Original Article the Aryl Hydrocarbon Receptor Agonist Benzo(A)Pyrene

Total Page:16

File Type:pdf, Size:1020Kb

Original Article the Aryl Hydrocarbon Receptor Agonist Benzo(A)Pyrene Am J Cancer Res 2016;6(5):1066-1077 www.ajcr.us /ISSN:2156-6976/ajcr0027753 Original Article The aryl hydrocarbon receptor agonist benzo(a)pyrene reactivates LINE-1 in HepG2 cells through canonical TGF-β1 signaling: implications in hepatocellular carcinogenesis Elsa M Reyes-Reyes, Irma N Ramos, Marco A Tavera-Garcia, Kenneth S Ramos Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Arizona College of Medicine, Tucson, Arizona 85721, USA Received March 8, 2016; Accepted March 16, 2016; Epub May 1, 2016; Published May 15, 2016 Abstract: Long interspersed nuclear element-1 (L1) is a genetic element that mobilizes throughout the mammalian genome via retrotransposition and damages host DNA via mutational insertions, chromosomal rearrangements, and reprogramming of gene expression. The cellular mechanisms responsible for aberrant L1 expression during cancer pathogenesis are unclear. Previously, we have shown that L1 reactivation in several human cell lines is dependent upon the activation of aryl hydrocarbon receptor (AhR), a ligand-activated transcription factor member of the PAS superfamily of proteins. We also showed that ectopic expression of L1 reprograms the HepG2 genome leading to epithelial-to-mesenchymal transition (EMT). Here we present evidence that reactivation of L1 and modu- lation of EMT in HepG2 cells by the AhR ligand benzo(a)pyrene (BaP) is effected through the canonical TGF-β1 signaling pathway. BaP increased TGF-β1 mRNA, SMAD2 phosphorylation and decreased expression of E-Cadherin. The functional relevance of these interactions and the involvement of TGFBR1/ALK5 and SMAD2/3 were confirmed by siRNA interference. Furthermore, expression of L1-encoded ORF1p was positively correlated with the activation of TGF-β1 signaling in human hepatocarcinoma samples at various stages of malignant progression. These results indicate that ligand-mediated AhR activation regulates L1 via canonical TGF-β1 signaling and raise important ques- tions about the molecular etiology of human hepatocarcinomas. Keywords: Long interspersed nuclear element-1, benzo(a)pyrene, AhR, TGF-β1, SMAD Introduction L1 retrotransposition is tightly regulated in somatic tissues via genetic and epigenetic Long interspersed nuclear element-1 (LINE-1 or mechanisms [5-7]. However, aberrant ORF1p L1) is a repetitive DNA sequence that mobilizes expression and new somatic L1 insertions have via a “copy and paste” retrotransposition mech- been detected in several epithelial cancers anism. A functional L1 element in humans is ~6 [8-11]. L1 retrotransposition is highly mutagen- kb in length and consists of a 5’ untranslated ic and may promote cancer through induction of region (UTR) with promoter activity, two open aberrant splicing, exon skipping, and genome reading frames, and a terminal 3’ UTR [1, 2]. L1 rearrangements that change gene expression encodes two proteins; ORF1p, a 40 kDa protein and promote genome instability [3, 4]. Our with nucleic acid binding activity and ORF2p, a group has shown that L1 reactivation exerts 150 kDa protein with endonuclease and retrotransposition-dependent and retrotrans- reverse transcriptase activities [3]. A complete position-independent functions that may be L1 