Estrogen Promotes Camp Production in Mesenchymal Stem Cells by Regulating ADCY2
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Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
Supplementary Table 2
Supplementary Table 2. Differentially Expressed Genes following Sham treatment relative to Untreated Controls Fold Change Accession Name Symbol 3 h 12 h NM_013121 CD28 antigen Cd28 12.82 BG665360 FMS-like tyrosine kinase 1 Flt1 9.63 NM_012701 Adrenergic receptor, beta 1 Adrb1 8.24 0.46 U20796 Nuclear receptor subfamily 1, group D, member 2 Nr1d2 7.22 NM_017116 Calpain 2 Capn2 6.41 BE097282 Guanine nucleotide binding protein, alpha 12 Gna12 6.21 NM_053328 Basic helix-loop-helix domain containing, class B2 Bhlhb2 5.79 NM_053831 Guanylate cyclase 2f Gucy2f 5.71 AW251703 Tumor necrosis factor receptor superfamily, member 12a Tnfrsf12a 5.57 NM_021691 Twist homolog 2 (Drosophila) Twist2 5.42 NM_133550 Fc receptor, IgE, low affinity II, alpha polypeptide Fcer2a 4.93 NM_031120 Signal sequence receptor, gamma Ssr3 4.84 NM_053544 Secreted frizzled-related protein 4 Sfrp4 4.73 NM_053910 Pleckstrin homology, Sec7 and coiled/coil domains 1 Pscd1 4.69 BE113233 Suppressor of cytokine signaling 2 Socs2 4.68 NM_053949 Potassium voltage-gated channel, subfamily H (eag- Kcnh2 4.60 related), member 2 NM_017305 Glutamate cysteine ligase, modifier subunit Gclm 4.59 NM_017309 Protein phospatase 3, regulatory subunit B, alpha Ppp3r1 4.54 isoform,type 1 NM_012765 5-hydroxytryptamine (serotonin) receptor 2C Htr2c 4.46 NM_017218 V-erb-b2 erythroblastic leukemia viral oncogene homolog Erbb3 4.42 3 (avian) AW918369 Zinc finger protein 191 Zfp191 4.38 NM_031034 Guanine nucleotide binding protein, alpha 12 Gna12 4.38 NM_017020 Interleukin 6 receptor Il6r 4.37 AJ002942 -
Epigenetic Modifications to Cytosine and Alzheimer's Disease
University of Kentucky UKnowledge Theses and Dissertations--Chemistry Chemistry 2017 EPIGENETIC MODIFICATIONS TO CYTOSINE AND ALZHEIMER’S DISEASE: A QUANTITATIVE ANALYSIS OF POST-MORTEM TISSUE Elizabeth M. Ellison University of Kentucky, [email protected] Digital Object Identifier: https://doi.org/10.13023/ETD.2017.398 Right click to open a feedback form in a new tab to let us know how this document benefits ou.y Recommended Citation Ellison, Elizabeth M., "EPIGENETIC MODIFICATIONS TO CYTOSINE AND ALZHEIMER’S DISEASE: A QUANTITATIVE ANALYSIS OF POST-MORTEM TISSUE" (2017). Theses and Dissertations--Chemistry. 86. https://uknowledge.uky.edu/chemistry_etds/86 This Doctoral Dissertation is brought to you for free and open access by the Chemistry at UKnowledge. It has been accepted for inclusion in Theses and Dissertations--Chemistry by an authorized administrator of UKnowledge. For more information, please contact [email protected]. STUDENT AGREEMENT: I represent that my thesis or dissertation and abstract are my original work. Proper attribution has been given to all outside sources. I understand that I am solely responsible for obtaining any needed copyright permissions. I have obtained needed written permission statement(s) from the owner(s) of each third-party copyrighted matter to be included in my work, allowing electronic distribution (if such use is not permitted by the fair use doctrine) which will be submitted to UKnowledge as Additional File. I hereby grant to The University of Kentucky and its agents the irrevocable, non-exclusive, and royalty-free license to archive and make accessible my work in whole or in part in all forms of media, now or hereafter known. -
Soluble Adenylyl Cyclase Inhibition Prevents Human Sperm Functions Essential for Fertilization
