Combined image and genomic analysis of high-grade serous ovarian cancer reveals PTEN loss as a common driver event and prognostic classifier

Background

TP53 and BRCA1/2 mutations are the main drivers in high-grade serous ovarian carcinoma (HGSOC). We hypothesise that combining tissue phenotypes from image analysis of tumour sections with genomic profiles could reveal other significant driver events.

Results

Automatic estimates of stromal content combined with genomic analysis of TCGA HGSOC tumours show that stroma strongly biases estimates of PTEN expression. Tumour-specific PTEN expression was tested in two independent cohorts using tissue microarrays containing 521 cases of HGSOC. PTEN loss or downregulation occurred in 77% of the first cohort by immunofluorescence and 52% of the validation group by immunohistochemistry, and is associated with worse survival in a multivariate Cox-regression model adjusted for study site, age, stage and grade. Reanalysis of TCGA data shows that hemizygous loss of PTEN is common (36%) and expression of PTEN and expression of androgen receptor are positively associated. Low androgen receptor expression was associated with reduced survival in data from TCGA and immunohistochemical analysis of the first cohort.

Conclusion

PTEN loss is a common event in HGSOC and defines a subgroup with significantly worse prognosis, suggesting the rational use of drugs to target PI3K and androgen receptor pathways for HGSOC. This work shows that integrative approaches combining tissue phenotypes from images with genomic analysis can resolve confounding effects of tissue heterogeneity and should be used to identify new drivers in other cancers.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0526-8) contains supplementary material, which is available to authorized users.     

Frequency of Antibiotic Resistance in a Swine Facility 2.5 Years After a Ban on Antibiotics

The addition of antibiotics to livestock feed has contributed to the selection of antibiotic-resistant bacteria in concentrated animal feeding operations and agricultural ecosystems. The objective of this study was to assess the occurrence of resistance to chlortetracycline and tylosin among bacterial populations at the Swine Complex of McGill University (Province of Quebec, Canada) in the absence of antibiotic administration to pigs for 2.5 years prior to the beginning of this study. Feces from ten pigs born from the same sow and provided feed without antibiotic were sampled during suckling (n = 6 for enumerations, n = 10 for PCR), weanling (n = 10 both for PCR and enumerations), growing (n = 10 both for PCR and enumerations), and finishing (n = 10 both for PCR and enumerations). The percentage of chlortetracycline-resistant anaerobic bacterial populations (Tet^R) was higher than that of tylosin-resistant anaerobic bacterial populations (Tyl^R) at weanling, growing, and finishing. Prior to the transportation of animals to the slaughterhouse, resistant populations varied between 6.5 and 9.4 Log colony-forming units g humid feces⁻¹. In all pigs, tet(L), tet(O), and erm(B) were detected at suckling and weanling, whereas only tet(O) was detected at growing and finishing. The abundance of tet(O) was similar between males and females at weanling and growing and reached 5.1 × 10⁵ and 5.6 × 10⁵ copies of tet(O)/ng of total DNA in males and females, respectively, at finishing. Results showed high abundances and proportions of Tet^R and Tyl^R anaerobic bacterial populations, as well as the occurrence of tet and erm resistance genes within these populations despite the absence of antibiotic administration to pigs at this swine production facility since January 2007, i.e., 2.5 years prior to the beginning of this study. This work showed that the occurrence of bacterial resistance to chlortetracycline and tylosin is high at the Swine Complex of McGill University.     

Production of Sophorolipids from Candida bombicola ATCC 22214 Using Turkish Corn Oil and Honey

The ability of Candida bombicola ATCC 22214 to produce sophorolipids using Turkish corn oil and honey was investigated. Shake flask experiments were carried out both with and without the addition of glucose as the second carbon source. The organism could produce sophorolipids under both conditions but higher production was obtained when corn oil was combined with glucose. The 3 L bioreactor was first operated in batch mode, using both corn oil and glucose. When all the glucose was consumed, ¹/₄th of the broth was pumped out and was replaced by freshly prepared medium containing 10 % [w/v] of cheap market honey as the sole carbon source. Feed was comprised of corn oil. High concentrations of sophorolipids (> 400 g/L) were produced. The crude products obtained from the batch cultivation could be solidified as very light brown solids when unused oil was removed by hexane, while the products of the two‐stage cultivation remained as viscous, honey‐like liquids after identical treatments.     

Identification of novel pro-migratory, cancer-associated genes using quantitative, microscopy-based screening

Background

Cell migration is a highly complex process, regulated by multiple genes, signaling pathways and external stimuli. To discover genes or pharmacological agents that can modulate the migratory activity of cells, screening strategies that enable the monitoring of diverse migratory parameters in a large number of samples are necessary.

Methodology

In the present study, we describe the development of a quantitative, high-throughput cell migration assay, based on a modified phagokinetic tracks (PKT) procedure, and apply it for identifying novel pro-migratory genes in a cancer-related gene library. In brief, cells are seeded on fibronectin-coated 96-well plates, covered with a monolayer of carboxylated latex beads. Motile cells clear the beads, located along their migratory paths, forming tracks that are visualized using an automated, transmitted-light screening microscope. The tracks are then segmented and characterized by multi-parametric, morphometric analysis, resolving a variety of morphological and kinetic features.

