CDC2 Mediates Progestin Initiated Endometrial Stromal Cell Proliferation: a PR Signaling to Gene Expression Independently of Its Binding to Chromatin
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RBP-J Signaling − Cells Through Notch Novel IRF8-Controlled
Sca-1+Lin−CD117− Mesenchymal Stem/Stromal Cells Induce the Generation of Novel IRF8-Controlled Regulatory Dendritic Cells through Notch −RBP-J Signaling This information is current as of September 25, 2021. Xingxia Liu, Shaoda Ren, Chaozhuo Ge, Kai Cheng, Martin Zenke, Armand Keating and Robert C. H. Zhao J Immunol 2015; 194:4298-4308; Prepublished online 30 March 2015; doi: 10.4049/jimmunol.1402641 Downloaded from http://www.jimmunol.org/content/194/9/4298 Supplementary http://www.jimmunol.org/content/suppl/2015/03/28/jimmunol.140264 http://www.jimmunol.org/ Material 1.DCSupplemental References This article cites 59 articles, 19 of which you can access for free at: http://www.jimmunol.org/content/194/9/4298.full#ref-list-1 Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision by guest on September 25, 2021 • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2015 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology Sca-1+Lin2CD1172 Mesenchymal Stem/Stromal Cells Induce the Generation of Novel IRF8-Controlled Regulatory Dendritic Cells through Notch–RBP-J Signaling Xingxia Liu,*,1 Shaoda Ren,*,1 Chaozhuo Ge,* Kai Cheng,* Martin Zenke,† Armand Keating,‡,x and Robert C. -
Genome-Wide DNA Methylation Analysis of KRAS Mutant Cell Lines Ben Yi Tew1,5, Joel K
www.nature.com/scientificreports OPEN Genome-wide DNA methylation analysis of KRAS mutant cell lines Ben Yi Tew1,5, Joel K. Durand2,5, Kirsten L. Bryant2, Tikvah K. Hayes2, Sen Peng3, Nhan L. Tran4, Gerald C. Gooden1, David N. Buckley1, Channing J. Der2, Albert S. Baldwin2 ✉ & Bodour Salhia1 ✉ Oncogenic RAS mutations are associated with DNA methylation changes that alter gene expression to drive cancer. Recent studies suggest that DNA methylation changes may be stochastic in nature, while other groups propose distinct signaling pathways responsible for aberrant methylation. Better understanding of DNA methylation events associated with oncogenic KRAS expression could enhance therapeutic approaches. Here we analyzed the basal CpG methylation of 11 KRAS-mutant and dependent pancreatic cancer cell lines and observed strikingly similar methylation patterns. KRAS knockdown resulted in unique methylation changes with limited overlap between each cell line. In KRAS-mutant Pa16C pancreatic cancer cells, while KRAS knockdown resulted in over 8,000 diferentially methylated (DM) CpGs, treatment with the ERK1/2-selective inhibitor SCH772984 showed less than 40 DM CpGs, suggesting that ERK is not a broadly active driver of KRAS-associated DNA methylation. KRAS G12V overexpression in an isogenic lung model reveals >50,600 DM CpGs compared to non-transformed controls. In lung and pancreatic cells, gene ontology analyses of DM promoters show an enrichment for genes involved in diferentiation and development. Taken all together, KRAS-mediated DNA methylation are stochastic and independent of canonical downstream efector signaling. These epigenetically altered genes associated with KRAS expression could represent potential therapeutic targets in KRAS-driven cancer. Activating KRAS mutations can be found in nearly 25 percent of all cancers1. -
Genome-Wide Assessment of REST Binding Profiles Reveals Distinctions Between Human and Mouse Hippocampus
