Sporadic colorectal cancer (CRC) is a result of complex interactions between the host and its environment. Environmental stressors act by causing host cell DNA alterations implicated in the onset of cancer. Here we investigate the stressor ability of CRC-associated gut dysbiosis as causal agent of host DNA alterations. The epigenetic nature of these alterations was investigated in humans and in mice. Germ-free mice receiving fecal samples from subjects with normal colonoscopy or from CRC patients were monitored for 7 or 14 wk. Aberrant crypt foci, luminal microbiota, and DNA alterations (colonic exome sequencing and methylation patterns) were monitored following human feces transfer. CRC-associated microbiota induced higher numbers of hypermethylated genes in murine colonic mucosa (vs. healthy controls’ microbiota recipients). Several gene promoters including SFRP1,2,3, PENK, NPY, ALX4, SEPT9, and WIF1 promoters were found hypermethylated in CRC but not in normal tissues or effluents from fecal donors. In a pilot study (n = 266), the blood methylation levels of 3 genes (Wif1, PENK, and NPY) were shown closely associated with CRC dysbiosis. In a validation study (n = 1,000), the cumulative methylation index (CMI) of these genes was significantly higher in CRCs than in controls. Further, CMI appeared as an independent risk factor for CRC diagnosis as shown by multivariate analysis that included fecal immunochemical blood test. Consequently, fecal bacterial species in individuals with higher CMI in blood were identified by whole metagenomic analysis. Thus, CRC-related dysbiosis induces methylation of host genes, and corresponding CMIs together with associated bacteria are potential biomarkers for CRC.

Because the use of spectral powers of blood pressure (BP) and R-R interval (RR) in the low (LF) and high frequencies (HF) to quantify sympathetic and parasympathetic activities is still under debate, we questioned whether nonlinear methods may give better results. The BP signal was recorded for 30 min before and after intravenous injection of hexamethonium (20 mg/kg), atropine (0.5 mg/kg), atenolol (1 mg/kg), and prazosin (1 mg/kg) in conscious, normotensive Wistar-Kyoto rats. Three nonlinear indexes [percentage of recurrence, percentage of determinism, and length index ( L max)] extracted from the recurrence plot method were used to analyze the BP signal. Sympathetic but not parasympathetic blockade reduced BP level and its LF component. RR increased and decreased after β- and α-blockades, respectively. Hexamethonium increased HF, and atropine reduced LF, of RR. Sympathetic blockade and, in particular, α-sympathetic blockade increased nonlinear indexes of BP. In contrast, parasympathetic blockade by atropine increased nonlinear indexes of RR. These results suggest that, compared with spectral indexes, nonlinear indexes may be more specific markers of sympathetic and parasympathetic tones.

Circulating triglycerides (TG) normally increase after a meal but are altered in pathophysiological conditions such as obesity. Although TG metabolism in the brain remains poorly understood, several brain structures express enzymes that process TG-enriched particles, including mesolimbic structures. For this reason, and because consumption of high fat diet alters dopamine signaling, we tested the hypothesis that TG might directly target mesolimbic reward circuits to control reward-seeking behaviors. We found that the delivery of small amounts of TG to the brain through the carotid artery rapidly reduced both spontaneous and amphetamine-induced locomotion, abolished preference for palatable food, and reduced the motivation to engage in food-seeking behavior. Conversely, targeted disruption of the TG-hydrolyzing enzyme lipoprotein lipase specifically in the nucleus accumbens increased palatable food preference and food seeking behavior. Finally, prolonged TG perfusion resulted in a return to normal palatable food preference despite continued locomotor suppression, suggesting that adaptive mechanisms occur. These findings reveal new mechanisms by which dietary fat may alter mesolimbic circuit function and reward seeking.

BackgroundOvarian granulosa cell tumors (GCTs) are the most frequent sex cord-stromal tumors. Several studies have shown that a somatic mutation leading to a C134W substitution in the transcription factor FOXL2 appears in more than 95% of adult-type GCTs. Its pervasive presence suggests that FOXL2 is the main cancer driver gene. However, other mutations and genomic changes might also contribute to tumor formation and/or progression.MethodsWe have performed a combined comparative genomic hybridization and transcriptomic analyses of 10 adult-type GCTs to obtain a picture of the genomic landscape of this cancer type and to identify new candidate co-driver genes.ResultsOur results, along with a review of previous molecular studies, show the existence of highly recurrent chromosomal imbalances (especially, trisomy 14 and monosomy 22) and preferential co-occurrences (i.e. trisomy 14/monosomy 22 and trisomy 7/monosomy 16q). In-depth analyses showed the presence of recurrently broken, amplified/duplicated or deleted genes. Many of these genes, such as AKT1, RUNX1 and LIMA1, are known to be involved in cancer and related processes. Further genomic explorations suggest that they are functionally related.ConclusionsOur combined analysis identifies potential candidate genes, whose alterations might contribute to adult-type GCT formation/progression together with the recurrent FOXL2 somatic mutation.Electronic supplementary materialThe online version of this article (doi:10.1186/s12885-015-1283-0) contains supplementary material, which is available to authorized users.

Recently, several theoretical and applied studies have shown that unsupervised Bayesian classification systems are of particular relevance for biological studies. However, these systems have not yet fully reached the biological community mainly because there are few freely available dedicated computer programs, and Bayesian clustering algorithms are known to be time consuming, which limits their usefulness when using personal computers. To overcome these limitations, we developed AutoClass@IJM, a computational resource with a web interface to AutoClass, a powerful unsupervised Bayesian classification system developed by the Ames Research Center at N.A.S.A. AutoClass has many powerful features with broad applications in biological sciences: (i) it determines the number of classes automatically, (ii) it allows the user to mix discrete and real valued data, (iii) it handles missing values. End users upload their data sets through our web interface; computations are then queued in our cluster server. When the clustering is completed, an URL to the results is sent back to the user by e-mail. AutoClass@IJM is freely available at: http://ytat2.ijm.univ-paris-diderot.fr/AutoclassAtIJM.html.

Extrahepatic cholangiocarcinoma (CCA) accounts for 3% of digestive cancers. The role of biliary microbiota as an environment-related modulator has been scarcely investigated in CCA, and the putative impact of associated diseases has not been yet assessed. We characterized the biliary microbiota in CCA patients in order to identify a specific CCA-related dysbiosis. The biliary effluents were collected through an endoscopic retrograde pancreatic cholangiography (ERCP) examination involving 28 CCA and 47 patients with gallstones, herein considered as controls. The biliary effluents were submitted to bacterial DNA extraction and 16S rRNA sequencing, using Illumina technology. Overall, 32% of CCA and 22% of controls displayed another associated disease, such as diabetes, pancreatitis, inflammatory bowel disease, or primary sclerosing cholangitis. Such associated diseases were considered in the comparisons that were made. Principal coordinate analysis (PCoA) detected a significant disparity of biliary microbiota composition between CCA patients and controls without an associated disease. Amongst the most abundant phyla, Proteobacteria did not significantly differ between CCA patients and controls, whereas Firmicutes levels were lower and Bacteroidetes higher in CCAs’ biliary microbiota than in the controls’ microbiota. The most abundant genera were Enterococcus, Streptococcus, Bacteroides, Klebsiella, and Pyramidobacter in CCA’s biliary microbiota. Additionally, levels of Bacteroides, Geobacillus, Meiothermus, and Anoxybacillus genera were significantly higher in CCA patients’ biliary microbiota, without an associated disease, in comparison with controls. A specific CCA-related dysbiosis was identified as compared to controls independently from associated diseases. This suggests that a microorganism community may be involved in CCA pathogenesis.

Beat-to-beat heart rate (HR) and blood pressure were measured by the Finapres system in 44 healthy and 64 diabetic subjects in the at-rest condition. Autonomic control in diabetic subjects was assessed by the Ewing test. HR variability was explored by both linear and nonlinear methods. Linear methods used HR standard deviation and power spectrum. The percentage of the spectrum in the low frequencies was used to assess the sympathetic tone of the autonomic control. The nonlinear method used the "recurrence plot." This method explored long parallel subsequences in the HR time series. These sequences characterize the dependence of the HR dynamics on initial values. The HR standard deviation was reduced in the diabetic subjects compared with the healthy subjects (2.80 +/- 1.17 vs. 3.64 +/- 1.45 beats/min; P < 0.001). In the diabetic subjects, the HR standard deviation and the percentage of the spectrum in the low frequencies showed no correlations with the Ewing score (P > 0.10). In contrast, the longest length index was very strongly correlated to the Ewing score (r = -0.60; P < 0.0001). The results suggest that nonlinear methods might be powerful to explore the autonomic dysfunction in diabetic subjects.

Cirrhosis is a lesion at risk of hepatocellular carcinoma (HCC). Identifying mechanisms associated with the transition from cirrhosis to HCC and characterizing biomarkers of cirrhosis at high risk of developing into cancer are crucial for improving early diagnosis and prognosis of HCC. We used MALDI imaging to compare mass spectra obtained from tissue sections of cirrhosis without HCC, cirrhosis with HCC, and HCC, and a top-down proteomics approach to characterize differential biomarkers. We identified a truncated form of monomeric ubiquitin lacking the two C-terminal glycine residues, Ubi(1-74), the level of which increased progressively, from cirrhosis without HCC to cirrhosis with HCC to HCC. We showed that kallikrein-related peptidase 6 (KLK6) catalysed the production of Ubi(1-74) from monomeric ubiquitin. Furthermore, we demonstrated that KLK6 was induced de novo in cirrhosis and increased in HCC in parallel with accumulation of Ubi(1-74). We investigated in vitro the possible consequences of Ubi(1-74) accumulation and demonstrated that Ubi(1-74) interferes with the normal ubiquitination machinery in what is likely to be a kinetic process. Our data suggest that de novo KLK6 expression during early liver carcinogenesis may induce production of Ubi(1-74) by post-translational modification of ubiquitin. Given the deleterious effect of Ubi(1-74) on protein ubiquitination and the major role of ubiquitin machinery in maintenance of cell homeostasis, Ubi(1-74) might severely impact a number of critical cellular functions during transition from cirrhosis to cancer. Ubi(1-74) and KLK6 may serve as markers of cancer risk in patients with cirrhosis.