bioRxiv preprint doi: https://doi.org/10.1101/2021.04.27.441671; this version posted April 28, 2021. 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. Soluble adenylyl cyclase inhibition prevents human sperm functions essential for fertilization Melanie Balbach1, Lubna Ghanem1, Thomas Rossetti1, Navpreet Kaur1, Carla Ritagliati1,3, Jacob Ferreira1, Dario Krapf3, Lis C Puga Molina4, Celia Maria Santi4, Jan Niklas Hansen5, Dagmar Wachten5, Makoto Fushimi2, Peter T. Meinke1,2, Jochen Buck1 & Lonny R. Levin1 1Department of Pharmacology, Weill Cornell Medicine, New York City, NY 2Tri-Institutional Therapeutics Discovery Institute, New York City, NY 3Laboratory of Cell Signal Transduction Networks, Instituto de Biología Molecular y Celular de Rosario, Rosario, Argentina 4Department of OB/GYN, Washington University School of Medicine, Saint Louis, Missouri 5Institute of Innate Immunity, Biophysical Imaging, Medical Faculty, University of Bonn, Bonn, Germany To whom correspondence should be addressed: Dr. Lonny R. Levin, Department of Pharmacology, Weill Cornell Medicine, 1300 York Avenue, New York City, NY, 10065; phone: +1 212 746 6752, email: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2021.04.27.441671; this version posted April 28, 2021. 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. 1 Abstract 2 Soluble adenylyl cyclase (sAC: ADCY10) is essential for activating dormant sperm. Studies of 3 freshly dissected mouse sperm identified sAC as needed for initiating capacitation and activating 4 motility. -
Detection of H3k4me3 Identifies Neurohiv Signatures, Genomic
viruses Article Detection of H3K4me3 Identifies NeuroHIV Signatures, Genomic Effects of Methamphetamine and Addiction Pathways in Postmortem HIV+ Brain Specimens that Are Not Amenable to Transcriptome Analysis Liana Basova 1, Alexander Lindsey 1, Anne Marie McGovern 1, Ronald J. Ellis 2 and Maria Cecilia Garibaldi Marcondes 1,* 1 San Diego Biomedical Research Institute, San Diego, CA 92121, USA; [email protected] (L.B.); [email protected] (A.L.); [email protected] (A.M.M.) 2 Departments of Neurosciences and Psychiatry, University of California San Diego, San Diego, CA 92103, USA; [email protected] * Correspondence: [email protected] Abstract: Human postmortem specimens are extremely valuable resources for investigating trans- lational hypotheses. Tissue repositories collect clinically assessed specimens from people with and without HIV, including age, viral load, treatments, substance use patterns and cognitive functions. One challenge is the limited number of specimens suitable for transcriptional studies, mainly due to poor RNA quality resulting from long postmortem intervals. We hypothesized that epigenomic Citation: Basova, L.; Lindsey, A.; signatures would be more stable than RNA for assessing global changes associated with outcomes McGovern, A.M.; Ellis, R.J.; of interest. We found that H3K27Ac or RNA Polymerase (Pol) were not consistently detected by Marcondes, M.C.G. Detection of H3K4me3 Identifies NeuroHIV Chromatin Immunoprecipitation (ChIP), while the enhancer H3K4me3 histone modification was Signatures, Genomic Effects of abundant and stable up to the 72 h postmortem. We tested our ability to use H3K4me3 in human Methamphetamine and Addiction prefrontal cortex from HIV+ individuals meeting criteria for methamphetamine use disorder or not Pathways in Postmortem HIV+ Brain (Meth +/−) which exhibited poor RNA quality and were not suitable for transcriptional profiling. -
Novel Modulation of Adenylyl Cyclase Type 2 Jason Michael Conley Purdue University
Purdue University Purdue e-Pubs Open Access Dissertations Theses and Dissertations Fall 2013 Novel Modulation of Adenylyl Cyclase Type 2 Jason Michael Conley Purdue University Follow this and additional works at: https://docs.lib.purdue.edu/open_access_dissertations Part of the Medicinal-Pharmaceutical Chemistry Commons Recommended Citation Conley, Jason Michael, "Novel Modulation of Adenylyl Cyclase Type 2" (2013). Open Access Dissertations. 