Regulatory Mechanisms of Tumor Suppressor P16<Sup>

Total Page:16

File Type:pdf, Size:1020Kb

Regulatory Mechanisms of Tumor Suppressor P16<Sup> CURRENT TOPIC pubs.acs.org/biochemistry Regulatory Mechanisms of Tumor Suppressor P16INK4A and Their Relevance to Cancer † ‡ § || Junan Li,*, , Ming Jye Poi, and Ming-Daw Tsai † ‡ Division of Environmental Health Sciences, College of Public Health, and Comprehensive Cancer Center and § Department of Pharmacy, The Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, Ohio 43210, United States Genomics) Research Center and Institute of Biological Chemistry, Academia Sinica, Taiwan ABSTRACT: P16INK4A (also known as P16 and MTS1), a protein consisting exclusively of four ankyrin repeats, is recognized as a tumor suppressor mainly because of the prevalence of genetic inactivation of the p16INK4A (or CDKN2A) gene in virtually all types of human cancers. However, it has also been shown that an elevated level of expression (upregulation) of P16 is involved in cellular senescence, aging, and cancer progression, indicating that the regulation of P16 is critical for its function. Here, we discuss the regulatory mechanisms of P16 function at the DNA level, the transcription level, and the posttranscriptional level, as well as their implications for the structureÀfunction relationship of P16 and for human cancers. 16, also designated as MTS1 and P16INK4A, is one of the most ’ BASIC BIOCHEMICAL FEATURES OF P16 Pextensively studied proteins in the past decades because of its In 1993, a truncated version of the p16 cDNA gene was first critical roles in cell cycle progression, cellular senescence, and the fi 1À5 identi ed in a yeast two-hybrid screen for proteins that development of human cancers. At the G1-to-S transition, interact with human CDK4.12,13 The cDNA encoded a P16 specifically inhibits cyclin-dependent kinase 4 and 6 (CDK4 polypeptide of 148 amino acid residues with an estimated and CDK6, respectively)-mediated phosphorylation of pRb, the molecular mass of ∼16 kDa that negatively modulated the retinoblastoma susceptible gene product, thus sequestering E2F kinase activity of CDK4 (Figure 2A). Consequently, it was transcription factors as incompetent pRbÀE2F complexes and designated as P16INK4A (for an inhibitor of CDK4) or consequently blocking cell cycle progression5 (Figure 1). CDKN2(forCDKinhibitor2).Oneyearlater,theMTS1 Furthermore, it has also been demonstrated that an elevated (multiple tumor suppressor 1) locus on human chromosome level of P16 expression induced by oncogenes, DNA damage 9p was described following the discovery that the p16 gene response, or aging can trigger and accelerate cellular sene- was frequently inactivated by homozygous deletion or muta- À scence.1 4 While genetic inactivation of the p16 gene (cyclin- tion in melanomas as well as a broad spectrum of additional 13 dependent kinase inhibitor 2a, CDKN2A) by deletion, methyla- human cancer types. The full-length p16 cDNA gene was tion, and point mutation has been found in nearly 50% of all reported soon thereafter, which encodes a protein with eight 6À9 additional amino acid residues at the N-terminus in compar- human cancers, the overexpression of P16 at both mRNA 14,15 and protein levels is also associated with poor prognosis for ison with the originally reported cDNA sequence (Figure 2A). Further studies have established that P16 is a cancers, including neuroblastoma, cervical, ovarian, and breast pivotal regulator of cell cycle progression with diverse phy- cancers, prostate tumors, and oral cancers.10 Together, these fi siological functions and unique structural and biophysical ndings demonstrate that both the transcriptional level and properties. translational status of P16 are critical for its overall ability to Function. P16 primarily functions in cell cycle control as a mediate cellular activities. However, while numerous studies À 16 fi negative regulator of the prominent pRb E2F pathway. In G0 have focused on de ning the genetic and/or epigenetic status and early G1 phases, pRb is hypophosphorylated and forms ff of p16 in di erent cancers in investigating the molecular complexes with members of the E2F family of transcription 6,11 mechanism(s) of carcinogenesis, the critical regulation of factors. These complexes sequester E2Fs and prevent their access P16 itself has been understudied until recently. Here we review recent findings in P16 regulation and discuss their significance