Policing Cancer: Vitamin D Arrests the Cell Cycle
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Screening and Identification of Key Biomarkers in Clear Cell Renal Cell Carcinoma Based on Bioinformatics Analysis
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.21.423889; this version posted December 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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. Screening and identification of key biomarkers in clear cell renal cell carcinoma based on bioinformatics analysis Basavaraj Vastrad1, Chanabasayya Vastrad*2 , Iranna Kotturshetti 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. 3. Department of Ayurveda, Rajiv Gandhi Education Society`s Ayurvedic Medical College, Ron, Karnataka 562209, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India bioRxiv preprint doi: https://doi.org/10.1101/2020.12.21.423889; this version posted December 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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 Clear cell renal cell carcinoma (ccRCC) is one of the most common types of malignancy of the urinary system. The pathogenesis and effective diagnosis of ccRCC have become popular topics for research in the previous decade. In the current study, an integrated bioinformatics analysis was performed to identify core genes associated in ccRCC. An expression dataset (GSE105261) was downloaded from the Gene Expression Omnibus database, and included 26 ccRCC and 9 normal kideny samples. Assessment of the microarray dataset led to the recognition of differentially expressed genes (DEGs), which was subsequently used for pathway and gene ontology (GO) enrichment analysis. -
The Retinoblastoma Tumor-Suppressor Gene, the Exception That Proves the Rule
Oncogene (2006) 25, 5233–5243 & 2006 Nature Publishing Group All rights reserved 0950-9232/06 $30.00 www.nature.com/onc REVIEW The retinoblastoma tumor-suppressor gene, the exception that proves the rule DW Goodrich Department of Pharmacology & Therapeutics, Roswell Park Cancer Institute, Buffalo, NY, USA The retinoblastoma tumor-suppressor gene (Rb1)is transmission of one mutationally inactivated Rb1 allele centrally important in cancer research. Mutational and loss of the remaining wild-type allele in somatic inactivation of Rb1 causes the pediatric cancer retino- retinal cells. Hence hereditary retinoblastoma typically blastoma, while deregulation ofthe pathway in which it has an earlier onset and a greater number of tumor foci functions is common in most types of human cancer. The than sporadic retinoblastoma where both Rb1 alleles Rb1-encoded protein (pRb) is well known as a general cell must be inactivated in somatic retinal cells. To this day, cycle regulator, and this activity is critical for pRb- Rb1 remains an exception among cancer-associated mediated tumor suppression. The main focus of this genes in that its mutation is apparently both necessary review, however, is on more recent evidence demonstrating and sufficient, or at least rate limiting, for the genesis of the existence ofadditional, cell type-specific pRb func- a human cancer. The simple genetics of retinoblastoma tions in cellular differentiation and survival. These has spawned the hope that a complete molecular additional functions are relevant to carcinogenesis sug- understanding of the Rb1-encoded protein (pRb) would gesting that the net effect of Rb1 loss on the behavior of lead to deeper insight into the processes of neoplastic resulting tumors is highly dependent on biological context. -
MYCL Promotes Ipsc-Like Colony Formation Via MYC Box 0 and 2 Domains
MYCL promotes iPSC-like colony formation via MYC Box 0 and 2 domains Chiaki Akifuji Department of Life Science Frontiers, Center for iPS cell Research and Application (CiRA), Kyoto University Mio Iwasaki Department of Life Science Frontiers, Center for iPS cell Research and Application (CiRA), Kyoto University Yuka Kawahara Department of Life Science Frontiers, Center for iPS cell Research and Application (CiRA), Kyoto University Chiho Sakurai Department of Life Science Frontiers, Center for iPS cell Research and Application (CiRA), Kyoto University Yusheng Cheng Department of Life Science Frontiers, Center for iPS cell Research and Application (CiRA), Kyoto University Takahiko Imai Department of Life Science Frontiers, Center for iPS cell