DOCSLIB.ORG

Original Article Abnormal Expression of YEATS4 Associates with Poor

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

Am J Cancer Res 2018;8(10):2076-2087 www.ajcr.us /ISSN:2156-6976/ajcr0084894 Original Article Abnormal expression of YEATS4 associates with poor prognosis and promotes cell proliferation of hepatic carcinoma cell by regulation the TCEA1/DDX3 axis Song You2,3*, Fuqiang Wang1,2*, Qing Hu4, Pengtao Li1,2, Changmao Zhang2,3, Yaqi Yu2, Yi Zhang2, Qiu Li2, Qing Bao2, Pingguo Liu1,2, Jie Li1,2* 1Department of Hepatobiliary Surgery, Zhongshan Hospital of Xiamen University, Xiamen, Fujian, China; 2Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma (Xiamen University Affiliated Zhongshan Hospital), Xiamen, Fujian, China; 3Graduate College of Fujian Medical University, Fuzhou, Fujian, China; 4Medicine Clinical Laboratory of Xiamen Xianyue Hospital, Xiamen, Fujian, China. *Equal contributors. Received August 31, 2018; Accepted September 14, 2018; Epub October 1, 2018; Published October 15, 2018 Abstract: YEATS domain containing 4 (YEATS4) is usually amplified and functions as an oncogene in several ma- lignancies, such as colorectum, ovarian, breast and lung. However, the biological role of YEATS4 in hepatocellular carcinoma (HCC) has not yet been discussed. Herein, we found that YEATS4 was significantly upregulated in HCC compared to para-cancerous tissues, and was associated with poor prognosis, large tumor size, poor differentia- tion and distant metastasis. In addition, YEATS4 promoted HCC cell proliferation and colony formation by binding to and increasing the transcriptional activity of the TCEA1 promoter. Concurrently, upregulation of TCEA1 increased the stability of the DDX3 protein, a member of the DEAD box RNA helicase family, and augmented the proliferative and colony forming ability of HCC cells. Furthermore, YEATS4 accelerated tumor growth in vivo in a xenograft HCC model. Taken together, our study provides evidence for the first time on the potential role of the YEATS4/TCEA1/ DDX3 axis in regulating HCC progression, and presents YEATS4 as a promising therapeutic target and prognosis maker for HCC. Keywords: YEATS4, TCEA1, DDX3, hepatic carcinoma, prognosis, proliferation Introduction the Wnt/β-catenin/TCF signaling pathway [5, 6]. YEATS4 is also upregulated in NSCLC and Hepatocellular carcinoma (HCC) is a malignant contributes to cancer cell proliferation and tumor of the liver, and has a high mortality rate tumor growth by inhibiting p53 expression [7]. with an annually increasing incidence world- Furthermore, it has been linked with increas- wide [1]. The poor prognosis of HCC patients is ed drug resistance in ovarian cancer [8]. Dow- largely attributed to the difficulty in early diag- nregulation of YEATS4 by miR-218 sensitized nosis, as well as the high metastasis, invasion colorectal cancer cells to L-OHP-induced cell and recurrence of this cancer [2]. Therefore, it apoptosis by weakening cytoprotective auto- is vital to explore the pathways involved in HCC phagy [9]. However, the precise function of initiation, and thereby identify early specific bio- YEATS4 in HCC, and underlying mechanisms markers and potential therapeutic targets for and patient prognosis is unclear. HCC. SOX is an important transcriptional elongation YEATS4 was first identified in the nucleolix [3]. factor that can directly bind to RNA polymerase High sequence homology to the human MLLT1 II, and allow it to read through various transcrip- and MLLT3 proteins indicated a transcription tion arrest sites [10, 11]. SOX has 3 distinct iso- factor function [4]. Recently, YEATS4 has been forms: the ubiquitously expressed TCEA1 that shown to be involved in the genesis and pro- was identified in the network-based protein- gression of various cancers. In the pancreatic protein interactions (PPI) for meningioma rela- and gastric cancers, it acts as an oncogene via tive to healthy controls, the testis-specific SOX2 YEATS4 promotes cell proliferation [12], and SOX3 which controls murine embry- Technology). The blots were then incubated onic stem cell (mESC) fate and maintains its with horseradish peroxidase-conjugated sec- pluripotency by regulating the Lefty1-Nodal- ondary antibodies (Pierce) and visualized by ch- Smad2 pathway [13]. TCEA1 is also up-regulat- emiluminescence. Experiments were repeated ed in HCC [14], although its potential role in triplicate independently. TCEA1 in liver cancer is not completely clear. Human tissue specimens DDX3 (DEAD box protein 3) belongs to the DEAD box RNA helicase family that are charac- Tumor samples were obtained with informed terized by the presence of a helicase domain consent from HCC patients at Zhongshan Hos- and involved in RNA post-transcriptional pro- pital Xiamen University, between 2007 and cession. They are also members of the DEAD/ 2011. The study was approved by the Xiamen H-box family [15], which are aberrantly expr- University Medical Ethics Committee. Overall essed in various solid and hematological ma- survival was calculated from the date of sur- lignancies [16-18]. Studies have shown that gery