Gene fusions involving neuregulin 1 (
) have been noted in multiple cancer types and have potential therapeutic implications. Although varying results have been reported in other cancer types, the ...efficacy of the HER-family kinase inhibitor afatinib in the treatment of
fusion-positive pancreatic ductal adenocarcinoma is not fully understood.
Forty-seven patients with pancreatic ductal adenocarcinoma received comprehensive whole-genome and transcriptome sequencing and analysis. Two patients with gene fusions involving
received afatinib treatment, with response measured by pretreatment and posttreatment PET/CT imaging.
Three of 47 (6%) patients with advanced pancreatic ductal adenocarcinoma were identified as
wild type by whole-genome sequencing. All
wild-type tumors were positive for gene fusions involving the ERBB3 ligand
. Two of 3 patients with
fusion-positive tumors were treated with afatinib and demonstrated a significant and rapid response while on therapy.
This work adds to a growing body of evidence that
gene fusions are recurrent, therapeutically actionable genomic events in pancreatic cancers. Based on the clinical outcomes described here, patients with
wild-type tumors harboring
gene fusions may benefit from treatment with afatinib.
.
Plant specialized metabolism (SM) enzymes produce lineage-specific metabolites with important ecological, evolutionary, and biotechnological implications. Using Arabidopsis thaliana as a model, we ...identified distinguishing characteristics of SM and GM (general metabolism, traditionally referred to as primary metabolism) genes through a detailed study of features including duplication pattern, sequence conservation, transcription, protein domain content, and gene network properties. Analysis of multiple sets of benchmark genes revealed that SM genes tend to be tandemly duplicated, coexpressed with their paralogs, narrowly expressed at lower levels, less conserved, and less well connected in gene networks relative to GM genes. Although the values of each of these features significantly differed between SM and GM genes, any single feature was ineffective at predicting SM from GM genes. Using machine learning methods to integrate all features, a prediction model was established with a true positive rate of 87% and a true negative rate of 71%. In addition, 86% of known SM genes not used to create the machine learning model were predicted. We also demonstrated that the model could be further improved when we distinguished between SM, GM, and junction genes responsible for reactions shared by SM and GM pathways, indicating that topological considerations may further improve the SM prediction model. Application of the prediction model led to the identification of 1,220 A. thaliana genes with previously unknown functions, each assigned a confidence measure called an SM score, providing a global estimate of SM gene content in a plant genome.
Targeted mutant models are common in mechanistic toxicology experiments investigating the absorption, metabolism, distribution, or elimination (ADME) of chemicals from individuals. Key models include ...those for xenosensing transcription factors and cytochrome P450s (CYP). Here we investigated changes in transcript levels, protein expression, and steroid hydroxylation of several xenobiotic detoxifying CYPs in constitutive androstane receptor (CAR)-null and two CYP-null mouse models that have subfamily members regulated by CAR; the Cyp3a-null and a newly described Cyp2b9/10/13-null mouse model. Compensatory changes in CYP expression that occur in these models may also occur in polymorphic humans, or may complicate interpretation of ADME studies performed using these models. The loss of CAR causes significant changes in several CYPs probably due to loss of CAR-mediated constitutive regulation of these CYPs. Expression and activity changes include significant repression of Cyp2a and Cyp2b members with corresponding drops in 6α- and 16β-testosterone hydroxylase activity. Further, the ratio of 6α-/15α-hydroxylase activity, a biomarker of sexual dimorphism in the liver, indicates masculinization of female CAR-null mice, suggesting a role for CAR in the regulation of sexually dimorphic liver CYP profiles. The loss of Cyp3a causes fewer changes than CAR. Nevertheless, there are compensatory changes including gender-specific increases in Cyp2a and Cyp2b. Cyp2a and Cyp2b were down-regulated in CAR-null mice, suggesting activation of CAR and potentially PXR following loss of the Cyp3a members. However, the loss of Cyp2b causes few changes in hepatic CYP transcript levels and almost no significant compensatory changes in protein expression or activity with the possible exception of 6α-hydroxylase activity. This lack of a compensatory response in the Cyp2b9/10/13-null mice is probably due to low CYP2B hepatic expression, especially in male mice. Overall, compensatory and regulatory CYP changes followed the order CAR-null > Cyp3a-null > Cyp2b-null mice.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Multiple preventive vaccines are being developed to counter the coronavirus disease 2019 pandemic. The leading candidates have now been evaluated in nonhuman primates (NHPs) and human phase 1 and/or ...phase 2 clinical trials. Several vaccines have already advanced into phase 3 efficacy trials, while others will do so before the end of 2020. Here, we summarize what is known of the antibody and T cell immunogenicity of these vaccines in NHPs and humans. To the extent possible, we compare how the vaccines have performed, taking into account the use of different assays to assess immunogenicity and inconsistencies in how the resulting data are presented. We also review the outcome of challenge experiments with severe acute respiratory syndrome coronavirus 2 in immunized macaques, while noting variations in the protocols used, including but not limited to the virus challenge doses. Press releases on the outcomes of vaccine efficacy trials are also summarized.