Research and Application (CiRA), Kyoto University Masato Nakagawa ( [email protected] ) Department of Life Science Frontiers, Center for iPS cell Research and Application (CiRA), Kyoto University Research Article Keywords: mycl, reprogramming, ipsc, eciency, induced Posted Date: August 19th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-817686/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License 1 MYCL promotes iPSC-like colony formation via MYC Box 0 and 2 domains 2 3 Authors 4 Chiaki Akifuji1, Mio Iwasaki1, Yuka Kawahara1, Chiho Sakurai1, Yusheng Cheng1, Takahiko 5 Imai1, and Masato Nakagawa1* 6 7 Affiliation 8 1 Department of Life Science Frontiers, Center for iPS cell Research and Application (CiRA), 9 Kyoto University, Kyoto 606-8507, Japan 10 11 *Correspondence: [email protected] 12 13 Abstract 14 Induced pluripotent stem cells (iPSCs) have the potential to differentiate into any cell in 15 the body and thus have attractive regenerative medicine potential. -
A Left/Right Comparison of Twice-Daily Calcipotriol Ointment and Calcitriol Ointment in Patients with Psoriasis: the Effect on Keratinocyte Subpopulations
Acta Derm Venereol 2004; 84: 195–200 INVESTIGATIVE REPORT A Left/Right Comparison of Twice-Daily Calcipotriol Ointment and Calcitriol Ointment in Patients with Psoriasis: The Effect on Keratinocyte Subpopulations Mannon E.J. FRANSSEN, Gys J. DE JONGH, Piet E.J. VAN ERP and Peter C.M. VAN DE KERKHOF Department of Dermatology, University Medical Centre Nijmegen, The Netherlands Vitamin D3 analogues are a first-line treatment of Calcipotriol (Daivonex1,50mg/g ointment, Leo chronic plaque psoriasis, but so far, comparative clinical Pharmaceutical Products, Denmark) has been investi- studies on calcipotriol and calcitriol ointment are sparse, gated intensively during the last decade, and has proven and in particular no comparative studies are available on to be a valuable tool in the management of chronic cell biological effects of these compounds in vivo. Using plaque psoriasis. A review by Ashcroft et al. (1), based on flow cytometric assessment, we investigated whether these a large number of randomized controlled trials, showed compounds had different effects on the composition and that calcipotriol was at least as effective as potent DNA synthesis of epidermal cell populations responsible topical corticosteroids, 1a,-25-dihydroxycholecalciferol for the psoriatic phenotype. For 8 weeks, 20 patients with (calcitriol), short-contact dithranol, tacalcitol and coal psoriasis vulgaris were treated twice daily with calcipo- tar. Recently, Scott et al. (2) presented an overview of triol and calcitriol ointment in a left/right comparative studies on the use of calcipotriol ointment in the study. Before and after treatment, clinical assessment of management of psoriasis. They reconfirmed the super- target lesions was performed, together with flow cyto- ior efficacy of a twice-daily calcipotriol ointment metric analysis of epidermal subpopulations with respect regimen to the treatments as mentioned above, and to keratin (K) 10, K6, vimentin and DNA distribution. -
G2 Phase Cell Cycle Regulation by E2F4 Following Genotoxic Stress
G2 Phase Cell Cycle Regulation by E2F4 Following Genotoxic Stress by MEREDITH ELLEN CROSBY Submitted in partial fulfillment of the requirements for the Degree of Doctor of Philosophy Thesis Advisor: Dr. Alex Almasan Department of Environmental Health Sciences CASE WESTERN RESERVE UNIVERSITY May, 2006 CASE WESTERN RESERVE UNIVERSITY SCHOOL OF GRADUATE STUDIES We hereby approve the dissertation of ______________________________________________________ candidate for the Ph.D. degree *. (signed)_______________________________________________ (chair of the committee) ________________________________________________ ________________________________________________ ________________________________________________ ________________________________________________ ________________________________________________ (date) _______________________ *We also certify that written approval has been obtained for any proprietary material contained therein. TABLE OF CONTENTS TABLE OF CONTENTS………………………………………………………………….1 LIST OF FIGURES……………………………………………………………………….5 LIST OF TABLES………………………………………………………………………...7 ACKNOWLEDGEMENTS……………………………………………………………….8 LIST OF ABBREVIATIONS……………………………………………………………10 ABSTRACT……………………………………………………………………………...15 CHAPTER 1. INTRODUCTION 1.1. CELL CYCLE REGULATION: HISTORICAL OVERVIEW………………...17 1.2. THE E2F FAMILY OF TRANSCRIPTION FACTORS……………………….22 1.3. E2F AND CELL CYCLE CONTROL 1.3.1. G0/G1 Phase Transition………………………………………………….28 1.3.2. S Phase…………………………………………………………………...28 1.3.3. G2/M Phase Transition…………………………………………………..30 1.4. -