to the date of death or final follow-up. high-levels of DDX3 could promote proliferation and neoplastic transformation of immortalized Hematoxylin-eosin and immunohistochemistry human breast cancer epithelial cells [19]. In staining addition, studies have hinted to DDX3 growth- regulatory functions of DDX3 in hepato-carcino- Tissues were fixed with 10% neutral formalin, genesis and progression [20, 21]. embedded in paraffin, and 3-μm-thick sections were prepared by the pathological technologist. In this study, we showed that YEATS4 transcrip- For Hematoxylin-Eosin (HE) staining, sections tionally activated TCEA1 expression TCEA1 by were deparaffinized and hydrated with a gra- binding to its promoter, TCEA1 and the latter dient alcohol. After soaking in PBS, sections upregulated DDX3 levels by increasing protein were stained with HE. For IHC, sections were stability. These interactions significantly accel- stained using the streptavidin-peroxidase (S-P) erated HCC cells proliferation and growth in method. In brief, sections were deparaffiniz- vitro and in vivo, thereby indicating that up-reg- ed, hydrated and soaked in 3% H2O2 for 10 ulation of YEATS4 is associated with poor prog- minutes at room temperature, and then incu- nosis in HCC patients. bated with Pygo2 polyclonal antibody (1:3000, ab109001, Abcam) at 4°C overnight. Biotiny- Materials and methods lated secondary antibody and diaminobenzi- dine (DAB) were purchased from Maixin Bio- Cell culture technology (Fuzhou, China). Human liver cancer cell lines were purchased Plasmid construction and lentivirus prepara- from the cell bank of Shanghai Institute of Cell tion Biology and cultured in medium (HyClone) sup- plemented with 10% fetal calf serum (Gibco), For target gene knockdown, control and shRNA 100 IU/ml penicillin and 100 μg/ml streptomy- sequences (shown in Table 1) against YEATS4 cin (Millipore). were cloned into the pLKO.1-Puro vector. For over-expression, genomic sequence of the Immunoblotting YEATS4 and TCEA1 coding region was respec- tively cloned into the backbone of the plv-Puro Cells were harvested and protein was extracted vector vector downstream of the CMV promot- using RIPA buffer (Sigma) with 1% v/v protease er. Then 293T cells were transfected with the inhibitor cocktail (Sigma) and 1% v/v phospha- above mentioned plasmids and packaging vec- tase inhibitor cocktail (Sigma). Equal amounts tors by using the Turbofect Transfection Re- of protein lysates were separated by SDS-PAGE agent (Thermo). Infected cells were cultured for and were transferred onto PVDF membranes. selection with puromycin (InvivoGen). The filters were probed with the following spe- cific primary antibodies: anti-YEATS4 and anti- RNA extraction and real-time PCR DDX3 (Abcam), anti-TCEA1 and anti-PCNA (Pro- teintech Group), anti-ha, anti-flag and anti-β- RNA was extracted from tissues or cell samples actin (Cell Signaling Technology) (Cell Signaling using the Trizol reagent (Invitrogen) according 2077 Am J Cancer Res 2018;8(10):2076-2087 YEATS4 promotes cell proliferation Table 1. YEATS4 abnormal expression correlates with clinic-patho- unting Kit-8 (CCK-8) assays logical factors of HCC patients were performed using the Kit Clinical-pathology Factors A abnormal expression N X2 P (#YB-K001, Yiyuan Biotechno- logies, Guangzhou, China) ac- Age (yr) cording to the manufacturer’s < 55 20 (80.0%) 25 0.125 0.724 instructions for the purpose of ≥ 55 40 (83.3%) 48 detecting cell proliferation ab- Gender ility. Optical density (OD) val- Male 35 (83.3%) 42 0.088 0.768 ues were measured at a wa- Female 25 (80.6%) 31 velength of 450 nm by a micro- Tumor size plate reader. All experiments < 5 cm 21 (70.0%) 30 5.172 0.023* were performed three times, ≥ 5 cm 39 (90.7%) 43 and the average results were Metastasis calculated. Yes 38 (92.7%) 41 7.033 0.008** EdU assay No 22 (68.8%) 32 Differentiation The EdU incorporation assay Poor 28 (93.3%) 30 5.074 0.034* was performed using the EdU Moderate 12 (85.7%) 14 assay kit (RiboBio, Guangzhou, Well 20 (71.4%) 28 China), according to the manu- facturer’s instructions. Briefly, Liver cirrhosis status cells were cultured in triplica- No 19 (73.1%) 26 2.261 0.200 te in 24-well plates. The cells Yes 41 (87.2%) 47 were then incubated with 50 Serum HBV level (cps/ml) nM EdU for an additional 2 h at < 1000 26 (83.9%) 31 0.166 0.684 37°C. The cells were fixed with ≥ 1000 28 (80.0%) 35 4% formaldehyde for 15 min at Serum AFP level (ug/L) room temperature and treat- < 400 27 (79.4%) 34 0.279 0.597 ed with 0.5% Triton X-100 for ≥ 400 32 (84.2%) 38 20 min at room temperature to *p < 0.05; **P < 0.01. permeabilize them. After three washes with phosphate-buff- ered saline (PBS), the cells we- to the manufacturer’s instructions. Primers re incubated with the Apollo reaction cocktail were designed and synthesized by BGI-Tech. (100 l/well) for 30 min. After being washed th- The sequences of the primer pairs are shown in ree times with phosphate buffered saline (PBS), Table S1.
Recommended publications
  • Antisense RNA Polymerase II Divergent Transcripts Are P-Tefb Dependent and Substrates for the RNA Exosome

