Combining chromosomal arm status and significantly aberrant genomic locations reveals new cancer subtypes.

Many types of tumors exhibit characteristic chromosomal losses or gains, as well as local amplifications and deletions. Within any given tumor type, sample specific amplifications and deletions are also observed. Typically, a region that is aberrant in more tumors, or whose copy number change is stronger, would be considered as a more promising candidate to be biologically relevant to cancer. We sought for an intuitive method to define such aberrations and prioritize them. We define V, the "volume" associated with an aberration, as the product of three factors: (a) fraction of patients with the aberration, (b) the aberration's length and (c) its amplitude. Our algorithm compares the values of V derived from the real data to a null distribution obtained by permutations, and yields the statistical significance (p-value) of the measured value of V. We detected genetic locations that were significantly aberrant, and combine them with chromosomal arm status (gain/loss) to create a succinct fingerprint of the tumor genome. This genomic fingerprint is used to visualize the tumors, highlighting events that are co-occurring or mutually exclusive. We apply the method on three different public array CGH datasets of Medulloblastoma and Neuroblastoma, and demonstrate its ability to detect chromosomal regions that were known to be altered in the tested cancer types, as well as to suggest new genomic locations to be tested. We identified a potential new subtype of Medulloblastoma, which is analogous to Neuroblastoma type 1.

An unusual cause of hemoptysis--aberrant origin of the left pulmonary artery from the ascending aorta in the adult.

Aberrant origin of a pulmonary artery from the ascending aorta is an uncommon congenital vascular malformation with poor survival without surgery. In this case report, we describe the unusual late diagnosis of this congenital malformation in an otherwise asymptomatic young man presenting with mild hemoptysis. We review the natural and modified history of this defect and the relevant aspects of follow-up in adult life.

Endoluminal surgical triangulation: overcoming challenges of colonic endoscopic submucosal dissections using a novel flexible endoscopic surgical platform: feasibility study in a porcine model.

BACKGROUND: Colonic endoscopic submucosal dissection (ESD) is challenging as a result of the limited ability of conventional endoscopic instruments to achieve traction and exposure. The aim of this study was to evaluate the feasibility of colonic ESD in a porcine model using a novel endoscopic surgical platform, the Anubiscope (Karl Storz, Tüttlingen, Germany), equipped with two working channels for surgical instruments with four degrees of freedom offering surgical triangulation. METHODS: Nine ESDs were performed by a surgeon without any ESD experience in three swine, at 25, 15, and 10 cm above the anal verge with the Anubiscope. Sixteen ESDs were performed by an experienced endoscopist in five swine using conventional endoscopic instruments. Major ESD steps included the following for both groups: scoring the area, submucosal injection of glycerol, precut, and submucosal dissection. Outcomes measured were as follows: dissection time and speed, specimen size, en bloc dissection, and complications. RESULTS: No perforations occurred in the Anubis group, while there were eight perforations (50 %) in the conventional group (p = 0.02). Complete and en bloc dissections were achieved in all cases in the Anubis group. Mean dissection time for completed cases was statistically significantly shorter in the Anubis group (32.3 ± 16.1 vs. 55.87 ± 7.66 min; p = 0.0019). Mean specimen size was higher in the conventional group (1321 ± 230 vs. 927.77 ± 229.96 mm(2); p = 0.003), but mean dissection speed was similar (35.95 ± 18.93 vs. 23.98 ± 5.02 mm(2)/min in the Anubis and conventional groups, respectively; p = 0.1). CONCLUSIONS: Colonic ESDs were feasible in pig models with the Anubiscope. This surgical endoscopic platform is promising for endoluminal surgical procedures such as ESD, as it is user-friendly, effective, and safe.

