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Sebaceous gland carcinoma (SGC) is a rare, but life-threatening condition with a predilection for the periocular region. Eyelid SGC can be broadly categorised into two subtypes, namely either nodular or pagetoid with the latter being more aggressive and requiring radical excision to save life. We have identified key altered microRNAs (miRNA) involved in SGC shared by both subtypes, hsa-miR-34a-5p and hsa-miR-16-5p. However, their gene targets BCL2 and MYC were differentially expressed with both overexpressed in pagetoid but unchanged in nodular suggesting different modes of action of these two miRNAs on BCL/MYC expression. Hsa-miR-150p is nodular-specifically overexpressed, and its target ZEB1 was significantly downregulated in nodular SGC suggesting a tumour suppressor role. Invasive pagetoid subtype demonstrated specific overexpression of hsa-miR-205 and downregulation of hsa-miR-199a. Correspondingly, miRNA gene targets, EZH2 (by hsa-miR-205) and CD44 (by hsa-miR-199a), were both overexpressed in pagetoid SGC. CD44 has been identified as a potential cancer stem cell marker in head and neck squamous cell carcinoma and its overexpression in pagetoid cells represents a novel treatment target. Aberrant miRNAs and their gene targets have been identified in both SGC subtypes, paving the way for better molecular understanding of these tumours and identifying new treatment targets.

Breast cancer is commonest cancer in women worldwide. Elucidation of underlying biology and molecular pathways is necessary for improving therapeutic options and clinical outcomes. Molecular alterations in breast cancer are complex and involve cross-talk between multiple signaling pathways. The aim of this study is to extract a unique mRNA fingerprint of breast cancer in Lebanese women using microarray technologies. Gene-expression profiles of 94 fresh breast tissue samples (84 cancerous/10 non-tumor adjacent samples) were analyzed using GeneChip Human Genome U133 Plus 2.0 arrays. Quantitative real-time PCR was employed to validate candidate genes. Differentially expressed genes between breast cancer and non-tumor tissues were screened. Significant differences in gene expression were established for COL11A1/COL10A1/MMP1/COL6A6/DLK1/S100P/CXCL11/SOX11/LEP/ADIPOQ/OXTR/FOSL1/ACSBG1 and C21orf37. Pathways/diseases representing these genes were retrieved and linked using PANTHER ® /Pathway Studio ® . Many of the deregulated genes are associated with extracellular matrix, inflammation, angiogenesis, metastasis, differentiation, cell proliferation and tumorigenesis. Characteristics of breast cancers in Lebanese were compared to those of women from Western populations to explain why breast cancer is more aggressive and presents a decade earlier in Lebanese victims. Delineating molecular mechanisms of breast cancer in Lebanese women led to key genes which could serve as potential biomarkers and/or novel drug targets for breast cancer.

High-throughput profiling has generated massive amounts of data across basic, clinical and translational research fields. However, open source comprehensive web tools for analysing data obtained from different platforms and technologies are still lacking. To fill this gap and the unmet computational needs of ongoing research projects, we developed O-miner, a rapid, comprehensive, efficient web tool that covers all the steps required for the analysis of both transcriptomic and genomic data starting from raw image files through in-depth bioinformatics analysis and annotation to biological knowledge extraction. O-miner was developed from a biologist end-user perspective. Hence, it is as simple to use as possible within the confines of the complexity of the data being analysed. It provides a strong analytical suite able to overlay and harness large, complicated, raw and heterogeneous sets of profiles with biological/clinical data. Biologists can use O-miner to analyse and integrate different types of data and annotations to build knowledge of relevant altered mechanisms and pathways in order to identify and prioritize novel targets for further biological validation. Here we describe the analytical workflows currently available using O-miner and present examples of use. O-miner is freely available at www.o-miner.org.

The immunological environment experienced by parasitic nematodes varies greatly between hosts and is particularly influenced by whether or not a host has been previously infected. How a parasitic nematode responds to these different environments is poorly understood, but may allow a parasite to ameliorate the adverse effects of host immunity on parasite fitness. Here we use a microarray approach to identify genes in the parasitic nematode Strongyloides ratti that exhibit differential transcription between different rat host immunological environments, and between replicate lines of S. ratti selected for either early or late reproduction. We hypothesise that such genes may be used by this species to cope with and respond to its host environment. Our results showed that, despite large phenotypic differences between S. ratti adults from different immunological environments, the S. ratti transcriptome exhibited a relatively stable pattern of expression. Thus, differential expression amongst treatments was limited to a small proportion of transcripts and generally involved only modest fold changes. These transcripts included a group of collagen genes up-regulated in parasites early in an infection, and in immunised host environments, which may be related to protection against the damage caused to a parasite by host immune responses. We found that later in an infection, a number of genes associated with muscle function and repair were up-regulated in immunised host environments; these may help parasites maintain their position in the host intestine. Differences in transcription between selection lines of S. ratti were only observed in immunised hosts and included genes associated with the response to the host's immunological environment., (Copyright © 2010 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.)