retrotransposition cycle consists of tran- critical to neoplastic transformation and cancer scription of L1 RNA, export into the cytoplasm, progression [12, 13]. Ectopic expression of wild translation of ORF1 and ORF2, association of type or a mutant L1 protein incapable of ret- L1 RNA with ORF1 and ORF2 proteins to form rotransposition modulates the expression of a ribonucleoprotein (RNP) particles, import into large number of genetic targets involved in can- the nucleus, reverse transcription, and integra- cer through changes in cellular adhesion, tion into new genomic locations [4]. inflammation and metabolism [12, 13]. L1 also BaP-mediated AhR activation regulates L1 via canonical TGF-β1 signaling disrupts epithelial cell differentiation programs common cellular processes e.g. cell cycle pro- and induces epithelial-to-mesenchymal transi- gression, apoptosis, cell adhesion and interac- tion (EMT) [13], a process that facilitates tion with extracellular matrix [23]. Several stud- metastasis by promoting cell motility and con- ies have shown that AhR can regulate TGF-β1 ferring transformed cells the ability to invade signaling, through deregulation of TGF-β1 [14]. secretion, modulation of TGF-β1 expression or down-regulation of the latency-associated pro- A master promoter of EMT is transforming tein (LTBP-1) expression [24-26]. TGF-β1 also growth factor-β1 (TGF-β1) [15], a potent immu- regulates AhR expression and CYP1A1/1B1 nosuppressive and pro-inflammatory cytokine enzyme activity in a cell/tissue specific manner [16]. TGF-β1 plays a dual role in carcinogenesis, [27-29]. Thus, different mechanisms have been having the ability to inhibit proliferation of can- proposed to explain AhR and TGF-β1 crosstalk cer cells or to activate migration and invasive- in endothelium [30], regulatory T cells [31], ness through EMT [15] or neoangiogenesis Th17 cells [32] or dendritic cells [33]. The com- [17]. TGF-β1 signaling is mediated through a plexity of tissue-context specific mechanisms complex that includes type I and two type II in the regulation of L1 by AhR/TGF-β1 crosstalk transmembrane receptors with serine/threo- is the primary focus of the present nine kinase activity. Type II receptors phosphor- investigation. ylate type I components, while type 1 receptors transduce the signal from the cell membrane to Materials and methods the nucleus canonically through a complex of SMAD proteins or alternatively, non-canonical- Materials ly, through other signaling pathways e.g. Jun BaP was purchased from Ultra Scientific N-terminal kinase (JNK), p38 and extracellu- (Kingstown, RI). Recombinant human TGF-β1 lar signal-regulated kinases/mitogen-activated was purchased from R&D Systems (Minnea- protein kinases (ERK/MAPK) [18]. Interestingly, polis, MN). Monoclonal anti-GAPDH, and hor- in silico analysis of the L1 regulatory genetic seradish peroxidase (HRP) linked anti-mouse network [12], and biological validation in HepG2 IgG antibodies were from Santa Cruz Biotech cells [13], showed that some of genetic targets (Dallas, TX). Rabbit anti-AhR (13790), anti-E- of L1 are also targets of TGF-β1 (e.g. CCL2, cadherin (24E10), anti-vimentin (D21H3), anti- VCAM, CXCL1) [19-21]. These data suggested SMAD2 (5339), anti-phospho-SMAD2 (3108), that L1 activation and TGF-β1 signaling in hepa- anti-SMAD2/3 (8685), anti-TGFBR1 (3712), toma cells may be cooperative and important