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1.
Nature ; 592(7853): 267-271, 2021 04.
Article in English | MEDLINE | ID: mdl-33658711

ABSTRACT

The behaviour of an animal is determined by metabolic, emotional and social factors1,2. Depending on its state, an animal will focus on avoiding threats, foraging for food or on social interactions, and will display the appropriate behavioural repertoire3. Moreover, survival and reproduction depend on the ability of an animal to adapt to changes in the environment by prioritizing the appropriate state4. Although these states are thought to be associated with particular functional configurations of large-brain systems5,6, the underlying principles are poorly understood. Here we use deep-brain calcium imaging of mice engaged in spatial or social exploration to investigate how these processes are represented at the neuronal population level in the basolateral amygdala, which is a region of the brain that integrates emotional, social and metabolic information. We demonstrate that the basolateral amygdala encodes engagement in exploratory behaviour by means of two large, functionally anticorrelated ensembles that exhibit slow dynamics. We found that spatial and social exploration were encoded by orthogonal pairs of ensembles with stable and hierarchical allocation of neurons according to the saliency of the stimulus. These findings reveal that the basolateral amygdala acts as a low-dimensional, but context-dependent, hierarchical classifier that encodes state-dependent behavioural repertoires. This computational function may have a fundamental role in the regulation of internal states in health and disease.


Subject(s)
Basolateral Nuclear Complex/physiology , Exploratory Behavior/physiology , Animals , Calcium/analysis , Male , Mice , Mice, Inbred C57BL , Social Behavior , Spatial Navigation/physiology
2.
Mol Cell ; 75(3): 483-497.e9, 2019 08 08.
Article in English | MEDLINE | ID: mdl-31253574

ABSTRACT

In mammals, ∼100 deubiquitinases act on ∼20,000 intracellular ubiquitination sites. Deubiquitinases are commonly regarded as constitutively active, with limited regulatory and targeting capacity. The BRCA1-A and BRISC complexes serve in DNA double-strand break repair and immune signaling and contain the lysine-63 linkage-specific BRCC36 subunit that is functionalized by scaffold subunits ABRAXAS and ABRO1, respectively. The molecular basis underlying BRCA1-A and BRISC function is currently unknown. Here we show that in the BRCA1-A complex structure, ABRAXAS integrates the DNA repair protein RAP80 and provides a high-affinity binding site that sequesters the tumor suppressor BRCA1 away from the break site. In the BRISC structure, ABRO1 binds SHMT2α, a metabolic enzyme enabling cancer growth in hypoxic environments, which we find prevents BRCC36 from binding and cleaving ubiquitin chains. Our work explains modularity in the BRCC36 DUB family, with different adaptor subunits conferring diversified targeting and regulatory functions.


Subject(s)
BRCA1 Protein/genetics , DNA Repair/genetics , DNA-Binding Proteins/genetics , Deubiquitinating Enzymes/genetics , Histone Chaperones/genetics , Neoplasms/genetics , Binding Sites/genetics , Carrier Proteins/genetics , Cell Nucleus/genetics , Cell Nucleus/immunology , Cytoplasm/genetics , Cytoplasm/immunology , DNA Breaks, Double-Stranded , DNA Repair/immunology , Deubiquitinating Enzymes/immunology , HeLa Cells , Humans , Immunity, Cellular/genetics , Multiprotein Complexes/chemistry , Multiprotein Complexes/genetics , Neoplasms/immunology , Nuclear Matrix-Associated Proteins/genetics , Protein Binding/genetics , Ubiquitin/genetics , Ubiquitin-Specific Proteases/genetics , Ubiquitination/genetics
3.
Am J Pathol ; 193(2): 161-181, 2023 02.
Article in English | MEDLINE | ID: mdl-36410420

ABSTRACT

The roof plate-specific spondin-leucine-rich repeat-containing G-protein coupled receptor 4/5 (LGR4/5)-zinc and ring finger 3 (ZNRF3)/ring finger protein 43 (RNF43) module is a master regulator of hepatic Wnt/ß-catenin signaling and metabolic zonation. However, its impact on nonalcoholic fatty liver disease (NAFLD) remains unclear. The current study investigated whether hepatic epithelial cell-specific loss of the Wnt/ß-catenin modulator Lgr4/5 promoted NAFLD. The 3- and 6-month-old mice with hepatic epithelial cell-specific deletion of both receptors Lgr4/5 (Lgr4/5dLKO) were compared with control mice fed with normal diet (ND) or high-fat diet (HFD). Six-month-old HFD-fed Lgr4/5dLKO mice developed hepatic steatosis and fibrosis but the control mice did not. Serum cholesterol-high-density lipoprotein and total cholesterol levels in 3- and 6-month-old HFD-fed Lgr4/5dLKO mice were decreased compared with those in control mice. An ex vivo primary hepatocyte culture assay and a comprehensive bile acid (BA) characterization in liver, plasma, bile, and feces demonstrated that ND-fed Lgr4/5dLKO mice had impaired BA secretion, predisposing them to develop cholestatic characteristics. Lipidome and RNA-sequencing analyses demonstrated severe alterations in several lipid species and pathways controlling lipid metabolism in the livers of Lgr4/5dLKO mice. In conclusion, loss of hepatic Wnt/ß-catenin activity by Lgr4/5 deletion led to loss of BA secretion, cholestatic features, altered lipid homeostasis, and deregulation of lipoprotein pathways. Both BA and intrinsic lipid alterations contributed to the onset of NAFLD.