    Antisense RNA Polymerase II Divergent Transcripts Are P-Tefb Dependent and Substrates for the RNA Exosome

    Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome Ryan A. Flynna,1,2, Albert E. Almadaa,b,1, Jesse R. Zamudioa, and Phillip A. Sharpa,b,3 aDavid H. Koch Institute for Integrative Cancer Research, Cambridge, MA 02139; and bDepartment of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139 Contributed by Phillip A. Sharp, May 12, 2011 (sent for review March 3, 2011) Divergent transcription occurs at the majority of RNA polymerase II PII carboxyl-terminal domain (CTD) at serine 2, DSIF, and (RNAPII) promoters in mouse embryonic stem cells (mESCs), and NELF results in the dissociation of NELF from the elongation this activity correlates with CpG islands. Here we report the char- complex and continuation of transcription (13). More recently acterization of upstream antisense transcription in regions encod- it was recognized, in mESCs, that c-Myc stimulates transcription ing transcription start site associated RNAs (TSSa-RNAs) at four at over a third of all cellular promoters by recruitment of P-TEFb divergent CpG island promoters: Isg20l1, Tcea1, Txn1, and Sf3b1. (12). Intriguingly in these same cells, NELF and DSIF have bi- We find that upstream antisense RNAs (uaRNAs) have distinct modal binding profiles at divergent TSSs. This suggests divergent capped 5′ termini and heterogeneous nonpolyadenylated 3′ ends. RNAPII complexes might be poised for signals controlling elon- uaRNAs are short-lived with average half-lives of 18 minutes and gation and opens up the possibility that in the antisense direction are present at 1–4 copies per cell, approximately one RNA per DNA P-TEF-b recruitment may be regulating release for productive template.
  • A Genome-Wide Library of MADM Mice for Single-Cell Genetic Mosaic Analysis