in and horseradish peroxidase (HRP) linked anti- hepatocarcinogenesis. rabbit IgG antibodies were from Cell Signaling Technology (Beverly, MA). Protein lysates from: The regulatory networks involved in L1 reactiva- normal limits liver tissue (male, case ID. tion during cell transformation and cancer pro- CU0000001489, Cat No. CP565754), staging I gression are not clear. We have previously hepatocellular liver carcinoma tissue (male, shown that L1 reactivation by the environmen- case ID. CU0000012132, Cat No. CP641361), tal carcinogen BaP is mediated through binding staging II hepatocellular liver carcinoma tissue to the aryl hydrocarbon receptor (AhR). AhR is a (male, case ID. CU0000005407, Cat No. ligand-activated transcription factor ubiqui- CP19427), staging IIIA hepatocellular liver car- tously distributed that translocates from the cinoma tissue (male, case ID. CU000001197, cytosol to the nucleus after ligation by polycy- Cat No. CP607175), and staging IV hepatocel- clic aromatic hydrocarbons. Ligand-bound AhR lular liver carcinoma tissue (male, case ID. forms a heterodimer with the AhR nuclear CU0000013002, Cat No. CP532216) were translocator (ARNT) and binds to a specific from OriGene (Rockville, MD). Pathological sequence to regulate gene expression. The staging of tissue samples followed established hallmark response of AhR activation is the tran- guidelines. DMSO was from American Type scriptional activation of cytochrome P4501A1 Culture Collection (ATCC). (CYP1A1) in hepatic parenchymal cells [22]. Polyclonal anti-human ORF1p antibody There exists a cell-specific and context-depen- dent crosstalk between AhR and TGF-β1. Both A custom made polyclonal antibody produced AhR and TGF-β1 participate in the regulation of by New England Peptide Inc. was diluted 1067 Am J Cancer Res 2016;6(5):1066-1077 BaP-mediated AhR activation regulates L1 via canonical TGF-β1 signaling Table 1. Oligonucleotides sequences used in this study 1% IGEPAL CA-630 (pH 7.5), supple- Sequence Description mented with protease and phospha- tase inhibitor cocktails (EMD Millipore) 5’-CCA AGTTGGAAAACACTCTGC-3’ ORF1-Forward-RT-PCR for 5 min at 4°C and then cleared by 5’-TGTGGCGTTCTCTGTATTTCC-3’ ORF1-Reverse-RT-PCR centrifugation at 16,000 × g for 10 5’-TCGACACATACACTCTCCCAAG-3’ ORF2-Forward-RT-PCR minutes at 4°C. All protein concentra- 5’-TGGTCCTGGACTCTTTTTGG-3’ ORF2-Reverse-RT-PCR tions were determined using the 5’-GGATACCAACTATTGCTTCAGCTCC-3’ TGF β1-Forward-RT-PCR bicinchoninic acid assay (Thermo 5’-AGGCTCCAAATATAGGGGCAGGGTC-3’ TGF β1-Reverse-RT-PCR Fisher Scientific). 5’-GATCATCAGCAATGCCTCCT-3’ GAPDH-Forward-RT-PCR Immunoblotting 5’-TGTGGTCATGAGTCCTTCCA-3’ GAPDH-Reverse-RT-PCR 5’-CGGAUGAAAUCCUGACGUAtt-3’ AHR-siRNA-Sense Total cell lysates were resolved by 5’-UACGUCAGGAUUUCAUCAGtt-3’ AHR-siRNA-Antisense SDS-Tris PAGE and transferred onto 5’-CAGUUACUGUGGAAGGAAUtt-3’ TGFBR1-siRNA-Sense polyvinylidine fluoride membranes
Recommended publications
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
    Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated.
    [Show full text]
  • 1714 Gene Comprehensive Cancer Panel Enriched for Clinically Actionable Genes with Additional Biologically Relevant Genes 400-500X Average Coverage on Tumor