Received: April 27, 2011 in understanding the roles of P16 in cancer from a biochemical Revised: May 26, 2011 perspective. Published: May 27, 2011 r 2011 American Chemical Society 5566 dx.doi.org/10.1021/bi200642e | Biochemistry 2011, 50, 5566–5582 Biochemistry CURRENT TOPIC resulting in entry into the S phase. Binding of P16 directly downregulates the kinase activities of CDK4 and CDK6, keeping pRb in a hypophosphorylated status. Furthermore, P16 can disrupt complexes of CDK4/6 and non-P16 CDK inhibitors such as P27 (CDKN1B), thus leading to the release of these non- P16 inhibitors, suppression of CDK2 activity, and increases in the level of expression of hypophosphorylated pRb.5 Consequently, these P16-dependent events culminate in cell arrest at the G1ÀS boundary. Interestingly, it has been reported recently that the suppressive impact of P16 on E2F-mediated gene expression can be enhanced by the physical association between P16 and GRIM- 19 (gene-associated retinoid-IFN-induced mortality-19), a proa- poptotic protein functioning in the IFN-β/RA-induced cell death pathway.19 A more detailed account of these findings is presented below. Figure 1. P16ÀCDK4/6ÀpRb pathway. Arrows and minus signs In addition to the pRbÀE2F pathway, P16 also contributes to represent positive and negative regulatory effects, respectively. P denotes cell cycle progression through alternate and independent reg- À phosphorylated. This figure was modified from ref 56. ulatory pathways.20 22 First, phosphorylation of the carboxyl- terminal domain (CTD) of the large subunit of RNA polymerase II by the CDK7 subunit of general transcription factor TFIIH is an essential regulatory event in transcription.20,21 P16 is able to interact with TFIIH in the preinitiation complex, inhibit phos- phorylation of the CTD, and contribute to the capacity of this pathway to induce cell cycle arrest. Second, it has been reported that P16 contacts the glycine-rich loop of c-jun N-terminal kinases 1 and 3 (JNK1 and JNK3, respectively) and suppresses their kinase activities.22 The loss of JNK activity negatively regulates UV-induced c-Jun phosphorylation in melanoma cells and consequently interferes with cell transformation promoted by the H-Ras-JNK-c-Jun-AP1 signaling axis.22 Additionally, accumulating evidence has shown that P16 is involved in cellular senescence and aging through molecular mechanisms yet to be explicitly elucidated.4,23,24 The level of expression of P16 increases remarkably with aging in a large number of rodent and human tissues in both healthy and disease states.4 This elevated level of P16 expression has been shown to induce cellular senescence and aging in various progenitor cells and premalignant tumor cells,3 including neural progenitor cells,25 pancreas islet progenitor cells,26 and hematopoietic stem cells.27 These findings suggest that an aging-associated increase in the level of P16 expression can contribute to the decline in replicative potential for certain self-renewing compartments, a characteristic of aging.4 Moreover, a number of recent studies have demonstrated that P16 could be involved in the cellular response to genotoxic agents.4,12 P16-compromised or P16- deficient cells demonstrated sensitivity to ultraviolet (UV) light-induced apoptosis, suggesting that the absence of functional P16 allows propagation of proapoptotic signaling.28 Conversely, Figure 2. Primary, secondary, and tertiary structures of P16. (A) following genotoxically induced DNA damage, an elevated level Sequence and secondary structure of P16. Italic residues at the N-ter- minus represent missing residues in the cDNA gene first reported. Red of expression of P16 in tumor cells resulted in cell cycle arrest and and dashed lines represent helical and loop regions, respectively. inhibition of apoptotic events such as cytochrome c release, Residues with asterisks are those with mutations in human cancers. mitochondrial membrane depolarization, and activation of the AR is the ankyrin repeat. (B) Tertiary structure and domains of P16. The caspase cascade. These findings demonstrate that P16 is able to solution structure of P16 (Protein Data Bank entry 2A5E) is presented mitigate the sensitivity of mitochondria to proapoptotic signals in here,30 in which D84, the residue critical for CDK4 inhibition, is cancer cells with damaged DNA.29 highlighted. JNK denotes c-Jun N-terminal kinases. Structure. P16 is exclusively composed of four ankyrin repeat (AR) motifs30 (Figure 2B). Ankyrin repeats are relatively con- to the promoters of proliferation-associated genes, such as cyclin served motifs of approximately 31À34 residues.30,31 They are B1 (CCNB), dihydrofolate reductase (DHFR), jun B proto- abundantly present in proteins of plants, prokaryotes, viruses, oncogene (JUNB), and thymidine kinase 1 (TK1)17,18 (Figure 1). yeast, invertebrates, and vertebrates and are involved in numer- Once committed to cell proliferation, pRb is progressively hyper- ous physiological processes through the mediation of proteinÀ phosphorylated by CDK4 and CDK6 in the late G1 phase, protein interactions.31 Like in other AR proteins, each AR motif 5567 dx.doi.org/10.1021/bi200642e |Biochemistry
Recommended publications
  • The P16 (Cdkn2a/Ink4a) Tumor-Suppressor Gene in Head
    The p16 (CDKN2a/INK4a) Tumor-Suppressor Gene in Head and Neck Squamous Cell Carcinoma: A Promoter Methylation and Protein Expression Study in 100 Cases Lingbao Ai, M.D., Krystal K. Stephenson, Wenhua Ling, M.D., Chunlai Zuo, M.D., Perkins Mukunyadzi, M.D., James Y. Suen, M.D., Ehab Hanna, M.D., Chun-Yang Fan, M.D., Ph.D. Departments of Pathology (LA, KKS, CZ, PM, CYF) and Otolaryngology-Head and Neck Surgery (CYF, JYS, EH), University of Arkansas for Medical Sciences; and School of Public Health (LA, WL), Sun-Yat Sen University, Guangzhou, China apparent loss of p16 protein expression appears to The p16 (CDKN2a/INK4a) gene is an important be an independent prognostic factor, although loss tumor-suppressor gene, involved in the p16/cyclin- of p16 protein may be used to predict overall pa- dependent kinase/retinoblastoma gene pathway of tient survival in early-stage head and neck squa- cell cycle control. The p16 protein is considered to mous cell carcinoma. be a negative regulator of the pathway. The gene encodes an inhibitor of cyclin-dependent kinases 4 KEY WORDS: Gene inactivation, Head and and 6, which regulate the phosphorylation of reti- neck squamous cell carcinoma, p16, Promoter noblastoma gene and the G1 to S phase transition of hypermethylation. the cell cycle. In the present study, p16 gene pro- Mod Pathol 2003;16(9):944–950 moter hypermethylation patterns and p16 protein expression were analyzed in 100 consecutive un- The development of head and neck squamous cell treated cases of primary head and neck squamous carcinoma is believed to be a multistep process, in cell carcinoma by methylation-specific PCR and im- which genetic and epigenetic events accumulate as munohistochemical staining.
    [Show full text]
  • 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]
  • Involvement of the Cyclin-Dependent Kinase Inhibitor P16 (Ink4a) in Replicative Senescence of Normal Human Fibroblasts
    Proc. Natl. Acad. Sci. USA Vol. 93, pp. 13742–13747, November 1996 Biochemistry Involvement of the cyclin-dependent kinase inhibitor p16 (INK4a) in replicative senescence of normal human fibroblasts DAVID A. ALCORTA*†,YUE XIONG‡,DAWN PHELPS‡,GREG HANNON§,DAVID BEACH§, AND J. CARL BARRETT* *Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709; ‡Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599; and §Howard Hughes Medical Institute, Cold Spring Harbor Laboratories, Cold Spring Harbor, NY 11724 Communicated by Raymond L. Erickson, Harvard University, Cambridge, MA, September 19, 1996 (received for review on May 15, 1996) ABSTRACT Human diploid fibroblasts (HDFs) can be viewed in ref. 5). In senescent fibroblasts, CDK2 is catalytically grown in culture for a finite number of population doublings inactive and the protein down-regulated (7). CDK4 is also before they cease proliferation and enter a growth-arrest state reported to be down-regulated in senescent cells (8), while the termed replicative senescence. The retinoblastoma gene prod- status of CDK6 has not been previously addressed. The uct, Rb, expressed in these cells is hypophosphorylated. To activating cyclins for these CDKs, cyclins D1 and E, are present determine a possible mechanism by which senescent human in senescent cells at similar or elevated levels relative to early fibroblasts maintain a hypophosphorylated Rb, we examined passage cells (8). A role of the CDK inhibitors in senescence the expression levels and interaction of the Rb kinases, CDK4 was revealed by the isolation of a cDNA of a highly expressed and CDK6, and the cyclin-dependent kinase inhibitors p21 message in senescent cells that encoded the CDK inhibitor, p21 and p16 in senescent HDFs.
