ZNRF3 and RNF43 cooperate to safeguard metabolic liver zonation and hepatocyte proliferation.

AXIN2 and LGR5 mark intestinal stem cells (ISCs) that require WNT/ß-Catenin signaling for constant homeostatic proliferation. In contrast, AXIN2/LGR5+ pericentral hepatocytes show low proliferation rates despite a WNT/ß-Catenin activity gradient required for metabolic liver zonation. The mechanisms restricting proliferation in AXIN2+ hepatocytes and metabolic gene expression in AXIN2+ ISCs remained elusive. We now show that restricted chromatin accessibility in ISCs prevents the expression of ß-Catenin-regulated metabolic enzymes, whereas fine-tuning of WNT/ß-Catenin activity by ZNRF3 and RNF43 restricts proliferation in chromatin-permissive AXIN2+ hepatocytes, while preserving metabolic function. ZNRF3 deletion promotes hepatocyte proliferation, which in turn becomes limited by RNF43 upregulation. Concomitant deletion of RNF43 in ZNRF3 mutant mice results in metabolic reprogramming of periportal hepatocytes and induces clonal expansion in a subset of hepatocytes, ultimately promoting liver tumors. Together, ZNRF3 and RNF43 cooperate to safeguard liver homeostasis by spatially and temporally restricting WNT/ß-Catenin activity, balancing metabolic function and hepatocyte proliferation.

Imaging Mass Cytometry and Single-Cell Genomics Reveal Differential Depletion and Repletion of B-Cell Populations Following Ofatumumab Treatment in Cynomolgus Monkeys.

Ofatumumab is the first, fully human, anti-CD20 monoclonal antibody in Phase 3 development for multiple sclerosis (MS). The study focused on changes in lymphocyte subsets in blood and lymphoid tissues and on potential novel biomarkers as a result of anti-CD20 antibody action in Cynomolgus monkeys treated with human equivalent doses of subcutaneous (s.c.) ofatumumab on Days 0, 7, and 14. Axillary lymph nodes (LNs) and blood samples were collected at various time points until Day 90. Lymphocyte subsets were quantified by flow cytometry, while morphological and immune cell changes were assessed by imaging mass cytometry (IMC), immunohistochemistry (IHC), in situ hybridization (ISH), and transcriptome analyses using single-cell methodology. Ofatumumab treatment resulted in a potent and rapid reduction of B cells along with a simultaneous drop in CD20+ T cell counts. At Day 21, IHC revealed B-cell depletion in the perifollicular and interfollicular area of axillary LNs, while only the core of the germinal center was depleted of CD20+CD21+ cells. By Day 62, the perifollicular and interfollicular areas were abundantly infiltrated by CD21+ B cells and this distribution returned to the baseline cytoarchitecture by Day 90. By IMC CD20+CD3+CD8+ cells could be identified at the margin of the follicles, with a similar pattern of distribution at Day 21 and 90. Single-cell transcriptomics analysis showed that ofatumumab induced reversible changes in t-distributed stochastic neighbor embedding (t-SNE) defined B-cell subsets that may serve as biomarkers for drug action. In summary, low dose s.c. ofatumumab potently depletes both B cells and CD20+ T cells but apparently spares marginal zone (MZ) B cells in the spleen and LN. These findings add to our molecular and tissue-architectural understanding of ofatumumab treatment effects on B-cell subsets.

Author Correction: Gut microbiome structure and metabolic activity in inflammatory bowel disease.

In the Supplementary Tables 2, 4 and 6 originally published with this Article, the authors mistakenly included sample identifiers in the form of UMCGs rather than UMCG IBDs in the validation cohort; this has now been amended.

Gut microbiome structure and metabolic activity in inflammatory bowel disease.