211. https://docs.lib.purdue.edu/open_access_dissertations/211 This document has been made available through Purdue e-Pubs, a service of the Purdue University Libraries. Please contact [email protected] for additional information. Graduate School ETD Form 9 (Revised 12/07) PURDUE UNIVERSITY GRADUATE SCHOOL Thesis/Dissertation Acceptance This is to certify that the thesis/dissertation prepared By Jason Michael Conley Entitled NOVEL MODULATION OF ADENYLYL CYCLASE TYPE 2 Doctor of Philosophy For the degree of Is approved by the final examining committee: Val Watts Chair Gregory Hockerman Ryan Drenan Donald Ready To the best of my knowledge and as understood by the student in the Research Integrity and Copyright Disclaimer (Graduate School Form 20), this thesis/dissertation adheres to the provisions of Purdue University’s “Policy on Integrity in Research” and the use of copyrighted material. Approved by Major Professor(s): ____________________________________Val Watts ____________________________________ Approved by: Jean-Christophe Rochet 08/16/2013 Head of the Graduate Program Date i NOVEL MODULATION OF ADENYLYL CYCLASE TYPE 2 A Dissertation Submitted to the Faculty of Purdue University by Jason Michael Conley In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy December 2013 Purdue University West Lafayette, Indiana ii For my parents iii ACKNOWLEDGEMENTS I am very grateful for the mentorship of Dr. -
Sex Chromosome Complement Regulates Expression of Mood-Related Genes Marianne L Seney1,2, Kokomma I Ekong1, Ying Ding3,4, George C Tseng3,5 and Etienne Sibille1,2,6*
Seney et al. Biology of Sex Differences 2013, 4:20 http://www.bsd-journal.com/content/4/1/20 RESEARCH Open Access Sex chromosome complement regulates expression of mood-related genes Marianne L Seney1,2, Kokomma I Ekong1, Ying Ding3,4, George C Tseng3,5 and Etienne Sibille1,2,6* Abstract Background: Studies on major depressive and anxiety disorders suggest dysfunctions in brain corticolimbic circuits, including altered gamma-aminobutyric acid (GABA) and modulatory (serotonin and dopamine) neurotransmission. Interestingly, sexual dimorphisms in GABA, serotonin, and dopamine systems are also reported. Understanding the mechanisms behind these sexual dimorphisms may help unravel the biological bases of the heightened female vulnerability to mood disorders. Here, we investigate the contribution of sex-related factors (sex chromosome complement, developmental gonadal sex, or adult circulating hormones) to frontal cortex expression of selected GABA-, serotonin-, and dopamine-related genes. Methods: As gonadal sex is determined by sex chromosome complement, the role of sex chromosomes cannot be investigated individually in humans. Therefore, we used the Four Core Genotypes (FCG) mouse model, in which sex chromosome complement and gonadal sex are artificially decoupled, to examine the expression of 13 GABA-related genes, 6 serotonin- and dopamine-related genes, and 8 associated signal transduction genes under chronic stress conditions. Results were analyzed by three-way ANOVA (sex chromosome complement × gonadal sex × circulating testosterone). A global perspective of gene expression changes was provided by heatmap representation and gene co-expression networks to identify patterns of transcriptional activities related to each main factor. Results: We show that under chronic stress conditions, sex chromosome complement influenced GABA/serotonin/ dopamine-related gene expression in the frontal cortex, with XY mice consistently having lower gene expression compared to XX mice. -
Systems Biology Understanding of the Effects of Lithium on Cancer
bioRxiv preprint doi: https://doi.org/10.1101/363077; this version posted August 24, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. Systems Biology Understanding of the Effects of Lithium on Cancer Weihao Ge1,2 and Eric Jakobsson1,2,3, * 1National Center for Supercomputing Applications, 2Center for Biophysics and Computational Biology, 3Department of Molecular and Integrative Physiology University of Illinois at Urbana-Champaign, Urbana, IL, USA Correspondence *Eric Jakobsson [email protected] Abstract Lithium has many widely varying biochemical and phenomenological effects, suggesting that a systems biology approach