Subject(s)
Non-alcoholic Fatty Liver Disease , Animals , Mice , Non-alcoholic Fatty Liver Disease/metabolism , beta Catenin/metabolism , Leucine/metabolism , Liver/metabolism , Cholesterol/metabolism , Receptors, G-Protein-Coupled/genetics , Receptors, G-Protein-Coupled/metabolism , Mice, Inbred C57BL , Diet, High-Fat/adverse effects
4.
Int Wound J ; 21(4): e14447, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38149752

ABSTRACT

A limited understanding of the pathology underlying chronic wounds has hindered the development of effective diagnostic markers and pharmaceutical interventions. This study aimed to elucidate the molecular composition of various common chronic ulcer types to facilitate drug discovery strategies. We conducted a comprehensive analysis of leg ulcers (LUs), encompassing venous and arterial ulcers, foot ulcers (FUs), pressure ulcers (PUs), and compared them with surgical wound healing complications (WHCs). To explore the pathophysiological mechanisms and identify similarities or differences within wounds, we dissected wounds into distinct subregions, including the wound bed, border, and peri-wound areas, and compared them against intact skin. By correlating histopathology, RNA sequencing (RNA-Seq), and immunohistochemistry (IHC), we identified unique genes, pathways, and cell type abundance patterns in each wound type and subregion. These correlations aim to aid clinicians in selecting targeted treatment options and informing the design of future preclinical and clinical studies in wound healing. Notably, specific genes, such as PITX1 and UPP1, exhibited exclusive upregulation in LUs and FUs, potentially offering significant benefits to specialists in limb preservation and clinical treatment decisions. In contrast, comparisons between different wound subregions, regardless of wound type, revealed distinct expression profiles. The pleiotropic chemokine-like ligand GPR15L (C10orf99) and transmembrane serine proteases TMPRSS11A/D were significantly upregulated in wound border subregions. Interestingly, WHCs exhibited a nearly identical transcriptome to PUs, indicating clinical relevance. Histological examination revealed blood vessel occlusions with impaired angiogenesis in chronic wounds, alongside elevated expression of genes and immunoreactive markers related to blood vessel and lymphatic epithelial cells in wound bed subregions. Additionally, inflammatory and epithelial markers indicated heightened inflammatory responses in wound bed and border subregions and reduced wound bed epithelialization. In summary, chronic wounds from diverse anatomical sites share common aspects of wound pathophysiology but also exhibit distinct molecular differences. These unique molecular characteristics present promising opportunities for drug discovery and treatment, particularly for patients suffering from chronic wounds. The identified diagnostic markers hold the potential to enhance preclinical and clinical trials in the field of wound healing.


Subject(s)
Diabetic Foot , Leg Ulcer , Pressure Ulcer , Soft Tissue Injuries , Humans , Pressure Ulcer/genetics , Pressure Ulcer/therapy , Diabetic Foot/therapy , Leg Ulcer/therapy , Gene Expression , Suppuration
5.
Nat Methods ; 17(3): 343-351, 2020 03.
Article in English | MEDLINE | ID: mdl-32123394

ABSTRACT

Virtual realities are powerful tools to analyze and manipulate interactions between animals and their environment and to enable measurements of neuronal activity during behavior. In many species, however, optical access to the brain and/or the behavioral repertoire are limited. We developed a high-resolution virtual reality for head-restrained adult zebrafish, which exhibit cognitive behaviors not shown by larvae. We noninvasively measured activity throughout the dorsal telencephalon by multiphoton calcium imaging. Fish in the virtual reality showed regular swimming patterns and were attracted to animations of conspecifics. Manipulations of visuo-motor feedback revealed neurons that responded selectively to the mismatch between the expected and the actual visual consequences of motor output. Such error signals were prominent in multiple telencephalic areas, consistent with models of predictive processing. A virtual reality system for adult zebrafish therefore provides opportunities to analyze neuronal processing mechanisms underlying higher brain functions including decision making, associative learning, and social interactions.


Subject(s)
Behavior, Animal , Brain/diagnostic imaging , Neurons/physiology , User-Computer Interface , Virtual Reality , Animals , Brain Mapping , Cognition , Decision Making , Female , Male , Motor Skills , Probability , Social Behavior , Swimming , Zebrafish
6.
Nat Chem Biol ; 17(3): 280-290, 2021 03.
Article in English | MEDLINE | ID: mdl-33462494

ABSTRACT

Although most acute skin wounds heal rapidly, non-healing skin ulcers represent an increasing and substantial unmet medical need that urgently requires effective therapeutics. Keratinocytes resurface wounds to re-establish the epidermal barrier by transitioning to an activated, migratory state, but this ability is lost in dysfunctional chronic wounds. Small-molecule regulators of keratinocyte plasticity with the potential to reverse keratinocyte malfunction in situ could offer a novel therapeutic approach in skin wound healing. Utilizing high-throughput phenotypic screening of primary keratinocytes, we identify such small molecules, including bromodomain and extra-terminal domain (BET) protein family inhibitors (BETi). BETi induce a sustained activated, migratory state in keratinocytes in vitro, increase activation markers in human epidermis ex vivo and enhance skin wound healing in vivo. Our findings suggest potential clinical utility of BETi in promoting keratinocyte re-epithelialization of skin wounds. Importantly, this novel property of BETi is exclusively observed after transient low-dose exposure, revealing new potential for this compound class.


