gcMECM: graph clustering of mutual exclusivity of cancer mutations

Background Next-generation sequencing platforms allow us to sequence millions of small fragments of DNA simultaneously, revolutionizing cancer research. Sequence analysis has revealed that cancer driver genes operate across multiple intricate pathways and networks with mutations often occurring in a mutually exclusive pattern. Currently, low-frequency mutations are understudied as cancer-relevant genes, especially in the context of networks. Results Here we describe a tool, gcMECM, that enables us to visualize the functionality of mutually exclusive genes in the subnetworks derived from mutation associations, gene–gene interactions, and graph clustering. These subnetworks have revealed crucial biological components in the canonical pathway, especially those mutated at low frequency. Examining the subnetwork, and not just the impact of a single gene, significantly increases the statistical power of clinical analysis and enables us to build models to better predict how and why cancer develops. Conclusions gcMECM uses a computationally efficient and scalable algorithm to identify subnetworks in a canonical pathway with mutually exclusive mutation patterns and distinct biological functions.

Cytosolic Sensor of Bacterial Lipopolysaccharide in Human Macrophages

Inflammasomes are cytosolic supramolecular organizing centers that, in response to pathogen-derived molecules and endogenous danger signals, assemble and activate innate immune responses. Bacterial lipopolysaccharide (LPS) is an inflammasome trigger and a major mediator of inflammation during infection, including during the potentially lethal condition sepsis. Activation of most inflammasomes is triggered by sensing of pathogen products by a specific host cytosolic nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing protein (NLRP) or other sensor protein that in turn activates a pro-inflammatory caspase. LPS that accesses the cell cytosol (cLPS) induces cell-autonomous activation of a non-canonical inflammasome that contains caspases-4/5 in humans or caspase-11 in mice1-3. Whereas the NLRPs that sense most pathogen triggers have been identified, no NLRP is known to sense cLPS, which together with the observation that caspases-4, -5, and -11 bind LPS in vitro4, has led to the postulate that inflammasome activation by cLPS occurs independent of an NLRP. Here we show that primate-specific NLRP11 senses cLPS and promotes the activation of caspase-4. We found that in response to infection by each of several gram-negative intracellular bacterial pathogens or to LPS transfection, efficient activation of the non-canonical pathway in human-derived macrophages depends on NLRP11. Further, we found that in both immortalized human-derived macrophages and primary human macrophages, the dependence of the non-canonical pathway on NLRP11 is due to detection of cLPS. Moreover, in cell lysates, NLRP11 binds LPS independently of caspase-4 and binds caspase-4 independently of LPS. Our results demonstrate that NLRP11 senses cLPS and promotes LPS-dependent activation of caspase-4. NLRP11 is a previously missing link in the human non-canonical inflammasome activation pathway.

A pro-resolving phenotype underpins the anti-inflammatory effects of inorganic nitrate

