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1.
Nature ; 547(7664): 453-457, 2017 07 27.
Article in English | MEDLINE | ID: mdl-28678785

ABSTRACT

Plasticity of the cell state has been proposed to drive resistance to multiple classes of cancer therapies, thereby limiting their effectiveness. A high-mesenchymal cell state observed in human tumours and cancer cell lines has been associated with resistance to multiple treatment modalities across diverse cancer lineages, but the mechanistic underpinning for this state has remained incompletely understood. Here we molecularly characterize this therapy-resistant high-mesenchymal cell state in human cancer cell lines and organoids and show that it depends on a druggable lipid-peroxidase pathway that protects against ferroptosis, a non-apoptotic form of cell death induced by the build-up of toxic lipid peroxides. We show that this cell state is characterized by activity of enzymes that promote the synthesis of polyunsaturated lipids. These lipids are the substrates for lipid peroxidation by lipoxygenase enzymes. This lipid metabolism creates a dependency on pathways converging on the phospholipid glutathione peroxidase (GPX4), a selenocysteine-containing enzyme that dissipates lipid peroxides and thereby prevents the iron-mediated reactions of peroxides that induce ferroptotic cell death. Dependency on GPX4 was found to exist across diverse therapy-resistant states characterized by high expression of ZEB1, including epithelial-mesenchymal transition in epithelial-derived carcinomas, TGFß-mediated therapy-resistance in melanoma, treatment-induced neuroendocrine transdifferentiation in prostate cancer, and sarcomas, which are fixed in a mesenchymal state owing to their cells of origin. We identify vulnerability to ferroptic cell death induced by inhibition of a lipid peroxidase pathway as a feature of therapy-resistant cancer cells across diverse mesenchymal cell-state contexts.


Subject(s)
Glutathione Peroxidase/metabolism , Lipid Peroxidation/drug effects , Neoplasms/drug therapy , Neoplasms/enzymology , Cadherins/metabolism , Cell Death , Cell Line, Tumor , Cell Lineage , Cell Transdifferentiation , Drug Resistance, Neoplasm/genetics , Epithelial-Mesenchymal Transition , Humans , Iron/metabolism , Lipid Peroxides/metabolism , Male , Melanoma/drug therapy , Melanoma/enzymology , Melanoma/metabolism , Melanoma/pathology , Mesoderm/drug effects , Mesoderm/enzymology , Mesoderm/metabolism , Mesoderm/pathology , Neoplasms/genetics , Neoplasms/pathology , Phospholipid Hydroperoxide Glutathione Peroxidase , Prostatic Neoplasms/drug therapy , Prostatic Neoplasms/enzymology , Prostatic Neoplasms/metabolism , Prostatic Neoplasms/pathology , Proteomics , Proto-Oncogene Proteins B-raf/genetics , Reproducibility of Results , Zinc Finger E-box-Binding Homeobox 1/genetics
2.
Nat Chem Biol ; 12(2): 109-16, 2016 Feb.
Article in English | MEDLINE | ID: mdl-26656090

ABSTRACT

Changes in cellular gene expression in response to small-molecule or genetic perturbations have yielded signatures that can connect unknown mechanisms of action (MoA) to ones previously established. We hypothesized that differential basal gene expression could be correlated with patterns of small-molecule sensitivity across many cell lines to illuminate the actions of compounds whose MoA are unknown. To test this idea, we correlated the sensitivity patterns of 481 compounds with ∼19,000 basal transcript levels across 823 different human cancer cell lines and identified selective outlier transcripts. This process yielded many novel mechanistic insights, including the identification of activation mechanisms, cellular transporters and direct protein targets. We found that ML239, originally identified in a phenotypic screen for selective cytotoxicity in breast cancer stem-like cells, most likely acts through activation of fatty acid desaturase 2 (FADS2). These data and analytical tools are available to the research community through the Cancer Therapeutics Response Portal.


Subject(s)
Gene Expression Regulation, Neoplastic/drug effects , Small Molecule Libraries/pharmacology , Aflatoxins/chemistry , Aflatoxins/pharmacology , Blotting, Western , Breast Neoplasms/drug therapy , Cell Line, Tumor , Computer Simulation , Drug Delivery Systems , Female , Humans , Molecular Structure , Principal Component Analysis , Real-Time Polymerase Chain Reaction
3.
Proc Natl Acad Sci U S A ; 106(50): 21453-8, 2009 Dec 15.
Article in English | MEDLINE | ID: mdl-19940241