Conclusions

In this screen we identified 4 novel genes derived from breast carcinoma related cDNA library, whose over-expression induces major alteration in the migration of the stationary MCF7 cells. This approach can serve for high throughput screening for novel ways to modulate cellular migration in pathological states such as tumor metastasis and invasion.     

Chemotaxonomy of fungi in the Rhizoctonia solani species complex performing GC/MS metabolite profiling

Hyphal anastomosis testing and molecular methods have been the primary criteria employed to understand the evolutionary and taxonomic relationships of the soil-borne fungal plant pathogen Rhizoctonia solani species complex. In this study, a metabolomics-based approach for characterizing and identifying isolates of R. solani using gas chromatography/mass spectrometry (GC/MS) metabolite profiling and footprinting was developed. Multivariate and hierarchical cluster analyses of GC/MS data provided resolution of isolates belonging to anastomosis groups (AGs) 1–6, 9, and 10 of R. solani. Clustering of R. solani AG-3 isolates, based on host origin, was also observed and attributed to metabolite-biomarkers belonging to amino, carboxylic and fatty acids. The chemotaxonomic approach using metabolomics is a high-throughput methodology that complements existing molecular approaches for the taxonomic investigation of Rhizoctonia isolates and monitoring of fungal metabolism.

     

Foaming and enzyme activity in fungal cultures grown on sugar beet cosette

Summary Enzyme synthesis, foaming behaviour and its effects were studied using two common cellulolytic fungi;Trichoderma reesei andSporotrichum pulverulentum in a medium containing sugar beet cosette as a cellulosic substrate. Cellulase enzyme activities in the culture broth were found to be higher than the enzyme activities in natural and experimentally forced foam layers.     

Mixing performance of air-lift fermenters against working volume and draft tube dimensions

Mixing characteristics of a laboratory scale internal loop air-lift fermenter has been investigated. The effects of different draft tube dimensions and positions as well as varying levels of liquid height over the draft tube, on mixing time were determined. The results indicate the existance of an optimum liquid height and thus liquid volume with respect to mixing performance especially for the taller draft tubes.List of Symbols A mm distance between draft tube and reactor base - A _D mm² area of the downcomer region - A _R mm² area of the riser region - B mm width of annulus - D _d mm draft tube diameter - D _t mm fermenter diameter - H _d mm draft tube height - H _l mm liquid height in the fermenter - H _t mm fermenter height - V _d m³ draft tube volume - V _t m³ fermenter volume - D _d /D _l - _B H _d /H _l - _F H _l /D _t      

Growth and reproduction of a stream population of Cobitis turcica in central Anatolia (Turkey)

Cobitis turcica is endemic to Anatolia, and being of a bottom‐dwelling nature is highly influenced by habitat degradation. Due to drought and water pollution, in 2006 this species was included in the IUCN Red List as endangered. Therefore in order to develop conservation strategies, knowledge of its life history traits is important. The study presents first time data on the basic life history traits of C. turcica captured in a small stream flowing from P?narba?? Springs to Kozanl? Gök Lake in central Anatolia. In total, 1356 specimens were caught between March 2003 and August 2004. The overall sex ratio (M : F) was 1 : 0.62. Longevity in females, which reaches a maximum age of 6+, is 1 year longer than for males. Females are longer and heavier than males of the same age group. Maximum observed total lengths were 103.6 mm in a 5+ year‐old male and 126.75 mm in a 6+ year‐old female. Length–weight relationships were calculated for males, females, and juveniles, with the b exponent of the relationships as 2.9068, 2.8326, and 3.6859, respectively. Spawning was fractional, beginning in April and continuing until the end of July. Mean total fecundity was 2238 at age 5+.     

Modeling above‐ground litterfall in eastern Mediterranean conifer forests using fractional tree cover,and remotely sensed and ground data

Question: How can we model above‐ground litterfall in Mediterranean conifer forests using remotely sensed and ground data, and geographic information systems (GIS)? Location: Eastern Mediterranean conifer forest of Turkey. Methods: Above‐ground litterfall from Mediterranean forest stands of Pinus nigra, Cedrus libani, Pinus brutia and Juniperus excelsa and mixed Abies cilicica, C. libani and P. nigra was modeled as a function of fractional tree cover using a regression tree algorithm, based on IKONOS and Landsat TM/ETM+data. Landsat TM/ETM+images for the study area were used to map actual stand patterns, based on a land‐cover map of species stands using a supervised classification. Results: Total amount of annual above‐ground litterfall for the entire study area (12 260 km²) was estimated at 417.2 Mg ha^?1 for P. brutia, 291.1 Mg ha^?1 for the mixed stand, 115.5 Mg ha^?1 for P. nigra, 54.6 Mg ha^?1 for J. excelsa and 45.9 Mg ha^?1 for C. libani. The maps generated indicate the distribution of the seasonal amount of total above‐ground litterfall for different species and the distribution of species stands in the study area. There was an increase in the amount of above‐ground litterfall for P. brutia stand in summer, for J. excelsa in autumn and for C. libani, P. nigra and the mixed stand of A. cilicica, P. nigra and C. libani in winter. Conclusion: Application of this model helps to improve the accuracy of estimated litterfall input to soil organic carbon pools in the Mediterranean conifer forests.