We compare the antigenicity and conformation of soluble, cleaved vs. uncleaved envelope glycoprotein (Env gp)140 trimers from the subtype A HIV type 1 (HIV-1) strain BG505. The impact of gp120–gp41 ...cleavage on trimer structure, in the presence or absence of trimer-stabilizing modifications (i.e., a gp120–gp41 disulfide bond and an I559P gp41 change, together designated SOSIP), was assessed. Without SOSIP changes, cleaved trimers disintegrate into their gp120 and gp41-ectodomain (gp41 ECTO) components; when only the disulfide bond is present, they dissociate into gp140 monomers. Uncleaved gp140s remain trimeric whether SOSIP substitutions are present or not. However, negative-stain electron microscopy reveals that only cleaved trimers form homogeneous structures resembling native Env spikes on virus particles. In contrast, uncleaved trimers are highly heterogeneous, adopting a variety of irregular shapes, many of which appear to be gp120 subunits dangling from a central core that is presumably a trimeric form of gp41 ECTO. Antigenicity studies with neutralizing and nonneutralizing antibodies are consistent with the EM images; cleaved, SOSIP-stabilized trimers express quaternary structure-dependent epitopes, whereas uncleaved trimers expose nonneutralizing gp120 and gp41 ECTO epitopes that are occluded on cleaved trimers. These findings have adverse implications for using soluble, uncleaved trimers for structural studies, and the rationale for testing uncleaved trimers as vaccine candidates also needs to be reevaluated.
The identification of multiple broadly neutralizing antibodies (bNAbs) against the HIV-1 envelope glycoprotein (Env) trimer has facilitated its structural characterization and guided Env immunogen ...design. Several recent studies constitute progress in utilizing this knowledge for the development of an HIV-1 vaccine that induces bNAbs. Native-like Env trimers can induce autologous NAb responses against resistant (Tier-2) viruses in several animal models. Here we review recent studies aimed at addressing the challenge of driving the strong but narrowly focused NAb responses to Env trimers towards ones with much greater breadth. Among strategies that merit pursuing are using multiple trimers as sequential or simultaneous immunogens, targeting the germline precursors of bNAbs, delivering sequential lineages of trimers derived from infected individuals who developed bNAbs, and presenting trimers as particulate antigens.
An activity-guided fractionation approach applied to thermally treated, enzymatically hydrolyzed mushroom, Agaricus bisporus L., protein led to the identification of several saltiness- and ...kokumi-enhancing peptides. The identification was accomplished by employing a combination of solid-phase extraction (SPE), gel-permeation chromatography (GPC), and semipreparative reverse-phase high-performance liquid chromatography (RP-HPLC), coupled with sensory analysis. As a result, this study led to the identification of a collection of common mushroom derived tastants, including 5′-mononucleotides and free amino acids, along with several taste-modulating pyroglutamyl dipeptides, including pyroglutamylcysteine (pGlu-Cys), pyroglutamylvaline (pGlu-Val), pyroglutamylaspartic acid (pGlu-Asp), pyroglutamylglutamic acid (pGlu-Glu), and pyroglutamylproline (pGlu-Pro). The taste-modulating thresholds for the pyroglutamyl dipeptides were calculated in a model mushroom broth containing natural concentrations of guanosine 5′-monophosphate and 14 amino acids, all with dose-over-threshold (DoT) factors ≥1. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was employed to quantitate the pyroglutamyl dipeptides, and their concentrations ranged from 2 to 58 μmol/L; however, they were determined to be present in the hydrolysate below their individual taste-modulating thresholds. Despite being present below their individual thresholds, when the dipeptides were collectively added to a model mushroom broth at their natural concentrations (143 μmol/L combined), both salty (p = 0.0061) and kokumi (p = 0.0025) taste attributes were significantly enhanced, demonstrating a synergistic subthreshold taste-modulating effect. This study lays the groundwork for future investigations on the saltiness-enhancing potential of mixtures of subthreshold levels of pyroglutamyl dipeptides found in mushrooms and other sources.