ABSTRACT

In mammals, the circadian oscillator generates approximately 24-h rhythms in feeding behavior, even under constant environmental conditions. Livers of mice held under constant darkness exhibit circadian rhythm in abundance in up to 15% of expressed transcripts. Therefore, oscillations in hepatic transcripts could be driven by rhythmic food intake or sustained by the hepatic circadian oscillator, or a combination of both. To address this question, we used distinct feeding and fasting paradigms on wild-type (WT) and circadian clock-deficient mice. We monitored temporal patterns of feeding and hepatic transcription. Both food availability and the temporal pattern of feeding determined the repertoire, phase, and amplitude of the circadian transcriptome in WT liver. In the absence of feeding, only a small subset of transcripts continued to express circadian patterns. Conversely, temporally restricted feeding restored rhythmic transcription of hundreds of genes in oscillator-deficient mouse liver. Our findings show that both temporal pattern of food intake and the circadian clock drive rhythmic transcription, thereby highlighting temporal regulation of hepatic transcription as an emergent property of the circadian system.


Subject(s)
Circadian Rhythm/genetics , Eating/genetics , Gene Expression Regulation , Liver/metabolism , Animals , Gene Expression Profiling , Male , Mice , Mice, Inbred C57BL , RNA, Messenger/analysis , Time Factors
4.
Cell Rep ; 31(13): 107841, 2020 06 30.
Article in English | MEDLINE | ID: mdl-32610142

ABSTRACT

Synthetic CRISPR-based gene-drive systems have tremendous potential in public health and agriculture, such as for fighting vector-borne diseases or suppressing crop pest populations. These elements can rapidly spread in a population by breaching the inheritance limit of 50% dictated by Mendel's law of gene segregation, making them a promising tool for population engineering. However, current technologies lack control over their propagation capacity, and there are important concerns about potential unchecked spreading. Here, we describe a gene-drive system in Drosophila that generates an analog inheritance output that can be tightly and conditionally controlled to between 50% and 100%. This technology uses a modified SpCas9 that responds to a synthetic, orally available small molecule, fine-tuning the inheritance probability. This system opens a new avenue to feasibility studies for spatial and temporal control of gene drives using small molecules.


Subject(s)
Drosophila melanogaster/genetics , Gene Drive Technology , Inheritance Patterns/genetics , Small Molecule Libraries/metabolism , Animals , Animals, Genetically Modified , CRISPR-Associated Protein 9/metabolism , Pharmaceutical Preparations
5.
Nat Genet ; 49(2): 274-281, 2017 Feb.
Article in English | MEDLINE | ID: mdl-27992416

ABSTRACT

Chronic sleep disturbances, associated with cardiometabolic diseases, psychiatric disorders and all-cause mortality, affect 25-30% of adults worldwide. Although environmental factors contribute substantially to self-reported habitual sleep duration and disruption, these traits are heritable and identification of the genes involved should improve understanding of sleep, mechanisms linking sleep to disease and development of new therapies. We report single- and multiple-trait genome-wide association analyses of self-reported sleep duration, insomnia symptoms and excessive daytime sleepiness in the UK Biobank (n = 112,586). We discover loci associated with insomnia symptoms (near MEIS1, TMEM132E, CYCL1 and TGFBI in females and WDR27 in males), excessive daytime sleepiness (near AR-OPHN1) and a composite sleep trait (near PATJ (INADL) and HCRTR2) and replicate a locus associated with sleep duration (at PAX8). We also observe genetic correlation between longer sleep duration and schizophrenia risk (rg = 0.29, P = 1.90 × 10-13) and between increased levels of excessive daytime sleepiness and increased measures for adiposity traits (body mass index (BMI): rg = 0.20, P = 3.12 × 10-9; waist circumference: rg = 0.20, P = 2.12 × 10-7).


Subject(s)
Genetic Loci/genetics , Mental Disorders/genetics , Metabolic Diseases/genetics , Sleep Wake Disorders/genetics , Sleep/genetics , Adiposity/genetics , Adult , Aged , Female , Genome-Wide Association Study/methods , Humans , Male , Middle Aged , Phenotype , Self Report , Waist Circumference/genetics
6.
Nat Commun ; 7: 10889, 2016 Mar 09.
Article in English | MEDLINE | ID: mdl-26955885

ABSTRACT

Our sleep timing preference, or chronotype, is a manifestation of our internal biological clock. Variation in chronotype has been linked to sleep disorders, cognitive and physical performance, and chronic disease. Here we perform a genome-wide association study of self-reported chronotype within the UK Biobank cohort (n=100,420). We identify 12 new genetic loci that implicate known components of the circadian clock machinery and point to previously unstudied genetic variants and candidate genes that might modulate core circadian rhythms or light-sensing pathways. Pathway analyses highlight central nervous and ocular systems and fear-response-related processes. Genetic correlation analysis suggests chronotype shares underlying genetic pathways with schizophrenia, educational attainment and possibly BMI. Further, Mendelian randomization suggests that evening chronotype relates to higher educational attainment. These results not only expand our knowledge of the circadian system in humans but also expose the influence of circadian characteristics over human health and life-history variables such as educational attainment.


