The results of mutational profiling of 287 patients with gastrointestinal cancer are presented, identifying for the first time IDH1 mutations in a significant subset of patients with intrahepatic cholangiocarcinoma.
Cancers of origin in the gallbladder and bile ducts are rarely curable with current modalities of cancer treatment. Our clinical application of broad-based mutational profiling for patients diagnosed with a gastrointestinal malignancy has led to the novel discovery of mutations in the gene encoding isocitrate dehydrogenase 1 (IDH1) in tumors from a subset of patients with cholangiocarcinoma. A total of 287 tumors from gastrointestinal cancer patients (biliary tract, colorectal, gastroesophageal, liver, pancreatic, and small intestine carcinoma) were tested during routine clinical evaluation for 130 site-specific mutations within 15 cancer genes. Mutations were identified within a number of genes, including KRAS (35%), TP53 (22%), PIK3CA (10%), BRAF (7%), APC (6%), NRAS (3%), AKT1 (1%), CTNNB1 (1%), and PTEN (1%). Although mutations in the metabolic enzyme IDH1 were rare in the other common gastrointestinal malignancies in this series (2%), they were found in three tumors (25%) of an initial series of 12 biliary tract carcinomas. To better define IDH1 and IDH2 mutational status, an additional 75 gallbladder and bile duct cancers were examined. Combining these cohorts of biliary cancers, mutations in IDH1 and IDH2 were found only in cholangiocarcinomas of intrahepatic origin (nine of 40, 23%) and in none of the 22 extrahepatic cholangiocarcinomas and none of the 25 gallbladder carcinomas. In an analysis of frozen tissue specimens, IDH1 mutation was associated with highly elevated tissue levels of the enzymatic product 2-hydroxyglutarate. Thus, IDH1 mutation is a molecular feature of cholangiocarcinomas of intrahepatic origin. These findings define a specific metabolic abnormality in this largely incurable type of gastrointestinal cancer and present a potentially new target for therapy.
Biliary tract cancer; Cholangiocarcinoma; IDH1; IDH2; 2-Hydroxyglutarate; Mutation
Mammalian microRNAs (miRNAs) pair to 3'UTRs of mRNAs to direct their posttranscriptional repression. Important for target recognition are ~7-nt sites that match the seed region of the miRNA. However, these seed matches are not always sufficient for repression, indicating that other characteristics help specify targeting. By combining computational and experimental approaches, we uncovered five general features of site context that boost site efficacy: AU-rich nucleotide composition near the site, proximity to sites for co-expressed miRNAs (which leads to cooperative action), proximity to residues pairing to miRNA nucleotides 13–16, and positioning within the 3'UTR at least 15 nt from the stop codon and away from the center of long UTRs. A model combining these context determinants quantitatively predicts site performance both for exogenously added miRNAs and for endogenous miRNA-message interactions. Because it predicts site efficacy without recourse to evolutionary conservation, the model also identifies effective nonconserved sites and siRNA off-targets.
Despite the general consensus that synaesthesia emerges at an early developmental stage and is only rarely acquired during adulthood, the transient induction of synaesthesia with chemical agents has been frequently reported in research on different psychoactive substances. Nevertheless, these effects remain poorly understood and have not been systematically incorporated. Here we review the known published studies in which chemical agents were observed to elicit synaesthesia. Across studies there is consistent evidence that serotonin agonists elicit transient experiences of synaesthesia. Despite convergent results across studies, studies investigating the induction of synaesthesia with chemical agents have numerous methodological limitations and little experimental research has been conducted. Cumulatively, these studies implicate the serotonergic system in synaesthesia and have implications for the neurochemical mechanisms underlying this phenomenon but methodological limitations in this research area preclude making firm conclusions regarding whether chemical agents can induce genuine synaesthesia.
drugs; serotonin; synaesthesia
Background. The degree of cross-immunity between human papillomavirus (HPV) types is fundamental both to the epidemiological dynamics of HPV and to the impact of HPV vaccination. Epidemiological data on HPV infections has been repeatedly interpreted as inconsistent with cross-immunity.
Methods. We reevaluate the epidemiological data using a model to determine the odds ratios of multiple to single infections expected in the presence or absence of cross-immunity. We simulate a virtual longitudinal survey to determine the effect cross-immunity has on the prevalence of multiple infections. We calibrate our model to epidemiological data and estimate the extent of type replacement following vaccination against specific HPV types.
Results. We find that cross-immunity can produce odds ratios of infection comparable with epidemiological observations. We show that the sample sizes underlying existing surveys have been insufficient to identify even intense cross-immunity. We also find that the removal of HPV type 16, type 18, and types 6 and 11 would increase the prevalence of nontargeted types by 50%, 29%, and 183%, respectively.