    [Show full text]
  • Transcriptional Regulation of the P16 Tumor Suppressor Gene
    ANTICANCER RESEARCH 35: 4397-4402 (2015) Review Transcriptional Regulation of the p16 Tumor Suppressor Gene YOJIRO KOTAKE, MADOKA NAEMURA, CHIHIRO MURASAKI, YASUTOSHI INOUE and HARUNA OKAMOTO Department of Biological and Environmental Chemistry, Faculty of Humanity-Oriented Science and Engineering, Kinki University, Fukuoka, Japan Abstract. The p16 tumor suppressor gene encodes a specifically bind to and inhibit the activity of cyclin-CDK specific inhibitor of cyclin-dependent kinase (CDK) 4 and 6 complexes, thus preventing G1-to-S progression (4, 5). and is found altered in a wide range of human cancers. p16 Among these CKIs, p16 plays a pivotal role in the regulation plays a pivotal role in tumor suppressor networks through of cellular senescence through inhibition of CDK4/6 activity inducing cellular senescence that acts as a barrier to (6, 7). Cellular senescence acts as a barrier to oncogenic cellular transformation by oncogenic signals. p16 protein is transformation induced by oncogenic signals, such as relatively stable and its expression is primary regulated by activating RAS mutations, and is achieved by accumulation transcriptional control. Polycomb group (PcG) proteins of p16 (Figure 1) (8-10). The loss of p16 function is, associate with the p16 locus in a long non-coding RNA, therefore, thought to lead to carcinogenesis. Indeed, many ANRIL-dependent manner, leading to repression of p16 studies have shown that the p16 gene is frequently mutated transcription. YB1, a transcription factor, also represses the or silenced in various human cancers (11-14). p16 transcription through direct association with its Although many studies have led to a deeper understanding promoter region.
    [Show full text]
  • The P16 Status of Tumor Cell Lines Identifies Small Molecule Inhibitors Specific for Cyclin-Dependent Kinase 41
    Vol. 5, 4279–4286, December 1999 Clinical Cancer Research 4279 The p16 Status of Tumor Cell Lines Identifies Small Molecule Inhibitors Specific for Cyclin-dependent Kinase 41 Akihito Kubo,2 Kazuhiko Nakagawa,2, 3 CDK4 kinase inhibitors that may selectively induce growth Ravi K. Varma, Nicholas K. Conrad, inhibition of p16-altered tumors. Jin Quan Cheng, Wen-Ching Lee, INTRODUCTION Joseph R. Testa, Bruce E. Johnson, INK4A 4 The p16 gene (also known as CDKN2A) encodes p16 , Frederic J. Kaye, and Michael J. Kelley which inhibits the CDK45:cyclin D and CDK6:cyclin D com- Medicine Branch [A. K., K. N., N. K. C., F. J. K., B. E. J.] and plexes (1). These complexes mediate phosphorylation of the Rb Developmental Therapeutics Program [R. K. V.], National Cancer Institute, Bethesda, Maryland 20889; Department of Medical protein and allow cell cycle progression beyond the G1-S-phase Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania checkpoint (2). Alterations of p16 have been described in a wide 19111 [J. Q. C., W-C. L., J. R. T.]; and Department of Medicine, variety of histological types of human cancers including astro- Duke University Medical Center, Durham, North Carolina 27710 cytoma, melanoma, leukemia, breast cancer, head and neck [M. J. K.] squamous cell carcinoma, malignant mesothelioma, and lung cancer. Alterations of p16 can occur through homozygous de- ABSTRACT letion, point mutation, and transcriptional suppression associ- ated with hypermethylation in cancer cell lines and primary Loss of p16 functional activity leading to disruption of tumors (reviewed in Refs. 3–5). the p16/cyclin-dependent kinase (CDK) 4:cyclin D/retino- Whereas the Rb gene is inactivated in a narrow range of blastoma pathway is the most common event in human tumor cells, the pattern of mutational inactivation of Rb is tumorigenesis, suggesting that compounds with CDK4 ki- inversely correlated with p16 alterations (6–8), suggesting that nase inhibitory activity may be useful to regulate cancer cell a single defect in the p16/CDK4:cyclin D/Rb pathway is suffi- growth.
