We present the results of a global study of dysregulated miRNAs in paired samples of normal mucosa and tumor from eight patients with colorectal cancer. Although there is existing data of miRNA contribution to colorectal tumorigenesis, these studies are typically small to medium scale studies of cell lines or non-paired tumor samples. The present study is to our knowledge unique in two respects. Firstly, the normal and adjacent tumor tissue samples are paired, thus taking into account the baseline differences between individuals when testing for differential expression. Secondly, we use high-throughput sequencing, thus enabling a comprehensive survey of all miRNAs expressed in the tissues. We use Illumina sequencing technology to perform sequencing and two different tools to statistically test for differences in read counts per gene between samples: edgeR when using the pair information and DESeq when ignoring this information, i.e., treating tumor and normal samples as independent groups. We identify 37 miRNAs that are significantly dysregulated in both statistical approaches, 19 down-regulated and 18 up-regulated. Some of these miRNAs are previously published as potential regulators in colorectal adenocarcinomas such as miR-1, miR-96 and miR-145. Our comprehensive survey of differentially expressed miRNAs thus confirms some existing findings. We have also discovered 16 dysregulated miRNAs, which to our knowledge have not previously been associated with colorectal carcinogenesis: the following significantly down-regulated miR-490-3p, -628-3p/-5p, -1297, -3151, -3163, -3622a-5p, -3656 and the up-regulated miR-105, -549, -1269, -1827, -3144-3p, -3177, -3180-3p, -4326. Although the study is preliminary with only eight patients included, we believe the results add to the present knowledge on miRNA dysregulation in colorectal carcinogenesis. As such the results would serve as a robust training set for validation of potential biomarkers in a larger cohort study. Finally, we also present data supporting the hypothesis that there are differences in miRNA expression between adenocarcinomas and neuroendocrine tumors of the colon.

Atlantic salmon (Salmo salar) is among the most sensitive organisms toward acidic, aluminum exposure. Main documented responses to this type of stress are a combination of hypoxia and loss of blood plasma ions. Physiological responses to stress in fish are often grouped into primary, secondary and tertiary responses, where the above mentioned effects are secondary responses, while primary responses include endocrine changes as measurable levels of catecholamines and corticosteroids. In this study we have exposed young (14 months) Atlantic salmon to acid/Al water (pH ≈ 5.6, Al(i) ≈ 80 μg L⁻¹) for 3 days, and obtained clear and consistent decrease of Na⁺ and Cl⁻ ions, and increases of glucose in blood plasma, hematocrit and P(CO₂) in blood. We did not measure plasma cortisol (primary response compound), but analyzed effects on microRNA level (miRNA) in muscle tissue, as this may represent initial markers of primary stress responses. miRNAs regulate diverse biological processes, many are evolutionarily conserved, and hundreds have been identified in various animals, although only in a few fish species. We used a novel high-throughput sequencing (RNA-Seq) method to identify miRNAs in Atlantic salmon and specific miRNAs as potential early markers for stress. A total of 18 miRNAs were significantly differentially expressed (FDR<0.1) in exposed compared to control fish, four down-regulated and 14 up-regulated. An unsupervised hierarchical clustering of significant miRNAs revealed two clusters representing exposed and non-exposed individuals. Utilizing the genome of the zebrafish and bioinformatic tools, we identified 224 unique miRNAs in the Atlantic salmon samples sequenced. Additional laboratory studies focusing on function, stress dose-responses and temporal expression of the identified miRNAs will facilitate their use as initial markers for stress responses.