Subject(s)
Cell Cycle Proteins/genetics , Epidermis/drug effects , Re-Epithelialization/drug effects , Skin Ulcer/drug therapy , Small Molecule Libraries/pharmacology , Transcription Factors/genetics , Wounds, Nonpenetrating/drug therapy , Animals , Cell Cycle Proteins/antagonists & inhibitors , Cell Cycle Proteins/metabolism , Disease Models, Animal , Epidermis/metabolism , Epidermis/pathology , Fluorescence Resonance Energy Transfer , Gene Expression Regulation , High-Throughput Screening Assays , Humans , Keratinocytes/drug effects , Keratinocytes/metabolism , Keratinocytes/pathology , Male , Mice , Mice, Inbred C57BL , Primary Cell Culture , Protein Isoforms/antagonists & inhibitors , Protein Isoforms/genetics , Protein Isoforms/metabolism , Protein Precursors/antagonists & inhibitors , Protein Precursors/genetics , Protein Precursors/metabolism , Re-Epithelialization/genetics , Skin Ulcer/genetics , Skin Ulcer/metabolism , Skin Ulcer/pathology , Small Molecule Libraries/chemistry , Structure-Activity Relationship , Transcription Factors/antagonists & inhibitors , Transcription Factors/metabolism , Transcription, Genetic , Wounds, Nonpenetrating/genetics , Wounds, Nonpenetrating/metabolism , Wounds, Nonpenetrating/pathology
7.
Mol Cell ; 42(3): 330-41, 2011 May 06.
Article in English | MEDLINE | ID: mdl-21549310

ABSTRACT

The Polycomb repressive complex 2 (PRC2) confers transcriptional repression through histone H3 lysine 27 trimethylation (H3K27me3). Here, we examined how PRC2 is modulated by histone modifications associated with transcriptionally active chromatin. We provide the molecular basis of histone H3 N terminus recognition by the PRC2 Nurf55-Su(z)12 submodule. Binding of H3 is lost if lysine 4 in H3 is trimethylated. We find that H3K4me3 inhibits PRC2 activity in an allosteric fashion assisted by the Su(z)12 C terminus. In addition to H3K4me3, PRC2 is inhibited by H3K36me2/3 (i.e., both H3K36me2 and H3K36me3). Direct PRC2 inhibition by H3K4me3 and H3K36me2/3 active marks is conserved in humans, mouse, and fly, rendering transcriptionally active chromatin refractory to PRC2 H3K27 trimethylation. While inhibition is present in plant PRC2, it can be modulated through exchange of the Su(z)12 subunit. Inhibition by active chromatin marks, coupled to stimulation by transcriptionally repressive H3K27me3, enables PRC2 to autonomously template repressive H3K27me3 without overwriting active chromatin domains.


Subject(s)
Chromatin/metabolism , Histones/metabolism , Lysine/metabolism , Repressor Proteins/metabolism , Amino Acid Sequence , Animals , Blotting, Western , Cell Line , Chromatin/genetics , Crystallography, X-Ray , Drosophila , Drosophila Proteins/chemistry , Drosophila Proteins/genetics , Drosophila Proteins/metabolism , Histone-Lysine N-Methyltransferase/chemistry , Histone-Lysine N-Methyltransferase/genetics , Histone-Lysine N-Methyltransferase/metabolism , Histones/chemistry , Humans , Lysine/chemistry , Methylation , Mice , Models, Molecular , Molecular Sequence Data , Mutation , Polycomb Repressive Complex 2 , Polycomb-Group Proteins , Protein Binding , Protein Structure, Tertiary , Repressor Proteins/chemistry , Repressor Proteins/genetics , Retinoblastoma-Binding Protein 4/chemistry , Retinoblastoma-Binding Protein 4/genetics , Retinoblastoma-Binding Protein 4/metabolism , Transcription, Genetic
8.
Nature ; 485(7397): 195-200, 2012 Apr 29.
Article in English | MEDLINE | ID: mdl-22575959

ABSTRACT

R-spondin proteins strongly potentiate Wnt signalling and function as stem-cell growth factors. Despite the biological and therapeutic significance, the molecular mechanism of R-spondin action remains unclear. Here we show that the cell-surface transmembrane E3 ubiquitin ligase zinc and ring finger 3 (ZNRF3) and its homologue ring finger 43 (RNF43) are negative feedback regulators of Wnt signalling. ZNRF3 is associated with the Wnt receptor complex, and inhibits Wnt signalling by promoting the turnover of frizzled and LRP6. Inhibition of ZNRF3 enhances Wnt/ß-catenin signalling and disrupts Wnt/planar cell polarity signalling in vivo. Notably, R-spondin mimics ZNRF3 inhibition by increasing the membrane level of Wnt receptors. Mechanistically, R-spondin interacts with the extracellular domain of ZNRF3 and induces the association between ZNRF3 and LGR4, which results in membrane clearance of ZNRF3. These data suggest that R-spondin enhances Wnt signalling by inhibiting ZNRF3. Our study provides new mechanistic insights into the regulation of Wnt receptor turnover, and reveals ZNRF3 as a tractable target for therapeutic exploration.