    [Show full text]
  • Identification of Potential Key Genes and Pathway Linked with Sporadic Creutzfeldt-Jakob Disease Based on Integrated Bioinformatics Analyses
    medRxiv preprint doi: https://doi.org/10.1101/2020.12.21.20248688; this version posted December 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Identification of potential key genes and pathway linked with sporadic Creutzfeldt-Jakob disease based on integrated bioinformatics analyses 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 NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. medRxiv preprint doi: https://doi.org/10.1101/2020.12.21.20248688; this version posted December 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Abstract Sporadic Creutzfeldt-Jakob disease (sCJD) is neurodegenerative disease also called prion disease linked with poor prognosis. The aim of the current study was to illuminate the underlying molecular mechanisms of sCJD. The mRNA microarray dataset GSE124571 was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened.
    [Show full text]
  • Transcriptomic and Proteomic Profiling Provides Insight Into
    BASIC RESEARCH www.jasn.org Transcriptomic and Proteomic Profiling Provides Insight into Mesangial Cell Function in IgA Nephropathy † † ‡ Peidi Liu,* Emelie Lassén,* Viji Nair, Celine C. Berthier, Miyuki Suguro, Carina Sihlbom,§ † | † Matthias Kretzler, Christer Betsholtz, ¶ Börje Haraldsson,* Wenjun Ju, Kerstin Ebefors,* and Jenny Nyström* *Department of Physiology, Institute of Neuroscience and Physiology, §Proteomics Core Facility at University of Gothenburg, University of Gothenburg, Gothenburg, Sweden; †Division of Nephrology, Department of Internal Medicine and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan; ‡Division of Molecular Medicine, Aichi Cancer Center Research Institute, Nagoya, Japan; |Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden; and ¶Integrated Cardio Metabolic Centre, Karolinska Institutet Novum, Huddinge, Sweden ABSTRACT IgA nephropathy (IgAN), the most common GN worldwide, is characterized by circulating galactose-deficient IgA (gd-IgA) that forms immune complexes. The immune complexes are deposited in the glomerular mesangium, leading to inflammation and loss of renal function, but the complete pathophysiology of the disease is not understood. Using an integrated global transcriptomic and proteomic profiling approach, we investigated the role of the mesangium in the onset and progression of IgAN. Global gene expression was investigated by microarray analysis of the glomerular compartment of renal biopsy specimens from patients with IgAN (n=19) and controls (n=22). Using curated glomerular cell type–specific genes from the published literature, we found differential expression of a much higher percentage of mesangial cell–positive standard genes than podocyte-positive standard genes in IgAN. Principal coordinate analysis of expression data revealed clear separation of patient and control samples on the basis of mesangial but not podocyte cell–positive standard genes.
