Nanoproteomic analysis of ischemia-dependent changes in signaling protein phosphorylation in colorectal normal and cancer tissue

Additional file 1: Table S1. Clinical data for the 20 patients analyzed in the study. Presents patient clinical data including tumor stage and grade

DNA damage induced by cis- and carboplatin as indicator for in vitro sensitivity of ovarian carcinoma cells

<p>Abstract</p> <p>Background</p> <p>The DNA damage by platinum cytostatics is thought to be the main cause of their cytotoxicity. Therefore the measurement of the DNA damage induced by cis- and carboplatin should reflect the sensitivity of cancer cells toward the platinum chemotherapeutics.</p> <p>Methods</p> <p>DNA damage induced by cis- and carboplatin in primary cells of ovarian carcinomas was determined by the alkaline comet assay. In parallel, the reduction of cell viability was measured by the fluorescein diacetate (FDA) hydrolysis assay.</p> <p>Results</p> <p>While in the comet assay the isolated cells showed a high degree of DNA damage after a 24 h treatment, cell viability revealed no cytotoxicity after that incubation time. The individual sensitivities to DNA damage of 12 tumour biopsies differed up to a factor of about 3. DNA damage after a one day treatment with cis- or carboplatin correlated well with the cytotoxic effects after a 7 day treatment (r = 0,942 for cisplatin r = 0.971 for carboplatin). In contrast to the platinum compounds the correlation of DNA damage and cytotoxicity induced by adriamycin was low (r = 0,692), or did not exist for gemcitabine.</p> <p>Conclusion</p> <p>The measurement of DNA damage induced by cis- and carboplatin is an accurate method to determine the in vitro chemosensitivity of ovarian cancer cells towards these cytostatics, because of its quickness, sensitivity, and low cell number needed.</p

The Genome of Mycobacterium Africanum West African 2 Reveals a Lineage-Specific Locus and Genome Erosion Common to the M. tuberculosis Complex

Mycobacterium africanum, a close relative of M. tuberculosis, is studied for the following reasons: M. africanum is commonly isolated from West African patients with tuberculosis yet has not spread beyond this region, it is more common in HIV infected patients, and it is less likely to lead to tuberculosis after one is exposed to an infectious case. Understanding this organism's unique biology gets a boost from the decoding of its genome, reported in this issue. For example, genome analysis reveals that M. africanum contains a region shared with “ancient” lineages in the M. tuberculosis complex and other mycobacterial species, which was lost independently from both M. tuberculosis and M. bovis. This region encodes a protein involved in transmembrane transport. Furthermore, M. africanum has lost genes, including a known virulence gene and genes for vitamin synthesis, in addition to an intact copy of a gene that may increase its susceptibility to antibiotics that are insufficiently active against M. tuberculosis. Finally, the genome sequence and analysis reported here will aid in the development of new diagnostics and vaccines against tuberculosis, which need to take into account the differences between M. africanum and other species in order to be effective worldwide

Identification and Validation of a Potential Marker of Tissue Quality Using Gene Expression Analysis of Human Colorectal Tissue

<div><p>Correlative studies have identified numerous biomarkers that are individualizing therapy across many medical specialties, including oncology. Accurate interpretation of these studies requires the collection of tissue samples of sufficient quality. Tissue quality can be measured by changes in levels of gene expression and can be influenced by many factors including pre-analytical conditions, ischemic effects and the surgical collection procedure itself. However, as yet there are no reliable biomarkers of tissue quality at researchers’ disposal. The aim of the current study was to identify genes with expression patterns that fluctuated reproducibly in response to typical post-surgical stress (ischemia) in order to identify a specific marker of tissue quality. All tissue samples were obtained from patients with primary colorectal carcinoma (CRC) (N = 40) either via colonoscopy prior to surgery, or by surgical resection. Surgically resected tissue samples were divided into three groups and subjected to cold ischemia for 10, 20 or 45 minutes. Normal colorectal tissue and CRC tissue was analyzed using microarray and quantitative real-time PCR (qPCR). Comparing changes in gene expression between pre- and post-surgical tissue using microarray analysis identified a list of potential tissue quality biomarkers and this list was validated using qPCR. Results revealed that post-operative ischemia significantly alters gene expression in normal and CRC tissue samples. Both microarray analysis and qPCR revealed regulator of G-protein signaling 1 (<i>RGS1</i>) as a potential marker of CRC tissue quality and eukaryotic translation elongation factor 1 alpha 1 (<i>EEF1A1</i>) as a potential reference gene of post-operative tissue quality. Larger studies with additional time points and endpoints will be needed to confirm these results.</p></div

Expression levels of <i>RGS1</i> following normalization to <i>UBC</i>, <i>GAPDH</i> and <i>EEF1A1</i> as well as to the combination of <i>GAPDH</i> and <i>UBC</i>.

<p>Comparison of <i>RGS1</i> gene expression changes in normal <b>(A)</b> and tumor <b>(B)</b> ischemic tissue samples of 20 individual patients. Patients pre-surgery samples (0) were set to 1 and individual fold changes of ischemic samples were calculated based on normalization to <i>UBC</i> (white box), <i>GAPDH</i> (light grey box), <i>EEF1A1</i> (grey box) or to a combination of <i>GAPDH</i> and <i>UBC</i> (dark grey box). Results were summarized by Box-Whisker Plots. Boxes represent first and third quartile, whiskers represent minima and maxima, solid lines within boxes indicate medians. Kruskal-Wallis test and Dunn’s multiple comparison test were used for statistical analysis to compare the four normalization approaches within each time point. n.s. = not significant; N = normal tissue; T = tumor tissue; 0 = before surgery; 10, 20, 45 = 10, 20, 45 minutes after resection.</p

Microarray data of genes with the lowest CV across ischemia time points in normal colorectal tissue.

<p>The 10 probe sets (nine genes) with the lowest CV including rank across all four time points (pre-surgery, 10, 20 and 45 minutes after resection) in normal colorectal tissue as well as the corresponding ranks in tumor colorectal tissue are shown. Additionally, CVs and ranks of <i>GAPDH</i> and <i>UBC</i> are included within this table. Table adapted from David K et al. Oncotarget 2014; 5. <b>[<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0133987#pone.0133987.ref005" target="_blank">5</a>]</b>.</p><p>Microarray data of genes with the lowest CV across ischemia time points in normal colorectal tissue.</p