The Reciprocal Interplay Between Tnfα and the Circadian Clock
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SHARP1 (BHLHE41) Mouse Monoclonal Antibody [Clone ID: OTI3H4] Product Data
OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for TA806354 SHARP1 (BHLHE41) Mouse Monoclonal Antibody [Clone ID: OTI3H4] Product data: Product Type: Primary Antibodies Clone Name: OTI3H4 Applications: IHC, WB Recommended Dilution: WB 1:2000, IHC 1:150 Reactivity: Human Host: Mouse Isotype: IgG1 Clonality: Monoclonal Immunogen: Human recombinant protein fragment corresponding to amino acids 1-297 of human BHLHE41(NP_110389) produced in E.coli. Formulation: PBS (PH 7.3) containing 1% BSA, 50% glycerol and 0.02% sodium azide. Concentration: 1 mg/ml Purification: Purified from mouse ascites fluids or tissue culture supernatant by affinity chromatography (protein A/G) Conjugation: Unconjugated Storage: Store at -20°C as received. Stability: Stable for 12 months from date of receipt. Predicted Protein Size: 50.3 kDa Gene Name: basic helix-loop-helix family member e41 Database Link: NP_110389 Entrez Gene 79365 Human Q9C0J9 Background: This gene encodes a basic helix-loop-helix protein expressed in various tissues. The encoded protein can interact with ARNTL or compete for E-box binding sites in the promoter of PER1 and repress CLOCK/ARNTL's transactivation of PER1. This gene is believed to be involved in the control of circadian rhythm and cell differentiation. Defects in this gene are associated with the short sleep phenotype. [provided by RefSeq, Feb 2014] This product is to be used for laboratory only. Not for diagnostic or therapeutic use. View online » ©2021 OriGene Technologies, Inc., 9620 Medical Center Drive, Ste 200, Rockville, MD 20850, US 1 / 2 SHARP1 (BHLHE41) Mouse Monoclonal Antibody [Clone ID: OTI3H4] – TA806354 Synonyms: BHLHB3; DEC2; hDEC2; SHARP1 Protein Families: Transcription Factors Protein Pathways: Circadian rhythm - mammal Product images: HEK293T cells were transfected with the pCMV6- ENTRY control (Left lane) or pCMV6-ENTRY BHLHE41 ([RC206882], Right lane) cDNA for 48 hrs and lysed. -
UNIVERSITY of CALIFORNIA Los Angeles
UNIVERSITY OF CALIFORNIA Los Angeles Circadian Gene Networks In Bone Regeneration A thesis submitted in partial satisfaction of the requirements for the degree Master of Science in Oral Biology by Nathaniel Raphael Hassan 2012 ABSTRACT OF THESIS Circadian Gene Networks In Bone Regeneration By Nathaniel Raphael Hassan Master of Science in Oral Biology University of California, Los Angeles, 2012 Professor Ichiro Nishimura, Chair BACKGROUND: Previous studies suggested that vitamin D played a significant role in bone regeneration, facilitating the establishment of implant osseointegration. A whole genome microarray study further suggested that the vitamin D axis might involve circadian rhythm gene expression in the bone peripheral tissue. OBJECTIVES: To identify key gene networks involved with vitamin D receptor in the bone regeneration process and to explore any correlation with circadian rhythm gene expression in bone marrow mesenchymal stromal/stem cells (BMSC). METHODS: The available whole gene microarray data was analyzed using the weighted gene correlation network analysis (WGCNA) R package and Cytoscape software. Any gene expression correlation was examined for vitamin D receptor (VDR) as well as circadian rhythm ii genes. Separately, Per 1 luciferase transgenic Wistar rats were then applied for in vitro evaluation on BMSC circadian rhythm. Per1::luc BMSCs were seeded on 35mm dishes and forskolin-synchronized luminescence was recorded across different media conditions. The recording media included growth medium containing F12 (10% Fetal Bovine Serum, 1% Pen- Strep and antibiotic) supplemented with or without 1 nM 1,25D. Luminescence was also recorded in F12 growth medium containing bone differentiation factors (beta glycerophosphate, Ascorbic acid and Dexamethasone) supplemented with 0, 1 or 10 nM 1,25D. -
NPAS2 As a Transcriptional Regulator of Non-Rapid Eye Movement Sleep: Genotype and Sex Interactions