Conclusions. Cross-immunity between HPV types is consistent with epidemiological data, contrary to previous interpretations. Cross-immunity may cause significant type replacement following vaccination, and therefore should be considered in future vaccine studies and epidemiological models.
A new immuno-TRAP technique overcomes limitations of spatial resolution and selection bias to identify gene locus associations with a nuclear subcompartment such as promyelocytic leukemia nuclear bodies.
Important insights into nuclear function would arise if gene loci physically interacting with particular subnuclear domains could be readily identified. Immunofluorescence microscopy combined with fluorescence in situ hybridization (immuno-FISH), the method that would typically be used in such a study, is limited by spatial resolution and requires prior assumptions for selecting genes to probe. Our new technique, immuno-TRAP, overcomes these limitations. Using promyelocytic leukemia nuclear bodies (PML NBs) as a model, we used immuno-TRAP to determine if specific genes localize within molecular dimensions with these bodies. Although we confirmed a TP53 gene–PML NB association, immuno-TRAP allowed us to uncover novel locus-PML NB associations, including the ABCA7 and TFF1 loci and, most surprisingly, the PML locus itself. These associations were cell type specific and reflected the cell’s physiological state. Combined with microarrays or deep sequencing, immuno-TRAP provides powerful opportunities for identifying gene locus associations with potentially any nuclear subcompartment.
MicroRNAs (miRNAs) are endogenous ~23-nt RNAs that can play important gene-regulatory roles in animals and plants by pairing to the mRNAs of protein-coding genes to direct their posttranscriptional repression. This review outlines the current understanding of miRNA target recognition in animals and discusses the widespread impact of miRNAs on both the expression and evolution of protein-coding genes.
When chromosomal DNA is damaged, progression through the cell cycle is halted to provide the cells with time to repair the genetic material before it is distributed between the mother and daughter cells. In Saccharomyces cerevisiae, this cell cycle arrest occurs at the G2/M transition. However, it is also necessary to restrain exit from mitosis by maintaining Bfa1-Bub2, the inhibitor of the Mitotic Exit Network (MEN), in an active state. While the role of Bfa1 and Bub2 in the inhibition of mitotic exit when the spindle is not properly aligned and the spindle position checkpoint is activated has been extensively studied, the mechanism by which these proteins prevent MEN function after DNA damage is still unclear. Here, we propose that the inhibition of the MEN is specifically required when telomeres are damaged but it is not necessary to face all types of chromosomal DNA damage, which is in agreement with previous data in mammals suggesting the existence of a putative telomere-specific DNA damage response that inhibits mitotic exit. Furthermore, we demonstrate that the mechanism of MEN inhibition when telomeres are damaged relies on the Rad53-dependent inhibition of Bfa1 phosphorylation by the Polo-like kinase Cdc5, establishing a new key role of this kinase in regulating cell cycle progression.
A key aspect of the division of cells is that the genomic material must be carefully duplicated, protected from damage, and correctly distributed during this process. When the cells detect problems that affect the integrity or the proper distribution of the genome, they trigger different surveillance mechanisms to stop the division process until the problem is fixed. The functionality of some of these surveillance mechanisms depends on the inhibition of the final stages of cell division, a process known as mitotic exit. This is the case for the DNA damage checkpoint (DDC), which is triggered by chromosomal DNA damage. Here, we propose that the inhibition of mitotic exit is specifically required by the DDC only when the telomeres (the chromosomal ends) are damaged. Additionally, we have demonstrated that the DDC blocks mitotic exit by inhibiting the key cell cycle regulator Cdc5, which triggers the inactivation of Bfa1 and Bub2, two negative regulators of the mitotic exit process.
Mutations in the central region of the signalling hub Adenomatous Polyposis Coli (APC) cause colorectal tumourigenesis. The structure of this region remained unknown. Here, we characterise the Mutation Cluster Region in APC (APC-MCR) as intrinsically disordered and propose a model how this structural feature may contribute to regulation of Wnt signalling by phosphorylation. APC-MCR was susceptible to proteolysis, lacked α-helical secondary structure and did not display thermal unfolding transition. It displayed an extended conformation in size exclusion chromatography and was accessible for phosphorylation by CK1ε in vitro. The length of disordered regions in APC increases with species complexity, from C. elegans to H. sapiens. We speculate that the large disordered region harbouring phosphorylation sites could be a successful strategy to stabilise tight regulation of Wnt signalling against single missense mutations.
The RNA interference (RNAi) pathway is found in most eukaryotic lineages but curiously is absent in others, including that of Saccharomyces cerevisiae. Here, we show that reconstituting RNAi in S. cerevisiae causes loss of a beneficial dsRNA virus, known as killer virus. Incompatibility between RNAi and killer viruses extends to other fungal species, in that RNAi is absent in all species known to possess dsRNA killer viruses, whereas killer viruses are absent in closely related species that retained RNAi. Thus, the advantage imparted by acquiring and retaining killer viruses explains the persistence of RNAi-deficient species during fungal evolution.