Subject(s)
Receptors, Wnt/metabolism , Thrombospondins/metabolism , Ubiquitin-Protein Ligases/deficiency , Ubiquitin-Protein Ligases/metabolism , Animals , Cell Polarity/physiology , Colorectal Neoplasms/genetics , DNA-Binding Proteins/deficiency , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Feedback, Physiological , Female , Frizzled Receptors/metabolism , HEK293 Cells , Humans , Low Density Lipoprotein Receptor-Related Protein-6/metabolism , Male , Mice , Mice, Knockout , Oncogene Proteins/deficiency , Oncogene Proteins/genetics , Oncogene Proteins/metabolism , Protein Stability , Protein Structure, Tertiary , Receptors, G-Protein-Coupled/deficiency , Receptors, G-Protein-Coupled/genetics , Receptors, G-Protein-Coupled/metabolism , Ubiquitin-Protein Ligases/chemistry , Ubiquitin-Protein Ligases/genetics , Ubiquitination , Wnt Signaling Pathway , Xenopus , Zebrafish , beta Catenin/metabolism
9.
PLoS Genet ; 11(8): e1005465, 2015 Aug.
Article in English | MEDLINE | ID: mdl-26295846

ABSTRACT

YAP1 is a major effector of the Hippo pathway and a well-established oncogene. Elevated YAP1 activity due to mutations in Hippo pathway components or YAP1 amplification is observed in several types of human cancers. Here we investigated its genomic binding landscape in YAP1-activated cancer cells, as well as in non-transformed cells. We demonstrate that TEAD transcription factors mediate YAP1 chromatin-binding genome-wide, further explaining their dominant role as primary mediators of YAP1-transcriptional activity. Moreover, we show that YAP1 largely exerts its transcriptional control via distal enhancers that are marked by H3K27 acetylation and that YAP1 is necessary for this chromatin mark at bound enhancers and the activity of the associated genes. This work establishes YAP1-mediated transcriptional regulation at distal enhancers and provides an expanded set of target genes resulting in a fundamental source to study YAP1 function in a normal and cancer setting.


Subject(s)
Adaptor Proteins, Signal Transducing/physiology , DNA-Binding Proteins/metabolism , Nuclear Proteins/metabolism , Phosphoproteins/physiology , Transcription Factors/metabolism , Acetylation , Base Sequence , Binding Sites , Cell Line, Tumor , Consensus Sequence , Enhancer Elements, Genetic , Histones/metabolism , Humans , Protein Binding , Protein Processing, Post-Translational , TEA Domain Transcription Factors , Transcriptional Activation , Transcriptome , YAP-Signaling Proteins
10.
BMC Genomics ; 17: 309, 2016 Apr 27.
Article in English | MEDLINE | ID: mdl-27121005

ABSTRACT

BACKGROUND: Hearing loss is the most common sensory defect afflicting several hundred million people worldwide. In most cases, regardless of the original cause, hearing loss is related to the degeneration and death of hair cells and their associated spiral ganglion neurons. Despite this knowledge, relatively few studies have reported regeneration of the auditory system. Significant gaps remain in our understanding of the molecular mechanisms underpinning auditory function, including the factors required for sensory cell regeneration. Recently, the identification of transcriptional activators and repressors of hair cell fate has been augmented by the discovery of microRNAs (miRNAs) associated with hearing loss. As miRNAs are central players of differentiation and cell fate, identification of miRNAs and their gene targets may reveal new pathways for hair cell regeneration, thereby providing new avenues for the treatment of hearing loss. RESULTS: In order to identify new genetic elements enabling regeneration of inner ear sensory hair cells, next-generation miRNA sequencing (miRSeq) was used to identify the most prominent miRNAs expressed in the mouse embryonic inner ear cell line UB/OC-1 during differentiation towards a hair cell like phenotype. Based on these miRSeq results eight most differentially expressed miRNAs were selected for further characterization. In UB/OC-1, miR-210 silencing in vitro resulted in hair cell marker expression, whereas ectopic expression of miR-210 resulted in new hair cell formation in cochlear explants. Using a lineage tracing mouse model, transdifferentiation of supporting epithelial cells was identified as the likely mechanism for this new hair cell formation. Potential miR-210 targets were predicted in silico and validated experimentally using a miR-trap approach. CONCLUSION: MiRSeq followed by ex vivo validation revealed miR-210 as a novel factor driving transdifferentiation of supporting epithelial cells to sensory hair cells suggesting that miR-210 might be a potential new factor for hearing loss therapy. In addition, identification of inner ear pathways regulated by miR-210 identified potential new drug targets for the treatment of hearing loss.