    A Genome-Wide Library of MADM Mice for Single-Cell Genetic Mosaic Analysis

    bioRxiv preprint doi: https://doi.org/10.1101/2020.06.05.136192; this version posted June 6, 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. Contreras et al., A Genome-wide Library of MADM Mice for Single-Cell Genetic Mosaic Analysis Ximena Contreras1, Amarbayasgalan Davaatseren1, Nicole Amberg1, Andi H. Hansen1, Johanna Sonntag1, Lill Andersen2, Tina Bernthaler2, Anna Heger1, Randy Johnson3, Lindsay A. Schwarz4,5, Liqun Luo4, Thomas Rülicke2 & Simon Hippenmeyer1,6,# 1 Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria 2 Institute of Laboratory Animal Science, University of Veterinary Medicine Vienna, Vienna, Austria 3 Department of Biochemistry and Molecular Biology, University of Texas, Houston, TX 77030, USA 4 HHMI and Department of Biology, Stanford University, Stanford, CA 94305, USA 5 Present address: St. Jude Children’s Research Hospital, Memphis, TN 38105, USA 6 Lead contact #Correspondence and requests for materials should be addressed to S.H. ([email protected]) 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.06.05.136192; this version posted June 6, 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. Contreras et al., SUMMARY Mosaic Analysis with Double Markers (MADM) offers a unique approach to visualize and concomitantly manipulate genetically-defined cells in mice with single-cell resolution.
  • Gene Regulation Underlies Environmental Adaptation in House Mice

    Gene Regulation Underlies Environmental Adaptation in House Mice

    Downloaded from genome.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Research Gene regulation underlies environmental adaptation in house mice Katya L. Mack,1 Mallory A. Ballinger,1 Megan Phifer-Rixey,2 and Michael W. Nachman1 1Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, California 94720, USA; 2Department of Biology, Monmouth University, West Long Branch, New Jersey 07764, USA Changes in cis-regulatory regions are thought to play a major role in the genetic basis of adaptation. However, few studies have linked cis-regulatory variation with adaptation in natural populations. Here, using a combination of exome and RNA- seq data, we performed expression quantitative trait locus (eQTL) mapping and allele-specific expression analyses to study the genetic architecture of regulatory variation in wild house mice (Mus musculus domesticus) using individuals from five pop- ulations collected along a latitudinal cline in eastern North America. Mice in this transect showed clinal patterns of variation in several traits, including body mass. Mice were larger in more northern latitudes, in accordance with Bergmann’s rule. We identified 17 genes where cis-eQTLs were clinal outliers and for which expression level was correlated with latitude. Among these clinal outliers, we identified two genes (Adam17 and Bcat2) with cis-eQTLs that were associated with adaptive body mass variation and for which expression is correlated with body mass both within and between populations. Finally, we per- formed a weighted gene co-expression network analysis (WGCNA) to identify expression modules associated with measures of body size variation in these mice.
  • Lack of Polymorphisms in the Coding Region of the Highly Conserved Gene Encoding Transcription Elongation Factor S-II (TCEA1)

    Lack of Polymorphisms in the Coding Region of the Highly Conserved Gene Encoding Transcription Elongation Factor S-II (TCEA1)

