Validation of a Multiplexed Gene Signature Assay for Diagnosis of Canine Cancers from Formalin-Fixed Paraffin-Embedded Tissues

Background

Use of molecular‐based diagnostics for companion animals is impeded by availability of technology platforms, tissue acquisition requirements, and species‐specific reagents.

Hypothesis/Objectives

To validate a quantitative nuclease protection assay (qNPA) to simultaneously measure RNA expression of multiple genes in archived formalin‐fixed paraffin‐embedded (FFPE) tumors from dogs.

Animals

All tumor biopsy samples were collected retrospectively from surgical biopsies and in the care of veterinarians.

Methods

Retrospective case series. A qNPA 96‐well ArrayPlate was built using 30 canine‐specific genes, 5 housekeeping genes, positive and negative controls with qualified gene‐specific oligonucleotides. Pearson's correlation, coefficient of variation (CV), and multivariate analysis were used to determine analytical performance using 40 FFPE dog tumors. Once validated, 70 FFPE dog tumors were analyzed for differences in gene expression using hierarchical clustering and analysis of variance of log transformed data. Immunohistochemistry (IHC) was performed to correlate gene expression and protein expression in a subset of tumors.

Results

The assay was linear with decreasing sample input (R² = 0.978), reproducible within and between 96‐well plates (r = 0.988 and 0.95, respectively) and between different laboratories (CV = 0.96). Hierarchical cluster analysis showed grouping of tumors by histogenesis and oncogenes. Significant differences were found between BCl2, E2F transcription factor 1, MDM2, COX‐2, MET proto‐oncogene receptor kinase, and other biologically relevant gene expression in tumor subtypes. Immunohistochemistry confirmed protein expression.

Conclusions and Clinical Implications

Because this technology works reliably on FFPE specimens, it can help expedite the broad introduction of multiplexed genomic information for improved diagnostics and discovery of new targets for therapies in veterinary oncology.

[Incidence of methicillin-resistant Staphylococcus aureus in community-onset paediatric skin infections: a retrospective study 2000-2005]

BACKGROUND

A dramatic increase in the incidence of methicillin-resistant Staphylococcus aureus (MRSA) in community-onset skin infections has been reported over the last 10 years in the USA. The emergence of MRSA has been recently described in France. The aims of this study were to assess the incidence of MRSA in community-onset skin infections and to analyse the characteristics of MRSA skin infections in a French paediatric population.

PATIENTS AND METHODS

This is a retrospective study covering the period January 2000 to December 2005. Patients aged under 15 years with S. aureus isolated from skin and a clinical diagnosis of skin infection were included.

RESULTS

One hundred and thirty-four children were included with a median age of 3.4 years. There were no significant differences in MRSA prevalence between the different years of the study. The overall prevalence of MRSA was 8.2% (n=11/134). None of the isolated strains presented an antimicrobial susceptibility profile suggestive of the ST80-type community-acquired MRSA described in France. Three MRSA strains were isolated from serious superantigen-mediated skin infections. The antimicrobial susceptibility and genetic profile (tst-positive agr2 MSRA) for one strain of S. aureus militated strongly in favour of an MRSA ST5 clone skin infection.

CONCLUSION

In this study we found no evidence of epidemic spread of MRSA in community-onset childhood skin infections between 2000-2005. Nevertheless, we report three cases of serious MRSA-induced superantigen-associated skin infection. This argues in favour of the presence of virulent community MRSA clones in France.

Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana

Arabidopsis thaliana is an important model system for plant biologists. In 1996 an international collaboration (the Arabidopsis Genome Initiative) was formed to sequence the whole genome of Arabidopsis and in 1999 the sequence of the first two chromosomes was reported. The sequence of the last three chromosomes and an analysis of the whole genome are reported in this issue. Here we present the sequence of chromosome 3, organized into four sequence segments (contigs). The two largest (13.5 and 9.2 Mb) correspond to the top (long) and the bottom (short) arms of chromosome 3, and the two small contigs are located in the genetically defined centromere. This chromosome encodes 5,220 of the roughly 25,500 predicted protein-coding genes in the genome. About 20% of the predicted proteins have significant homology to proteins in eukaryotic genomes for which the complete sequence is available, pointing to important conserved cellular functions among eukaryotes.