Subject(s)
Cell Transdifferentiation , Hair Cells, Auditory, Inner/cytology , MicroRNAs/metabolism , Organ of Corti/cytology , Regeneration , Animals , Cell Line , Gene Knock-In Techniques , High-Throughput Nucleotide Sequencing , Mice , Mice, Inbred BALB C , Mice, Inbred C57BL , Mice, Transgenic , MicroRNAs/genetics , Organ Culture Techniques , SOXB1 Transcription Factors/genetics , Sequence Analysis, RNA
11.
BMC Genomics ; 17(1): 723, 2016 09 09.
Article in English | MEDLINE | ID: mdl-27613601

ABSTRACT

BACKGROUND: Genome-wide CRISPR-Cas9 dropout screens can identify genes whose knockout affects cell viability. Recent CRISPR screens detected thousands of essential genes required for cellular survival and key cellular processes; however discovering novel lineage-specific genetic dependencies from the many hits still remains a challenge. RESULTS: To assess whether CRISPR-Cas9 dropout screens can help identify cancer dependencies, we screened two human cancer cell lines carrying known and distinct oncogenic mutations using a genome-wide sgRNA library. We found that the gRNA targeting the driver mutation EGFR was one of the highest-ranking candidates in the EGFR-mutant HCC-827 lung adenocarcinoma cell line. Likewise, sgRNAs for NRAS and MAP2K1 (MEK1), a downstream kinase of mutant NRAS, were identified among the top hits in the NRAS-mutant neuroblastoma cell line CHP-212. Depletion of these genes targeted by the sgRNAs strongly correlated with the sensitivity to specific kinase inhibitors of the EGFR or RAS pathway in cell viability assays. In addition, we describe other dependencies such as TBK1 in HCC-827 cells and TRIB2 in CHP-212 cells which merit further investigation. CONCLUSIONS: We show that genome-wide CRISPR dropout screens are suitable for the identification of oncogenic drivers and other essential genes.


Subject(s)
CRISPR-Cas Systems , Cell Transformation, Neoplastic/genetics , Genome-Wide Association Study , Mutation , Oncogenes , Calcium-Calmodulin-Dependent Protein Kinases/metabolism , Cell Line, Tumor , Cell Survival/drug effects , Cell Survival/genetics , Drug Screening Assays, Antitumor , Gene Knockout Techniques , Humans , Intracellular Signaling Peptides and Proteins/metabolism , Phenotype , Protein Kinase Inhibitors/pharmacology , Protein Serine-Threonine Kinases/metabolism , RNA, Guide, Kinetoplastida/genetics
12.
Hepatology ; 62(5): 1497-510, 2015 Nov.
Article in English | MEDLINE | ID: mdl-26173433

ABSTRACT

UNLABELLED: The Yes-associated protein (YAP)/Hippo pathway has been implicated in tissue development, regeneration, and tumorigenesis. However, its role in cholangiocarcinoma (CC) is not established. We show that YAP activation is a common feature in CC patient biopsies and human CC cell lines. Using microarray expression profiling of CC cells with overexpressed or down-regulated YAP, we show that YAP regulates genes involved in proliferation, apoptosis, and angiogenesis. YAP activity promotes CC growth in vitro and in vivo by functionally interacting with TEAD transcription factors (TEADs). YAP activity together with TEADs prevents apoptosis induced by cytotoxic drugs, whereas YAP knockdown sensitizes CC cells to drug-induced apoptosis. We further show that the proangiogenic microfibrillar-associated protein 5 (MFAP5) is a direct transcriptional target of YAP/TEAD in CC cells and that secreted MFAP5 promotes tube formation of human microvascular endothelial cells. High YAP activity in human CC xenografts and clinical samples correlates with increased MFAP5 expression and CD31(+) vasculature. CONCLUSIONS: These findings establish YAP as a key regulator of proliferation and antiapoptotic mechanisms in CC and provide first evidence that YAP promotes angiogenesis by regulating the expression of secreted proangiogenic proteins.


Subject(s)
Bile Duct Neoplasms/pathology , Bile Ducts, Intrahepatic , Cholangiocarcinoma/pathology , DNA-Binding Proteins/physiology , Drug Resistance, Neoplasm , Neovascularization, Pathologic/etiology , Nuclear Proteins/physiology , Transcription Factors/physiology , Animals , Apoptosis , Bile Duct Neoplasms/blood supply , Bile Duct Neoplasms/drug therapy , Cell Cycle Proteins , Cell Proliferation , Cholangiocarcinoma/blood supply , Cholangiocarcinoma/drug therapy , Contractile Proteins/genetics , Female , Gene Expression Regulation, Neoplastic , Glycoproteins/genetics , Humans , Intercellular Signaling Peptides and Proteins , Mice , Oncogenes , TEA Domain Transcription Factors
13.
Nat Chem Biol ; 10(5): 343-9, 2014 May.
Article in English | MEDLINE | ID: mdl-24633354