Sexual concurrency poses significant HIV/STI transmission risk. The correlates of concurrency have not been examined among homeless men. A representative sample of 305 heterosexually active homeless men utilizing meal programs in the Skid Row area of Los Angeles reported on their mental health, substance use, and social network characteristics. Nearly 40% of men reported concurrency with one of their four most recent sex partners. Results indicated that HIV seropositivity (OR = 4.39, CI: 1.10, 17.46; p = 0.04), PTSD (OR = 2.29, CI: 1.05, 5.01; p = 0.04), hard drug use (OR = 2.45, CI: 1.07, 5.58; p = 0.03), and the perception that network alters engage in risky sex (OR = 3.72, CI: 1.49, 9.30; p = 0.01) were associated with increased odds of concurrency. Programs aimed at reducing HIV/STI transmission in this vulnerable population must take into account the roles that behavioral health and social networks may play in sexual concurrency.
Stress during the prenatal and early postnatal periods (perinatal stress, PS) is known to impact offspring cognitive, behavioral, and physical development, but effects on skeletal growth are not clear. Our objective was to analyze effects of variable, mild, daily PS exposure on adult offspring long bone length.
Twelve pregnant rat dams were randomly assigned to receive variable stress from gestational days 14-21 (Prenatal group), postpartum days 2-9 (Postnatal), both periods (Pre-Post), or no stress (Control). Differences in adult offspring tibia and femur length were analyzed among treatment groups.
Mean tibia length differed among groups for males (p=0.016) and females (p=0.009), and differences for femur length approached significance for males (p=0.051). Long bone length was shorter among PS-exposed offspring, especially those exposed to postnatal stress (Postnatal and Pre-Post groups). Results persisted when controlling for nose-tail length. These differences might reflect early stunting that is maintained in adulthood, or delayed growth among PS-exposed offspring.
This study suggests that PS results in shorter long bones in adulthood, independently of effects on overall body size. Stunting and growth retardation are major global health burdens. Our study adds to a growing body of evidence suggesting that PS is a risk factor for poor linear growth.
perinatal stress; pregnancy; skeletal growth; programming
Sorafenib is a raf kinase and angiogenesis inhibitor with activity in multiple cancers. This phase II study in heavily pretreated non-small cell lung cancer (NSCLC) patients (≥ two prior therapies) utilized a randomized discontinuation design.
Patients received 400 mg of sorafenib orally twice daily for two cycles (two months) (Step 1). Responding patients on Step 1 continued on sorafenib; progressing patients went off study, and patients with stable disease were randomized to placebo or sorafenib (Step 2), with crossover from placebo allowed upon progression. The primary endpoint of this study was the proportion of patients having stable or responding disease two months after randomization.
: There were 299 patients evaluated for Step 1 with 81 eligible patients randomized on Step 2 who received sorafenib (n=50) or placebo (n=31). The two-month disease control rates following randomization were 54% and 23% for patients initially receiving sorafenib and placebo respectively, p=0.005. The hazard ratio for progression on Step 2 was 0.51 (95% CI 0.30, 0.87, p=0.014) favoring sorafenib. A trend in favor of overall survival with sorafenib was also observed (13.7 versus 9.0 months from time of randomization), HR 0.67 (95% CI 0.40-1.11), p=0.117. A dispensing error occurred which resulted in unblinding of some patients, but not before completion of the 8 week initial step 2 therapy. Toxicities were manageable and as expected.
: The results of this randomized discontinuation trial suggest that sorafenib has single agent activity in a heavily pretreated, enriched patient population with advanced NSCLC. These results support further investigation with sorafenib as a single agent in larger, randomized studies in NSCLC.
NSCLC; sorafenib; randomized discontinuation trial
Chronic kidney disease (CKD) is histologically characterized by interstitial fibrosis, which may be driven by peritubular capillary dropout and hypoxia. Surprisingly, peritubular capillaries have little repair capacity. We sought to establish long-term cultures of rat kidney endothelial cells to investigate their growth regulatory properties.
Kidney endothelial cells from adult rats (AKEC) or young rats (YKEC) were isolated using CD31 based isolation techniques and sustained in long-term cultures.
Although YKEC grew slightly better than AKEC, both performed poorly compared to endothelial cells of the rat adult pulmonary microvasculature (PMVEC), pulmonary artery (PAEC), or HUVEC cells. PMVEC and PAEC contained a large percentage of cells with high colony forming potential. By contrast, KECs were incapable of forming large colonies and most remained as single non-dividing cells. KEC expressed high levels of mRNA for VEGF receptors but were surprisingly insensitive to VEGF stimulation. KECs did not form branching structures on Matrigel when cultured alone, but in mixed cultures KECs incorporated into branching structures with PMVECs.