Subject(s)
Circadian Rhythm , Genetic Loci , Genome, Human , White People/genetics , Adult , Aged , Cohort Studies , Female , Genome-Wide Association Study , Humans , Male , Middle Aged , United Kingdom
7.
Nat Commun ; 7: 11987, 2016 06 22.
Article in English | MEDLINE | ID: mdl-27329820

ABSTRACT

Identifying therapeutic targets in rare cancers remains challenging due to the paucity of established models to perform preclinical studies. As a proof-of-concept, we developed a patient-derived cancer cell line, CLF-PED-015-T, from a paediatric patient with a rare undifferentiated sarcoma. Here, we confirm that this cell line recapitulates the histology and harbours the majority of the somatic genetic alterations found in a metastatic lesion isolated at first relapse. We then perform pooled CRISPR-Cas9 and RNAi loss-of-function screens and a small-molecule screen focused on druggable cancer targets. Integrating these three complementary and orthogonal methods, we identify CDK4 and XPO1 as potential therapeutic targets in this cancer, which has no known alterations in these genes. These observations establish an approach that integrates new patient-derived models, functional genomics and chemical screens to facilitate the discovery of targets in rare cancers.


Subject(s)
Cyclin-Dependent Kinase 4/genetics , Karyopherins/genetics , Rare Diseases/genetics , Receptors, Cytoplasmic and Nuclear/genetics , Sarcoma/genetics , A549 Cells , Animals , Antineoplastic Combined Chemotherapy Protocols/therapeutic use , CRISPR-Cas Systems , Cell Cycle , Cell Line, Tumor , Doxorubicin/administration & dosage , Drug Screening Assays, Antitumor , Exome , Female , Genomics , Humans , Hydrazines/administration & dosage , Mice , Mice, Nude , Neoplasm Metastasis , Neoplasm Recurrence, Local , Neoplasm Transplantation , Piperazines/administration & dosage , Pyridines/administration & dosage , RNA Interference , Rare Diseases/drug therapy , Sarcoma/drug therapy , Sequence Analysis, RNA , Triazoles/administration & dosage , Exportin 1 Protein
8.
Cell Metab ; 22(5): 789-98, 2015 Nov 03.
Article in English | MEDLINE | ID: mdl-26411343

ABSTRACT

A diurnal rhythm of eating-fasting promotes health, but the eating pattern of humans is rarely assessed. Using a mobile app, we monitored ingestion events in healthy adults with no shift-work for several days. Most subjects ate frequently and erratically throughout wakeful hours, and overnight fasting duration paralleled time in bed. There was a bias toward eating late, with an estimated <25% of calories being consumed before noon and >35% after 6 p.m. "Metabolic jetlag" resulting from weekday/weekend variation in eating pattern akin to travel across time zones was prevalent. The daily intake duration (95% interval) exceeded 14.75 hr for half of the cohort. When overweight individuals with >14 hr eating duration ate for only 10-11 hr daily for 16 weeks assisted by a data visualization (raster plot of dietary intake pattern, "feedogram") that we developed, they reduced body weight, reported being energetic, and improved sleep. Benefits persisted for a year.


Subject(s)
Eating/physiology , Energy Intake/physiology , Feeding Behavior/physiology , Smartphone , Adult , Body Weight , Female , Humans , Male
9.
Science ; 347(6227): 1265-9, 2015 Mar 13.
Article in English | MEDLINE | ID: mdl-25766238

ABSTRACT

Circadian clocks orchestrate periods of rest or activity and feeding or fasting over the course of a 24-hour day and maintain homeostasis. To assess whether a consolidated 24-hour cycle of feeding and fasting can sustain health, we explored the effect of time-restricted feeding (TRF; food access limited to daytime 12 hours every day) on neural, peripheral, and cardiovascular physiology in Drosophila melanogaster. We detected improved sleep, prevention of body weight gain, and deceleration of cardiac aging under TRF, even when caloric intake and activity were unchanged. We used temporal gene expression profiling and validation through classical genetics to identify the TCP-1 ring complex (TRiC) chaperonin, the mitochondrial electron transport chain complexes, and the circadian clock as pathways mediating the benefits of TRF.