ABSTRACT

Hedgehog (Hh) signaling determines cell fate during development and can drive tumorigenesis. We performed a screen for new compounds that can impinge on Hh signaling downstream of Smoothened (Smo). A series of cyclohexyl-methyl aminopyrimidine chemotype compounds ('CMAPs') were identified that could block pathway signaling in a Smo-independent manner. In addition to inhibiting Hh signaling, the compounds generated inositol phosphates through an unknown GPCR. Correlation of GPCR mRNA expression levels with compound activity across cell lines suggested the target to be the orphan receptor GPR39. RNA interference or cDNA overexpression of GPR39 demonstrated that the receptor is necessary for compound activity. We propose a model in which CMAPs activate GPR39, which signals to the Gli transcription factors and blocks signaling. In addition to the discovery of GPR39 as a new target that impinges on Hh signaling, we report on small-molecule modulators of the receptor that will enable in vitro interrogation of GPR39 signaling in different cellular contexts.


Subject(s)
Hedgehog Proteins/antagonists & inhibitors , Receptors, G-Protein-Coupled/metabolism , Chromatography, Affinity , Proteomics , Signal Transduction , Tandem Mass Spectrometry
14.
FASEB J ; 29(7): 2980-92, 2015 Jul.
Article in English | MEDLINE | ID: mdl-25854701

ABSTRACT

Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common cause of autosomal-dominant forms of Parkinson's disease. LRRK2 is a modular, multidomain protein containing 2 enzymatic domains, including a kinase domain, as well as several protein-protein interaction domains, pointing to a role in cellular signaling. Although enormous efforts have been made, the exact pathophysiologic mechanisms of LRRK2 are still not completely known. In this study, we used a chemical genetics approach to identify LRRK2 substrates from mouse brain. This approach allows the identification of substrates of 1 particular kinase in a complex cellular environment. Several of the identified peptides are involved in the regulation of microtubule (MT) dynamics, including microtubule-associating protein (MAP)/microtubule affinity-regulating kinase 1 (MARK1). MARK1 is a serine/threonine kinase known to phosphorylate MT-binding proteins such as Tau, MAP2, and MAP4 at KXGS motifs leading to MT destabilization. In vitro kinase assays and metabolic-labeling experiments in living cells confirmed MARK1 as an LRRK2 substrate. Moreover, we also showed that LRRK2 and MARK1 are interacting in eukaryotic cells. Our findings contribute to the identification of physiologic LRRK2 substrates and point to a potential mechanism explaining the reported effects of LRRK2 on neurite morphology.


Subject(s)
Protein Serine-Threonine Kinases/genetics , Protein Serine-Threonine Kinases/metabolism , Amino Acid Sequence , Animals , Brain/metabolism , HEK293 Cells , Humans , Leucine-Rich Repeat Serine-Threonine Protein Kinase-2 , Mice , Mice, Knockout , Microtubules/metabolism , Molecular Sequence Data , Mutant Proteins/chemistry , Mutant Proteins/genetics , Mutant Proteins/metabolism , Parkinson Disease/genetics , Parkinson Disease/metabolism , Protein Serine-Threonine Kinases/chemistry , Protein Serine-Threonine Kinases/deficiency , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Substrate Specificity
15.
Dev Biol ; 390(2): 181-90, 2014 Jun 15.
Article in English | MEDLINE | ID: mdl-24680895

ABSTRACT

Lgr4 and Lgr5 are known markers of adult and embryonic tissue stem cells in various organs. However, whether Lgr4 and Lgr5 are important for embryonic development remains unclear. To study their functions during intestinal crypt, skin and kidney development we now generated mice lacking either Lgr4 (Lgr4KO), Lgr5 (Lgr5KO) or both receptors (Lgr4/5dKO). E16.5 Lgr4KO mice displayed complete loss of Lgr5+/Olfm4+intestinal stem cells, compromised Wnt signaling and impaired proliferation and differentiation of gut epithelium. Similarly, E16.5 Lgr4KO mice showed reduced basal cell proliferation and hair follicle numbers in the developing skin, as well as dilated kidney tubules and ectatic Bowman׳s spaces. Although Lgr4KO and Lgr5KO mice both died perinatally, Lgr5 deletion did not compromise embryonic development of gut, kidney or skin. Concomitant deletion of Lgr4 and Lgr5 did not prevent perinatal lethality, in contrast to a previous report that suggested rescue of Lgr5 KO perinatal lethality by a hypomorphic Lgr4 mutant. While the double deletion did not further promote the phenotypes observed in Lgr4KO intestines, impaired kidney cell proliferation, reduced epidermal thickness, loss of Lgr5+follicular epithelium and impaired hair follicle development were only observed in Lgr4/5dKO mice. This supports complementary functions of both receptors. Our findings clearly establish the importance of Lgr4 and Lgr5 during embryonic gut, skin and kidney development, with a dominant role of Lgr4.