    Drug Discov Ther 2007;1(1):9-11. Brief Report Lack of polymorphisms in the coding region of the highly conserved gene encoding transcription elongation factor S-II (TCEA1) Takahiro Ito1, Kent Doi2, 3, Naoko Matsumoto4, Fumiko Kakihara4, Eisei Noiri2, Setsuo Hasegawa4, Katsushi Tokunaga3, Kazuhisa Sekimizu1, * 1 Division of Developmental Biochemistry, Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo, Japan; 2 Department of Nephrology and Endocrinology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan; 3 Department of Human Genetics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan; 4 Sekino Clinical Pharmacology Clinic, Tokyo, Japan. ABSTRACT: Transcription elongation factor been identified in many eukaryotes including budding S-II stimulates mRNA chain elongation catalyzed yeast, fruit fly, mouse, and human (6-9). The human by RNA polymerase II. S-II is highly conserved S-II gene, designated TCEA1, was initially reported among eukaryotes and is essential for definitive to be a 2.5-kb intronless gene mapped on 3p22- > hematopoiesis in mice. In the present study, we p21.3 (10). We previously reported that the murine report the identification of five novel nucleotide S-II gene consists of 10 exons and maps on the variations in the human S-II gene in the Japanese proximal region of mouse chromosome 1, which is population. All five variations were located in syntenic to human chromosome 8q (11). Consistent introns, and no polymorphisms were found in the with the synteny between the mouse and human protein-coding region, suggesting strong negative chromosomes, recent progress in the human genome selection during gene evolution.
  • A High-Throughput Approach to Uncover Novel Roles of APOBEC2, a Functional Orphan of the AID/APOBEC Family

    A High-Throughput Approach to Uncover Novel Roles of APOBEC2, a Functional Orphan of the AID/APOBEC Family

    Rockefeller University Digital Commons @ RU Student Theses and Dissertations 2018 A High-Throughput Approach to Uncover Novel Roles of APOBEC2, a Functional Orphan of the AID/APOBEC Family Linda Molla Follow this and additional works at: https://digitalcommons.rockefeller.edu/ student_theses_and_dissertations Part of the Life Sciences Commons A HIGH-THROUGHPUT APPROACH TO UNCOVER NOVEL ROLES OF APOBEC2, A FUNCTIONAL ORPHAN OF THE AID/APOBEC FAMILY A Thesis Presented to the Faculty of The Rockefeller University in Partial Fulfillment of the Requirements for the degree of Doctor of Philosophy by Linda Molla June 2018 © Copyright by Linda Molla 2018 A HIGH-THROUGHPUT APPROACH TO UNCOVER NOVEL ROLES OF APOBEC2, A FUNCTIONAL ORPHAN OF THE AID/APOBEC FAMILY Linda Molla, Ph.D. The Rockefeller University 2018 APOBEC2 is a member of the AID/APOBEC cytidine deaminase family of proteins. Unlike most of AID/APOBEC, however, APOBEC2’s function remains elusive. Previous research has implicated APOBEC2 in diverse organisms and cellular processes such as muscle biology (in Mus musculus), regeneration (in Danio rerio), and development (in Xenopus laevis). APOBEC2 has also been implicated in cancer. However the enzymatic activity, substrate or physiological target(s) of APOBEC2 are unknown. For this thesis, I have combined Next Generation Sequencing (NGS) techniques with state-of-the-art molecular biology to determine the physiological targets of APOBEC2. Using a cell culture muscle differentiation system, and RNA sequencing (RNA-Seq) by polyA capture, I demonstrated that unlike the AID/APOBEC family member APOBEC1, APOBEC2 is not an RNA editor. Using the same system combined with enhanced Reduced Representation Bisulfite Sequencing (eRRBS) analyses I showed that, unlike the AID/APOBEC family member AID, APOBEC2 does not act as a 5-methyl-C deaminase.
  • Oral Administration of Lactobacillus Plantarum 299V

    Oral Administration of Lactobacillus Plantarum 299V

    Genes Nutr (2015) 10:10 DOI 10.1007/s12263-015-0461-7 RESEARCH PAPER Oral administration of Lactobacillus plantarum 299v modulates gene expression in the ileum of pigs: prediction of crosstalk between intestinal immune cells and sub-mucosal adipocytes 1 1,4 1,5 1 Marcel Hulst • Gabriele Gross • Yaping Liu • Arjan Hoekman • 2 1,3 1,3 Theo Niewold • Jan van der Meulen • Mari Smits Received: 19 November 2014 / Accepted: 28 March 2015 / Published online: 11 April 2015 Ó The Author(s) 2015. This article is published with open access at Springerlink.com Abstract To study host–probiotic interactions in parts of ileum. A higher expression level of several B cell-specific the intestine only accessible in humans by surgery (je- transcription factors/regulators was observed, suggesting junum, ileum and colon), pigs were used as model for that an influx of B cells from the periphery to the ileum humans. Groups of eight 6-week-old pigs were repeatedly and/or the proliferation of progenitor B cells to IgA-com- orally administered with 5 9 1012 CFU Lactobacillus mitted plasma cells in the Peyer’s patches of the ileum was plantarum 299v (L. plantarum 299v) or PBS, starting with stimulated. Genes coding for enzymes that metabolize a single dose followed by three consecutive daily dosings leukotriene B4, 1,25-dihydroxyvitamin D3 and steroids 10 days later. Gene expression was assessed with pooled were regulated in the ileum. Bioinformatics analysis pre- RNA samples isolated from jejunum, ileum and colon dicted that these metabolites may play a role in the scrapings of the eight pigs per group using Affymetrix crosstalk between intestinal immune cells and sub-mucosal porcine microarrays.
  • Gene Regulation and the Genomic Basis of Speciation and Adaptation in House Mice (Mus Musculus)

    Gene Regulation and the Genomic Basis of Speciation and Adaptation in House Mice (Mus Musculus)

    Gene regulation and the genomic basis of speciation and adaptation in house mice (Mus musculus) By Katya L. Mack A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Integrative Biology in the Graduate Division of the University of California, Berkeley Committee in charge: Professor Michael W. Nachman, Chair Professor Rasmus Nielsen Professor Craig T. Miller Fall 2018 Abstract Gene regulation and the genomic basis of speciation and adaptation in house mice (Mus musculus) by Katya Mack Doctor of Philosophy in Integrative Biology University of California, Berkeley Professor Michael W. Nachman, Chair Gene expression is a molecular phenotype that is essential to organismal form and fitness. However, how gene regulation evolves over evolutionary time and contributes to phenotypic differences within and between species is still not well understood. In my dissertation, I examined the role of gene regulation in adaptation and speciation in house mice (Mus musculus). In chapter 1, I reviewed theoretical models and empirical data on the role of gene regulation in the origin of new species. I discuss how regulatory divergence between species can result in hybrid dysfunction and point to areas that could benefit from future research. In chapter 2, I characterized regulatory divergence between M. m. domesticus and M. m. musculus associated with male hybrid sterility. The major model for the evolution of post-zygotic isolation proposes that hybrid sterility or inviability will evolve as a product of deleterious interactions (i.e., negative epistasis) between alleles at different loci when joined together in hybrids. As the regulation of gene expression is inherently based on interactions between loci, disruption of gene regulation in hybrids may be a common mechanism for post-zygotic isolation.
  • Variation in Protein Coding Genes Identifies Information Flow

    Variation in Protein Coding Genes Identifies Information Flow

    bioRxiv preprint doi: https://doi.org/10.1101/679456; this version posted June 21, 2019. 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. Animal complexity and information flow 1 1 2 3 4 5 Variation in protein coding genes identifies information flow as a contributor to 6 animal complexity 7 8 Jack Dean, Daniela Lopes Cardoso and Colin Sharpe* 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Institute of Biological and Biomedical Sciences 25 School of Biological Science 26 University of Portsmouth, 27 Portsmouth, UK 28 PO16 7YH 29 30 * Author for correspondence 31 [email protected] 32 33 Orcid numbers: 34 DLC: 0000-0003-2683-1745 35 CS: 0000-0002-5022-0840 36 37 38 39 40 41 42 43 44 45 46 47 48 49 Abstract bioRxiv preprint doi: https://doi.org/10.1101/679456; this version posted June 21, 2019. 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. Animal complexity and information flow 2 1 Across the metazoans there is a trend towards greater organismal complexity. How 2 complexity is generated, however, is uncertain. Since C.elegans and humans have 3 approximately the same number of genes, the explanation will depend on how genes are 4 used, rather than their absolute number.
  • Single-Cell Transcriptome Reveals a Testis-Specific Expression Profile Of