An Amino-Terminal Domain of Mxil Mediates Anti-Myc Oncogenic Activity and Interacts with a Homolog of the Yeast Transcriptional Repressor SIN3
CORE Metadata, citation and similar papers at core.ac.uk Provided by Elsevier - Publisher Connector Cell, Vol, 80, 777-786, March 10, 1995, Copyright © 1995 by Cell Press An Amino-Terminal Domain of Mxil Mediates Anti-Myc Oncogenic Activity and Interacts with a Homolog of the Yeast Transcriptional Repressor SIN3 Nicole Schreiber-Agus,*t Lynda Chin,*tt Ken Chen,t et al., 1990), and a carboxy-terminal a-helical domain re- Richard Torres, t Govinda Rao,§ Peter Guida,t quired for dimerization with another basic region-helix- Arthur h Skoultchi,§ and Ronald A. DePinhot Ioop-helix-leucine zipper (bHLH-LZ) protein, Max (Black- "rDepartments of Microbiology and Immunology wood and Eisenman, 1991; Prendergast et al., 1991). and of Medicine Many of the biochemical and biological activities of Myc §Department of Cell Biology appear to be highly dependent upon its association with ~Division of Dermatology Max (Blackwood and Eisenman, 1991 ; Prendergast et al., Albert Einstein College of Medicine 1991; Kretzner et al., 1992; Amati et al., 1993a, 1993b). Bronx, New York 10461 In addition to its key role as an obligate partner in transacti- vation-competent Myc-Max complexes, Max may also re- press Myc-responsive genes through the formation of Summary transactivation-inert complexes that are capable of bind- ing the Myc-Max recognition sequence (Blackwood et al., Documented interactions among members of the Myc 1992; Kato et al., 1992; Kretzner et al., 1992; Makela et superfamily support a yin-yang model for the regula- al., 1992; Mukherjee et al., 1992; Prendergast et al., 1992; tion of Myc-responsive genes in which t ransactivation- Ayer et al., 1993; Zervos et al., 1993). -
The E–Id Protein Axis Modulates the Activities of the PI3K–AKT–Mtorc1
Downloaded from genesdev.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press The E–Id protein axis modulates the activities of the PI3K–AKT–mTORC1– Hif1a and c-myc/p19Arf pathways to suppress innate variant TFH cell development, thymocyte expansion, and lymphomagenesis Masaki Miyazaki,1,8 Kazuko Miyazaki,1,8 Shuwen Chen,1 Vivek Chandra,1 Keisuke Wagatsuma,2 Yasutoshi Agata,2 Hans-Reimer Rodewald,3 Rintaro Saito,4 Aaron N. Chang,5 Nissi Varki,6 Hiroshi Kawamoto,7 and Cornelis Murre1 1Department of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA; 2Department of Biochemistry and Molecular Biology, Shiga University of Medical School, Shiga 520-2192, Japan; 3Division of Cellular Immunology, German Cancer Research Center, D-69120 Heidelberg, Germany; 4Department of Medicine, University of California at San Diego, La Jolla, California 92093, USA; 5Center for Computational Biology, Institute for Genomic Medicine, University of California at San Diego, La Jolla, California 92093, USA; 6Department of Pathology, University of California at San Diego, La Jolla, California 92093, USA; 7Department of Immunology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan It is now well established that the E and Id protein axis regulates multiple steps in lymphocyte development. However, it remains unknown how E and Id proteins mechanistically enforce and maintain the naı¨ve T-cell fate. Here we show that Id2 and Id3 suppressed the development and expansion of innate variant follicular helper T (TFH) cells. Innate variant TFH cells required major histocompatibility complex (MHC) class I-like signaling and were associated with germinal center B cells. -
Original Article MYCN-Mediated Regulation of the HES1 Promoter Enhances the Chemoresistance of Small-Cell Lung Cancer by Modulating Apoptosis