    xO GENE PANEL 1714 gene comprehensive cancer panel enriched for clinically actionable genes with additional biologically relevant genes 400-500x average coverage on tumor Genes A-C Genes D-F Genes G-I Genes J-L AATK ATAD2B BTG1 CDH7 CREM DACH1 EPHA1 FES G6PC3 HGF IL18RAP JADE1 LMO1 ABCA1 ATF1 BTG2 CDK1 CRHR1 DACH2 EPHA2 FEV G6PD HIF1A IL1R1 JAK1 LMO2 ABCB1 ATM BTG3 CDK10 CRK DAXX EPHA3 FGF1 GAB1 HIF1AN IL1R2 JAK2 LMO7 ABCB11 ATR BTK CDK11A CRKL DBH EPHA4 FGF10 GAB2 HIST1H1E IL1RAP JAK3 LMTK2 ABCB4 ATRX BTRC CDK11B CRLF2 DCC EPHA5 FGF11 GABPA HIST1H3B IL20RA JARID2 LMTK3 ABCC1 AURKA BUB1 CDK12 CRTC1 DCUN1D1 EPHA6 FGF12 GALNT12 HIST1H4E IL20RB JAZF1 LPHN2 ABCC2 AURKB BUB1B CDK13 CRTC2 DCUN1D2 EPHA7 FGF13 GATA1 HLA-A IL21R JMJD1C LPHN3 ABCG1 AURKC BUB3 CDK14 CRTC3 DDB2 EPHA8 FGF14 GATA2 HLA-B IL22RA1 JMJD4 LPP ABCG2 AXIN1 C11orf30 CDK15 CSF1 DDIT3 EPHB1 FGF16 GATA3 HLF IL22RA2 JMJD6 LRP1B ABI1 AXIN2 CACNA1C CDK16 CSF1R DDR1 EPHB2 FGF17 GATA5 HLTF IL23R JMJD7 LRP5 ABL1 AXL CACNA1S CDK17 CSF2RA DDR2 EPHB3 FGF18 GATA6 HMGA1 IL2RA JMJD8 LRP6 ABL2 B2M CACNB2 CDK18 CSF2RB DDX3X EPHB4 FGF19 GDNF HMGA2 IL2RB JUN LRRK2 ACE BABAM1 CADM2 CDK19 CSF3R DDX5 EPHB6 FGF2 GFI1 HMGCR IL2RG JUNB LSM1 ACSL6 BACH1 CALR CDK2 CSK DDX6 EPOR FGF20 GFI1B HNF1A IL3 JUND LTK ACTA2 BACH2 CAMTA1 CDK20 CSNK1D DEK ERBB2 FGF21 GFRA4 HNF1B IL3RA JUP LYL1 ACTC1 BAG4 CAPRIN2 CDK3 CSNK1E DHFR ERBB3 FGF22 GGCX HNRNPA3 IL4R KAT2A LYN ACVR1 BAI3 CARD10 CDK4 CTCF DHH ERBB4 FGF23 GHR HOXA10 IL5RA KAT2B LZTR1 ACVR1B BAP1 CARD11 CDK5 CTCFL DIAPH1 ERCC1 FGF3 GID4 HOXA11 IL6R KAT5 ACVR2A
    [Show full text]
  • Silencing of ZNF217 Gene Influences the Biological Behavior of a Human Ovarian Cancer Cell Line
    1065-1071 5/4/08 14:33 Page 1065 INTERNATIONAL JOURNAL OF ONCOLOGY 32: 1065-1071, 2008 Silencing of ZNF217 gene influences the biological behavior of a human ovarian cancer cell line GUIQIN SUN1, JUN ZHOU2, AILAN YIN1, YANQING DING2 and MEI ZHONG1 1Department of Obstetrics and Gynecology, Nanfang Hospital, 2Department of Pathology, Southern Medical University, Guangzhou 510515, Guangdong Province, P.R. China Received January 7, 2008; Accepted February 22, 2008 Abstract. Zinc-finger protein 217 (ZNF217), a candidate and environmental factors, but its pathogenesis is still unclear. oncogene on 20q13.2, can lead cultured human ovarian and Most cancer development including ovarian cancer could mammary epithelial cells to immortalization, which indicates attribute to an accumulation of genetic and/or epigenetic selective expression of ZNF217 affecting 20q13 ampli- changes (2). fication during critical early stages of cancer progression. Zinc-finger protein 217 (ZNF217), recently cloned by In this study, we tested the hypothesis that ZNF217 is a key positional cloning, is thought as one of the strong candidate factor in regulating ovarian cancer proliferation and pro- oncogenes at 20q13.2 in breast cancer (3). Its amplification gression. We examined the effect of the inhibition of ZNF217 at 20q13.2 has also been frequently found in ovarian cancer expression on proliferation and invasion by establishing and other tumors (4-6) associated with aggressive tumor the ZNF217 knockdown ovarian cancer cell line using RNA behavior (7). Additionally, ZNF217 is presumed to encode interference (RNAi). Our results showed that silencing of alternately spliced, Kruppel-like transcription factors of ZNF217 resulted in the effective inhibition of ovarian cancer 1,062 and 1,108 aa, each having a DNA-binding domain cell growth and invasive ability.