Subject(s)
Intestines/embryology , Kidney/embryology , Receptors, G-Protein-Coupled/physiology , Skin/embryology , Wnt Signaling Pathway/physiology , Animals , Blotting, Southern , DNA Primers/genetics , Gene Components , Genotype , Green Fluorescent Proteins , Immunohistochemistry , Mice , Mice, Inbred BALB C , Mice, Knockout , Polymerase Chain Reaction , Receptors, G-Protein-Coupled/genetics , Reverse Transcriptase Polymerase Chain Reaction , Stem Cells/physiology , Wnt Signaling Pathway/genetics
16.
Nature ; 461(7264): 614-20, 2009 Oct 01.
Article in English | MEDLINE | ID: mdl-19759537

ABSTRACT

The stability of the Wnt pathway transcription factor beta-catenin is tightly regulated by the multi-subunit destruction complex. Deregulated Wnt pathway activity has been implicated in many cancers, making this pathway an attractive target for anticancer therapies. However, the development of targeted Wnt pathway inhibitors has been hampered by the limited number of pathway components that are amenable to small molecule inhibition. Here, we used a chemical genetic screen to identify a small molecule, XAV939, which selectively inhibits beta-catenin-mediated transcription. XAV939 stimulates beta-catenin degradation by stabilizing axin, the concentration-limiting component of the destruction complex. Using a quantitative chemical proteomic approach, we discovered that XAV939 stabilizes axin by inhibiting the poly-ADP-ribosylating enzymes tankyrase 1 and tankyrase 2. Both tankyrase isoforms interact with a highly conserved domain of axin and stimulate its degradation through the ubiquitin-proteasome pathway. Thus, our study provides new mechanistic insights into the regulation of axin protein homeostasis and presents new avenues for targeted Wnt pathway therapies.


Subject(s)
Repressor Proteins/metabolism , Signal Transduction/drug effects , Tankyrases/antagonists & inhibitors , Wnt Proteins/antagonists & inhibitors , Axin Protein , Cell Division/drug effects , Cell Line , Cell Line, Tumor , Colorectal Neoplasms/drug therapy , Colorectal Neoplasms/metabolism , Heterocyclic Compounds, 3-Ring/pharmacology , Humans , Proteasome Endopeptidase Complex/metabolism , Protein Binding , Proteomics , Repressor Proteins/chemistry , Tankyrases/metabolism , Transcription, Genetic/drug effects , Ubiquitin/metabolism , Ubiquitination , Wnt Proteins/metabolism , beta Catenin/antagonists & inhibitors , beta Catenin/metabolism
17.
Proc Natl Acad Sci U S A ; 108(17): 6739-44, 2011 Apr 26.
Article in English | MEDLINE | ID: mdl-21502533

ABSTRACT

The search for novel therapeutic interventions for viral disease is a challenging pursuit, hallmarked by the paucity of antiviral agents currently prescribed. Targeting of viral proteins has the inextricable challenge of rise of resistance. Safe and effective vaccines are not possible for many viral pathogens. New approaches are required to address the unmet medical need in this area. We undertook a cell-based high-throughput screen to identify leads for development of drugs to treat respiratory syncytial virus (RSV), a serious pediatric pathogen. We identified compounds that are potent (nanomolar) inhibitors of RSV in vitro in HEp-2 cells and in primary human bronchial epithelial cells and were shown to act postentry. Interestingly, two scaffolds exhibited broad-spectrum activity among multiple RNA viruses. Using the chemical matter as a probe, we identified the targets and identified a common cellular pathway: the de novo pyrimidine biosynthesis pathway. Both targets were validated in vitro and showed no significant cell cytotoxicity except for activity against proliferative B- and T-type lymphoid cells. Corollary to this finding was to understand the consequences of inhibition of the target to the host. An in vivo assessment for antiviral efficacy failed to demonstrate reduced viral load, but revealed microscopic changes and a trend toward reduced pyrimidine pools and findings in histopathology. We present here a discovery program that includes screen, target identification, validation, and druggability that can be broadly applied to identify and interrogate other host factors for antiviral effect starting from chemical matter of unknown target/mechanism of action.


Subject(s)
Antiviral Agents , Respiratory Syncytial Virus Infections/drug therapy , Respiratory Syncytial Virus Infections/metabolism , Respiratory Syncytial Viruses/metabolism , Animals , Antiviral Agents/chemical synthesis , Antiviral Agents/chemistry , Antiviral Agents/pharmacology , B-Lymphocytes/metabolism , B-Lymphocytes/pathology , B-Lymphocytes/virology , Cell Proliferation/drug effects , Chlorocebus aethiops , Dogs , Dose-Response Relationship, Drug , HeLa Cells , Humans , Jurkat Cells , Respiratory Syncytial Virus Infections/pathology , T-Lymphocytes/metabolism , T-Lymphocytes/pathology , T-Lymphocytes/virology , Vero Cells
18.
Science ; 385(6704): 91-99, 2024 Jul 05.
Article in English | MEDLINE | ID: mdl-38963839

ABSTRACT

Sickle cell disease (SCD) is a prevalent, life-threatening condition attributable to a heritable mutation in ß-hemoglobin. Therapeutic induction of fetal hemoglobin (HbF) can ameliorate disease complications and has been intently pursued. However, safe and effective small-molecule inducers of HbF remain elusive. We report the discovery of dWIZ-1 and dWIZ-2, molecular glue degraders of the WIZ transcription factor that robustly induce HbF in erythroblasts. Phenotypic screening of a cereblon (CRBN)-biased chemical library revealed WIZ as a previously unknown repressor of HbF. WIZ degradation is mediated by recruitment of WIZ(ZF7) to CRBN by dWIZ-1, as resolved by crystallography of the ternary complex. Pharmacological degradation of WIZ was well tolerated and induced HbF in humanized mice and cynomolgus monkeys. These findings establish WIZ degradation as a globally accessible therapeutic strategy for SCD.