bioRxiv preprint doi: https://doi.org/10.1101/2020.07.07.192229; this version posted July 7, 2020. 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-NC-ND 4.0 International license. Genome-wide assessment of REST binding profiles reveals distinctions between human and mouse hippocampus James C. McGann1,2#, Michael Spinner1#, Saurabh K. Garg1,3#, Karin Mullendorf1,4, Randall L. Woltjer5 and Gail Mandel1*. 1 Vollum Institute, Oregon Health and Science University, Portland, OR, USA. 2 Cancer Early Detection Advanced Research Center, Oregon Health and Science Institute, Portland, OR, USA. 3 Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA. 4 Universidad San Sebastian, Puerto Montt, Chile 5 Department of Pathology, Division of Neuropathology, Oregon Health and Science University, Portland, OR, USA. *Corresponding author # These authors contributed equally Abstract Background The transcriptional repressor, RE1 Silencing Transcription Factor (REST), recognized historically as a master regulator of neuronal gene expression during mouse development, has recently been ascribed roles in human aging and neurodegenerative disorders. However, REST’s role in healthy adult human brain, and how faithfully mouse models reproduce REST function in human brain, is not known. Results Here, we present the first genome-wide binding profile for REST in both mouse and human postnatal hippocampus. We find the majority of REST-bound sites in human hippocampus are unique compared to both mouse hippocampus and to all other reported human ENCODE cell types. -
Mir-376C Promotes Carcinogenesis and Serves As a Plasma Marker for Gastric Carcinoma
RESEARCH ARTICLE miR-376c promotes carcinogenesis and serves as a plasma marker for gastric carcinoma Pei-Shih Hung1, Chin-Yau Chen2, Wei-Ting Chen2, Chen-Yu Kuo3, Wen-Liang Fang4,5, Kuo-Hung Huang4,5, Peng-Chih Chiu5, Su-Shun Lo2,6* 1 Department of Education and Medical Research, National Yang-Ming University Hospital, Yilan, Taiwan, 2 Department of Surgery, National Yang-Ming University Hospital, Yilan, Taiwan, 3 Department of Medicine, National Yang-Ming University Hospital, Yilan, Taiwan, 4 Division of General Surgery, Veterans General Hospital±Taipei, Taipei, Taiwan, 5 Department of Dentistry, National Yang-Ming University Hospital, Yilan, Taiwan, 6 School of Medicine, National Yang-Ming University, Taipei, Taiwan a1111111111 [email protected] a1111111111 * a1111111111 a1111111111 a1111111111 Abstract Gastric carcinoma is highly prevalent throughout the world. Understanding the pathogenesis of this disease will benefit diagnosis and resolution. Studies show that miRNAs are involved in the tumorigenesis of gastric carcinoma. An initial screening followed by subsequent vali- OPEN ACCESS dation identified that miR-376c is up-regulated in gastric carcinoma tissue and the plasma Citation: Hung P-S, Chen C-Y, Chen W-T, Kuo C-Y, of patients with the disease. In addition, the urinary level of miR-376c is also significantly Fang W-L, Huang K-H, et al. (2017) miR-376c increased in gastric carcinoma patients. The plasma miR-376c level was validated as a bio- promotes carcinogenesis and serves as a plasma marker for gastric carcinoma. PLoS ONE 12(5): marker for gastric carcinoma, including early stage tumors. The induction of miR-376c was e0177346. -
HCC and Cancer Mutated Genes Summarized in the Literature Gene Symbol Gene Name References*
HCC and cancer mutated genes summarized in the literature Gene symbol Gene name References* A2M Alpha-2-macroglobulin (4) ABL1 c-abl oncogene 1, receptor tyrosine kinase (4,5,22) ACBD7 Acyl-Coenzyme A binding domain containing 7 (23) ACTL6A Actin-like 6A (4,5) ACTL6B Actin-like 6B (4) ACVR1B Activin A receptor, type IB (21,22) ACVR2A Activin A receptor, type IIA (4,21) ADAM10 ADAM metallopeptidase domain 10 (5) ADAMTS9 ADAM metallopeptidase with thrombospondin type 1 motif, 9 (4) ADCY2 Adenylate cyclase 2 (brain) (26) AJUBA Ajuba LIM protein (21) AKAP9 A kinase (PRKA) anchor protein (yotiao) 9 (4) Akt AKT serine/threonine kinase (28) AKT1 v-akt murine thymoma viral oncogene