Regulation of endothelial nitric oxide synthase (eNOS) in hepatocytes may be an important target in nonalcoholic fatty liver disease (NAFLD) development and progression to nonalcoholic ...steatohepatitis (NASH). In this study, we show genetic deletion and viral knockdown of hepatocyte-specific eNOS exacerbated hepatic steatosis and inflammation, decreased hepatic mitochondrial fatty acid oxidation and respiration, increased mitochondrial H
O
emission, and impaired the hepatic mitophagic (BNIP3 and LC3II) response. Conversely, overexpressing eNOS in hepatocytes in vitro and in vivo increased hepatocyte mitochondrial respiration and attenuated Western diet-induced NASH. Moreover, patients with elevated NAFLD activity score (histology score of worsening steatosis, hepatocyte ballooning, and inflammation) exhibited reduced hepatic eNOS expression, which correlated with reduced hepatic mitochondrial fatty acid oxidation and lower hepatic protein expression of mitophagy protein BNIP3. The current study reveals an important molecular role for hepatocyte-specific eNOS as a key regulator of NAFLD/NASH susceptibility and mitochondrial quality control with direct clinical correlation to patients with NASH.
•Glycan microarray technology tracked polysaccharide changes during winemaking.•Polyphenols extracted using enzyme maceration were more polymerized and galloylated.•Enzyme-crafted Cabernet Sauvignon ...wines were more astringent but not more bitter.•Higher polyphenol levels correlated with harder more astringent wines.•Higher arabinogalactan protein levels correlated with softer less astringent wines.
Pectolytic enzyme maceration is common for producing red wines, but the effects on bitterness and astringency are not well understood. Glycan microarrays assessed polysaccharide diversity and with polyphenol analysis was correlated with sensory data on descriptors of astringency and their perceived levels in enzyme-crafted Cabernet Sauvignon wines. Enzyme use is shown to have no effect on bitterness, but enzyme-macerated wines are more astringent. The data suggests that pectolytic enzymes are much more pronounced in their effect on the cell wall matrix than the ripeness of the berries at harvest and subsequent sensory perception. Enzyme-macerated red wines showed higher levels of polyphenol which were more polymerized and galloylated. The polyphenol-rich wines were described as hard, chalky, grippy, grainy and dry. The non-enzyme wines had elevated levels of arabinogalactan protein and pectin epitopes (notably biomarker mAbs JIM8 and JIM13) with the wines being characterized as soft, fine and velvety.
HIV's envelope glycoprotein (Env) is the sole target for neutralizing antibodies. The structures of many broadly neutralizing antibodies (bNAbs) in complex with truncated Env subunits or components ...have been reported. However, their interaction with the intact Env trimer, and the structural determinants that underlie neutralization resistance in this more native context are less well understood. Here we use hydrogen/deuterium exchange to examine the interactions between a panel of bNAbs and native-like Env trimers (SOSIP.664 trimers). Highly potent bNAbs cause only localized effects at their binding interface, while the binding of less potent antibodies is associated with elaborate changes throughout the trimer. In conjunction with binding kinetics, our results suggest that poorly neutralizing antibodies can only bind when the trimer transiently samples an open state. We propose that the kinetics of such opening motions varies among isolates, with Env from neutralization-sensitive viruses opening more frequently than Env from resistant viruses.
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