Since induced sputum has become a widely used non-invasive method of recovering cells from the surfaces of the bronchial airways, isolating specific cell populations will be necessary in order to learn more about their specific role in innate immunity and inflammation in the airways. Several studies have demonstrated the ability to conduct ex vivo analyses on sputum cells such as phagocytosis and surface marker measurements, but these have not been performed on isolated cell types. [1][2][3] This study demonstrates the capability to isolate sputum macrophages from human volunteers in order to advance our understanding of macrophage biology in the airways. To this end, techniques that can enrich and isolate cells without significant activation would prove extremely useful. We compared two common methods for isolating and enriching macrophages in sputum: (1) magnetic bead separation; and (2) Percoll gel density gradient centrifugation. Cell purity and markers of cell activation (mRNA tumour necrosis factor a (TNFa)) and interleukin1b (IL1b)) were measured at various time points in the isolation process.Nine healthy subjects underwent induced sputum. Sputum collection and sputum processing has been described in detail previously.4 For measuring natural cell activation over time, we incubated the processed sputum cells for 3 h at 37˚C and analysed mRNA TNFa and IL1-b at 0 h (baseline) and 3 h. In the positive control experiment we incubated the processed sputum cells with 1 ng/ml LPS (E coli, Sigma). For Percoll (Amersham Biosciences) separation, 600 ml of sputum cell suspension (1610 6 cells/ ml) was layered over Percoll solution (42%) and centrifuged at 560 g for 10 min. Sputum macrophages were removed and incubated at 37˚C for 1, 2 and 3 h, respectively, and a pre-incubation sample was also collected. The macrophages were further pelleted and stored at 270˚C . For Dynabead separation, CELLection Pan Mouse IgG Kit (Dynal, Norway) was used for immunomagnetic separation of airway macrophages coated with mouse monoclonal IgG2b HLA-DR antibody (Diatec, Norway). Bead coating and cell isolation was performed according to the protocol from the manufacturer. The isolated cells were incubated at 37˚C for 1, 2 and 3 h, respectively, and a pre-incubation sample was also collected. The samples were further pelleted and stored at 270˚C. Total RNA was extracted (Qiagen) from all the cell samples and reverse transcription was performed (Superscript III, Invitrogen). We used pre-developed PCR primers and probes for TNFa and the housekeeping gene PGK (Applied Biosystems). Specific primers and probes were designed for IL1b using ProbeLibrary (Exiqon ProbeLibrary). Quantification of mRNA was performed using the ABI Prism 7700 (Applied Biosystems), and the relative standard curve method was used to calculate the relative gene expression.The results show that the median (range) proportion of macrophages in the pre-isolation sputum sample was 61 (34-70)%. Bead isolation produced 99 (95-99)% macrophage purity compared with 88 (85-94)% w...

Monoclonal antibodies targeting the epidermal growth factor receptor have expanded the range of treatment options for patients with metastatic colorectal cancer. However, somatic mutations in the KRAS and BRAF genes have proven to be molecular predictors of resistance to treatment with anti-epidermal growth factor receptor therapy in these patients. Thus, we have developed a sensitive mutation assay, wobble-enhanced amplification refractory mutation system, for detecting the 8 most commonly reported mutations of clinical importance in the KRAS and BRAF genes; KRAS g.34G>C (p.G12R), g.34G>A (p.G12S), g.34G>T (p.G12C), g.35G>A (p.G12D), g.35G>C (p.G12A), g.35G>T (p.G12V), g.38G>A (p.G13D), and BRAF g.1799T>A (p.V600E). A total of 28 candidate setups were designed based on bioinformatics and primer/probe design. Eight candidate setups were thus selected using a synthetic oligonucleotide model. The setups were further validated through several experiments using formalin-fixed paraffin-embedded tissue and cell lines. The results confirm that the wobble-enhanced amplification refractory mutation system method is quick, cost effective, and sensitive. The method is optimized to handle a typical template input of 1 to 20 ng DNA per polymerase chain reaction and can be implemented in any laboratory with ease with a real-time polymerase chain reaction instrument capable of handling TaqMan techonology. The steps used to develop this method can be implemented to design assays for other mutations located in KRAS, BRAF, or other candidate genes.

Bacterial single cell protein (BSCP) is used as a protein enrichment in livestock and fish feed, and is extracted from dried bacterial mass. In the production of BSCP, workers are exposed to organic dust containing high levels of endotoxins that may induce acute airway inflammation. However, the long term effect on the airways of such exposure is not known, and we have examined inflammatory markers in induced sputum and blood among BSCP exposed workers. We included 21 non-smoking production workers (age 31-42 (range; mean 35)) without respiratory symptoms and 21 healthy non-exposed references (age 21-52 (range; mean 34)). Airborne endotoxin concentrations were measured, and induced sputum samples and blood samples were collected from the workers and non-exposed references. The airborne endotoxin concentration measured in inhaled air during the work shift was 430 EU/m(3) (50-2000) (median (range)). The percentage of neutrophils in induced sputum was 79% (66-93) (median (25th-75th percentiles)) and 31% (25-45) (p < 0.001) for operators and references, respectively. Protein analysis in induced sputum supernatant showed significantly elevated levels of interleukins IL-1beta and IL-12 (p < 0.05), while blood analysis showed significantly elevated levels of PDGF-BB (platelet-derived growth factor-BB) and RANTES (regulated upon activation normally T cell expressed and secreted) (p < 0.05). Workers exposed to BSCP had an airway inflammation characterized by a high level of neutrophils. However, only a few cytokines were elevated in lung and blood, which could imply low inflammatory activity suggestive of possible adaptation mechanisms due to daily exposure to BSCP, or that the inflammation reaction was a dose-related response occurring at higher levels.