Subject(s)
Circadian Clocks , Drosophila melanogaster/physiology , Animals , Chaperonins/genetics , Chaperonins/metabolism , Drosophila Proteins/genetics , Drosophila Proteins/metabolism , Drosophila melanogaster/genetics , Electron Transport , Energy Intake , Feeding Behavior , Flight, Animal , Heart/physiology , Male , Metabolic Networks and Pathways , Mitochondria/metabolism , Myocardial Contraction , Sleep , Transcriptome , Weight Gain
10.
Elife ; 3: e03357, 2014 Jul 17.
Article in English | MEDLINE | ID: mdl-25035422

ABSTRACT

The robustness and limited plasticity of the master circadian clock in the suprachiasmatic nucleus (SCN) is attributed to strong intercellular communication among its constituent neurons. However, factors that specify this characteristic feature of the SCN are unknown. Here, we identified Lhx1 as a regulator of SCN coupling. A phase-shifting light pulse causes acute reduction in Lhx1 expression and of its target genes that participate in SCN coupling. Mice lacking Lhx1 in the SCN have intact circadian oscillators, but reduced levels of coupling factors. Consequently, the mice rapidly phase shift under a jet lag paradigm and their behavior rhythms gradually deteriorate under constant condition. Ex vivo recordings of the SCN from these mice showed rapid desynchronization of unit oscillators. Therefore, by regulating expression of genes mediating intercellular communication, Lhx1 imparts synchrony among SCN neurons and ensures consolidated rhythms of activity and rest that is resistant to photic noise.


Subject(s)
Circadian Clocks/genetics , Jet Lag Syndrome/genetics , LIM-Homeodomain Proteins/genetics , Neurons/metabolism , Period Circadian Proteins/genetics , Suprachiasmatic Nucleus/metabolism , Transcription Factors/genetics , Animals , Cell Communication , Gene Expression Profiling , Gene Expression Regulation , Jet Lag Syndrome/metabolism , Jet Lag Syndrome/pathology , LIM-Homeodomain Proteins/metabolism , Male , Mice , Mice, Knockout , Neurons/pathology , Period Circadian Proteins/metabolism , Photoperiod , Signal Transduction , Suprachiasmatic Nucleus/pathology , Transcription Factors/metabolism
11.
Cell Metab ; 15(6): 848-60, 2012 Jun 06.
Article in English | MEDLINE | ID: mdl-22608008

ABSTRACT

While diet-induced obesity has been exclusively attributed to increased caloric intake from fat, animals fed a high-fat diet (HFD) ad libitum (ad lib) eat frequently throughout day and night, disrupting the normal feeding cycle. To test whether obesity and metabolic diseases result from HFD or disruption of metabolic cycles, we subjected mice to either ad lib or time-restricted feeding (tRF) of a HFD for 8 hr per day. Mice under tRF consume equivalent calories from HFD as those with ad lib access yet are protected against obesity, hyperinsulinemia, hepatic steatosis, and inflammation and have improved motor coordination. The tRF regimen improved CREB, mTOR, and AMPK pathway function and oscillations of the circadian clock and their target genes' expression. These changes in catabolic and anabolic pathways altered liver metabolome and improved nutrient utilization and energy expenditure. We demonstrate in mice that tRF regimen is a nonpharmacological strategy against obesity and associated diseases.


Subject(s)
Diet, High-Fat/adverse effects , Eating , Energy Intake , Metabolic Diseases/prevention & control , Adenylate Kinase/metabolism , Adipose Tissue, Brown/metabolism , Adipose Tissue, Brown/pathology , Adipose Tissue, White/metabolism , Adiposity , Animals , Bile Acids and Salts/biosynthesis , Cholesterol/blood , Circadian Rhythm , Cyclic AMP Response Element-Binding Protein/metabolism , Cytokines/genetics , Cytokines/metabolism , Energy Metabolism , Fatty Liver/etiology , Fatty Liver/metabolism , Fatty Liver/prevention & control , Gene Expression , Glucose/metabolism , Homeostasis , Lipid Metabolism , Liver/metabolism , Liver/pathology , Male , Metabolic Diseases/etiology , Metabolic Diseases/metabolism , Mice , Mice, Inbred C57BL , Oxygen Consumption , Phosphorylation , Ribosomal Protein S6 Kinases/metabolism , TOR Serine-Threonine Kinases/metabolism , Time Factors , Weight Gain
12.
Cell Metab ; 13(6): 613-4, 2011 Jun 08.
Article in English | MEDLINE | ID: mdl-21641540

ABSTRACT

The diurnally active fruit flies prefer a major meal in the morning. Feeding the flies in the evening uncouples their metabolic cycle from circadian activity rhythms. A paper by Xu et al. in this issue of Cell Metabolism found that such uncoupled rhythms reduce egg laying.

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