is required to understand its action. Multiple lines of evidence point to lithium as a significant factor in development of cancer, showing that understanding lithium action is of high importance. In this paper we undertake first steps towards a systems approach by analyzing mutual enrichment between the interactomes of lithium-sensitive enzymes and the pathways associated with cancer. This work integrates information from two important databases, STRING and KEGG pathways. We find that for the majority of cancer pathways the mutual enrichment is many times greater than chance, reinforcing previous lines of evidence that lithium is an important influence on cancer. bioRxiv preprint doi: https://doi.org/10.1101/363077; this version posted August 24, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. -
Maternal Folic Acid Impacts DNA Methylation Profile in Male Rat Offspring Implicated in Neurodevelopment and Learning/Memory
Wang et al. Genes & Nutrition (2021) 16:1 https://doi.org/10.1186/s12263-020-00681-1 RESEARCH Open Access Maternal folic acid impacts DNA methylation profile in male rat offspring implicated in neurodevelopment and learning/memory abilities Xinyan Wang1, Zhenshu Li1, Yun Zhu2,3, Jing Yan3,4, Huan Liu1,3, Guowei Huang1,3 and Wen Li1,3* Abstract Background: Periconceptional folic acid (FA) supplementation not only reduces the incidence of neural tube defects, but also improves cognitive performances in offspring. However, the genes or pathways that are epigenetically regulated by FA in neurodevelopment were rarely reported. Methods: To elucidate the underlying mechanism, the effect of FA on the methylation profiles in brain tissue of male rat offspring was assessed by methylated DNA immunoprecipitation chip. Differentially methylated genes (DMGs) and gene network analysis were identified using DAVID and KEGG pathway analysis. Results: Compared with the folate-normal diet group, 1939 DMGs were identified in the folate-deficient diet group, and 1498 DMGs were identified in the folate-supplemented diet group, among which 298 DMGs were overlapped. The pathways associated with neurodevelopment and learning/memory abilities were differentially methylated in response to maternal FA intake during pregnancy, and there were some identical and distinctive potential mechanisms under FA deficiency or FA-supplemented conditions. Conclusions: In conclusion, genes and pathways associated with neurodevelopment and learning/memory abilities were differentially -
ADCY2, ADCY5, and GRIA1 Are the Key Genes of Camp Signaling Pathway to Participate in Osteoporotic Spinal Fracture After the Manipulation of Wnt Signaling
ADCY2, ADCY5, and GRIA1 are the key genes of cAMP signaling pathway to participate in osteoporotic spinal fracture after the manipulation of Wnt signaling Type Research paper Keywords Wnt signaling pathway, Spinal Fractures, GRIA1, cAMP signaling Abstract Introduction Osteoporotic spinal fracture, characterized by high morbidity and mortality, has become a health burden for the aging population. The inactivation of the Wnt signaling has been proved to promote osteoporotic fractures. Our study is to identify the key genes, miRNAs, and pathways that possibly lead to osteoporosis and osteoporotic spinal fracture after the aberrant activation or mutation of Wnt signaling pathway. Material and methods Impute R package was used to screen out the differently expressed genes (DEGs) and differently expressed miRNAs in GEO datasets. STRING and Metascape were used to construct protein-protein interactions (PPI) network, gene ontology (GO) enrichment and pathway enrichment. The relative expression of ADCY2, ADCY5, and GRIA1 in bone tissues was measured by RT-qPCR. Results 562 DEGs were screened out using Impute R package, and a PPI network involving the 562 DEGs was constructed using STRING and Metascape. GO enrichment and pathway enrichment showed that the 562 DEGs were associated with membrane protein-related signaling pathways. Then, 75 genes between the target genesPreprint of miR-18a-3p and 562 DEGs were overlapped using Venny 2.1.0. Finally, the cAMP signaling pathway was identified as the key pathway, whilst ADCY2, ADCY5, and GRIA1 were identified the key genes that possibly participate in osteoporotic spinal fracture after the manipulation of Wnt signaling pathway, which was further proved by their excessive downregulation in osteoporotic patients with spinal fracture. -