Subject(s)
Anemia, Sickle Cell , Fetal Hemoglobin , Fetal Hemoglobin/genetics , Fetal Hemoglobin/metabolism , Animals , Anemia, Sickle Cell/genetics , Anemia, Sickle Cell/metabolism , Humans , Mice , Transcription Factors/metabolism , Transcription Factors/genetics , Ubiquitin-Protein Ligases/metabolism , Ubiquitin-Protein Ligases/genetics , Proteolysis , Macaca fascicularis , Adaptor Proteins, Signal Transducing/metabolism , Adaptor Proteins, Signal Transducing/genetics , Small Molecule Libraries/pharmacology , Small Molecule Libraries/chemistry , Crystallography, X-Ray
19.
Cell Stem Cell ; 31(4): 554-569.e17, 2024 Apr 04.
Article in English | MEDLINE | ID: mdl-38579685

ABSTRACT

The YAP/Hippo pathway is an organ growth and size regulation rheostat safeguarding multiple tissue stem cell compartments. LATS kinases phosphorylate and thereby inactivate YAP, thus representing a potential direct drug target for promoting tissue regeneration. Here, we report the identification and characterization of the selective small-molecule LATS kinase inhibitor NIBR-LTSi. NIBR-LTSi activates YAP signaling, shows good oral bioavailability, and expands organoids derived from several mouse and human tissues. In tissue stem cells, NIBR-LTSi promotes proliferation, maintains stemness, and blocks differentiation in vitro and in vivo. NIBR-LTSi accelerates liver regeneration following extended hepatectomy in mice. However, increased proliferation and cell dedifferentiation in multiple organs prevent prolonged systemic LATS inhibition, thus limiting potential therapeutic benefit. Together, we report a selective LATS kinase inhibitor agonizing YAP signaling and promoting tissue regeneration in vitro and in vivo, enabling future research on the regenerative potential of the YAP/Hippo pathway.


Subject(s)
Protein Kinase Inhibitors , Protein Serine-Threonine Kinases , YAP-Signaling Proteins , Animals , Humans , Mice , Cell Proliferation , Protein Serine-Threonine Kinases/antagonists & inhibitors , Protein Serine-Threonine Kinases/metabolism , Stem Cells/metabolism , Transcription Factors/metabolism , YAP-Signaling Proteins/agonists , YAP-Signaling Proteins/drug effects , YAP-Signaling Proteins/metabolism , Protein Kinase Inhibitors/chemistry , Protein Kinase Inhibitors/pharmacology
20.
J Biol Chem ; 286(22): 19489-500, 2011 Jun 03.
Article in English | MEDLINE | ID: mdl-21471202

ABSTRACT

Humans lacking sclerostin display progressive bone overgrowth due to increased bone formation. Although it is well established that sclerostin is an osteocyte-secreted bone formation inhibitor, the underlying molecular mechanisms are not fully elucidated. We identified in tandem affinity purification proteomics screens LRP4 (low density lipoprotein-related protein 4) as a sclerostin interaction partner. Biochemical assays with recombinant proteins confirmed that sclerostin LRP4 interaction is direct. Interestingly, in vitro overexpression and RNAi-mediated knockdown experiments revealed that LRP4 specifically facilitates the previously described inhibitory action of sclerostin on Wnt1/ß-catenin signaling. We found the extracellular ß-propeller structured domain of LRP4 to be required for this sclerostin facilitator activity. Immunohistochemistry demonstrated that LRP4 protein is present in human and rodent osteoblasts and osteocytes, both presumed target cells of sclerostin action. Silencing of LRP4 by lentivirus-mediated shRNA delivery blocked sclerostin inhibitory action on in vitro bone mineralization. Notably, we identified two mutations in LRP4 (R1170W and W1186S) in patients suffering from bone overgrowth. We found that these mutations impair LRP4 interaction with sclerostin and its concomitant sclerostin facilitator effect. Together these data indicate that the interaction of sclerostin with LRP4 is required to mediate the inhibitory function of sclerostin on bone formation, thus identifying a novel role for LRP4 in bone.


Subject(s)
Bone Morphogenetic Proteins/metabolism , LDL-Receptor Related Proteins/metabolism , Osteocytes/metabolism , Osteogenesis , Adaptor Proteins, Signal Transducing , Amino Acid Substitution , Animals , Bone Morphogenetic Proteins/genetics , Genetic Markers/genetics , HEK293 Cells , Humans , LDL-Receptor Related Proteins/genetics , Mice , Mutation, Missense , Signal Transduction/genetics , Wnt1 Protein/genetics , Wnt1 Protein/metabolism , beta Catenin/genetics , beta Catenin/metabolism
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