    [Show full text]
  • Supplementary Material Computational Prediction of SARS
    Supplementary_Material Computational prediction of SARS-CoV-2 encoded miRNAs and their putative host targets Sheet_1 List of potential stem-loop structures in SARS-CoV-2 genome as predicted by VMir. Rank Name Start Apex Size Score Window Count (Absolute) Direct Orientation 1 MD13 2801 2864 125 243.8 61 2 MD62 11234 11286 101 211.4 49 4 MD136 27666 27721 104 205.6 119 5 MD108 21131 21184 110 204.7 210 9 MD132 26743 26801 119 188.9 252 19 MD56 9797 9858 128 179.1 59 26 MD139 28196 28233 72 170.4 133 28 MD16 2934 2974 76 169.9 71 43 MD103 20002 20042 80 159.3 403 46 MD6 1489 1531 86 156.7 171 51 MD17 2981 3047 131 152.8 38 87 MD4 651 692 75 140.3 46 95 MD7 1810 1872 121 137.4 58 116 MD140 28217 28252 72 133.8 62 122 MD55 9712 9758 96 132.5 49 135 MD70 13171 13219 93 130.2 131 164 MD95 18782 18820 79 124.7 184 173 MD121 24086 24135 99 123.1 45 176 MD96 19046 19086 75 123.1 179 196 MD19 3197 3236 76 120.4 49 200 MD86 17048 17083 73 119.8 428 223 MD75 14534 14600 137 117 51 228 MD50 8824 8870 94 115.8 79 234 MD129 25598 25642 89 115.6 354 Reverse Orientation 6 MR61 19088 19132 88 197.8 271 10 MR72 23563 23636 148 188.8 286 11 MR11 3775 3844 136 185.1 116 12 MR94 29532 29582 94 184.6 271 15 MR43 14973 15028 109 183.9 226 27 MR14 4160 4206 89 170 241 34 MR35 11734 11792 111 164.2 37 52 MR5 1603 1652 89 152.7 118 53 MR57 18089 18132 101 152.7 139 94 MR8 2804 2864 122 137.4 38 107 MR58 18474 18508 72 134.9 237 117 MR16 4506 4540 72 133.8 311 120 MR34 10010 10048 82 132.7 245 133 MR7 2534 2578 90 130.4 75 146 MR79 24766 24808 75 127.9 59 150 MR65 21528 21576 99 127.4 83 180 MR60 19016 19049 70 122.5 72 187 MR51 16450 16482 75 121 363 190 MR80 25687 25734 96 120.6 75 198 MR64 21507 21544 70 120.3 35 206 MR41 14500 14542 84 119.2 94 218 MR84 26840 26894 108 117.6 94 Sheet_2 List of stable stem-loop structures based on MFE.
    [Show full text]
  • Connecting the Missing Dots: Ncrnas As Critical Regulators of Therapeutic Susceptibility in Breast Cancer
    cancers Review Connecting the Missing Dots: ncRNAs as Critical Regulators of Therapeutic Susceptibility in Breast Cancer Elena-Georgiana Dobre 1,2 , Sorina Dinescu 2,3,* and Marieta Costache 2,3 1 AMS Genetic Lab, 030882 Bucharest, Romania; [email protected] 2 Department of Biochemistry and Molecular Biology, University of Bucharest, 050095 Bucharest, Romania; [email protected] 3 The Research Institute of the University of Bucharest, 050095 Bucharest, Romania * Correspondence: [email protected] Received: 8 August 2020; Accepted: 14 September 2020; Published: 21 September 2020 Simple Summary: Despite considerable improvements in diagnosis and treatment, drug resistance remains the main cause of death in BC. Multiple lines of evidence demonstrated that ncRNAs play a vital role in BC resistance. Here, we summarized the molecular mechanisms by which miRNAs and lncRNAs may impact the therapeutic response in BC, highlighting that these molecules can be further exploited as predictive biomarkers and therapeutic targets. By merging data from various studies, we concluded that several ncRNAs, such as miR-221, miR-222, miR-451, UCA1, and GAS5 are strong candidates for pharmacological interventions since they are involved in resistance to all forms of therapies in BC. Therefore, we believe that our review provides an important reservoir of molecules that may translate into clinically useful biomarkers, laying the ground for the adoption of ncRNAs within mainstream routine oncology clinical practice. Abstract: Whether acquired or de novo, drug resistance remains a significant hurdle in achieving therapeutic success in breast cancer (BC). Thus, there is an urge to find reliable biomarkers that will help in predicting the therapeutic response.