Am J Cancer Res 2019;9(9):1938-1956 www.ajcr.us /ISSN:2156-6976/ajcr0100301 Original Article MYCN-mediated regulation of the HES1 promoter enhances the chemoresistance of small-cell lung cancer by modulating apoptosis Qin Tong1,2*, Shuming Ouyang3*, Rui Chen1, Jie Huang4, Linlang Guo1 1Department of Pathology, Zhujiang Hospital, Southern Medical University, 253 Gongye Road, Guangzhou 510282, People’s Republic of China; Departments of 2Radiation Oncology, 3Reproductive Medicine, The First Affiliated Hospital of University of South China, Hengyang 421001, People’s Republic of China; 4Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People’s Hospital & Guangdong Academy of Medical Sciences, Guangzhou 510080, People’s Republic of China. *Equal contributors. Received June 29, 2019; Accepted August 10, 2019; Epub September 1, 2019; Published September 15, 2019 Abstract: MYCN, a member of the MYC family, is correlated with tumorigenesis, metastasis and therapy in many malig nancies; however, its role in small-cell lung cancer (SCLC) remains unclear. In this study, we sought to identify the function of MYCN in SCLC chemoresistance and found that MYCN is overexpressed in chemoresistant SCLC cells. We used MYCN gain- and loss-of- function experiments to demonstrate that MYCN promotes in vitro and in vivo chemoresistance in SCLC by inhibiting apoptosis. Mechanistic investigations showed that MYCN binds to the HES1 promoter and exhibits transcriptional activity. Furthermore, MYCN mediated SCLC chemoresistance through HES1. Accordingly, the NOTCH inhibitor FLI-60 derepressed HES1 and diminished MYCN-induced chemoresistance in SCLC. Finally, the positive correlation between HES1 and MYCN was confirmed in SCLC patients. -
P53 Regulates Myogenesis by Triggering the Differentiation
CORE Metadata, citation and similar papers at core.ac.uk Provided by PubMed Central p53 Regulates Myogenesis by Triggering the Differentiation Activity of pRb Alessandro Porrello, Maria Antonietta Cerone, Sabrina Coen, Aymone Gurtner, Giulia Fontemaggi, Letizia Cimino, Giulia Piaggio, Ada Sacchi, and Silvia Soddu Molecular Oncogenesis Laboratory, Regina Elena Cancer Institute, Center for Experimental Research, 00158 Rome, Italy Abstract. The p53 oncosuppressor protein regulates mary myoblasts, pRb is hypophosphorylated and prolif- cell cycle checkpoints and apoptosis, but increasing evi- eration stops. However, these cells do not upregulate dence also indicates its involvement in differentiation pRb and have reduced MyoD activity. The transduction and development. We had previously demonstrated of exogenous TP53 or Rb genes in p53-defective myo- that in the presence of differentiation-promoting stim- blasts rescues MyoD activity and differentiation poten- uli, p53-defective myoblasts exit from the cell cycle but tial. Additionally, in vivo studies on the Rb promoter do not differentiate into myocytes and myotubes. To demonstrate that p53 regulates the Rb gene expression identify the pathways through which p53 contributes at transcriptional level through a p53-binding site. to skeletal muscle differentiation, we have analyzed Therefore, here we show that p53 regulates myoblast the expression of a series of genes regulated during differentiation by means of pRb without affecting its myogenesis in parental and dominant–negative p53 cell cycle–related functions. (dnp53)-expressing C2C12 myoblasts. We found that in dnp53-expressing C2C12 cells, as well as in p53Ϫ/Ϫ pri- Key words: p53 • Rb • MyoD • differentiation • muscle Introduction The differentiation of skeletal myoblasts is characterized review, see Wright, 1992). -
Isolation and Characterisation of Lymphatic Endothelial Cells From
www.nature.com/scientificreports OPEN Isolation and characterisation of lymphatic endothelial cells from lung tissues afected by lymphangioleiomyomatosis Koichi Nishino1,2*, Yasuhiro Yoshimatsu3,4, Tomoki Muramatsu5, Yasuhito Sekimoto1,2, Keiko Mitani1,2, Etsuko Kobayashi1,2, Shouichi Okamoto1,2, Hiroki Ebana1,2,6,7, Yoshinori Okada8, Masatoshi Kurihara2,6, Kenji Suzuki9, Johji Inazawa5, Kazuhisa Takahashi1, Tetsuro Watabe3 & Kuniaki Seyama1,2 Lymphangioleiomyomatosis (LAM) is a rare pulmonary disease characterised by the proliferation of smooth muscle-like cells (LAM cells), and an abundance of lymphatic vessels in LAM lesions. Studies reported that vascular endothelial growth factor-D (VEGF-D) secreted by LAM cells contributes to LAM-associated lymphangiogenesis, however, the precise mechanisms of lymphangiogenesis and characteristics of lymphatic endothelial cells (LECs) in LAM lesions have not yet been elucidated. In this study, human