homolog 1 (5,21,22) AKT2 v-akt murine thymoma viral oncogene homolog 2 (4) ALB Albumin (4) ALK Anaplastic lymphoma receptor tyrosine kinase (22) AMPH Amphiphysin (24) ANK3 Ankyrin 3, node of Ranvier (ankyrin G) (4) ANKRD12 Ankyrin repeat domain 12 (4) ANO1 Anoctamin 1, calcium activated chloride channel (4) APC Adenomatous polyposis coli (4,5,21,22,25,28) APOB Apolipoprotein B [including Ag(x) antigen] (4) AR Androgen receptor (5,21-23) ARAP1 ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1 (4) ARHGAP35 Rho GTPase activating protein 35 (21) ARID1A AT rich interactive domain 1A (SWI-like) (4,5,21,22,24,25,27,28) ARID1B AT rich interactive domain 1B (SWI1-like) (4,5,22) ARID2 AT rich interactive domain 2 (ARID, RFX-like) (4,5,22,24,25,27,28) ARID4A AT rich interactive domain 4A (RBP1-like) (28) ARID5B AT rich interactive domain 5B (MRF1-like) (21) ASPM Asp (abnormal -
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 -
Functional Haplotypes of ARID4A Affect Promoter Activity and Semen
Animal Reproduction Science xxx (xxxx) xxx–xxx Contents lists available at ScienceDirect Animal Reproduction Science journal homepage: www.elsevier.com/locate/anireprosci Functional haplotypes of ARID4A affect promoter activity and semen quality of bulls Chunhong Yanga,1, Jinpeng Wanga,1, Juan Liua,1, Yan Suna, Yijun Guoa,b, Qiang Jianga, Zhihua Jua, Qican Gaoa,b, Xiuge Wanga, Jinming Huanga, ⁎ Changfa Wanga, a Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan 250131, PR China b College of Life Science, Shandong Normal University, Jinan, PR China ARTICLE INFO ABSTRACT Keywords: The AT-rich interaction domain 4 A (ARID4A) has an important role in regulating Sertoli cell Bovine function and male fertility. Its molecular mechanisms, however, remain largely unknown. In this ARID4A study, two single nucleotide polymorphisms (SNPs) (g.53 G > T, ss 1966531596, and SNP g.826 G > A, rs 210809648) were identified in the promoter region of ARID4A in 215 Chinese Haplotype Holstein bulls using polymerase chain reaction (PCR)-restriction fragment length polymorphism Semen quality and created restriction site-PCR. Results revealed that bulls with g.53 G > T-GG and g.826 G > A-G G genotype exhibited higher sperm deformity rate than those with g.53 G > T- TT and g.826 G > A-AA genotype (P < 0.01). Furthermore, three haplotypes (H1 (GG), H3 (TG), H4 (TA)) and six haplotype combinations (H1H1, H1H3, H1H4, H3H3, H3H4, H4H4) were obtained. The bulls with H4H4 exhibited lower sperm deformity rate than those with H1H1 and H1H3 (P < 0.05). In addition, results of bioinformatics analysis revealed that ARID4A has two promoters and that two SNPs of ARID4A are located in transcription factor binding sites. -
Appendix 2. Significantly Differentially Regulated Genes in Term Compared with Second Trimester Amniotic Fluid Supernatant
Appendix 2. Significantly Differentially Regulated Genes in Term Compared With Second Trimester Amniotic Fluid Supernatant Fold Change in term vs second trimester Amniotic Affymetrix Duplicate Fluid Probe ID probes Symbol Entrez Gene Name 1019.9 217059_at D MUC7 mucin 7, secreted 424.5 211735_x_at D SFTPC surfactant protein C 416.2 206835_at STATH statherin 363.4 214387_x_at D SFTPC surfactant protein C 295.5 205982_x_at D SFTPC surfactant protein C 288.7 1553454_at RPTN repetin solute carrier family 34 (sodium 251.3 204124_at SLC34A2 phosphate), member 2 238.9 206786_at HTN3 histatin 3 161.5 220191_at GKN1 gastrokine 1 152.7 223678_s_at D SFTPA2 surfactant protein A2 130.9 207430_s_at D MSMB microseminoprotein, beta- 99.0 214199_at SFTPD surfactant protein D major histocompatibility complex, class II, 96.5 210982_s_at D HLA-DRA DR alpha 96.5 221133_s_at D CLDN18 claudin 18 94.4 238222_at GKN2 gastrokine 2 93.7 1557961_s_at D LOC100127983 