Introduction Increasing evidence highlights the critical role of chronic inflammation in cardiovascular disease (CVD). Targeting inflammatory pathways in patients with CVD has been associated with improved CV function in pre-clinical (Gee, 2017), early clinical (Yndestad, 2006; Velmurugan 2013; Jones, 2016) and large phase III studies (Ridker, 2017). The resolution of inflammation is an active process and its failure has also been proposed to contribute to CVD progression. At least one mechanism thought to underlie this failure is dysfunction of the canonical pathway for anti-inflammatory nitric oxide (NO) production. Restoring NO through provision of inorganic nitrate (NO3-) and subsequent bioactivation via the non-canonical pathway may offer therapeutic benefit. Aim To test whether dietary NO3–derived NO accelerates resolution of inflammation. Methods Randomised, double-blind, placebo-controlled, parallel limb study of 8–10mmol dietary NO3- supplementation versus NO3–deplete placebo beetroot juice in 36 healthy male volunteers (NCT03183830). Using a cantharadin-induced skin blister model (Day, 2001), acute (24h) and chronic (72h)-phase blisters were harvested pre- and post-treatment. Blister exudate was analysed for leucocyte activation state (CD11b, CD62L, CD162) by flow cytometry and cytokine/chemokine composition by ELISA. Ozone chemiluminescence established NO3-/NO2- levels in key biological matrices: plasma, urine and saliva. Results 9.3mmol inorganic NO3- led to a significant rise (versus placebo, p<0.001) of NO3-/NO2- in plasma, saliva and urine NO2- (p<0.02). No differences were seen in blister volumes, cell counts or markers of systemic inflammation. Whilst no differences were seen in the proportions of cellular infiltrate in 24h blisters, there were significant reductions of neutrophil (p=0.017) and intermediate monocyte proportions (p=0.001) and cellular adhesion molecules across inflammatory, intermediate and resolving monocytes at 72h (Figure 1). Generally, no differences in blister cytokine/chemokine profile was evident except for borderline significant suppression of TNFα at 24hrs with dietary NO3- treatment (P=0.057). Conclusion Whilst dietary inorganic NO3- does not impair the essential host defence response it does accelerate resolution: enhanced pro- to anti-inflammatory monocyte subtype switching and curtailed neutrophil recruitment, likely via attenuated TNFα production. These actions offer a novel, easy to administer, approach to influence inflammatory responses without impairing host defence. FUNDunding Acknowledgement Type of funding sources: Public Institution(s). Main funding source(s): Derek Willoughby Trust and British Heart Foundation

A Novel Model for the RNase MRP-Induced Switch between the Formation of Different Forms of 5.8S rRNA

Processing of the RNA polymerase I pre-rRNA transcript into the mature 18S, 5.8S, and 25S rRNAs requires removing the “spacer” sequences. The canonical pathway for the removal of the ITS1 spacer involves cleavages at the 3′ end of 18S rRNA and at two sites inside ITS1. The process can generate either a long or a short 5.8S rRNA that differs in the number of ITS1 nucleotides retained at the 5.8S 5′ end. Here we document a novel pathway to the long 5.8S, which bypasses cleavage within ITS1. Instead, the entire ITS1 is degraded from its 5′ end by exonuclease Xrn1. Mutations in RNase MRP increase the accumulation of long relative to short 5.8S rRNA. Traditionally this is attributed to a decreased rate of RNase MRP cleavage at its target in ITS1, called A3. However, results from this work show that the MRP-induced switch between long and short 5.8S rRNA formation occurs even when the A3 site is deleted. Based on this and our published data, we propose that the link between RNase MRP and 5.8S 5′ end formation involves RNase MRP cleavage at unknown sites elsewhere in pre-rRNA or in RNA molecules other than pre-rRNA.

MUC16 Is Overexpressed in Idiopathic Pulmonary Fibrosis and Induces Fibrotic Responses Mediated by Transforming Growth Factor-β1 Canonical Pathway

Several transmembrane mucins have demonstrated that they contribute intracellularly to induce fibrotic processes. The extracellular domain of MUC16 is considered as a biomarker for disease progression and death in IPF patients. However, there is no evidence regarding the signalling capabilities of MUC16 that contribute to IPF development. Here, we demonstrate that MUC16 was overexpressed in the lung tissue of IPF patients (n = 20) compared with healthy subjects (n = 17) and localised in fibroblasts and hyperplastic alveolar type II cells. Repression of MUC16 expression by siRNA-MUC16 transfection inhibited the TGF-β1-induced fibrotic processes such as mesenchymal/ myofibroblast transformations of alveolar type II A549 cells and lung fibroblasts, as well as fibroblast proliferation. SiRNA-MUC16 transfection also decreased the TGF-β1-induced SMAD3 phosphorylation, thus inhibiting the Smad Binding Element activation. Immunoprecipitation assays and confocal immunofluorescence showed the formation of a protein complex between MUC16/p-SMAD3 in the cell membrane after TGF-β1 stimulation. This study shows that MUC16 is overexpressed in IPF and collaborates with the TGF-β1 canonical pathway to induce fibrotic processes. Therefore, direct or indirect targeting of MUC16 could be a potential drug target for human IPF.

