position and shape occurs. Our results show that nonrigid registration can correctly detect these shape and position changes in MR images. Validation was performed using manual delineations. For delineations of the manilible, parotid and submandibular gland in the head-and-neck patient, the maximal centroid error decreases from 6 mm to 2 mm, while the minimal Dice similarity criterium (DSC) overlap measure increases from 0.70 to 0.84. In the rectal cancer patients, the maximal centroid error drops from 15 mm to 5 mm, while the minimal DSC rises from 0.22 to 0.57. Similar experiments were performed on CT images. The validation here was infeasible due to significant inaccuracies in the manual delineations

Glycerol used for denitrification in full-scale wastewater treatment plants: nitrous oxide emissions, sludge acclimatization, and other insights

Glycerol is commonly employed for denitrification purposes in full-scale wastewater treatment. In non-acclimatized biomass, the glycerol is very inefficient resulting in a high C/N ratio and low-standard denitrification rates. The acclimatization is driven by the microbial enrichment of Saccharimonadales and Propionibacteriales as found in different sampled municipal sludges flanking the dominant presence of Burkholderiales. The selective strategy is based on a very efficient process in terms of C/N ratios and standard denitrification rates, but it leads to nitrite accumulation. As a result, severe and unexpected nitrous oxide emissions were found in full-scale with emission factors up to 2.5% kgN2O (kgKJNremoved)−1. Simultaneous dosage of isobutirate in a full-scale experiment could counter the nitrous oxide emissions. As nitrous oxide emissions were found proportional to the dosed glycerol-based COD, the authors suggest that, in case of acclimatization of biomass to glycerol, an emission factor based on the dosed COD should substitute the general nitrous oxide emission factors based on incoming or removed nitrogen to the plant. HIGHLIGHTS Acclimatization to glycerol leads to an increase in C/N ratios and standard denitrification rates.; We observed microbial enrichment of Saccharimonadales and Propionibacteriales and nitrite accumulation.; N2O emission factors reached up to 2.5% kgN2O/kgKJNremoved.; In case of acclimatization, the N2O emission factor is best expressed in function of the dosed glycerol COD.; Simultaneous isobutirate dosage countered the N2O emissions.

FOXP1 inhibits cell growth and attenuates tumorigenicity of neuroblastoma

Background: Segmental genomic copy number alterations, such as loss of 11q or 3p and gain of 17q, are well established markers of poor outcome in neuroblastoma, and have been suggested to comprise tumor suppressor genes or oncogenes, respectively. The gene forkhead box P1 (FOXP1) maps to chromosome 3p14.1, a tumor suppressor locus deleted in many human cancers including neuroblastoma. FoxP1 belongs to a family of winged-helix transcription factors that are involved in processes of cellular proliferation, differentiation and neoplastic transformation. Methods: Microarray expression profiles of 476 neuroblastoma specimens were generated and genes differentially expressed between favorable and unfavorable neuroblastoma were identified. FOXP1 expression was correlated to clinical markers and patient outcome. To determine whether hypermethylation is involved in silencing of FOXP1, methylation analysis of the 5' region of FOXP1 in 47 neuroblastomas was performed. Furthermore, FOXP1 was re-expressed in three neuroblastoma cell lines to study the effect of FOXP1 on growth characteristics of neuroblastoma cells. Results: Low expression of FOXP1 is associated with markers of unfavorable prognosis like stage 4, age > 18 months and MYCN amplification and unfavorable gene expression-based classification (P < 0.001 each). Moreover, FOXP1 expression predicts patient outcome accurately and independently from well-established prognostic markers. Array-based CGH analysis of 159 neuroblastomas revealed that heterozygous loss of the FOXP1 locus was a rare event (n = 4), but if present, was associated with low FOXP1 expression. By contrast, DNA methylation analysis in 47 neuroblastomas indicated that hypermethylation is not regularly involved in FOXP1 gene silencing. Re-expression of FoxP1 significantly impaired cell proliferation, viability and colony formation in soft agar. Furthermore, induction of FOXP1 expression led to cell cycle arrest and apoptotic cell death of neuroblastoma cells. Conclusions: Our results suggest that down-regulation of FOXP1 expression is a common event in high-risk neuroblastoma pathogenesis and may contribute to tumor progression and unfavorable patient outcome