    [Show full text]
  • Target Gene Gene Description Validation Diana Miranda
    Supplemental Table S1. Mmu-miR-183-5p in silico predicted targets. TARGET GENE GENE DESCRIPTION VALIDATION DIANA MIRANDA MIRBRIDGE PICTAR PITA RNA22 TARGETSCAN TOTAL_HIT AP3M1 adaptor-related protein complex 3, mu 1 subunit V V V V V V V 7 BTG1 B-cell translocation gene 1, anti-proliferative V V V V V V V 7 CLCN3 chloride channel, voltage-sensitive 3 V V V V V V V 7 CTDSPL CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase-like V V V V V V V 7 DUSP10 dual specificity phosphatase 10 V V V V V V V 7 MAP3K4 mitogen-activated protein kinase kinase kinase 4 V V V V V V V 7 PDCD4 programmed cell death 4 (neoplastic transformation inhibitor) V V V V V V V 7 PPP2R5C protein phosphatase 2, regulatory subunit B', gamma V V V V V V V 7 PTPN4 protein tyrosine phosphatase, non-receptor type 4 (megakaryocyte) V V V V V V V 7 EZR ezrin V V V V V V 6 FOXO1 forkhead box O1 V V V V V V 6 ANKRD13C ankyrin repeat domain 13C V V V V V V 6 ARHGAP6 Rho GTPase activating protein 6 V V V V V V 6 BACH2 BTB and CNC homology 1, basic leucine zipper transcription factor 2 V V V V V V 6 BNIP3L BCL2/adenovirus E1B 19kDa interacting protein 3-like V V V V V V 6 BRMS1L breast cancer metastasis-suppressor 1-like V V V V V V 6 CDK5R1 cyclin-dependent kinase 5, regulatory subunit 1 (p35) V V V V V V 6 CTDSP1 CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 1 V V V V V V 6 DCX doublecortin V V V V V V 6 ENAH enabled homolog (Drosophila) V V V V V V 6 EPHA4 EPH receptor A4 V V V V V V 6 FOXP1 forkhead box P1 V
    [Show full text]
  • Comparative Gene Expression in Cells Competent in Or Lacking DNA-Pkcs Kinase Activity
    bioRxiv preprint doi: https://doi.org/10.1101/2020.09.17.300129; this version posted September 19, 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. 1 Comparative gene expression in cells competent in or lacking DNA-PKcs kinase activity 2 following etoposide exposure reveal differences in gene expression associated with 3 histone modifications, inflammation, cell cycle regulation, Wnt signaling, and 4 differentiation. 5 6 Sk Imran Ali1, Mohammad J.Najaf-Panah1, Johnny Sena2, Faye D. Schilkey2 and Amanda K. 7 Ashley1,3 8 9 1Department of Chemistry and Biochemistry, New Mexico state university, Las Cruces, NM. 10 2National center for Genome Resources, Santa Fe, NM. 11 12 3Correspondence should be addressed to Amanda K. Ashley; [email protected]. 13 14 Abstract 15 16 Maintenance of the genome is essential for cell survival, and impairment of the DNA damage 17 response is associated with multiple pathologies including cancer and neurological 18 abnormalities. DNA-PKcs is a DNA repair protein and a core component of the classical 19 nonhomologous end-joining pathway, but it may have roles in modulating gene expression and 20 thus, the overall cellular response to DNA damage. Using cells producing either wild-type (WT) 21 or kinase-inactive (KR) DNA-PKcs, we assessed global alterations in gene expression in the 22 absence or presence of DNA damage. We evaluated differential gene expression in untreated 23 cells and observed differences in genes associated with cellular adhesion, cell cycle regulation, 24 and inflammation-related pathways.
    [Show full text]
  • KCNMA1 Expression Is Downregulated in Colorectal Cancer Via Epigenetic Mechanisms
    Article KCNMA1 Expression is Downregulated in Colorectal Cancer via Epigenetic Mechanisms Maria Sofia Basile 1, Paolo Fagone 1,*, Katia Mangano 1, Santa Mammana 2, Gaetano Magro 3, Lucia Salvatorelli 3, Giovanni Li Destri 3, Gaetano La Greca 3, Ferdinando Nicoletti 1, Stefano Puleo 3 and Antonio Pesce 3 1 Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 89, 95123 Catania, Italy; [email protected] (M.S.B.); [email protected] (K.M.); [email protected] (F.N.) 2 IRCCS Centro Neurolesi “Bonino-Pulejo”, Strada Statale 113, C.da Casazza, 98124 Messina, Italy; [email protected] 3 Department of Medical and Surgical Sciences and Advanced Technology “G.F. Ingrassia”, University of Catania, Via Santa Sofia 86, 95123 Catania, Italy; [email protected] (G.M.); [email protected] (L.S.); [email protected] (G.L.D.); [email protected] (G.L.G.); [email protected] (S.P.); [email protected] (A.P.) * Correspondence: [email protected] Received: 17 December 2018; Accepted: 16 February 2019; Published: 19 February 2019 Abstract: KCNMA1 is a gene located at 10q22 that encodes the pore-forming α-subunit of the large-conductance Ca2+-activated K+ channel. KCNMA1 is down-regulated in gastric carcinoma tumors, through hypermethylation of its promoter. In the present study, we have evaluated the expression levels of KCNMA1 both in a mouse model of Colorectal Cancer (CRC) and in human CRC samples. Additionally, epigenetic mechanisms of KCNMA1 gene regulation were investigated. We observed a significant down-regulation of KCNMA1 both in a human and mouse model of CRC.
