ETBF and <i>Fusobacterium</i> are found at significantly higher levels in late stage (III/IV) cancers.

<p>For <i>Fusobacterium</i>, individual stages were compared in a pairwise manner using Dunn’s test. For ETBF, individual stages were compared in a pairwise manner using Fisher’s exact test. <i>Fusobacterium</i> is found at significantly higher levels in stage III CRCs compared to stage I or II CRCs. ETBF is found more frequently in stage III or IV CRCs compared to stage I or II CRCs; and in the corresponding normal mucosa of stage IV CRCs compared to stage I CRCs.</p

Summary of BLAST search query to identify intimin subtypes.

<p>Samples highlighted in bold were used to determine the effect of FFPE fixation on the ability to detect EPEC by qPCR. ND: not determined.</p><p>Summary of BLAST search query to identify intimin subtypes.</p

<i>Fusobacterium</i> clinicopathological associations.

<p>High-level colonisation by <i>Fusobacterium</i> is significantly more prevalent in younger patients, males and patients of Black ethnicity. Due to the disproportionately high number of young, black patients seen in our cohort the relationship between ethnicity and levels of colonisation by <i>Fusobacterium</i> was assessed using the subset of patients ≤ 50 years. A borderline significant relationship was seen between high-level colonisation by <i>Fusobacterium</i> and MSI-H compared to MSS/MSI-L (In our cohort three MSI-L cases were included with the MSS cohort). The vertical and horizontal dotted lines in the bottom right Fig. represent the cutoff for high-level colonisation by <i>pks+ E</i>. <i>coli</i> and <i>Fusobacterium</i>, respectively (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0119462#sec002" target="_blank">methods</a> for further detail). FB: <i>Fusobacterium</i>; B: Black; C: Caucasian; I: Indian; M: Mixed Ancestry; N: normal tissue; F: Female; M: Male.</p

Summary of the putative oncogenic mechansims and the bacterial components implicated in CRC pathogenesis for the six bacterial species quantified in this study.

<p>Summary of the putative oncogenic mechansims and the bacterial components implicated in CRC pathogenesis for the six bacterial species quantified in this study.</p

Quantification of bacteria in colorectal cancer and adjacent normal tissues.

<p>T and N denote adenocarcinoma and adjacent normal mucosa, respectively. Rates of concurrent colonisation in T and N samples were calculated as a fraction of the number of patients who were infected in T and/or N with a particular bacterium.</p><p>Quantification of bacteria in colorectal cancer and adjacent normal tissues.</p

ETBF and afaC+ <i>E</i>. <i>coli</i> are significantly more prevalent in colon vs. rectal cancers.

<p>This applies to both tumour and normal tissue in the case of ETBF (FDR = 0.002, 0.001, respectively) and normal tissue only in the case of afaC (FDR = 0.03).</p

Clinicopathological characteristics of the cohort of fresh-frozen tissues (N = 55).

<p>In the case of age and BMI mean values and their standard deviations (SD) are reported. The numbers in column 1 in brackets represent the number of patients with missing data in each category.</p><p>Clinicopathological characteristics of the cohort of fresh-frozen tissues (N = 55).</p

qPCR quantification of bacteria in paired patient samples, expressed as log10 bacteria/50ng of patient DNA.

<p>Each bar represents one samples (either tumour or normal) and the order of samples are the same for each bacterium. Red (tumour); blue (normal); *(Not determined).</p

Comparative Reevaluation of FASP and Enhanced FASP Methods by LC–MS/MS

Filter-aided sample preparation is a proteomic technique for the preparation and on column proteolysis of proteins. Recently an enhanced FASP protocol was developed that uses deoxycholic acid (DCA) and that reportedly enhances trypsin proteolysis, resulting in increases cytosolic and membrane protein representation. FASP and eFASP were re-evaluated by ultra-high-performance liquid chromatography coupled to a quadrupole mass filter Orbitrap analyzer (Q Exactive). Although there was no difference in trypsin activity, 14 099 and 13 414 peptides, describing 1723 and 1793 protein groups, from <i>Escherichia coli</i> K12 were identified using FASP and eFASP, respectively. Characterization of the physicochemical properties of identified peptides showed no significant differences other than eFASP extracting slightly more basic peptides. At the protein level, both methods extracted essentially the same number of hydrophobic transmembrane helix-containing proteins as well as proteins associated with the cytoplasm or the cytoplasmic and outer membranes. By employing state-of-the-art LC–MS/MS shot gun proteomics, our results indicate that FASP and eFASP showed no significant differences at the protein level. However, because of the slight differences in selectivity at the physicochemical level of peptides, these methods can be seen to be somewhat complementary for analyses of complex peptide mixtures

Quantitative label-free proteomic analysis of human urine to identify novel candidate protein biomarkers for schistosomiasis

<div><p>Background</p><p>Schistosomiasis is a chronic neglected tropical disease that is characterized by continued inflammatory challenges to the exposed population and it has been established as a possible risk factor in the aetiology of bladder cancer. Improved diagnosis of schistosomiasis and its associated pathology is possible through mass spectrometry to identify biomarkers among the infected population, which will influence early detection of the disease and its subtle morbidity.</p><p>Methodology</p><p>A high-throughput proteomic approach was used to analyse human urine samples for 49 volunteers from Eggua, a schistosomiasis endemic community in South-West, Nigeria. The individuals were previously screened for <i>Schistosoma haematobium</i> and structural bladder pathologies via microscopy and ultrasonography respectively. Samples were categorised into schistosomiasis, schistosomiasis with bladder pathology, bladder pathology, and a normal healthy control group. These samples were analysed to identify potential protein biomarkers.</p><p>Results</p><p>A total of 1306 proteins and 9701 unique peptides were observed in this study (FDR = 0.01). Fifty-four human proteins were found to be potential biomarkers for schistosomiasis and bladder pathologies due to schistosomiasis by label-free quantitative comparison between groups. Thirty-six (36) parasite-derived potential biomarkers were also identified, which include some existing putative schistosomiasis biomarkers that have been previously reported. Some of these proteins include Elongation factor 1 alpha, phosphopyruvate hydratase, histone H4 and heat shock proteins (HSP 60, HSP 70).</p><p>Conclusion</p><p>These findings provide an in-depth analysis of potential schistosoma and human host protein biomarkers for diagnosis of chronic schistosomiasis caused by <i>Schistosoma haematobium</i> and its pathogenesis.</p></div