    Single-Cell Transcriptome Reveals a Testis-Specific Expression Profile Of

    bioRxiv preprint doi: https://doi.org/10.1101/2021.03.10.434830; this version posted March 11, 2021. 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 4.0 International license. Single-cell transcriptome reveals a testis-specific expression profile of​ TCEA ​in human spermatogenesis 1† 2† Pankaew, S.​ ​ and Pramoj Na Ayutthaya, P.​ *​ 1Aix-Marseille​ Université, CNRS, INSERM, CIML, 13009 Marseille, France 2Department​ of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany † =​ equal contribution * = corresponding author Contact information Pankaew, S. = [email protected] Pramoj Na Ayutthaya, P. = [email protected] Abstract Transcription elongation factor A (​TCEA​) is a eukaryotic transcriptional molecule, required for a formation of initiation and elongation of gene transcription-mediated RNA polymerase II (RNAPII) complex, to promote transcription-coupled nucleotide excision repair (TC-NER) after RNAPII backtracking recovery. ​TCEA shares three isoforms in which ​TCEA1 is ubiquitously expressed among all eukaryotic cells. We found a spermatogenesis ​TCEA1 ​and TCEA2 ​expression profile has a unique transcriptional programme, compared with embryogenesis. Moreover, the testis-specific ​TCEA2 ​profile correlates with gene transcription, whereas ​TCEA1 ​specifically correlates with genes transcribed for Nuclear excision repair (NER) during
  • Molecular Targeting and Enhancing Anticancer Efficacy of Oncolytic HSV-1 to Midkine Expressing Tumors

    Molecular Targeting and Enhancing Anticancer Efficacy of Oncolytic HSV-1 to Midkine Expressing Tumors

    University of Cincinnati Date: 12/20/2010 I, Arturo R Maldonado , hereby submit this original work as part of the requirements for the degree of Doctor of Philosophy in Developmental Biology. It is entitled: Molecular Targeting and Enhancing Anticancer Efficacy of Oncolytic HSV-1 to Midkine Expressing Tumors Student's name: Arturo R Maldonado This work and its defense approved by: Committee chair: Jeffrey Whitsett Committee member: Timothy Crombleholme, MD Committee member: Dan Wiginton, PhD Committee member: Rhonda Cardin, PhD Committee member: Tim Cripe 1297 Last Printed:1/11/2011 Document Of Defense Form Molecular Targeting and Enhancing Anticancer Efficacy of Oncolytic HSV-1 to Midkine Expressing Tumors A dissertation submitted to the Graduate School of the University of Cincinnati College of Medicine in partial fulfillment of the requirements for the degree of DOCTORATE OF PHILOSOPHY (PH.D.) in the Division of Molecular & Developmental Biology 2010 By Arturo Rafael Maldonado B.A., University of Miami, Coral Gables, Florida June 1993 M.D., New Jersey Medical School, Newark, New Jersey June 1999 Committee Chair: Jeffrey A. Whitsett, M.D. Advisor: Timothy M. Crombleholme, M.D. Timothy P. Cripe, M.D. Ph.D. Dan Wiginton, Ph.D. Rhonda D. Cardin, Ph.D. ABSTRACT Since 1999, cancer has surpassed heart disease as the number one cause of death in the US for people under the age of 85. Malignant Peripheral Nerve Sheath Tumor (MPNST), a common malignancy in patients with Neurofibromatosis, and colorectal cancer are midkine- producing tumors with high mortality rates. In vitro and preclinical xenograft models of MPNST were utilized in this dissertation to study the role of midkine (MDK), a tumor-specific gene over- expressed in these tumors and to test the efficacy of a MDK-transcriptionally targeted oncolytic HSV-1 (oHSV).
  • Knockdown of High Mobility Group Box 3 Impairs Cell Viability and Colony Formation but Increases Apoptosis in A549 Human Non‑Small Cell Lung Cancer Cells