    [Show full text]
  • A Role for Mediator Complex Subunit MED13L in Rb&Sol;E2F-Induced
    Oncogene (2012) 31, 4709 --4717 & 2012 Macmillan Publishers Limited All rights reserved 0950-9232/12 www.nature.com/onc ORIGINAL ARTICLE A role for Mediator complex subunit MED13L in Rb/E2F-induced growth arrest SP Angus and JR Nevins The Rb/E2F pathway is deregulated in virtually all human tumors. It is clear that, in addition to Rb itself, essential cofactors required for transcriptional repression and silencing of E2F target genes are mutated or lost in cancer. To identify novel cofactors required for Rb/E2F-mediated inhibition of cell proliferation, we performed a genome-wide short hairpin RNA screen. In addition to several known Rb cofactors, the screen identified components of the Mediator complex, a large multiprotein coactivator required for RNA polymerase II transcription. We show that the Mediator complex subunit MED13L is required for Rb/E2F control of cell growth, the complete repression of cell cycle target genes, and cell cycle inhibition. Oncogene (2012) 31, 4709--4717; doi:10.1038/onc.2011.622; published online 16 January 2012 Keywords: tumor suppressor; cell cycle; senescence INTRODUCTION Typically, the levels of CDKN2A are greatly increased, leading to The retinoblastoma tumor suppressor (Rb) is a critical negative the accumulation of active, hypophosphorylated Rb. Senescent regulator of cellular proliferation that is frequently inactivated in cells characteristically exhibit flat-cell morphology and are positive 20 human cancer.1,2 In its active form, Rb binds to the members of for senescence-associated beta-galactosidase (SA-b-gal) activity. 21 the E2F family of transcription factors and either suppresses their Additionally, Narita et al. described the formation of senescence- transactivation function or assembles an active repressor com- associated heterochromatic foci at E2F promoters during V12 plex.3 E2F family members are essential regulators of genes Ras -induced senescence.
    [Show full text]
  • Chromo Cytoband Accession Gene Symbol Gene Name Comment 1
    Chromo Cytoband Accession Gene symbol Gene name Comment 1 1p34 H09082 Homo sapiens, clone IMAGE:4449283, mRNA 3 3p14 AA424807 KIAA0107 KIAA0107 gene product 4 4q21 W42723 GRO1 GRO1 oncogene (melanoma growth stimulating activity, alpha) candidate 6 6q22 AA676836 ASM3A acid sphingomyelinase-like phosphodiesterase 6 6q23 T69450 ENPP1 ectonucleotide pyrophosphatase/phosphodiesterase 1 6 6q23 AA608730 HBS1L HBS1 (S. cerevisiae)-like 8 8p11 T48411 HTPAP HTPAP protein 8 8q21 AA459100 TPD52 tumor protein D52 candidate 8 8q21 H84926 ESTs, Moderately similar to AF091457 1 zinc finger protein RIN ZF [R.norvegicus] 8 8q21 N29918 ESTs 8 8q21 AA464518 ESTs 8 8q21 H72538 DECR1 2,4-dienoyl CoA reductase 1, mitochondrial 8 8q22 R38161 Human clone 23548 mRNA sequence 8 8q24 AA453783 MAL2 mal, T-cell differentiation protein 2 8 8q24 AA167188 ZHX1 zinc-fingers and homeoboxes 1 8 8q24 AA676805 KIAA0429 KIAA0429 gene product 8 8q24 R48004 MYC v-myc avian myelocytomatosis viral oncogene homolog oncogene 8 8q24 AA173423 BM-009 hypothetical protein 11 11q13 H09958 CHK choline kinase 11 11q13 AA487486 CCND1 cyclin D1 (PRAD1: parathyroid adenomatosis 1) oncogene 13 13q14 AA485369 ESTs 15 15q21 H91651 GABPB2 GA-binding protein transcription factor, beta subunit 2 (47kD) 15 15q24 AA188168 DKFZP434K2235 DKFZP434K2235 protein 15 15q26 AA453473 Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 25206 15 15q26 R33031 AP3S2 adaptor-related protein complex 3, sigma 2 subunit 15 15q26 AA487575 SIP2-28 calcium and integrin binding protein 17 17q11 AA598826 TRAF4 TNF