These data suggest that the intrinsic growth of rat kidney endothelial cells is limited by unknown mechanisms. The low growth rate may relate to the minimal intrinsic regenerative capacity of renal capillaries.
angiogenesis; progenitor; hypoxia; CKD
This study explores physical effects associated with the application of cryopreservation via vitrification using a class of compounds which are defined here as synthetic ice modulators (SIMs). The general classification of SIMs includes molecules that modulate ice nucleation and growth, or possess properties of stabilizing the amorphous state, by virtue of their chemical structure and at concentrations that are not explained on a purely colligative basis. A subcategory of SIMs, referred to in the literature as synthetic ice blockers (SIBs), are compounds that interact directly with ice nuclei or crystals to modify their structure and/or rate of growth. The current study is part of an ongoing effort to characterize thermo-mechanical effects during vitrification, with emphasis on measuring the physical property of thermal expansion—the driving mechanism to thermo-mechanical stress. Materials under investigation are the cryoprotective agent (CPA) cocktail DP6 in combination with one of the following SIMs: 12% polyethylene glycol 400, 6% 1,3 cyclohexanediol, and 6% 2,3 butanediol. Results are presented for the CPA-SIM cocktail in the absence and presence of bovine muscle and goat artery specimens. This study focuses on the upper part of the cryogenic temperature range, where the CPA behaves as a fluid for all practical applications. Results of this study indicate that the addition of SIMs to DP6 allows lower cooling rates to ensure vitrification and extends the range of measurements. It is demonstrated that the combination of SIM with DP6 increases the thermal expansion of the cocktail, with implications for the likelihood of fracture formation—the most dramatic outcome of thermo-mechanical stress.
Thermal Expansion; Solid Mechanics; Vitrification; Synthetic Ice Blockers; Synthetic Ice Modulators
P-873 is a novel compound in the RX-04 pyrrolocytosine series of protein synthesis inhibitors currently under development by Rib-X Pharmaceuticals. We evaluated the pharmacodynamic and pharmacokinetic properties of this compound against Klebsiella pneumoniae using a murine neutropenic thigh infection model. P-873 demonstrated potent and rapid in vivo activity against this organism with enhanced penetration and duration of exposure in thigh tissue.
The eosinophil is a multifunctional granulocyte best known for providing host defense against parasites. Paradoxically, eosinophils are also implicated in the pathogenesis of allergic inflammation, asthma, and hypereosinophilic syndromes. Emerging evidence also supports the potential for harnessing the cytotoxic power of eosinophils and redirecting it to kill solid tumors. Central to eosinophil physiology is interleukin-5 (IL-5) and its receptor (IL-5R) which is composed of a ligand-specific alpha chain (IL-5Rα) and the common beta chain (βc). Eosinophil activation can lead to their degranulation, resulting in rapid release of an arsenal of tissue-destructive proinflammatory mediators and cytotoxic proteins that can be both beneficial and detrimental to the host. This review discusses eosinophil immunobiology and therapeutic strategies for targeting of IL-5 and IL-5R, as well as the potential for harnessing eosinophil cytotoxicity as a tumoricide.
Eosinophil; Interleukin-5 (IL-5); IL-5 receptor (IL-5R); Anti-IL-5 antibodies; Anti-IL-5R antibodies; Allergic inflammation; Asthma; Eosinophilic syndromes; Cancer; Therapeutic; Treatment; Hypereosinophilic disorders
Cognitive-behavioural therapy (CBT) has proven to be effective for anxiety-based school refusal, but it is still unknown how CBT for school refusal works, or through which mechanisms.
Innovative statistical approaches for analyzing small uncontrolled samples were used to investigate the role of self-efficacy in mediating CBT outcomes for anxiety-based school refusal.
Participants were 19 adolescents (12 to 17 years) who completed a manual-based cognitive-behavioural treatment. Primary outcomes (school attendance; school-related fear; anxiety) and secondary outcomes (depression; internalizing problems) were assessed at post-treatment and 2-month follow-up.
Post-treatment increases in school attendance and decreases in fear about attending school the next day were found to be mediated by self-efficacy. Mediating effects were not observed at 2-month follow-up.
These findings provide partial support for the role of self-efficacy in mediating the outcome of CBT for school refusal. They contribute to a small body of literature suggesting that cognitive change enhances CBT outcomes for young people with internalizing problems. Regarding methodology, the product of coefficient test appears to be a valuable way to study mediation in outcome studies involving small samples.
CBT; mediators; school refusal; anxiety; self-efficacy