Cerebral Pericytes and Endothelial Cells Communicate through Inflammasome-Dependent Signals

By upregulation of cell adhesion molecules and secretion of proinflammatory cytokines, cells of the neurovascular unit, including pericytes and endothelial cells, actively participate in neuroinflammatory reactions. As previously shown, both cell types can activate inflammasomes, cerebral endothelial cells (CECs) through the canonical pathway, while pericytes only through the noncanonical pathway. Using complex in vitro models, we demonstrate here that the noncanonical inflammasome pathway can be induced in CECs as well, leading to a further increase in the secretion of active interleukin-1β over that observed in response to activation of the canonical pathway. In parallel, a more pronounced disruption of tight junctions takes place. We also show that CECs respond to inflammatory stimuli coming from both the apical/blood and the basolateral/brain directions. As a result, CECs can detect factors secreted by pericytes in which the noncanonical inflammasome pathway is activated and respond with inflammatory activation and impairment of the barrier properties. In addition, upon sensing inflammatory signals, CECs release inflammatory factors toward both the blood and the brain sides. Consequently, CECs activate pericytes by upregulating their expression of NLRP3 (NOD-, LRR-, and pyrin domain-containing protein 3), an inflammasome-forming pattern recognition receptor. In conclusion, cerebral pericytes and endothelial cells mutually activate each other in inflammation.

Significance of the Wnt canonical pathway in radiotoxicity via oxidative stress of electron beam radiation and its molecular control in mice

Radiation triggers the cell death events through signaling proteins, but the combined mechanism of events is unexplored. We intend to investigate how the combined cascade works throughout the radiation process and its significance over radiotoxicity. Thirty adult mice were irradiated with electron beam radiation, and five were served as a control (Non treated). Mice were sacrificed after post 24 hours and 30 days of irradiation. We assessed the oxidative stress parameter and mRNA profile (Liver, Kidney, spleen, and germ cells), sperm viability, and motility. The mRNA profile study established the network of combined cascade work during radiation to combat oxidative response and cell survival. The quantitative examination of mRNA uncovers unique critical changes in all mRNA levels in all the cases, particularly in germ cells. Recuperation was likewise seen in post 30 days radiation in the liver, spleen, and kidney followed by oxidative stress parameters, however not in germ cells. It proposes reproductive physiology is exceptionally sensitive towards radiation, even at the molecular level. It also suggests the suppression of Lef1/axin2 could be the main reason for permanent failure in the sperm function process. Post irradiation likewise influences the morphology of sperms. The decrease in mRNA level of Lef1, Axin2, survivin, Ku70 suggests radiation inhibits the Wnt canonical pathway and failure in DNA repair mechanism in a coupled manner. Likewise, the increase in BAX and BCL2 suggests apoptosis activation followed by the decreased expression of enzymatic antioxidants. In summary, controlled several interlinked cascades execute when body exposure to radiation may further be used in a study to counterpart and better comprehend medication focus on radiation treatment.

Loss of EGFR Mutation Expression Induced by NF1 Mutation in Non-Small Cell Lung Cancer: Non-Canonical Pathway of Tyrosine Kinase Inhibitors’ Resistance

Non-small cell lung carcinoma (NSCLC) is considered the first cause of cancer-related death worldwide and many therapies have been developed against the presence of actionable mutations. For example, targeting the EGFR mutation has changed the overall prognosis in NSCLC. However, resistance to treatment has emerged and many canonical mechanisms have already been described. NF1 mutation causes partial or total loss of function of neurofibromin, which activates several intracellular pathways (MAPK / ERK, PI3K / AKT, TGF -β / Smad), producing cellular proliferation, migration, apoptosis resistance and genetic instability, leading to loss of EGFR expression. Herein, we describe a case of a novel activation of a non-canonical pathway that led to treatment resistance by NF1 mutation.