Colonic perianastomotic carcinogenesis in an experimental model

Background To examine the effect of anastomosis on experimental carcinogenesis in the colon of rats. Methods Forty-three 10-week-old male and female Sprague-Dawley rats were operated on by performing an end-to-side ileorectostomy. Group A:16 rats received no treatment. Group B: 27 rats received 18 subcutaneous injections weekly at a dose of 21 mg/kg wt of 1–2 dimethylhydrazine (DMH), from the eighth day after the intervention. Animals were sacrificed between 25–27 weeks. The number of tumours, their localization, size and microscopic characteristics were recorded. A paired chi-squared analysis was performed comparing tumoral induction in the perianastomotic zone with the rest of colon with faeces. Results No tumours appeared in the dimethylhydrazine-free group. The percentage tumoral area was greater in the perianastomotic zone compared to tumours which had developed in the rest of colon with faeces (p = 0.014). Conclusion We found a cocarcinogenic effect due to the creation of an anastomosis, when using an experimental model of colonic carcinogenesis induced by DMH in rats.

In this issue.

A new issue, once again a bouquet of attractive papers. First of all the paper by Droit-Dupré et al. (10.1007/s00428-015-1724-9). The group studied colonic adenocarcinomas, not otherwise specified, by immunohistochemistry for the expression of markers of intestinal epithelial cell differentiation. Hierarchical clustering analysis identified a major cluster of two thirds of the case series, expressing cytokeratin 20, CDX2 and MUC2 and invariably mismatch repair competent, which they called crypt-like. In stage III colon cancer, the crypt-like cluster had a better prognosis. The paper is a relatively simple example of what is happening in cancer classification beyond morphology: multiparameter differentiation and (epi)genomic markers defining new subtypes of cancer with potential clinical significance in clinical decision making.

Targeting Oxidative Stress and Aberrant Critical Period Plasticity in the Developmental Trajectory to Schizophrenia.

Schizophrenia is a neurodevelopmental disorder reflecting a convergence of genetic risk and early life stress. The slow progression to first psychotic episode represents both a window of vulnerability as well as opportunity for therapeutic intervention. Here, we consider recent neurobiological insight into the cellular and molecular components of developmental critical periods and their vulnerability to redox dysregulation. In particular, the consistent loss of parvalbumin-positive interneuron (PVI) function and their surrounding perineuronal nets (PNNs) as well as myelination in patient brains is consistent with a delayed or extended period of circuit instability. This linkage to critical period triggers (PVI) and brakes (PNN, myelin) implicates mistimed trajectories of brain development in mental illness. Strategically introduced antioxidant treatment or later reinforcement of molecular brakes may then offer a novel prophylactic psychiatry.

Aberrant features of the Messinian coral reefs, Spain

Se describen someramente los principales arrecifes del Messiniense en España, haciendo hincapié en el conjunto de 'anomalias' presentan los arrecifes del Neógeno inferior en comparación con las asociaciones arrecifales actuales. Se discute la importancia y significado de Porites sp. como coral claramente dominante, y a menudo exclusivo, en la construcción de edificios arrecifales.

The Influence of Diet and Microbes on Colonic Immune Regulation and their Implications on Type 1 Diabetes

Dietary and microbial factors are thought to contribute to the rapidly increasing prevalence of T1D in many countries worldwide. The impact of these factors on immune regulation and diabetes development in non-obese diabetic (NOD) mice are investigated in this thesis. Diabetes can be prevented in NOD mice through dietary manipulation. Diet affects the composition of intestinal microbiota, which may subsequently influence intestinal immune homeostasis. However, the specific effects of anti-diabetogenic diets on gut immunity and the explicit associations between intestinal immune disruption and type 1 diabetes onset remain unclear. The research presented herein demonstrates that newly weaned NOD mice suffer from a mild level of colitis, which shifts the colonic immune cell balance towards a proinflammatory status. Several aberrations can also be observed in the peritoneal B cells of NOD mice; an increase in activation marker expression, increased trafficking to the pancreatic lymph nodes and significantly higher antigen presenting cell (APC) efficiency towards insulin-specific T cells. A shift towards inflammation is likewise observed in the colon of germ-free NOD mice, but signs of peritoneal B cell activation are lacking in these mice. Remarkably, most of the abnormalities in the colon, peritoneal macrophages and the peritoneal B cell APC activity of NOD mice are abrogated when NOD mice are maintained on a diabetes-preventive, soy-based diet (ProSobee) from the time of weaning. Dietary and microbial factors hence have a significant impact on colonic immune regulation and peritoneal B cell activation and it is suggested that these factors influence diabetes development in NOD mice.

