Padhan BMC Cancer 2016 Supplemental Results

File contains the test statistic (T) for each possible combination of 1-3 features, including the constructed features (column 5 and 6). One combination is shown per row with the name of the feature combination in the first column and the header explaining the value in each column in the first row

Raw Protein RPAs

The relative peak area (RPA), i.e. peak area value of the 23 different activity levels of the 7 signal transducers after normalization to the HSP70 level analyzed in parallel in each sample (columns 2-24). This file contains one sample per row and one protein per column with the sample name in the first column and the protein name in the first row. Columns 25-27 contain the result of the mutation analysis of KRAS and BRAF. One in column 25 (MutationKRAS) indicate that KRAS is mutated in the sample, one in column 26 (MutationBRAF) indicates that BRAF is mutated, while one in column 27 (Wildtype) indicate that neither KRAS nor BRAF is mutated. A one in the binary variables in column 28-31 indicate the classification of each sample as normal mucosa, colorectal cancer (CRC) stage II, CRC stage IV, or metastasis. NaN is used to indicate that no measurement was done

Additional file 1: of High sensitivity isoelectric focusing to establish a signaling biomarker for the diagnosis of human colorectal cancer

Figure S1. Validation of antibodies used in the study by conventional immunoblotting. All antibodies showed immunoreactivity with the expected molecular species, in conventional immunoblotting on endothelial lysates. Figure S2. Detection of MEK1/2 protein by isoelectric focusing. There was no significant difference in MEK protein expression between normal, CRCII and CRCIV tissues. Detailed description of computational analyses; “Characterization of the data set and errors”. Figure S3. Distribution function for data subsets by Monte Carlo simulation. (DOCX 1215 kb

Raw Protein RPAs Constructed features replicate corrected

File shows the relative peak area (RPA), i.e. peak area value of the measured protein after normalization to the HSP70 level analyzed in parallel in each sample (columns 2-24, 28-42). This file contains one sample per row and one protein per column with the sample name in the first column and the protein name in the first row. Column 25-27 contain the result of the mutation analysis of KRAS and BRAF. One in column 25 (MutationKRAS) indicate that KRAS is mutated in the sample, one in column 26 (MutationBRAF) indicates that BRAF is mutated, while one in column 27 (Wildtype) indicate that neither KRAS nor BRAF is mutated. Columns 28 to 42 contain the RPA values of the constructed features, i.e. features that are calculated based on the 23 different activity levels of the 7 signal transducers in column 2-24. The four replicates of each constructed feature contains the minimum, maximum, mean, and median value based on all possible ways to combine the replicates of the proteins used to construct the feature. A one in the binary variables in column 43-46 indicate the classification of each sample as normal mucosa, colorectal cancer (CRC) stage II, CRC stage IV, or metastasis. In the last column the classification is 1 = normal mucosa, 2 = colorectal cancer (CRC) stage II, 3 = CRC stage IV, or 5 = metastasis. NaN is used to indicate that no measurement was done

The anticancer effect of mebendazole may be due to M1 monocyte/macrophage activation via ERK1/2 and TLR8-dependent inflammasome activation

<p>Mebendazole (MBZ), a drug commonly used for helminitic infections, has recently gained substantial attention as a repositioning candidate for cancer treatment. However, the mechanism of action behind its anticancer activity remains unclear. To address this problem, we took advantage of the curated MBZ-induced gene expression signatures in the LINCS Connectivity Map (CMap) database. The analysis revealed strong negative correlation with MEK/ERK1/2 inhibitors. Moreover, several of the most upregulated genes in response to MBZ exposure were related to monocyte/macrophage activation. The MBZ-induced gene expression signature in the promyeloblastic HL-60 cell line was strongly enriched in genes involved in monocyte/macrophage pro-inflammatory (M1) activation. This was subsequently validated using MBZ-treated THP-1 monocytoid cells that demonstrated gene expression, surface markers and cytokine release characteristic of the M1 phenotype. At high concentrations MBZ substantially induced the release of IL-1β and this was further potentiated by lipopolysaccharide (LPS). At low MBZ concentrations, cotreatment with LPS was required for MBZ-stimulated IL-1β secretion to occur. Furthermore, we show that the activation of protein kinase C, ERK1/2 and NF-kappaB were required for MBZ-induced IL-1β release. MBZ-induced IL-1β release was found to be dependent on NLRP3 inflammasome activation and to involve TLR8 stimulation. Finally, MBZ induced tumor-suppressive effects in a coculture model with differentiated THP-1 macrophages and HT29 colon cancer cells. In summary, we report that MBZ induced a pro-inflammatory (M1) phenotype of monocytoid cells, which may, at least partly, explain MBZ’s anticancer activity observed in animal tumor models and in the clinic.</p

Chemotherapeutic drug sensitivity of primary cultures of epithelial ovarian cancer cells from patients in relation to tumour characteristics and therapeutic outcome

<div><p></p><p><i>Background.</i> A number of chemotherapeutic drugs are active in epithelial ovarian cancer (EOC) but so far choice of drugs for treatment is mostly empirically based. Testing of drug activity in tumour cells from patients might provide a rationale for a more individualised approach for drug selection. <i>Material and methods.</i> Sensitivity of EOC to chemotherapeutic drugs was analysed in 125 tumour samples from 112 patients using a short-term primary culture assay based on the concept of total cell kill. Sensitivity was related to tumour histology, treatment status and clinical tumour response. <i>Results.</i> For most EOC standard drugs serous high grade and clear cell EOC were the most sensitive subtypes and the mucinous tumours the most resistant subtype. Docetaxel, however, tended to show the opposite pattern. Samples from previously treated patients tended to be more resistant than those from treatment naïve patients. The activity of cisplatin correlated with that of other drugs with the exception of docetaxel. Tumour samples from two sites in the same patient at the same occasion showed similar cisplatin sensitivity in contrast to samples taken at different occasions. Samples from patients responding in the clinic to treatment were more sensitive to most drugs than samples from non-responding patients. At the individual patient level, drug sensitivity in vitro compared with clinical response showed sensitivities and specificities in the 83–100% and 55–83% ranges, respectively. <i>Conclusions.</i> Assessment of EOC tumour cell drug sensitivity in vitro provides clinically relevant and potentially useful information for the optimisation of drug treatment.</p></div