uncharacterized LOC100127983 93.1 229584_at LRRK2 leucine-rich repeat kinase 2 HOXD cluster antisense RNA 1 (non- 88.6 242042_s_at D HOXD-AS1 protein coding) 86.0 205569_at LAMP3 lysosomal-associated membrane protein 3 85.4 232698_at BPIFB2 BPI fold containing family B, member 2 84.4 205979_at SCGB2A1 secretoglobin, family 2A, member 1 84.3 230469_at RTKN2 rhotekin 2 82.2 204130_at HSD11B2 hydroxysteroid (11-beta) dehydrogenase 2 81.9 222242_s_at KLK5 kallikrein-related peptidase 5 77.0 237281_at AKAP14 A kinase (PRKA) anchor protein 14 76.7 1553602_at MUCL1 mucin-like 1 76.3 216359_at D MUC7 mucin 7, -
Epigenetic Driver Mutations in ARID1A Shape Cancer Immune Phenotype and Immunotherapy
Epigenetic driver mutations in ARID1A shape cancer immune phenotype and immunotherapy Jing Li, … , Arul M. Chinnaiyan, Weiping Zou J Clin Invest. 2020;130(5):2712-2726. https://doi.org/10.1172/JCI134402. Research Article Immunology Graphical abstract Find the latest version: https://jci.me/134402/pdf RESEARCH ARTICLE The Journal of Clinical Investigation Epigenetic driver mutations in ARID1A shape cancer immune phenotype and immunotherapy Jing Li,1,2 Weichao Wang,1,2 Yajia Zhang,3 Marcin Cieślik,3,4,5 Jipeng Guo,1,2 Mengyao Tan,3 Michael D. Green,1,2,6 Weimin Wang,1,2 Heng Lin,1,2 Wei Li,1,2 Shuang Wei,1,2 Jiajia Zhou,1,2 Gaopeng Li,1,2 Xiaojun Jing,3 Linda Vatan,1,2 Lili Zhao,7 Benjamin Bitler,8 Rugang Zhang,8 Kathleen R. Cho,3,5 Yali Dou,3,5 Ilona Kryczek,1,2 Timothy A. Chan,9 David Huntsman,10,11 Arul M. Chinnaiyan,3,6,12,13,14 and Weiping Zou1,2,3,5,15 1Department of Surgery, University of Michigan School of Medicine, Ann Arbor, Michigan, USA. 2Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan, USA. 3Department of Pathology, 4Department of Computational Medicine and Bioinformatics, 5University of Michigan Rogel Cancer Center, and 6Department of Radiation Oncology, University of Michigan School of Medicine, Ann Arbor, Michigan, USA. 7Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA. 8Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, Pennsylvania, USA. 9Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA. -
Functional Annotation of Human Long Noncoding Rnas Using Chromatin
bioRxiv preprint doi: https://doi.org/10.1101/2021.01.13.426305; this version posted January 14, 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 Funconal annotaon of human long noncoding RNAs using chroman conformaon data Saumya Agrawal1, Tanvir Alam2, Masaru Koido1,3, Ivan V. Kulakovskiy4,5, Jessica Severin1, Imad ABugessaisa1, Andrey Buyan5,6, Josee Dos&e7, Masayoshi Itoh1,8, Naoto Kondo9, Yunjing Li10, Mickaël Mendez11, Jordan A. Ramilowski1,12, Ken Yagi1, Kayoko Yasuzawa1, CHi Wai Yip1, Yasushi Okazaki1, MicHael M. Ho9man11,13,14,15, Lisa Strug10, CHung CHau Hon1, CHikashi Terao1, Takeya Kasukawa1, Vsevolod J. Makeev4,16, Jay W. SHin1, Piero Carninci1, MicHiel JL de Hoon1 1RIKEN Center for Integra&ve Medical Sciences, YokoHama, Japan. 2College of Science and Engineering, Hamad Bin KHalifa University, DoHa, Qatar. 3Ins&tute of Medical Science, THe University of Tokyo, Tokyo, Japan. 4Vavilov Ins&tute of General Gene&cs, Russian Academy of Sciences, Moscow, Russia. 5Ins&tute of Protein ResearcH, Russian Academy of Sciences, PusHcHino, Russia. 6Faculty of Bioengineering and Bioinforma&cs, Lomonosov Moscow State University, Moscow, Russia. 7Department of BiocHemistry, Rosalind and Morris Goodman Cancer ResearcH Center, McGill University, Montréal, QuéBec, Canada. 8RIKEN Preven&ve Medicine and Diagnosis Innova&on Program, Wako, Japan. 9RIKEN Center for Life Science TecHnologies, YokoHama, Japan. 10Division of Biosta&s&cs, Dalla Lana ScHool of PuBlic HealtH, University of Toronto, Toronto, Ontario, Canada. 11Department of Computer Science, University of Toronto, Toronto, Ontario, Canada. 12Advanced Medical ResearcH Center, YokoHama City University, YokoHama, Japan. -