    [Show full text]
  • AP-1 in Cell Proliferation and Survival
    Oncogene (2001) 20, 2390 ± 2400 ã 2001 Nature Publishing Group All rights reserved 0950 ± 9232/01 $15.00 www.nature.com/onc AP-1 in cell proliferation and survival Eitan Shaulian1 and Michael Karin*,1 1Laboratory of Gene Regulation and Signal Transduction, Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, La Jolla, California, CA 92093-0636, USA A plethora of physiological and pathological stimuli extensively discussed previously (Angel and Karin, induce and activate a group of DNA binding proteins 1991; Karin, 1995). that form AP-1 dimers. These proteins include the Jun, The mammalian AP-1 proteins are homodimers and Fos and ATF subgroups of transcription factors. Recent heterodimers composed of basic region-leucine zipper studies using cells and mice de®cient in individual AP-1 (bZIP) proteins that belong to the Jun (c-Jun, JunB proteins have begun to shed light on their physiological and JunD), Fos (c-Fos, FosB, Fra-1 and Fra-2), Jun functions in the control of cell proliferation, neoplastic dimerization partners (JDP1 and JDP2) and the closely transformation and apoptosis. Above all such studies related activating transcription factors (ATF2, LRF1/ have identi®ed some of the target genes that mediate the ATF3 and B-ATF) subfamilies (reviewed by (Angel eects of AP-1 proteins on cell proliferation and death. and Karin, 1991; Aronheim et al., 1997; Karin et al., There is evidence that AP-1 proteins, mostly those that 1997; Liebermann et al., 1998; Wisdom, 1999). In belong to the Jun group, control cell life and death addition, some of the Maf proteins (v-Maf, c-Maf and through their ability to regulate the expression and Nrl) can heterodimerize with c-Jun or c-Fos (Nishiza- function of cell cycle regulators such as Cyclin D1, p53, wa et al., 1989; Swaroop et al., 1992), whereas other p21cip1/waf1, p19ARF and p16.
    [Show full text]
  • Open Data for Differential Network Analysis in Glioma
    International Journal of Molecular Sciences Article Open Data for Differential Network Analysis in Glioma , Claire Jean-Quartier * y , Fleur Jeanquartier y and Andreas Holzinger Holzinger Group HCI-KDD, Institute for Medical Informatics, Statistics and Documentation, Medical University Graz, Auenbruggerplatz 2/V, 8036 Graz, Austria; [email protected] (F.J.); [email protected] (A.H.) * Correspondence: [email protected] These authors contributed equally to this work. y Received: 27 October 2019; Accepted: 3 January 2020; Published: 15 January 2020 Abstract: The complexity of cancer diseases demands bioinformatic techniques and translational research based on big data and personalized medicine. Open data enables researchers to accelerate cancer studies, save resources and foster collaboration. Several tools and programming approaches are available for analyzing data, including annotation, clustering, comparison and extrapolation, merging, enrichment, functional association and statistics. We exploit openly available data via cancer gene expression analysis, we apply refinement as well as enrichment analysis via gene ontology and conclude with graph-based visualization of involved protein interaction networks as a basis for signaling. The different databases allowed for the construction of huge networks or specified ones consisting of high-confidence interactions only. Several genes associated to glioma were isolated via a network analysis from top hub nodes as well as from an outlier analysis. The latter approach highlights a mitogen-activated protein kinase next to a member of histondeacetylases and a protein phosphatase as genes uncommonly associated with glioma. Cluster analysis from top hub nodes lists several identified glioma-associated gene products to function within protein complexes, including epidermal growth factors as well as cell cycle proteins or RAS proto-oncogenes.
    [Show full text]
  • UC San Diego UC San Diego Electronic Theses and Dissertations
    UC San Diego UC San Diego Electronic Theses and Dissertations Title Regulation of gene expression programs by serum response factor and megakaryoblastic leukemia 1/2 in macrophages Permalink https://escholarship.org/uc/item/8cc7d0t0 Author Sullivan, Amy Lynn Publication Date 2009 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA, SAN DIEGO Regulation of Gene Expression Programs by Serum Response Factor and Megakaryoblastic Leukemia 1/2 in Macrophages A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Biomedical Sciences by Amy Lynn Sullivan Committee in charge: Professor Christopher K. Glass, Chair Professor Stephen M. Hedrick Professor Marc R. Montminy Professor Nicholas J. Webster Professor Joseph L. Witztum 2009 Copyright Amy Lynn Sullivan, 2009 All rights reserved. The Dissertation of Amy Lynn Sullivan is approved, and it is acceptable in quality and form for publication on microfilm and electronically: ______________________________________________________________ ______________________________________________________________ ______________________________________________________________ ______________________________________________________________ ______________________________________________________________ Chair University of California, San Diego 2009 iii DEDICATION To my husband, Shane, for putting up with me through all of the long hours, last minute late nights, and for not letting me quit no matter how many times my projects fell apart. To my son, Tyler, for always making me smile and for making every day an adventure. To my gifted colleagues, for all of the thought-provoking discussions, technical help and moral support through the roller- coaster ride that has been my graduate career. To my family and friends, for all of your love and support. I couldn’t have done it without you! iv EPIGRAPH If at first you don’t succeed, try, try, again.