NPAS2 as a transcriptional regulator of non-rapid eye movement sleep: Genotype and sex interactions Paul Franken*†‡, Carol A. Dudley§, Sandi Jo Estill§, Monique Barakat*, Ryan Thomason¶, Bruce F. O’Hara¶, and Steven L. McKnight‡§ §Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390; *Department of Biological Sciences, Stanford University, Stanford, CA 94305; ¶Department of Biology, University of Kentucky, Lexington, KY 40506; and †Center for Integrative Genomics, University of Lausanne, CH-1015 Lausanne-Dorigny, Switzerland Contributed by Steven L. McKnight, March 13, 2006 Because the transcription factor neuronal Per-Arnt-Sim-type sig- delta frequency range is a sensitive marker of time spent awake (4, nal-sensor protein-domain protein 2 (NPAS2) acts both as a sensor 7) and local cortical activation (8) and is therefore widely used as and an effector of intracellular energy balance, and because sleep an index of NREMS need and intensity. is thought to correct an energy imbalance incurred during waking, The PAS-domain proteins, CLOCK, BMAL1, PERIOD-1 we examined NPAS2’s role in sleep homeostasis using npas2 (PER1), and PER2, play crucial roles in circadian rhythm gener- knockout (npas2؊/؊) mice. We found that, under conditions of ation (9). The NPAS2 paralog CLOCK, like NPAS2, can induce the increased sleep need, i.e., at the end of the active period or after transcription of per1, per2, cryptochrome-1 (cry1), and cry2. PER and sleep deprivation (SD), NPAS2 allows for sleep to occur at times CRY proteins, in turn, inhibit CLOCK- and NPAS2-induced when mice are normally awake. Lack of npas2 affected electroen- transcription, thereby closing a negative-feedback loop that is cephalogram activity of thalamocortical origin; during non-rapid thought to underlie circadian rhythm generation. -
Targeting Glioblastoma Stem Cells Through Disruption of the Circadian Clock
Published OnlineFirst August 27, 2019; DOI: 10.1158/2159-8290.CD-19-0215 RESEARCH ARTICLE Targeting Glioblastoma Stem Cells through Disruption of the Circadian Clock Zhen Dong1, Guoxin Zhang1, Meng Qu2, Ryan C. Gimple1,3, Qiulian Wu1, Zhixin Qiu1, Briana C. Prager1,3, Xiuxing Wang1, Leo J.Y. Kim1,3, Andrew R. Morton3, Deobrat Dixit1, Wenchao Zhou4, Haidong Huang4, Bin Li5, Zhe Zhu1, Shideng Bao4, Stephen C. Mack6, Lukas Chavez7, Steve A. Kay2, and Jeremy N. Rich1 Downloaded from cancerdiscovery.aacrjournals.org on September 24, 2021. © 2019 American Association for Cancer Research. Published OnlineFirst August 27, 2019; DOI: 10.1158/2159-8290.CD-19-0215 ABSTRACT Glioblastomas are highly lethal cancers, containing self-renewing glioblastoma stem cells (GSC). Here, we show that GSCs, differentiated glioblastoma cells (DGC), and nonmalignant brain cultures all displayed robust circadian rhythms, yet GSCs alone displayed exquisite dependence on core clock transcription factors, BMAL1 and CLOCK, for optimal cell growth. Downregulation of BMAL1 or CLOCK in GSCs induced cell-cycle arrest and apoptosis. Chromatin immu- noprecipitation revealed that BMAL1 preferentially bound metabolic genes and was associated with active chromatin regions in GSCs compared with neural stem cells. Targeting BMAL1 or CLOCK attenu- ated mitochondrial metabolic function and reduced expression of tricarboxylic acid cycle enzymes. Small-molecule agonists of two independent BMAL1–CLOCK negative regulators, the cryptochromes and REV-ERBs, downregulated stem cell factors and reduced GSC growth. Combination of cryp- tochrome and REV-ERB agonists induced synergistic antitumor effi cacy. Collectively, these fi ndings show that GSCs co-opt circadian regulators beyond canonical circadian circuitry to promote stemness maintenance and metabolism, offering novel therapeutic paradigms. -
Neurobiological Functions of the Period Circadian Clock 2 Gene, Per2
Review Biomol Ther 26(4), 358-367 (2018) Neurobiological Functions of the Period Circadian Clock 2 Gene, Per2 Mikyung Kim, June Bryan de la Peña, Jae Hoon Cheong and Hee Jin Kim* Department of Pharmacy, Uimyung Research Institute for Neuroscience, Sahmyook University, Seoul 01795, Republic of Korea Abstract Most organisms have adapted to a circadian rhythm that follows a roughly 24-hour cycle, which is modulated by both internal (clock-related genes) and external (environment) factors. In such organisms, the central nervous system (CNS) is influenced by the circadian rhythm of individual cells. Furthermore, the period circadian clock 2 (Per2) gene is an important component of the circadian clock, which modulates the circadian rhythm. Per2 is mainly expressed in the suprachiasmatic nucleus (SCN) of the hypothalamus as well as other brain areas, including the midbrain and forebrain. This indicates that Per2 may affect various neurobiological activities such as sleeping, depression, and addiction. In this review, we focus on the neurobiological functions of Per2, which could help to better understand its roles in the CNS. Key Words: Circadian rhythm, Per2 gene, Sleep, Depression, Addiction, Neurotransmitter INTRODUCTION and lives in organisms because it can impart effects from the level of cells to organs including the brain. Thus, it is neces- A circadian rhythm is any physiological process that displays sary to understand clock-related genes that are controlling the a roughly 24 hour cycle in living beings, such as mammals, circadian rhythm endogenously. plants, fungi and cyanobacteria (Albrecht, 2012). In organ- The Period2 (Per2) gene is a member of the Period family isms, most biological functions such as sleeping and feeding of genes consisting of Per1, Per2, and Per3, and is mainly patterns are adapted to the circadian rhythm. -
Circadian- and Sex-Dependent Increases in Intravenous Cocaine Self-Administration in Npas2 Mutant Mice
bioRxiv preprint doi: https://doi.org/10.1101/788786; this version posted October 1, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Circadian- and sex-dependent increases in intravenous cocaine self-administration in Npas2 mutant mice Lauren M. DePoy1,2, Darius D. Becker-Krail1,2, Neha M. Shah1, Ryan W. Logan1,2,3, Colleen A. McClung1,2,3 1Department of Psychiatry, Translational Neuroscience Program, University of Pittsburgh School of Medicine 2Center for Neuroscience, University of Pittsburgh 3Center for Systems Neurogenetics of Addiction, The Jackson Laboratory Contact: Lauren DePoy, PhD 450 Technology Dr. Ste 223 Pittsburgh, PA 15219 412-624-5547 [email protected] Running Title: Increased self-administration in female Npas2 mutant mice Key words: circadian, sex-differences, cocaine, self-administration, addiction, Npas2 Abstract: 250 Body: 3996 Figures: 6 Tables: 1 Supplement: 3 Figures Acknowledgements: We Would like to thank Mariah Hildebrand and Laura Holesh for animal care and genotyping. We thank Drs. Steven McKnight and David Weaver for providing the Npas2 mutant mice. This work was funded by the National Institutes of Health: DA039865 (PI: Colleen McClung, PhD) and DA046117 (PI: Lauren DePoy). Disclosures: All authors have no financial disclosures or conflicts of interest to report. 1 bioRxiv preprint doi: https://doi.org/10.1101/788786; this version posted October 1, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Background: Addiction is associated With disruptions in circadian rhythms. -
Circadian Rhythmicity and the Influence of 'Clock
2311 Z Kiss and P M Ghosh Prostate cancer and the 23:11 T123–T134 Thematic Review ‘clock’ genes WOMEN IN CANCER THEMATIC REVIEW Circadian rhythmicity and the influence of ‘clock’ genes on prostate cancer Zsofia Kiss1,2 and Paramita M Ghosh1,2,3 1VA Northern California Health Care System, Mather, California, USA Correspondence 2Department of Urology, University of California at Davis, Sacramento, California, USA should be addressed 3Department of Biochemistry and Molecular Medicine, University of California at Davis, Sacramento, to P M Ghosh California, USA Email [email protected] Abstract Key Words The androgen receptor (AR) plays a key role in the development and progression f circadian clock of prostate cancer (CaP). Since the mid-1990s, reports in the literature pointed out f androgen receptor higher incidences of CaP in some select groups, such as airline pilots and night shift f melatonin workers in comparison with those working regular hours. The common finding in these f per1 ‘high-risk’ groups was that they all experienced a deregulation of the body’s internal f bmal1 circadian rhythm. Here, we discuss how the circadian rhythm affects androgen levels and modulates CaP development and progression. Circadian rhythmicity of androgen Endocrine-Related Cancer Endocrine-Related production is lost in CaP patients, with the clock genes Per1 and Per2 decreasing, and Bmal1 increasing, in these individuals. Periodic expression of the clock genes was restored upon administration of the neurohormone melatonin, thereby suppressing CaP progression. Activation of the melatonin receptors and the AR antagonized each other, and therefore the tumour-suppressive effects of melatonin and the clock genes were most clearly observed in the absence of androgens, that is, in conjunction with androgen deprivation therapy (ADT). -
Correlation Between Circadian Gene Variants and Serum Levels of Sex Steroids and Insulin-Like Growth Factor-I
3268 Correlation between Circadian Gene Variants and Serum Levels of Sex Steroids and Insulin-like Growth Factor-I Lisa W. Chu,1,2 Yong Zhu,3 Kai Yu,1 Tongzhang Zheng,3 Anand P. Chokkalingam,4 Frank Z. Stanczyk,5 Yu-Tang Gao,6 and Ann W. Hsing1 1Division of Cancer Epidemiology and Genetics and 2Cancer Prevention Fellowship Program, Office of Preventive Oncology, National Cancer Institute, NIH, Bethesda, Maryland; 3Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, Connecticut; 4Division of Epidemiology, School of Public Health, University of California at Berkeley, Berkeley, California; 5Department of Obstetrics and Gynecology, Keck School of Medicine, University of Southern California, Los Angeles, California; and 6Department of Epidemiology, Shanghai Cancer Institute, Shanghai, China Abstract A variety of biological processes, including steroid the GG genotype. In addition, the PER1 variant was hormone secretion, have circadian rhythms, which are associated with higher serum levels of sex hormone- P influenced by nine known circadian genes. Previously, binding globulin levels ( trend = 0.03), decreasing we reported that certain variants in circadian genes 5A-androstane-3A,17B-diol glucuronide levels P P were associated with risk for prostate cancer. To pro- ( trend = 0.02), and decreasing IGFBP3 levels ( trend = vide some biological insight into these findings, we 0.05). Furthermore, the CSNK1E variant C allele was examined the relationship of five variants of circadian associated with higher -
Integrative Bulk and Single-Cell Profiling of Premanufacture T-Cell Populations Reveals Factors Mediating Long-Term Persistence of CAR T-Cell Therapy
Published OnlineFirst April 5, 2021; DOI: 10.1158/2159-8290.CD-20-1677 RESEARCH ARTICLE Integrative Bulk and Single-Cell Profiling of Premanufacture T-cell Populations Reveals Factors Mediating Long-Term Persistence of CAR T-cell Therapy Gregory M. Chen1, Changya Chen2,3, Rajat K. Das2, Peng Gao2, Chia-Hui Chen2, Shovik Bandyopadhyay4, Yang-Yang Ding2,5, Yasin Uzun2,3, Wenbao Yu2, Qin Zhu1, Regina M. Myers2, Stephan A. Grupp2,5, David M. Barrett2,5, and Kai Tan2,3,5 Downloaded from cancerdiscovery.aacrjournals.org on October 1, 2021. © 2021 American Association for Cancer Research. Published OnlineFirst April 5, 2021; DOI: 10.1158/2159-8290.CD-20-1677 ABSTRACT The adoptive transfer of chimeric antigen receptor (CAR) T cells represents a breakthrough in clinical oncology, yet both between- and within-patient differences in autologously derived T cells are a major contributor to therapy failure. To interrogate the molecular determinants of clinical CAR T-cell persistence, we extensively characterized the premanufacture T cells of 71 patients with B-cell malignancies on trial to receive anti-CD19 CAR T-cell therapy. We performed RNA-sequencing analysis on sorted T-cell subsets from all 71 patients, followed by paired Cellular Indexing of Transcriptomes and Epitopes (CITE) sequencing and single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) on T cells from six of these patients. We found that chronic IFN signaling regulated by IRF7 was associated with poor CAR T-cell persistence across T-cell subsets, and that the TCF7 regulon not only associates with the favorable naïve T-cell state, but is maintained in effector T cells among patients with long-term CAR T-cell persistence. -
The Nuclear Receptor REV-Erbα Modulates Th17 Cell-Mediated Autoimmune Disease
The nuclear receptor REV-ERBα modulates Th17 cell-mediated autoimmune disease Christina Changa,b, Chin-San Looa,b, Xuan Zhaoc, Laura A. Soltd, Yuqiong Lianga, Sagar P. Bapata,c,e, Han Choc, Theodore M. Kameneckad, Mathias Leblanca, Annette R. Atkinsc, Ruth T. Yuc, Michael Downesc, Thomas P. Burrisf, Ronald M. Evansc,g,1, and Ye Zhenga,1 aNOMIS Center for Immunobiology and Microbial Pathogenesis, The Salk Institute for Biological Studies, La Jolla, CA 92037; bDivision of Biological Sciences, University of California San Diego, La Jolla, CA 92093; cGene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037; dDepartment of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL 33458; eMedical Scientist Training Program, University of California San Diego, La Jolla, CA 