Molecular Typing of Lung Adenocarcinoma on Cytological Samples Using a Multigene Next Generation Sequencing Panel

Identification of driver mutations in lung adenocarcinoma has led to development of targeted agents that are already approved for clinical use or are in clinical trials. Therefore, the number of biomarkers that will be needed to assess is expected to rapidly increase. This calls for the implementation of methods probing the mutational status of multiple genes for inoperable cases, for which limited cytological or bioptic material is available. Cytology specimens from 38 lung adenocarcinomas were subjected to the simultaneous assessment of 504 mutational hotspots of 22 lung cancer-associated genes using 10 nanograms of DNA and Ion Torrent PGM next-generation sequencing. Thirty-six cases were successfully sequenced (95%). In 24/36 cases (67%) at least one mutated gene was observed, including EGFR, KRAS, PIK3CA, BRAF, TP53, PTEN, MET, SMAD4, FGFR3, STK11, MAP2K1. EGFR and KRAS mutations, respectively found in 6/36 (16%) and 10/36 (28%) cases, were mutually exclusive. Nine samples (25%) showed concurrent alterations in different genes. The next-generation sequencing test used is superior to current standard methodologies, as it interrogates multiple genes and requires limited amounts of DNA. Its applicability to routine cytology samples might allow a significant increase in the fraction of lung cancer patients eligible for personalized therapy.     

The effects of seed availability on habitat use by a specialist seed predator

Space-use patterns of seed predators are strongly affected by spatiotemporal variation in the abundance of different tree seeds, their major food source. However, most studies have measured relationships between overall food availability and space use, and there are few cases where effects of different food resources have been explored. We studied the effects of two food resources, Norway spruce and silver fir seeds, on space and habitat use in red squirrel in a subalpine conifer forest from 2000 to 2006. Fir seeds disperse in the autumn of the year they are produced, spruce the following spring. We estimated spruce and fir seed availability within individual home ranges and monitored home-range size using radiotelemetry. Males had larger home ranges than females and the sexes responded differently to variation in food and density. Spruce seed availability negatively affected home-range and core-area sizes of males in spring–summer. Space use was not affected by fir seed availability. Squirrels positively selected spruce for foraging and spruce was always preferred over fir. Our results showed that spruce, but not fir, affected space and habitat use of squirrels, suggesting they do not behaviourally respond to early seed dispersal in fir.     

A putative role for Discoidin Domain Receptor 1 in cancer chemoresistance

ABSTRACT

The Discoidin Domain Receptor 1 (DDR1) receptor tyrosine kinase performs pleiotropic functions in the control of cell adhesion, proliferation, survival, migration, and invasion. Aberrant DDR1 function as a consequence of either mutations or increased expression has been associated with various human diseases including cancer. Pharmacological inhibition of DDR1 results in significant therapeutic benefit in several pre-clinical cancer models. Here, we discuss the potential implication of DDR1-dependent pro-survival functions in the development of cancer resistance to chemotherapeutic regimens and speculate on the molecular mechanisms that might mediate such important feature.     

Demography of alpine red squirrel populations in relation to fluctuations in seed crop size

Vertebrate population dynamics, social organisation and space use often are closely associated with the distribution of critical resources, such as food. Tree squirrels are ideal models to study these relationships, since both key demographic parameters (reproduction, survival and dispersal) and spatio-temporal variation in food supplies (measured as seed-crop size) can be reliably estimated. In this paper we test the following two predictions underlying the association between annual food abundance and demography in six alpine red squirrel populations, both with and without time-lag effects: 1) between-season and between-year fluctuations in survival rate, population density and increase parallel those in food availability; and 2) individuals follow a resource tracking strategy and increase in density mainly the year after a rich seed-crop. Red squirrels occurred at higher densities in Scots pine forest, characterised by stable seed-crops, than in Norway spruce with more abundant but more variable seed crops. Fluctuations in numbers were positively correlated with food availability, measured as annual conifer seed-crop sizes. Overall, adult survival rates were higher than those of subadults, and survival substantially fluctuated between seasons and years. Autumn densities and rates of population increase (summer-autumn) were strongly correlated with the same year's autumn seed-crop, while correlations with the previous year's seed-crop (time-lag models) were either weak (population density) or absent (population increase). Results of this paper show that fluctuations in red squirrel densities in habitats with strong temporal variation in seed production are more closely linked with food availability than in more stable habitats. In addition, in the Alpine conifer forests squirrel population sizes, in autumn, increase in synchrony with food resources, eliminating the population lag normally present when resources are produced in pulses.     

Exclusive core areas and intrasexual territoriality in Eurasian red squirrels (<Emphasis Type="Italic">Sciurus vulgaris</Emphasis>) revealed by incremental cluster polygon analysis

When animal home ranges overlap extensively in species lacking overt territorial behaviours, identifying exclusive core areas within individual ranges can be difficult. By analysing the size and overlap of successively smaller core areas among individual Eurasian red squirrels (Sciurus vulgaris), we determined exclusive areas within the home ranges of resident males and females. Possible effects of habitat composition and food supplies were explored by monitoring squirrels in different conifer forests and during years with low and high tree seed production. Using outlier-exclusive cores (OEC) revealed that the total ranges consisted of large sally zones (on average, 35% of the total minimum convex polygon [MCP] range) around home ranges with multi-nucleate cores. The mean OEC home range size did not differ between the sexes but was larger with poor food availability. Home ranges (99% incremental cluster polygons [ICP]) overlapped extensively between sexes (average overlap high food–low food: males by females 21–40%, females by males 43–45%) and among males (males by males 26–44%), while intrasexual overlap among females was low (9–10%). The overlap of inner cores among females rapidly approached zero, suggesting the intrasexual territoriality of 75% core areas. This was not the case among male squirrels, for which intrasexual overlap averaged only 4% at 50% but 18% at 75% core areas. Even the smallest inner cores had some degree of intersexual overlap, indicating that complete territoriality did not occur in this species. Female home ranges were more strongly affected by annual fluctuations in food supplies than male ranges. Females reduced the size of their food-based intrasexual territories when food availability increases. Males probably benefit from using larger home ranges and core areas, which overlap with the ranges of several females, by increasing their probability of successful mating.     

Management of cytological material,pre‐analytical procedures and bio‐banking in effusion cytopathology

Serous effusion fluid is one of the most commonly encountered specimens in routine cytopathology practice. It provides invaluable information about the patient and the clinical status; but to get the most of it, specimen handling and processing must be carried out properly. Cytomorphology is the basis of a successful analysis which should complemented by ancillary tests when needed. A wide spectrum of ancillary techniques ‐ ranging from immunocytochemistry and flow cytometry to different assays of molecular pathology ‐ can be applied to serous effusions. This article describes the acquisition and management of serous effusion fluids, methods for preservation and transportation, different techniques of cytopreparation, application of immunocytochemistry, flow cytometry, and fluorescence in‐situ hybridization (FISH), as well as DNA extraction for polymerase chain reaction (PCR) and next generation sequencing (NGS). Principles of bio‐banking of effusion samples are also discussed which is getting more important in correlation with the developments in personalized medicine.