primary-cultured LECs were obtained both from LAM-afected lung tissues (LAM-LECs) and normal lung tissues (control LECs) using fuorescence-activated cell sorting (FACS). We found that LAM-LECs had signifcantly higher ability of proliferation and migration compared to control LECs. VEGF-D signifcantly promoted migration of LECs but not proliferation of LECs in vitro. cDNA microarray and FACS analysis revealed the expression of vascular endothelial growth factor receptor (VEGFR)-3 and integrin α9 were elevated in LAM-LECs. Inhibition of VEGFR-3 suppressed proliferation and migration of LECs, and blockade of integrin α9 reduced VEGF-D-induced migration of LECs. Our data uncovered the distinct features of LAM-associated LECs, increased proliferation and migration, which may be due to higher expression of VEGFR-3 and integrin α9. Furthermore, we also found VEGF-D/VEGFR-3 and VEGF-D/ integrin α9 signaling play an important role in LAM-associated lymphangiogenesis. -
The First Genome-Wide View of Vitamin D Receptor Locations and Their Mechanistic Implications
ANTICANCER RESEARCH 32: 271-282 (2012) Review The First Genome-wide View of Vitamin D Receptor Locations and Their Mechanistic Implications CARSTEN CARLBERG1, SABINE SEUTER2 and SAMI HEIKKINEN1 1Department of Biosciences, University of Eastern Finland, Kuopio, Finland; 2Life Sciences Research Unit, University of Luxembourg, Luxembourg, Luxembourg Abstract. The transcription factor vitamin D receptor Physiological Impact of Vitamin D (VDR) is the nuclear sensor for the biologically most active in the Immune System metabolite of vitamin D, 1α,25-dihydroxyvitamin D3 (1α,25(OH)2D3). The physiological actions of the VDR and Vitamin D is a micronutrient which under ultraviolet (UV) its ligand are not only the well-known regulation of calcium radiation can also be produced in the skin (1). The most and phosphorus uptake and transport controlling bone abundant form of vitamin D is its liver hydroxylation product formation, but also their significant involvement in the 25-hydroxyvitamin D3 (25(OH)D3), serum concentrations of control of immune functions and of cellular growth and which indicate the vitamin D status of the human individual differentiation. For a general understanding of the (2). The biologically most active vitamin D metabolite is mechanisms of 1α,25(OH)2D3 signaling, it is essential to obtained from further hydroxylation of 25(OH)D3 in the monitor the genome-wide location of VDR in relation to kidney to 1α,25(OH)2D3 (3). Interestingly, the hydroxylation primary 1α,25(OH)2D3 target genes. Within the last months, of vitamin D can also take place in other tissues and a few of two chromatin immunoprecipitation sequencing (ChIP-Seq) them, such as keratinocytes and macrophages, have the studies using cells of the hematopoietic system, capacity for the full conversion of vitamin D to lymphoblastoids and monocytes, were published. -
Investigation of the Underlying Hub Genes and Molexular Pathogensis in Gastric Cancer by Integrated Bioinformatic Analyses
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.20.423656; this version posted December 22, 2020. 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. Investigation of the underlying hub genes and molexular pathogensis in gastric cancer by integrated bioinformatic analyses Basavaraj Vastrad1, Chanabasayya Vastrad*2 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India bioRxiv preprint doi: https://doi.org/10.1101/2020.12.20.423656; this version posted December 22, 2020. 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 The high mortality rate of gastric cancer (GC) is in part due to the absence of initial disclosure of its biomarkers. The recognition of important genes associated in GC is therefore recommended to advance clinical prognosis, diagnosis and and treatment outcomes. The current investigation used the microarray dataset GSE113255 RNA seq data from the Gene Expression Omnibus database to diagnose differentially expressed genes (DEGs). Pathway and gene ontology enrichment analyses were performed, and a proteinprotein interaction network, modules, target genes - miRNA regulatory network and target genes - TF regulatory network were constructed and analyzed. Finally, validation of hub genes was performed. The 1008 DEGs identified consisted of 505 up regulated genes and 503 down regulated genes.