A system for detecting high impact-low frequency mutations in primary tumors and metastases.

Tumor complexity and intratumor heterogeneity contribute to subclonal diversity. Despite advances in next-generation sequencing (NGS) and bioinformatics, detecting rare mutations in primary tumors and metastases contributing to subclonal diversity is a challenge for precision genomics. Here, in order to identify rare mutations, we adapted a recently described epithelial reprograming assay for short-term propagation of epithelial cells from primary and metastatic tumors. Using this approach, we expanded minor clones and obtained epithelial cell-specific DNA/RNA for quantitative NGS analysis. Comparative Ampliseq Comprehensive Cancer Panel sequence analyses were performed on DNA from unprocessed breast tumor and tumor cells propagated from the same tumor. We identified previously uncharacterized mutations present only in the cultured tumor cells, a subset of which has been reported in brain metastatic but not primary breast tumors. In addition, whole-genome sequencing identified mutations enriched in liver metastases of various cancers, including Notch pathway mutations/chromosomal inversions in 5/5 liver metastases, irrespective of cancer types. Mutations/rearrangements in FHIT, involved in purine metabolism, were detected in 4/5 liver metastases, and the same four liver metastases shared mutations in 32 genes, including mutations of different HLA-DR family members affecting OX40 signaling pathway, which could impact the immune response to metastatic cells. Pathway analyses of all mutated genes in liver metastases showed aberrant tumor necrosis factor and transforming growth factor signaling in metastatic cells. Epigenetic regulators including KMT2C/MLL3 and ARID1B, which are mutated in >50% of hepatocellular carcinomas, were also mutated in liver metastases. Thus, irrespective of cancer types, organ-specific metastases may share common genomic aberrations. Since recent studies show independent evolution of primary tumors and metastases and in most cases mutation burden is higher in metastases than primary tumors, the method described here may allow early detection of subclonal somatic alterations associated with metastatic progression and potentially identify therapeutically actionable, metastasis-specific genomic aberrations.

Quantitative analysis of wear and wear debris from metal-on-metal hip prostheses tested in a physiological hip joint simulator.

Osteolysis and loosening of artificial joints caused by UHMWPE wear debris has prompted renewed interest in metal-on-metal (MOM) hip prostheses. This study investigated the wear and wear debris morphology generated by MOM prostheses in a physiological anatomical hip simulator for different carbon content cobalt chrome alloys. The low carbon pairings demonstrated significantly higher "bedding in" and steady state wear rates than the mixed and high carbon pairings. The in vitro wear rates reported here were up to one or two orders of magnitude lower than the clinical wear rates for first-generation MOM hip prostheses. Two methods for characterising the metal wear debris were developed, involving digestion, scanning electron microscopy and transmission electron microscopy. The metal wear particles characterised by the two methods were similar in size, 25-36 nm, and comparable to particles isolated from periprosthetic tissues from first and second-generation MOM hip prostheses. Due to the small size of the metal particles, the number of particles generated per year for MOM prostheses in vitro was estimated to be up to 100 times higher than the number of polyethylene particles generated per year in vivo. The volumetric wear rates were affected by the carbon content of the cobalt chrome alloy and the material combinations used. However, particle size and morphology was not affected by method of particle characterisation, the carbon content of the alloy or material combination.

Cell-mediated immunity to the mycelial phase of Malassezia spp. in patients with pityriasis versicolor and controls.

BACKGROUND: Malassezia is the aetiological agent of pityriasis versicolor. The mycelial phase of the organism predominates in lesions of pityriasis versicolor. OBJECTIVES: To evaluate the cell-mediated immune (CMI) response to the mycelial phase of Malassezia in patients with this disease, which has not previously been studied. METHODS: The CMI status of 12 patients with pityriasis versicolor and 12 age- and sex-matched controls to mycelial antigen(s) of the organism was examined. The responses to the mycelial form of three strains of the organism were assessed using lymphocyte transformation and leucocyte migration inhibition assays. RESULTS: The transformation responses of the lymphocytes from both patients and controls gave transformation indices < or = 3, although the responses of lymphocytes from patients with pityriasis versicolor to the mycelial form of Malassezia strains were generally higher than those of the controls. In the leucocyte migration inhibition assay, leucocytes from patients with pityriasis versicolor and controls responded to the mycelial antigens of three different Malassezia strains; however, there was no significant difference in leucocyte response between patients with pityriasis versicolor and controls. CONCLUSIONS: Patients with pityriasis versicolor do not therefore have a CMI deficiency to Malassezia mycelial antigens but fail to generate a protective CMI response to mycelial antigens over and above that of control individuals during active disease.

Production of the mycelial phase of Malassezia in vitro.

To study the pathogenicity of Malassezia, the agent of pityriasis versicolor, it is necessary to obtain the mycelial form in vitro. A range of different components and conditions were tested to induce yeast cells of the organism to produce mycelia in vitro using different culture media. A mycelial culture medium was developed that consisted of bacteriological peptone, glucose, yeast extract, ox bile, glycerol, glycerol monostearate, Tween 80, squalene, glycine, potassium nitrate, sodium chloride, ferrous sulphate and magnesium sulphate with or without agar. The liquid and solid medium had a pH of 5.6 and the temperature of incubation was 30 degrees C. Cultures were incubated in air. This medium was able to induce some strains of Malassezia to produce up to 40% mycelium in vitro. In total, 33 different strains of Malassezia obtained from the skin of the healthy individuals and patients with pityriasis versicolor were tested for mycelium production. The strains of Malassezia capable of producing mycelium in vitro all possessed the serovar A antigen.