The inflammatory bowel diseases (IBDs), which include Crohn's disease (CD) and ulcerative colitis (UC), are multifactorial chronic conditions of the gastrointestinal tract. While IBD has been associated with dramatic changes in the gut microbiota, changes in the gut metabolome-the molecular interface between host and microbiota-are less well understood. To address this gap, we performed untargeted metabolomic and shotgun metagenomic profiling of cross-sectional stool samples from discovery (n = 155) and validation (n = 65) cohorts of CD, UC and non-IBD control patients. Metabolomic and metagenomic profiles were broadly correlated with faecal calprotectin levels (a measure of gut inflammation). Across >8,000 measured metabolite features, we identified chemicals and chemical classes that were differentially abundant in IBD, including enrichments for sphingolipids and bile acids, and depletions for triacylglycerols and tetrapyrroles. While > 50% of differentially abundant metabolite features were uncharacterized, many could be assigned putative roles through metabolomic 'guilt by association' (covariation with known metabolites). Differentially abundant species and functions from the metagenomic profiles reflected adaptation to oxidative stress in the IBD gut, and were individually consistent with previous findings. Integrating these data, however, we identified 122 robust associations between differentially abundant species and well-characterized differentially abundant metabolites, indicating possible mechanistic relationships that are perturbed in IBD. Finally, we found that metabolome- and metagenome-based classifiers of IBD status were highly accurate and, like the vast majority of individual trends, generalized well to the independent validation cohort. Our findings thus provide an improved understanding of perturbations of the microbiome-metabolome interface in IBD, including identification of many potential diagnostic and therapeutic targets.

FR171456 is a specific inhibitor of mammalian NSDHL and yeast Erg26p.

FR171456 is a natural product with cholesterol-lowering properties in animal models, but its molecular target is unknown, which hinders further drug development. Here we show that FR171456 specifically targets the sterol-4-alpha-carboxylate-3-dehydrogenase (Saccharomyces cerevisiae--Erg26p, Homo sapiens--NSDHL (NAD(P) dependent steroid dehydrogenase-like)), an essential enzyme in the ergosterol/cholesterol biosynthesis pathway. FR171456 significantly alters the levels of cholesterol pathway intermediates in human and yeast cells. Genome-wide yeast haploinsufficiency profiling experiments highlight the erg26/ERG26 strain, and multiple mutations in ERG26 confer resistance to FR171456 in growth and enzyme assays. Some of these ERG26 mutations likely alter Erg26 binding to FR171456, based on a model of Erg26. Finally, we show that FR171456 inhibits an artificial Hepatitis C viral replicon, and has broad antifungal activity, suggesting potential additional utility as an anti-infective. The discovery of the target and binding site of FR171456 within the target will aid further development of this compound.

An integrated approach for identification and target validation of antifungal compounds active against Erg11p.

Systemic life-threatening fungal infections represent a significant unmet medical need. Cell-based, phenotypic screening can be an effective means of discovering potential novel antifungal compounds, but it does not address target identification, normally required for compound optimization by medicinal chemistry. Here, we demonstrate a combination of screening, genetic, and biochemical approaches to identify and characterize novel antifungal compounds. We isolated a set of novel non-azole antifungal compounds for which no target or mechanism of action is known, using a screen for inhibition of Saccharomyces cerevisiae proliferation. Haploinsufficiency profiling of these compounds in S. cerevisiae suggests that they target Erg11p, a cytochrome P450 family member, which is the target of azoles. Consistent with this, metabolic profiling in S. cerevisiae revealed a buildup of the metabolic intermediates prior to Erg11p activity, following compound treatment. Further, human cytochrome P450 is also inhibited in in vitro assays by these compounds. We modeled the Erg11p protein based on the human CYP51 crystal structure, and in silico docking of these compounds suggests that they interact with the heme center in a manner similar to that of azoles. Consistent with these docking observations, Candida strains carrying azole-resistant alleles of ERG11 are also resistant to the compounds in this study. Thus, we have identified non-azole Erg11p inhibitors, using a systematic approach for ligand and target characterization.

Noise-induced coherence and network oscillations in a reduced bursting model.

The dynamics of the Hindmarsh-Rose (HR) model of bursting thalamic neurons is reduced to a system of two linear differential equations that retains the subthreshold resonance properties of the HR model. Introducing a reset mechanism after a threshold crossing, we turn this system into a resonant integrate-and-fire (RIF) model. Using Monte-Carlo simulations and mathematical analysis, we examine the effects of noise and the subthreshold dynamic properties of the RIF model on the occurrence of coherence resonance (CR). Synchronized burst firing occurs in a network of such model neurons with excitatory pulse-coupling. The coherence level of the network oscillations shows a stochastic resonance-like dependence on the noise level. Stochastic analysis of the equations shows that the slow recovery from the spike-induced inhibition is crucial in determining the frequencies of the CR and the subthreshold resonance in the original HR model. In this particular type of CR, the oscillation frequency strongly depends on the intrinsic time scales but changes little with the noise intensity. We give analytical quantities to describe this CR mechanism and illustrate its influence on the emerging network oscillations. We discuss the profound physiological roles this kind of CR may have in information processing in neurons possessing a subthreshold resonant frequency and in generating synchronized network oscillations with a frequency that is determined by intrinsic properties of the neurons.