    [Show full text]
  • Heme Related Genes Solid Tumor Related Genes Gene
    xT GENE PANEL, For use with xT | 596 gene panel reports 596 gene panel focused on actionable mutations by DNA sequencing • Specimen: tumor and matched normal (peripheral blood or saliva) • SNVs (single nucleotide variants), indels, and copy number variants are detected in all 596 genes • Genomic rearrangements are detected on a 21 gene subset by DNA Sequencing (others detected by RNA sequencing) • Microsatellite instability status and tumor mutational burden are included in the xT report • Average coverage ~ 500x Full transcriptome by RNA sequencing • Specimen: tumor only • Unbiased gene rearrangement detection from fusion transcripts and research use only expression changes • Sequenced at a minimum of 25 million reads, average 50 million reads HEME RELATED GENES ARHGAP26 BIRC3 CIITA DDX3X ETV6 HDAC1 LEF1 MAPK1 NUP98 POT1 SMARCA1 STAT5B TCL1A WHSC1 BCL10 CBLB CKS1B DNM2 FBXO11 HDAC4 MAF MIB1 P2RY8 RAD21 SMC1A STAT6 TNFRSF17 ZRSR2 BCL11B CBLC CSF3R EBF1 FHIT HIST1H1E MAFB MKI67 PCBP1 RHOA SMC3 SUZ12 TP63 BCL7A CD22 CUX1 ECT2L FOXO1 HIST1H3B MALT1 NCOR2 PHF6 SETBP1 SRSF2 TBL1XR1 TRAF3 BCR CD70 CXCR4 EPOR FOXO3 KMT2B MAP3K7 NT5C2 PIM1 SGK1 STAT5A TCF3 TUSC3 BOTH HEME AND SOLID TUMOR RELATED GENES ABCB1 AURKB CARD11 CDKN2B EGFR** FANCD2 FLT1 IDH1 KEAP1 MITF NOTCH1 PIK3R2 SDHA S TAT4 ABCC3 AXIN1 CBFB CDKN2C EP300 FANCE FLT3 IDH2 KIT MLH1** NOTCH2 PLCG2 SDHB ** STK11** ABL1 AXL CBL CEBPA** EPHA7 FANCF F LT4 IKBKE KLHL6 MPL NPM1 PPP2R1A SDHC** SUFU AKT1 B2M CCND1 CHD2 EPHB1 FANCG FOXL2 IKZF1 KMT2A MRE11A NRAS PRDM1 SDHD** TAF1 AKT2 BAP1 CCND2
    [Show full text]
  • Supplemental Solier
    Supplementary Figure 1. Importance of Exon numbers for transcript downregulation by CPT Numbers of down-regulated genes for four groups of comparable size genes, differing only by the number of exons. Supplementary Figure 2. CPT up-regulates the p53 signaling pathway genes A, List of the GO categories for the up-regulated genes in CPT-treated HCT116 cells (p<0.05). In bold: GO category also present for the genes that are up-regulated in CPT- treated MCF7 cells. B, List of the up-regulated genes in both CPT-treated HCT116 cells and CPT-treated MCF7 cells (CPT 4 h). C, RT-PCR showing the effect of CPT on JUN and H2AFJ transcripts. Control cells were exposed to DMSO. β2 microglobulin (β2) mRNA was used as control. Supplementary Figure 3. Down-regulation of RNA degradation-related genes after CPT treatment A, “RNA degradation” pathway from KEGG. The genes with “red stars” were down- regulated genes after CPT treatment. B, Affy Exon array data for the “CNOT” genes. The log2 difference for the “CNOT” genes expression depending on CPT treatment was normalized to the untreated controls. C, RT-PCR showing the effect of CPT on “CNOT” genes down-regulation. HCT116 cells were treated with CPT (10 µM, 20 h) and CNOT6L, CNOT2, CNOT4 and CNOT6 mRNA were analysed by RT-PCR. Control cells were exposed to DMSO. β2 microglobulin (β2) mRNA was used as control. D, CNOT6L down-regulation after CPT treatment. CNOT6L transcript was analysed by Q- PCR. Supplementary Figure 4. Down-regulation of ubiquitin-related genes after CPT treatment A, “Ubiquitin-mediated proteolysis” pathway from KEGG.
    [Show full text]