Influence of preoperative supplementation of omega-3 fatty acid in the healing of colonic anastomoses in malnourished rats receiving paclitaxel

OBJECTIVE: To evaluate the effect of preoperative supplementation of omega-3 fatty acids on the healing of colonic anastomoses in malnourished rats receiving paclitaxel. METHODS: we studied 160 male Wistar rats, divided in two groups: one subjected to malnutrition by pair feeding (M) for four weeks, and another that received food ad libitum (W). In the fourth week, the groups were further divided into two subgroups that received omega-3 or olive oil by gavage. The animals were submitted to colonic transection and end-to-end anastomosis. After the operation, each of the four groups was divided into two subgroups that received intraperitoneal isovolumetric solutions of saline or paclitaxel. RESULTS: mortality was 26.8% higher in the group of animals that received paclitaxel (p = 0.003). The complete rupture strength was greater in well-nourished-oil Paclitaxel group (WOP) compared with the the malnourished-oil Paclitaxel one (MOP). The collagen maturation index was higher in well-nourished-oil saline group (WOS) in relation to the malnutrition-oil-saline group (MOS), lower in malnourished-oil-saline group (MOS) in relation to malnourished-ômega3-saline one (M3S) and lower in the well-nourished-omega3-saline group (W3S) compared with the malnourished-omega3-saline (M3S). The blood vessel count was higher in the malnourished-oil-saline group (MOS) than in the malnourished-oil-paclitaxel group (MOP) and lower in the malnourished-oil-saline group (MOS) in relation to the malnourished-omega3-paclitaxel group (M3P). CONCLUSION: supplementation with omega-3 fatty acids was associated with a significant increase in the production of mature collagen in malnourished animals, with a reversal of the harmful effects caused by malnutrition associated with the use of paclitaxel on the rupture strength, and with a stimulus to neoangiogenesis in the group receiving paclitaxel.

Effect of Carapa guianensis Aublet (Andiroba) and Orbignya phalerata (Babassu) in colonic healing in rats

Objective: to evaluate the healing effect of the babassu aqueous extract and andiroba oil on open wounds in the cecum of rats. Methods: fifty-four Wistar rats were divided into three groups of 18: 1) babassu group with application of aqueous extract of babassu; 2) andiroba group with application of the oil; and 3) control group, with application of saline solution. All procedures were done by gavage. Each group was divided into three subgroups of six animals according to the observation period of 7, 14 or 21 days. From each animal was removed caecum fragment of 1.5cm² diameter. The areas of the lesions were analyzed macroscopically and resected specimens by light microscopy using hematoxylin-eosin and Masson's trichrome. Results: abscess and infection were observed in two aroeira group animals, and in one only hematoma. In relationship to adhesions degree, babassu group had higher incidence of grade II while in the control and aroeira groups predominated adhesions grade I. On microscopic examination on day 7 fibroblast proliferation was greater in aroeira and lower in babassu group (p=0.028). On the 14th day polymorphonuclear were less pronounced in babassu (p=0.007). As for the resistance test of air insufflation, it was observed that in all andiroba group in all tested days showed be higher. As for collagen, on the 7th day it was present in 100% of animals of aroeira group. On the 14th day was more pronounced in the control group and at day 21 similar results were found in the control and aroeira groups. Conclusion: animals in babassu and andiroba groups showed better cecum healing compared to the control group.

Total and segmental colonic transit time in constipated patients with Chagas’ disease without megaesophagus or megacolon

Manometric and pharmacological tests have shown that motor abnormalities may occur in the non-dilated colons of chagasic patients. In order to investigate the presence of abnormalities of colonic function in constipated patients with Chagas’ disease (ChC) without megaesophagus or megacolon, studies of total and segmental colonic transit time with radiopaque markers were performed on 15 ChC patients, 27 healthy volunteers and 17 patients with idiopathic constipation (IC). The values obtained for the control group were similar to those reported in the literature (total colonic time: 34.1 ± 15.6 h; right colon: 9.9 ± 7.3 h; left colon: 10.8 ± 10 h, and rectosigmoid: 12.6 ± 9.9 h). Colonic transit time data permitted us to divide both IC and ChC patients into groups with normal transit and those with slow colonic transit. Colonic inertia was detected in 41% of IC patients and in 13% of ChC patients; left colon isolated stasis (hindgut dysfunction) was detected in 12% of IC patients and 7% of ChC patients, and outlet obstruction was detected in 6% of IC patients and 7% of ChC patients. There were no significant differences in total or segmental colonic transit times between slow transit IC and slow transit ChC patients. In conclusion, an impairment of colonic motility was detected in about 30% of constipated patients with Chagas’ disease without megaesophagus or megacolon. This subgroup of patients presented no distinctive clinical feature or pattern of colonic dysmotility when compared to patients with slow transit idiopathic constipation.