WNT and DKK determine hair follicle spacing through a reaction-diffusion mechanism.

Mathematical reaction-diffusion models have been suggested to describe formation of animal pigmentation patterns and distribution of epidermal appendages. However, the crucial signals and in vivo mechanisms are still elusive. Here we identify WNT and its inhibitor DKK as primary determinants of murine hair follicle spacing, using a combined experimental and computational modeling approach. Transgenic DKK overexpression reduces overall appendage density. Moderate suppression of endogenous WNT signaling forces follicles to form clusters during an otherwise normal morphogenetic program. These results confirm predictions of a WNT/DKK-specific mathematical model and provide in vivo corroboration of the reaction-diffusion mechanism for epidermal appendage formation.

Membrane resonance and stochastic resonance modulate firing patterns of thalamocortical neurons.

We examined the interactions of subthreshold membrane resonance and stochastic resonance using whole-cell patch clamp recordings in thalamocortical neurons of rat brain slices, as well as with a Hodgkin-Huxley-type mathematical model of thalamocortical neurons. The neurons exhibited the subthreshold resonance when stimulated with small amplitude sine wave currents of varying frequency, and stochastic resonance when noise was added to sine wave inputs. Stochastic resonance was manifest as a maximum in signal-to-noise ratio of output response to subthreshold periodic input combined with noise. Stochastic resonance in conjunction with subthreshold resonance resulted in action potential patterns that showed frequency selectivity for periodic inputs. Stochastic resonance was maximal near subthreshold resonance frequency and a high noise level was required for detection of high frequency signals. We speculate that combined membrane and stochastic resonances have physiological utility in coupling synaptic activity to preferred firing frequency and in network synchronization under noise.

The influences of Ih on temporal summation in hippocampal CA1 pyramidal neurons: a modeling study.

Recent experimental and theoretical studies have found that active dendritic ionic currents can compensate for the effects of electrotonic attenuation. In particular, temporal summation, the percentage increase in peak somatic voltage responses invoked by a synaptic input train, is independent of location of the synaptic input in hippocampal CA1 pyramidal neurons under normal conditions. This independence, known as normalization of temporal summation, is destroyed when the hyperpolarization-activated current, Ih, is blocked [Magee JC (1999a), Nature Neurosci. 2: 508-514]. Using a compartmental model derived from morphological recordings of hippocampal CA1 pyramidal neurons, we examined the hypothesis that Ih was primarily responsible for normalization of temporal summation. We concluded that this hypothesis was incomplete. With a model that included Ih, the persistent Na(+) current (INaP), and the transient A-type K+ current (IA), however, we observed normalization of temporal summation across a wide range of synaptic input frequencies, in keeping with experimental observations.

Resonances and noise in a stochastic Hindmarsh-Rose model of thalamic neurons.

Thalamic neurons exhibit subthreshold resonance when stimulated with small sine wave signals of varying frequency and stochastic resonance when noise is added to these signals. We study a stochastic Hindmarsh-Rose model using Monte-Carlo simulations to investigate how noise, in conjunction with subthreshold resonance, leads to a preferred frequency in the firing pattern. The resulting stochastic resonance (SR) exhibits a preferred firing frequency that is approximately exponential in its dependence on the noise amplitude. In similar experiments, frequency dependent SR is found in the reliability of detection of alpha-function inputs under noise, which are more realistic inputs for neurons. A mathematical analysis of the equations reveals that the frequency preference arises from the dynamics of the slow variable. Noise can then transfer the resonance over the firing threshold because of the proximity of the fast subsystem to a Hopf bifurcation point. Our results may have implications for the behavior of thalamic neurons in a network, with noise switching the membrane potential between different resonance modes.