    [Show full text]
  • Expression of P16 INK4A and P14 ARF in Hematological Malignancies
    Leukemia (1999) 13, 1760–1769 1999 Stockton Press All rights reserved 0887-6924/99 $15.00 http://www.stockton-press.co.uk/leu Expression of p16INK4A and p14ARF in hematological malignancies T Taniguchi1, N Chikatsu1, S Takahashi2, A Fujita3, K Uchimaru4, S Asano5, T Fujita1 and T Motokura1 1Fourth Department of Internal Medicine, University of Tokyo, School of Medicine; 2Division of Clinical Oncology, Cancer Chemotherapy Center, Cancer Institute Hospital; 3Department of Hematology, Showa General Hospital; 4Third Department of Internal Medicine, Teikyo University, School of Medicine; and 5Department of Hematology/Oncology, Institute of Medical Science, University of Tokyo, Tokyo, Japan The INK4A/ARF locus yields two tumor suppressors, p16INK4A tumor suppressor genes.10,11 In human hematological malig- ARF and p14 , and is frequently deleted in human tumors. We nancies, their inactivation occurs mainly by means of homo- studied their mRNA expressions in 41 hematopoietic cell lines and in 137 patients with hematological malignancies; we used zygous deletion or promoter region hypermethylation a quantitative reverse transcription-PCR assay. Normal periph- (reviewed in Ref. 12). In tumors such as pancreatic adenocar- eral bloods, bone marrow and lymph nodes expressed little or cinomas, esophageal squamous cell carcinomas and familial undetectable p16INK4A and p14ARF mRNAs, which were readily melanomas, p16INK4A is often inactivated by point mutation, detected in 12 and 17 of 41 cell lines, respectively. Patients with 12 INK4A which is not the case in hematological malignancies. On hematological malignancies frequently lacked p16 INK4C INK4D ARF the other hand, genetic aberrations of p18 or p19 expression (60/137) and lost p14 expression less frequently 12 (19/137, 13.9%).
    [Show full text]
  • Uncommon Association of Germline Mutations of RET Proto-Oncogene
    European Journal of Endocrinology (2008) 158 417–422 ISSN 0804-4643 CASE REPORT Uncommon association of germline mutations of RET proto-oncogene and CDKN2A gene L Foppiani1, F Forzano2, I Ceccherini3, W Bruno4, P Ghiorzo4, F Caroli3, P Quilici5, R Bandelloni5, A Arlandini6, G Sartini6, M Cabria7 and P Del Monte1 1Endocrinology 2Genetics Laboratory, Galliera Hospital, 16128 Genova, Italy, 3Laboratory of Molecular Genetics, G Gaslini Institute, 16148 Genova, Italy, 4Department of Oncology, Biology and Genetics/Medical Genetics Service, University of Genova, 1632 Genova, Italy, 5Pathology Unit, 6Division of Surgery and 7Nuclear Medicine, Galliera Hospital, 16128 Genova, Italy (Correspondence should be addressed to L Foppiani who is now at S S D Endocrinologia, Mura delle Cappuccine 14, 16128 Genova, Italy; Email: [email protected]) Abstract Introduction: Calcitonin measurement is advised in the diagnosis of thyroid nodules, as it is an accurate marker of medullary thyroid carcinoma (MTC). C-cell hyperplasia (CCH)-induced hypercalcitoninemia cannot be distinguished from that induced by MTC, unless surgery is performed. Case: We report the clinical and biological features of a patient with a family history of cancer, including melanoma and pancreatic cancer, who had previously undergone surgery for melanoma. He presented the unusual association of papillary thyroid carcinoma (PTC), normocalcemic hyperpara- thyroidism, and hypercalcitoninemia with a pathological response to pentagastrin, which was histologically deemed secondary to CCH. Multiple endocrine neoplasia (MEN) 2A was diagnosed. RET gene analysis showed a p.V804M missense mutation in exon 14, a low- but variably penetrant defect found in both sporadic and MEN2A-associated MTC/CCH, and a p.G691S polymorphism in exon 11.
    [Show full text]