    Knockdown of High Mobility Group Box 3 Impairs Cell Viability and Colony Formation but Increases Apoptosis in A549 Human Non‑Small Cell Lung Cancer Cells

    ONCOLOGY LETTERS 17: 2937-2945, 2019 Knockdown of high mobility group box 3 impairs cell viability and colony formation but increases apoptosis in A549 human non‑small cell lung cancer cells NING SONG1*, BAOHUA WANG2*, GUISHAN FENG3, LIN DUAN1, SHENGFANG YUAN1, WEIHUA JIA1 and YI LIU1 Departments of 1Infectious Diseases and 2Thoracic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei 050000; 3Department of Internal Medicine, Hebei Yi County Hospital, Baoding, Hebei 074200, P.R. China Received August 25, 2017; Accepted February 22, 2018 DOI: 10.3892/ol.2019.9927 Abstract. Previous research has linked high mobility group of NSCLC; however, owing to the heterogeneity and genetic box 3 (HMGB3) overexpression to the malignant progression instability of NSCLC cells, therapeutic methods that are being and poor prognosis of non-small cell lung cancer (NSCLC). The used in the clinic, including chemotherapy, radiation therapy present study investigated the role of HMGB3 in cell survival or targeted therapy such as epithelial growth factor receptor and colony formation of NSCLC cells. Stable knockdown of (EGFR)-tyrosine kinase inhibitors, often exhibit short-lived HMGB3 in A549 cells was achieved by lentiviral-based shRNA treatment response (4). Novel therapeutic targets or methods interference and verified by detection of the transcriptional and are therefore required. translational level of HMGB3 with reverse transcription-quan- A previous study revealed that high mobility group box 3 titative polymerase chain reaction and western blotting, (HMGB3) overexpression is an independent risk factor for respectively. The influence of HMGB3 knockdown on A549 NSCLC progression, lymph node metastasis and poor survival cell viability and apoptotic rate was evaluated by Cell Counting rates of patients (5), indicating the prognostic value and the onco- Kit‑8 assay and flow cytometry following annexin V staining, genic role of HMGB3 overexpression in NSCLC development.
  • Evolution of Vertebrate Opioid Receptors

    Evolution of Vertebrate Opioid Receptors

    Evolution of vertebrate opioid receptors Susanne Dreborg, Go¨ rel Sundstro¨ m, Tomas A. Larsson, and Dan Larhammar* Department of Neuroscience, Uppsala University, Box 593, SE-75124 Uppsala, Sweden Edited by Tomas Ho¨kfelt, Karolinska Institutet, Stockholm, Sweden, and approved August 15, 2008 (received for review June 9, 2008) The opioid peptides and receptors have prominent roles in pain Many vertebrate gene families have been found to have transmission and reward mechanisms in mammals. The evolution expanded in the early stages of vertebrate evolution, before the of the opioid receptors has so far been little studied, with only a radiation of jawed vertebrates. However, the high degree of few reports on species other than tetrapods. We have investigated sequence divergence over such large evolutionary distances species representing a broader range of vertebrates and found that often obscures orthology–paralogy relationships. Investigation the four opioid receptor types (delta, kappa, mu, and NOP) are of conserved synteny may facilitate identification of orthologs present in most of the species. The gene relationships were and gives important clues to the mechanisms by which the genes deduced by using both phylogenetic analyses and chromosomal were duplicated. We used this approach to investigate the location relative to 20 neighboring gene families in databases of evolution of a few other gene families, namely the neuropeptide assembled genomes. The combined results show that the verte- Y (NPY) family of peptides (27) and the large family of NPY brate opioid receptor gene family arose by quadruplication of a receptors (28). These families were found to have expanded as large chromosomal block containing at least 14 other gene fami- a result of extensive chromosome duplications, most likely lies.