Dietary fiber intake, stool frequency and colonic transit time in chronic functional constipation in children

The objective of the present study was to evaluate associations between fiber intake, colonic transit time and stool frequency. Thirty-eight patients aged 4 to 14 years were submitted to alimentary evaluation and to measurement of colonic transit time. The median fiber intake of the total sample was age + 10.3 g/day. Only 18.4% of the subjects presented a daily dietary fiber intake below the levels recommended by the American Health Foundation. In this group, the median left colonic transit time was shorter than in the group with higher dietary fiber intake (11 vs 17 h, P = 0.067). The correlation between stool frequency and colonic transit time was negative and weak for left colon (r = -0.3, P = 0.04), and negative and moderate for rectosigmoid and total colon (r = -0.5, P<0.001 and r = -0.5, P<0.001, respectively). The stool frequency was lower in the group with slow transit time (0.8 vs 2.3 per week, P = 0.014). In conclusion, most patients with chronic functional constipation had adequate dietary fiber intake. The negative correlation between stool frequency and colonic transit time increased progressively from proximal segments to distal segments of the colon. Patients with normal and prolonged colonic transit time differ in terms of stool frequency.

Trypanosoma cruzi infection and/or administration of the nonsteroidal anti-inflammatory nimesulide increase the number of colonic crypts overexpressing metallothioneins in rat colon carcinogenesis

Trypanosoma cruzi infection and nonsteroidal anti-inflammatory drugs inhibit colorectal carcinogenesis by mechanisms not completely known and metallothionein proteins (MTs) may be involved in this process. Sixty-six male Wistar rats weighing 90 to 120 g were randomly divided into seven groups (GI to GVII). GI, GII and GIII animals were subcutaneously infected with 200,000 trypomastigote forms of the Y strain of T. cruzi. After 8 weeks, GI, GII, GIV, and GVI were injected with one weekly subcutaneous dose of 12 mg/kg dimethylhydrazine for 4 weeks. In sequence, GI, GIV and GV were treated with nimesulide (10 mg/kg per dose, five times per week for 8 weeks). Groups I, III, IV, and VI had 12 animals, and each of the other groups had 6 animals. All the animals were euthanized 8 weeks after the last dimethylhydrazine injection. The colons were fixed and processed for MT immunohistochemistry. The index of MT-overexpressing colonic crypts (MTEC) was estimated as the percentage of MT-stained crypts in relation to the total number of crypts scored. Five hundred crypts per animal were scored. Data were analyzed by the Kruskal-Wallis test followed by the Dunn test. There was an increase in MTEC index in the groups either infected with T. cruzi or treated with nimesulide or both infected and treated when compared to control (401, 809, and 1011%, respectively). We suggest that the increased formation of MTEC may be related to the protection against carcinogenesis provided both by T. cruzi infection and nimesulide.

Aberrant signaling in T-cell acute lymphoblastic leukemia: biological and therapeutic implications

T-cell acute lymphoblastic leukemia (T-ALL) is a biologically heterogeneous disease with respect to phenotype, gene expression profile and activation of particular intracellular signaling pathways. Despite very significant improvements, current therapeutic regimens still fail to cure a portion of the patients and frequently implicate the use of aggressive protocols with long-term side effects. In this review, we focused on how deregulation of critical signaling pathways, in particular Notch, PI3K/Akt, MAPK, Jak/STAT and TGF-ß, may contribute to T-ALL. Identifying the alterations that affect intracellular pathways that regulate cell cycle and apoptosis is essential to understanding the biology of this malignancy, to define more effective markers for the correct stratification of patients into appropriate therapeutic regimens and to identify novel targets for the development of specific, less detrimental therapies for T-ALL.