The Master Regulator Gene PRDM2 Controls C2C12 Myoblasts
Open Access Insights in Biology and Medicine Research Article The master regulator gene PRDM2 controls C2C12 myoblasts proliferation ISSN 2639-6769 and Differentiation switch and PRDM4 and PRDM10 expression Di Zazzo Erika1#, Bartollino Silvia1*# and Moncharmont Bruno1 1Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, Italy #These authors contributed equally to this work *Address for Correspondence: Silvia Bartollino, Abstract Department of Medicine and Health Sciences, “V. Tiberio”, University of Molise Via F. De Sanctis, The Positive Regulatory Domain (PRDM) protein family gene is involved in a spectrum variety of biological 86100 Campobasso, Italy, Tel.: +39 0874404886, processes, including proliferation, differentiation and apoptosis: its member seem to be transcriptional E-mail: [email protected] regulators highly cell type and tissue peculiar, towards histones modifi cations or recruitment of specifi c Submitted: 11 August 2017 interaction patters to modify the expression of target genes. In this study we analyzed the expression profi le of Approved: 20 September 2017 different member of PRDM gene family focusing our attention on the role of PRDM2, PRDM4 and PRDM10 genes Published: 25 September 2017 in mouse C2C12 cell line, during the differentiation of myoblasts into myotubes and speculate about the role of the protein Retinoblastoma protein-interacting zinc fi nger protein 1-RIZ1, coded by PRDM2 gene, as a regulator Copyright: 2017 Di Zazzo E, et al. This is an open access article distributed under the of the proliferation/differentiation switch. Creative Commons Attribution License, which permits unrestricted use, distribution, and Results showed a reduction of PRDM2, PRDM4 and PRDM10 expression level during the commitment of the reproduction in any medium, provided the differentiation of myoblasts into myotubes. -
Transcriptional Repressor HIC1 Contributes to Suppressive Function of Human Induced Regulatory T Cells
This is an electronic reprint of the original article. This reprint may differ from the original in pagination and typographic detail. Ubaid Ullah, Ullah; Andrabi, Syed Bilal Ahmad; Tripathi, Subhash Kumar; Dirasantha, Obaiah; Kanduri, Kartiek; Rautio, Sini; Gross, Catharina C.; Lehtimäki, Sari; Bala, Kanchan; Tuomisto, Johanna; Bhatia, Urvashi; Chakroborty, Deepankar; Elo, Laura L.; Lähdesmäki, Harri; Wiendl, Heinz; Rasool, Omid; Lahesmaa, Riitta Transcriptional Repressor HIC1 Contributes to Suppressive Function of Human Induced Regulatory T Cells Published in: Cell Reports DOI: 10.1016/j.celrep.2018.01.070 Published: 20/02/2018 Document Version Publisher's PDF, also known as Version of record Published under the following license: CC BY-NC-ND Please cite the original version: Ubaid Ullah, U., Andrabi, S. B. A., Tripathi, S. K., Dirasantha, O., Kanduri, K., Rautio, S., Gross, C. C., Lehtimäki, S., Bala, K., Tuomisto, J., Bhatia, U., Chakroborty, D., Elo, L. L., Lähdesmäki, H., Wiendl, H., Rasool, O., & Lahesmaa, R. (2018). Transcriptional Repressor HIC1 Contributes to Suppressive Function of Human Induced Regulatory T Cells. Cell Reports, 22(8), 2094-2106. https://doi.org/10.1016/j.celrep.2018.01.070 This material is protected by copyright and other intellectual property rights, and duplication or sale of all or part of any of the repository collections is not permitted, except that material may be duplicated by you for your research use or educational purposes in electronic or print form. You must obtain permission for any other use. Electronic or print copies may not be offered, whether for sale or otherwise to anyone who is not an authorised user.