92093; fCenter for Clinical Pharmacology, Washington University School of Medicine and St. Louis College of Pharmacy, St. Louis, MO 63104; and gHoward Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037 Contributed by Ronald M. Evans, July 29, 2019 (sent for review May 9, 2019; reviewed by Ming O. Li and David D. Moore) T helper 17 (Th17) cells produce interleukin-17 (IL-17) cytokines In this study, we show that REV-ERBα is also a key feedback and drive inflammatory responses in autoimmune diseases such as regulator of RORγt in Th17 cells. REV-ERBα is specifically up- multiple sclerosis. The differentiation of Th17 cells is dependent on regulated during Th17 differentiation and plays a dual role in the retinoic acid receptor-related orphan nuclear receptor RORγt. Th17 cells. When expressed at a low level, REV-ERBα promotes Here, we identify REV-ERBα (encoded by Nr1d1), a member of the RORγt expression via the suppression of negative regulator nuclear hormone receptor family, as a transcriptional repressor NFIL3 as reported previously (15, 16). -
Effects of PM Exposure on the Methylation of Clock Genes in a Population of Subjects with Overweight Or Obesity
International Journal of Environmental Research and Public Health Article Effects of PM Exposure on the Methylation of Clock Genes in A Population of Subjects with Overweight or Obesity Paola Monti 1 , Simona Iodice 2, Letizia Tarantini 2, Francesca Sacchi 2, Luca Ferrari 2 , Massimiliano Ruscica 3 , Massimiliano Buoli 4,5 , Luisella Vigna 1,6 , Angela Cecilia Pesatori 1,2 and Valentina Bollati 2,* 1 Department of Preventive Medicine, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; [email protected] (P.M.); [email protected] (L.V.); [email protected] (A.C.P.) 2 EPIGET—Epidemiology, Epigenetics and Toxicology Lab, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, 20122 Milan, Italy; [email protected] (S.I.); [email protected] (L.T.); [email protected] (F.S.); [email protected] (L.F.) 3 Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, 20133 Milan, Italy; [email protected] 4 Department of Pathophysiology and Transplantation, Università degli Studi di Milano, 20122 Milan, Italy; [email protected] 5 Department of Neurosciences and Mental Health, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy 6 Center of Obesity and Work EASO Collaborating Centers for Obesity Management, 20122 Milan, Italy * Correspondence: [email protected]; Tel.: +39-025-032-0127 Abstract: The expression of clock genes, regulating the synchronization of metabolic and behavioral processes with environmental light/dark cycles, is regulated by methylation and might be influenced by short-term exposure to airborne particulate matter (PM), especially in individuals that are hyper- Citation: Monti, P.; Iodice, S.; sensitive to proinflammatory cues. -
Supplementary Table 1
Supplementary Table 1. 492 genes are unique to 0 h post-heat timepoint. The name, p-value, fold change, location and family of each gene are indicated. Genes were filtered for an absolute value log2 ration 1.5 and a significance value of p ≤ 0.05. Symbol p-value Log Gene Name Location Family Ratio ABCA13 1.87E-02 3.292 ATP-binding cassette, sub-family unknown transporter A (ABC1), member 13 ABCB1 1.93E-02 −1.819 ATP-binding cassette, sub-family Plasma transporter B (MDR/TAP), member 1 Membrane ABCC3 2.83E-02 2.016 ATP-binding cassette, sub-family Plasma transporter C (CFTR/MRP), member 3 Membrane ABHD6 7.79E-03 −2.717 abhydrolase domain containing 6 Cytoplasm enzyme ACAT1 4.10E-02 3.009 acetyl-CoA acetyltransferase 1 Cytoplasm enzyme ACBD4 2.66E-03 1.722 acyl-CoA binding domain unknown other containing 4 ACSL5 1.86E-02 −2.876 acyl-CoA synthetase long-chain Cytoplasm enzyme family member 5 ADAM23 3.33E-02 −3.008 ADAM metallopeptidase domain Plasma peptidase 23 Membrane ADAM29 5.58E-03 3.463 ADAM metallopeptidase domain Plasma peptidase 29 Membrane ADAMTS17 2.67E-04 3.051 ADAM metallopeptidase with Extracellular other thrombospondin type 1 motif, 17 Space ADCYAP1R1 1.20E-02 1.848 adenylate cyclase activating Plasma G-protein polypeptide 1 (pituitary) receptor Membrane coupled type I receptor ADH6 (includes 4.02E-02 −1.845 alcohol dehydrogenase 6 (class Cytoplasm enzyme EG:130) V) AHSA2 1.54E-04 −1.6 AHA1, activator of heat shock unknown other 90kDa protein ATPase homolog 2 (yeast) AK5 3.32E-02 1.658 adenylate kinase 5 Cytoplasm kinase AK7