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Recent studies suggest that microRNAs show promise as excellent biomarkers for breast cancer; however there is still a high degree of variability between studies making the findings difficult to interpret. In addition to blood, ductal lavage (DL) and nipple aspirate fluids represent an excellent opportunity for biomarker detection because they can be obtained in a less invasive manner than biopsies and circumvent the limitations of evaluating blood biomarkers with regards to tissue of origin specificity. In this study, we have investigated for the first time, through a real-time PCR array, the expression of 742 miRNAs in the ductal lavage fluid collected from 22 women with unilateral breast tumors. We identified 17 differentially expressed miRNAs between tumor and paired normal samples from patients with ductal breast carcinoma. Most of these miRNAs have various roles in breast cancer tumorigenesis, invasion and metastasis, therapeutic response, or are associated with several clinical and pathological characteristics of breast tumors. Moreover, some miRNAs were also detected in other biological fluids of breast cancer patients such as serum (miR-23b, -133b, -181a, 338-3p, -625), plasma (miR-200a), and breast milk (miR-181a). A systems biology analysis of these differentially expressed miRNAs points out possible pathways and cellular processes previously described as having an important role in breast cancer such as Wnt, ErbB, MAPK, TGF-β, mTOR, PI3K-Akt, p53 signaling pathways. We also observed a difference in the miRNA expression with respect to the histological type of the tumors. In conclusion, our findings suggest that miRNA analysis of breast ductal fluid is feasible and potentially very useful for the detection of breast cancer.

Purpose: Visually guided ocular growth is facilitated by scleral extracellular matrix remodeling at the posterior pole of the eye. Coincident with scleral remodeling, significant changes in choroidal morphology, blood flow, and protein synthesis have been shown to occur in eyes undergoing ocular growth changes. The current study is designed to identify gene expression changes that may occur in the choroid/retinal pigment epithelium (RPE) of marmoset eyes during their compensation for hyperopic defocus as compared to eyes compensating for myopic defocus., Methods: Total RNA was isolated from choroid/RPE from four common marmosets (Callithrix jacchus) undergoing binocular lens treatment using extended wear soft contact lenses of equal magnitude but opposite sign (+/-5 diopter [D]). After reverse transcription, cDNA was labeled and hybridized to a human oligonucleotide microarray and gene transcript expression profiles were determined. Real-time polymerase chain reaction (PCR) and western blot analysis were used to confirm genes and proteins of interest, respectively., Results: Microarray analyses in choroid/RPE indicated 204 genes were significantly changed in minus lens-treated as compared with plus lens-treated eyes (p<0.05, Student's t-test). Differential choroid/RPE expression of protein tyrosine phosphatase, receptor type, B (PTPRB), transforming growth factor beta-induced (TGFBI), and basic fibroblast growth factor 2 (FGF-2) were confirmed by real-time PCR. TGFBIp was confirmed at the protein level by western blot analysis in marmoset and human cornea, choroid/RPE, and sclera., Conclusions: The present study demonstrated that significant gene expression changes occur in the marmoset choroid/RPE during visually guided ocular growth. The identification of novel candidate genes in choroid/RPE of marmoset eyes actively accelerating or decelerating their rates of ocular elongation may elucidate the choroidal response during the regulation of postnatal ocular growth and may lead to the identification of choroid/RPE signaling molecules that participate in scleral remodeling.

This report presents computational methods of analysis of cellular processes, functions, and pathways affected by differentially expressed microRNA, a statistical basis of the gene enrichment analysis method, a modification of enrichment analysis method accounting for combinatorial targeting of Gene Ontology categories by multiple miRNAs and examples of the global functional profiling of predicted targets of differentially expressed miRNAs in cancer. We have also summarized an application of Ingenuity Pathway Analysis tools for in depth analysis of microRNA target sets that may be useful for the biological interpretation of microRNA profiling data. To illustrate the utility of these methods, we report the main results of our recent computational analysis of five published datasets of aberrantly expressed microRNAs in five human cancers (pancreatic cancer, breast cancer, colon cancer, lung cancer, and lymphoma). Using a combinatorial target prediction algorithm and statistical enrichment analysis, we have determined Gene Ontology categories as well as biological functions, disease categories, toxicological categories, and signaling pathways that are: targeted by multiple microRNAs; statistically significantly enriched with target genes; and known to be affected in specific cancers. Our recent computational analysis of predicted targets of co-expressed miRNAs in five human cancers suggests that co-expressed miRNAs provide systemic compensatory response to the abnormal phenotypic changes in cancer cells by targeting a broad range of functional categories and signaling pathways reportedly affected in a particular cancer.

A new type of noncoding short single-stranded RNA molecules, microRNA (miRNA), has recently emerged as one of the most important new classes of cellular regulators. Recent advances in miRNA research have provided evidence that aberrant expression of specific miRNAs is associated with a broad spectrum of human diseases, such as cancer, diabetes, cardiovascular diseases, psychological disorders and others. Global microRNAome profiling has demonstrated drastic changes in expression of multiple miRNAs in many common human cancers. miRNA expression signatures have been shown to provide a more accurate method of classifying cancer subtypes than transcriptome profiling of an entire set of known protein-coding genes. miRNA profiling also allows classification of different stages in tumor progression and can predict disease outcome in some cases. Further characterization of these abnormal miRNA expression signatures and identification of the most significant and informative aberrantly expressed miRNAs could lead to the development of tissue- and biofluid-specific diagnostic markers, as well as a new type of oligonucleotide-based therapeutics. As researchers continue to study miRNA expression in cancer and focus on most relevant miRNAs, the further advancement of miRNA-detection technologies and bioinformatics algorithms is critical for successful identification of the most informative diagnostics markers among the tissue-specific miRNAs.

microRNAs are functional, 22 nt, noncoding RNAs that negatively regulate gene expression. Disturbance of microRNA expression may play a role in the initiation and progression of certain diseases. A microRNA expression signature has been identified that is associated with pancreatic cancer. This has been accomplished with the application of real-time PCR profiling of over 200 microRNA precursors on specimens of human pancreatic adenocarcinoma, paired benign tissue, normal pancreas, chronic pancreatitis and nine pancreatic cancer cell lines. Hierarchical clustering was able to distinguish tumor from normal pancreas, pancreatitis and cell lines. The PAM algorithm correctly classified 28 of 28 tumors, 6 of 6 normal pancreas and 11 of 15 adjacent benign tissues. One hundred microRNA precursors were aberrantly expressed in pancreatic cancer or desmoplasia (p < 0.01), including microRNAs previously reported as differentially expressed in other human cancers (miR-155, miR-21, miR-221 and miR-222) as well as those not previously reported in cancer (miR-376a and miR-301). Most of the top aberrantly expressed miRNAs displayed increased expression in the tumor. Expression of the active, mature microRNA was validated using a real-time PCR assay to quantify the mature microRNA and Northern blotting. Reverse transcription in situ PCR showed that three of the top differentially expressed miRNAs (miR-221, -376a and -301) were localized to tumor cells and not to stroma or normal acini or ducts. Aberrant microRNA expression may offer new clues to pancreatic tumorigenesis and may provide diagnostic biomarkers for pancreatic adenocarcinoma., (Copyright 2006 Wiley-Liss, Inc.)