An Integrated Analysis Reveals Geniposide Extracted from Gardenia Jasminoides Ellis Regulates Calcium Signaling Pathway Essential for Infuenza a Virus Replication
An Integrated Analysis Reveals Geniposide Extracted From Gardenia Jasminoides Ellis Regulates Calcium Signaling Pathway Essential for Inuenza a Virus Replication LiRun Zhou China Academy of Chinese Medical Sciences https://orcid.org/0000-0002-1350-940X Lei Bao China Academy of Chinese Medical Sciences Yaxin Wang China Academy of Chinese Medical Sciences Mengping Chen China Academy of Chinese Medical Sciences Yingying Zhang Beijing University of Chinese Medicine Aliated Dongzhimen Hospital Zihan Geng China Academy of Chinese Medical Sciences Ronghua Zhao China Academy of Chinese Medical Sciences Jing Sun China Academy of Chinese Medical Sciences Yanyan Bao China Academy of Chinese Medical Sciences Yujing Shi China Academy of Chinese Medical Sciences Rongmei Yao China Academy of Chinese Medical Sciences Shanshan Guo ( [email protected] ) China Academy of Chinese Medical Sciences Xiaolan Cui China Academy of Chinese Medical Sciences Research Page 1/30 Keywords: Geniposide, Inuenza A virus, RNA polymerase, Calcium signaling pathway, CAMKII Posted Date: August 9th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-764303/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 2/30 Abstract Background Geniposide, an iridoid glycoside puried from the fruit of Gardenia jasminoides Ellis, has been reported to possess pleiotropic activity against different diseases. In particular, geniposide possesses a variety of biological activities and exerts good therapeutic effects in the treatment of several strains of the inuenza virus. However, the molecular mechanism for the therapeutic effect has not been well dened. Methods This study aimed to investigate the mechanism of geniposide on inuenza A virus (IAV). -
Activin a Receptor, Type IC; ADCY1: Adenylate Cyclase 1; ADCY2
ABBREVIATIONS ACVR1C: activin A receptor, type IC; ADCY1: adenylate cyclase 1; ADCY2: adenylate cyclase 2; ADRA1B: adrenergic, alpha-1B-, receptor; AKT3: v-akt murine thymoma viral oncogene homolog 3; BMP6: bone morphogenetic protein 6; BMPR2: bone morphogenetic protein receptor, type II; CACNB2: calcium channel, voltage-dependent, beta 2 subunit; CALM1: calmodulin 1; CBL: Cbl proto-oncogene, E3 ubiquitin protein ligase; CD86: CD86 molecule; CDKN1B: cyclin-dependent kinase inhibitor 1B; DGKB: diacylglycerol kinase, beta 90kDa; DUSP8: dual specificity phosphatase 8; E2F5: E2F transcription factor 5, p130-binding; EIF4E: eukaryotic translation initiation factor 4E family member 2; EIF4E2: eukaryotic translation initiation factor 4E family member 2; ERBB2IP: erbb2 interacting protein; F2R: coagulation factor II (thrombin) receptor; FBXW11: F-box and WD repeat domain containing 11; FZD3: frizzled family receptor 3; FZD6: frizzled family receptor 6; GAB1: GRB2- associated binding protein 1; IFNAR1: interferon (alpha, beta and omega) receptor 1; IL13RA1: interleukin 13 receptor, alpha 1; IL15RA: interleukin 15 receptor, alpha; IL9R: interleukin 9 receptor; ITGA4: integrin, alpha 4; KAT2B: K(lysine) acetyltransferase 2B; MAML1: mastermind-like 1; MAP3K14: mitogen-activated protein kinase kinase kinase 14; MAP3K2: mitogen-activated protein kinase kinase kinase 2; MAP3K3: mitogen-activated protein kinase kinase kinase 3; MAP3K5: mitogen-activated protein kinase kinase kinase 5; MAP4K3: mitogen-activated protein kinase kinase kinase kinase 3; MAP4K4: