DOCSLIB.ORG

Deconvolution of Sarcoma Methylomes Reveals Varying Degrees of Immune Cell Infiltrates with Association to Genomic Aberrations

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Deconvolution of Sarcoma Methylomes Reveals Varying Degrees of Immune Cell Infiltrates with Association to Genomic Aberrations Simon et al. J Transl Med (2021) 19:204 https://doi.org/10.1186/s12967-021-02858-7 Journal of Translational Medicine RESEARCH Open Access Deconvolution of sarcoma methylomes reveals varying degrees of immune cell infltrates with association to genomic aberrations Malte Simon1,3†, Sadaf S. Mughal1†, Peter Horak2,5, Sebastian Uhrig1, Jonas Buchloh1, Bogac Aybey1, Albrecht Stenzinger4, Hanno Glimm6,7, Stefan Fröhling2,5, Benedikt Brors1,2,5 and Charles D. Imbusch1* Abstract Background: Soft-tissue sarcomas (STS) are a heterogeneous group of mesenchymal tumors for which response to immunotherapies is not well established. Therefore, it is important to risk-stratify and identify STS patients who will most likely beneft from these treatments. Results: To reveal shared and distinct methylation signatures present in STS, we performed unsupervised decon- volution of DNA methylation data from the TCGA sarcoma and an independent validation cohort. We showed that leiomyosarcoma can be subclassifed into three distinct methylation groups. More importantly, we identifed a com- ponent associated with tumor-infltrating leukocytes, which suggests varying degrees of immune cell infltration in STS subtypes and an association with prognosis. We further investigated the genomic alterations that may infuence tumor infltration by leukocytes including RB1 loss in undiferentiated pleomorphic sarcomas and ELK3 amplifcation in dediferentiated liposarcomas. Conclusions: In summary, we have leveraged unsupervised methylation-based deconvolution to characterize the immune compartment and molecularly stratify subtypes in STS, which may beneft precision medicine in the future. Keywords: Sarcoma, Deconvolution, Survival analysis, Tumor-infltrating leukocytes Background six subtypes including dediferentiated liposarcoma Soft-tissue sarcomas (STS) are rare cancers of mes- (DDLPS), leiomyosarcoma (LMS), undiferentiated enchymal origin that represent < 1% of adult solid pleomorphic sarcoma (UPS), myxofbrosarcoma (MFS), malignancies. Teir high diversity in terms of genetic malignant peripheral nerve sheath tumor (MPNST) aberrations and histological appearance results in and synovial sarcoma (SS). By analyzing genetic, epige- a subclassifcation into more than 70 subtypes [1]. netic, mRNA and protein expression data, the authors Recently, the TCGA consortium released a study com- stated that subtypes with complex karyotypes are prising the characterization of 206 sarcomas from mostly driven by copy number alterations instead of mutations, and that the presence of certain inferred immune cell types and methylation states associates *Correspondence: [email protected] †Malte Simon and Sadaf S Mughal contributed equally to this work with disease-specifc survival [2]. Several clinical tri- 1 Division of Applied Bioinformatics, German Cancer Research Center als on immunotherapies in STS have found low over- (DKFZ), Heidelberg, Germany all response rates, which highlights the importance of Full list of author information is available at the end of the article © The Author(s) 2021. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http:// creat iveco mmons. org/ licen ses/ by/4. 0/. The Creative Commons Public Domain Dedication waiver (http:// creat iveco mmons. org/ publi cdoma in/ zero/1. 0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Simon et al. J Transl Med (2021) 19:204 Page 2 of 17 a more detailed characterization of immune infltrates We validated the immune-cell associated signature as and the development of robust predictors of clinical well as associated genomic aberrations in independent beneft in these tumors [3, 4]. While a global compari- cohorts. son of immunogenicity in diferent tumor types has been previously presented, to date, no study focused on Results sarcomas [5, 6]. Deconvolution of methylation data results In this study, we reanalyzed the TCGA-SARC dataset in subtype‑specifc patterns from an epigenetic perspective by employing unsuper- To identify shared methylation patterns (hereafter vised deconvolution of the methylation data to dis- referred to as latent methylation components, LMCs), cover shared as well as subtype-specifc methylation we analyzed the TCGA sarcoma methylation data aggre- profles. By correlating distinct methylation changes gated within equidistant and non-overlapping genomic with mRNA abundances, we derived gene signatures windows and performed a deconvolution using MeDe- for each profle and showed their biological relevance Com [7]. We chose a factorization into nine LMCs based and usability for subclassifcation. Importantly, we on a low cross-validation error and high stability of the identifed an immune cell-associated component that resulting methylation patterns (Additional fle 1: Fig- implies varying degrees of immune cell infltration in ure S1). Hierarchical clustering on the proportions of STS with enrichment in UPS, DDLPS and MFS cases, the LMCs, which represent the relative occurrence of whereas it was substantially lower in LMS and SS. In the respective patterns in the tumor samples, showed addition genomic aberrations could be identifed that clear associations to histopathological subtypes for sev- harbour the potential to infuence tumor infltration. eral components (Fig. 1). Te strongest association was found for LMC9 and synovial sarcoma (point biserial Fig. 1 MeDeCom deconvolves subtype-specifc methylation patterns. Proportions for the deconvolution of TCGA-SARC methylation data using 9 LMCs and λ 0.01 are shown. Unsupervised deconvolution based on non-negative matrix factorization resulted in methylation components = associated with histological subtypes and tumor tissue sites. LMS, leiomyosarcoma; DDLPS, dediferentiated liposarcoma; MFS, myxofbrosarcoma; UPS, undiferentiated pleomorphic sarcoma; SS, synovial sarcoma; MPNST, malignant peripheral nerve sheath tumor Simon et al. J Transl Med (2021) 19:204 Page 3 of 17 correlation coefcient (rpb) = 0.97) refecting the dramatic Figure S6B). In particular, we were interested in meth- changes to their methylome, which occur in this subtype ylation changes resulting in upregulation of gene expres- as a consequence of an SS18-SSX gene fusion [8]. We fur- sion, since these provide insights on gene activity in the ther observed a global hypomethylation in SS compared LMC-associated tumors and might constitute potential to the other subtypes (Additional fle 1: Figure S2). LMC1 new biomarkers. We calculated the Pearson’s correlation was associated with uterine LMS (ULMS, rpb = 0.72), between methylation and gene expression to further flter whereas LMC7 represented a methylation pattern com- VMRs. Te cutof for a signifcant correlation was greater mon in most nongynecological LMS (STLMS, rpb = 0.81). than 0.3 for hypermethylation-upregulation or smaller Although having a weaker association, LMC2 was pre- than -0.3 for hypomethylation-upregulation. dominantly shared among UPS cases (rpb = 0.36), and Following this approach, we identifed 100 genes for LMC4 showed the strongest association with DDLPS STLMS-associated LMC7 (Fig. 2), which we termed as (rpb = 0.46). Whereas, LMCs 3, 5, 6, and 8 were shared ‘STLMS core signature’. 42 of these genes had hypometh- among the diferent sarcoma subtypes. ylated and 58 had hypermethylated VMRs. 55% of the We validated our fndings using an independent meth- LMS tumors had the highest proportion in LMC7, with ylation dataset (MASTER) from 56 sarcoma samples the majority of the samples belonging to retroperitoneal/ (Additional fle 1: Figure S3). In concordance with the upper abdominal region and only one uterine sample deconvolution results from TCGA-SARC, subtype-asso- (LMS group 1). ciated methylation patterns were consistently observed Te STLMS core signature also contained the previ- for LMS and SS. In addition, we also found unique meth- ously known immunohistochemical markers such as ylation patterns for gastrointestinal stromal tumors MYLK and CASQ2 [9, 10]. Next, we performed func- (GIST), solitary fbrous tumors (SFT) and myxoid lipo- tional annotation of these genes and found enrichments sarcoma (MLS). Hierarchical clustering of the LMCs in gene sets associated with muscle function (Additional from the independent deconvolution of TCGA-SARC fle 2: Table S1) such as focal adhesion (P < 0.004), actin and HIPO showed a high similarity of the methylation binding (P < 0.007) and muscle contraction (P = 0.131) patterns associated with the subtypes present in both (Fisher’s exact test and Benjamini - Hochberg correction) datasets (LMS and SS, Additional fle 1: Figure S4). Tis indicating that LMS group 1 is mostly associated with confrms that these subtypes have distinct methylation smooth muscle function. changes, which are consistently observed
Load more

Recommended publications
  • Small RAB Gtpases Regulate Multiple Steps of Mitosis
    CORE Metadata, citation and similar papers at core.ac.uk Provided by CONICET Digital REVIEW published: 17 February 2016 doi: 10.3389/fcell.2016.00002 Small RAB GTPases Regulate Multiple Steps of Mitosis Stéphanie Miserey-Lenkei 1* and María I. Colombo 2 1 Institut Curie, PSL Research University, Molecular Mechanisms of Intracellular Transport Group, CNRS UMR 144, Paris, France, 2 Laboratorio de Biología Celular y Molecular, Instituto de Histología y Embriología-CONICET, Facultad de Ciencias Médicas, Universidad Nacional de Cuyo, Mendoza, Argentina GTPases of the RAB family are key regulators of multiple steps of membrane trafficking. Several members of the RAB GTPase family have been implicated in mitotic progression. In this review, we will first focus on the function of endosome-associated RAB GTPases reported in early steps of mitosis, spindle pole maturation, and during cytokinesis. Second, we will discuss the role of Golgi-associated RAB GTPases at the metaphase/anaphase transition and during cytokinesis. Keywords: RABs GTPases, mitosis, endosomes, golgi complex, trafficking INTRODUCTION Edited by: In mammalian cells, GTPases of the RAB family are key regulators of multiple steps of membrane Letizia Lanzetti, traffic. RAB GTPases play a central role in the formation of transport carriers from a donor University of Turin, Italy membrane, movement of these carriers along cytoskeletal tracks and finally anchoring/fusion Reviewed by: to the correct acceptor membrane (Stenmark, 2009). RAB GTPases represent a large family Andrew Alexander Peden, of small guanosine triphosphate (GTP)-binding proteins that comprise more than 60 known University of Sheffield, UK Anna Akhmanova, members. RAB GTPases are localized on distinct membrane-bound compartments and cycle Utrecht University, Netherlands between an active GTP-bound form and an inactive guanosine diphosphate (GDP)-bound *Correspondence: form.
    [Show full text]
  • Role and Regulation of the P53-Homolog P73 in the Transformation of Normal Human Fibroblasts
    Role and regulation of the p53-homolog p73 in the transformation of normal human fibroblasts Dissertation zur Erlangung des naturwissenschaftlichen Doktorgrades der Bayerischen Julius-Maximilians-Universität Würzburg vorgelegt von Lars Hofmann aus Aschaffenburg Würzburg 2007 Eingereicht am Mitglieder der Promotionskommission: Vorsitzender: Prof. Dr. Dr. Martin J. Müller Gutachter: Prof. Dr. Michael P. Schön Gutachter : Prof. Dr. Georg Krohne Tag des Promotionskolloquiums: Doktorurkunde ausgehändigt am Erklärung Hiermit erkläre ich, dass ich die vorliegende Arbeit selbständig angefertigt und keine anderen als die angegebenen Hilfsmittel und Quellen verwendet habe. Diese Arbeit wurde weder in gleicher noch in ähnlicher Form in einem anderen Prüfungsverfahren vorgelegt. Ich habe früher, außer den mit dem Zulassungsgesuch urkundlichen Graden, keine weiteren akademischen Grade erworben und zu erwerben gesucht. Würzburg, Lars Hofmann Content SUMMARY ................................................................................................................ IV ZUSAMMENFASSUNG ............................................................................................. V 1. INTRODUCTION ................................................................................................. 1 1.1. Molecular basics of cancer .......................................................................................... 1 1.2. Early research on tumorigenesis ................................................................................. 3 1.3. Developing
    [Show full text]
  • Structure of the APPL1 BAR-PH Domain and EMBO Characterization of Its Interaction with Rab5 Open
    The EMBO Journal (2007) 26, 3484–3493 | & 2007 European Molecular Biology Organization | Some Rights Reserved 0261-4189/07 www.embojournal.org TTHEH E EEMBOMBO JJOURNALOURN AL Structure of the APPL1 BAR-PH domain and EMBO characterization of its interaction with Rab5 open This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits distribution, and reproductioninany medium, provided the original authorand source are credited. This license does not permit commercial exploitation or the creation of derivative works without specific permission. Guangyu Zhu1, Jia Chen2, Jay Liu3, Introduction Joseph S Brunzelle4, Bo Huang2, Endocytosis induced by ligandÀreceptor interaction has been Nancy Wakeham1, Simon Terzyan1, 2 2 3 directly linked to signal transduction mediated by Rab5 and Xuemei Li , Zihe Rao , Guangpu Li its effector APPL1 (Adaptor protein containing PH domain 1,2, and Xuejun C Zhang * PTB domain and Leucine zipper motif; Miaczynska et al, 1Crystallography Research Program, Oklahoma Medical Research 2004; Mao et al, 2006). The small GTPase Rab5 is a generally Foundation, Oklahoma City, OK, USA, 2National Laboratory of acknowledged prominent regulator of vesicle trafficking en- Biomacromolecules, Institute of Biophysics, Chinese Academy of route from the plasma membrane to early endosomes (Li, 3 Sciences, Beijing, China, Department of Biochemistry and Molecular 1996), whereas APPL1 (also called DIP13a) is identified with Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA and 4Department of Molecular Pharmacology and signaling pathways of adiponectin, insulin, EGF, follicle Biological Chemistry, Feinberg Medical School, Northwestern stimulating hormone receptor, neurotrophin receptor University, Chicago, IL, USA (TrkA), oxidative stress, and DCC-mediated apoptosis (Liu et al, 2002; Miaczynska et al, 2004; Lin et al, 2006; Mao et al, APPL1 is an effector of the small GTPase Rab5.
    [Show full text]
  • Mouse Rab21 Knockout Project (CRISPR/Cas9)
    https://www.alphaknockout.com Mouse Rab21 Knockout Project (CRISPR/Cas9) Objective: To create a Rab21 knockout Mouse model (C57BL/6N) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Rab21 gene (NCBI Reference Sequence: NM_024454 ; Ensembl: ENSMUSG00000020132 ) is located on Mouse chromosome 10. 7 exons are identified, with the ATG start codon in exon 1 and the TAA stop codon in exon 7 (Transcript: ENSMUST00000020343). Exon 2~6 will be selected as target site. Cas9 and gRNA will be co-injected into fertilized eggs for KO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Exon 2 starts from about 23.12% of the coding region. Exon 2~6 covers 56.46% of the coding region. The size of effective KO region: ~7921 bp. The KO region does not have any other known gene. Page 1 of 8 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele 5' gRNA region gRNA region 3' 1 2 3 4 5 6 7 Legends Exon of mouse Rab21 Knockout region Page 2 of 8 https://www.alphaknockout.com Overview of the Dot Plot (up) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 2000 bp section upstream of Exon 2 is aligned with itself to determine if there are tandem repeats. No significant tandem repeat is found in the dot plot matrix. So this region is suitable for PCR screening or sequencing analysis. Overview of the Dot Plot (down) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 2000 bp section downstream of Exon 6 is aligned with itself to determine if there are tandem repeats.
    [Show full text]
  • Datasheet: MCA5197Z Product Details
    Datasheet: MCA5197Z Description: MOUSE ANTI HUMAN RAB21:Preservative Free Specificity: RAB21 Format: Preservative Free Product Type: Monoclonal Antibody Clone: 1F6 Isotype: IgG1 Quantity: 0.1 mg Product Details Applications This product has been reported to work in the following applications. This information is derived from testing within our laboratories, peer-reviewed publications or personal communications from the originators. Please refer to references indicated for further information. For general protocol recommendations, please visit www.bio-rad-antibodies.com/protocols. Yes No Not Determined Suggested Dilution Immunohistology - Paraffin 0.1 - 10 ug/ml Western Blotting 0.1 - 10 ug/ml Immunofluorescence 0.1 - 10 ug/ml Where this product has not been tested for use in a particular technique this does not necessarily exclude its use in such procedures. Suggested working dilutions are given as a guide only. It is recommended that the user titrates the product for use in their own system using appropriate negative/positive controls. Target Species Human Product Form Purified IgG - liquid Preparation Purified IgG prepared by affinity chromatography on Protein A Buffer Solution Phosphate buffered saline Preservative None present Stabilisers Approx. Protein Ig concentration 0.5 mg/ml Concentrations Immunogen Recombinant protein corresponding to aa 116-226 of human RAB21. External Database Links UniProt: Q9UL25 Related reagents Entrez Gene: 23011 RAB21 Related reagents Page 1 of 2 Synonyms KIAA0118 Fusion Partners Spleen cells from BALB/c mice were fused with cells from the Sp2/0 myeloma cell line. Specificity Mouse anti Human RAB21 antibody, clone 1F6 recognizes human Ras-related protein Rab-21, also known as RAB21.
    [Show full text]
  • Original Article Identification of Prognostic Genes in Paediatric Medulloblastoma from Mrna Expression Profiles
    Int J Clin Exp Med 2016;9(10):19925-19929 www.ijcem.com /ISSN:1940-5901/IJCEM0017954 Original Article Identification of prognostic genes in paediatric medulloblastoma from mRNA expression profiles Changjun Cao, Wei Wang, Pucha Jiang Department of Neurosurgery, Zhongnan Hospital of Wuhan University, China Received October 15, 2015; Accepted March 1, 2016; Epub October 15, 2016; Published October 30, 2016 Abstract: Medulloblastoma is the most common malignant brain tumour of childhood. The identification of prognos- tic biomarkers correlated with overall survival remains a crucial step towards the refinement of medulloblastoma treatment. A total of 100 medulloblastoma samples from two independent cohorts were included in this study. The statistical modelling approach, Bayesian Model Averaging algorithm, was used to discover the prognostic biomark- ers. Six genes including BICD2, CD300LG, RAB21, RAD18, SYNRG and TNFSF13 were identified to be related to medulloblastoma overall survival. We demonstrated this six-gene signature could successfully discriminate low-risk group from high-risk groups in two independent medulloblastoma cohorts. We have successfully identified a six- gene medulloblastoma prognostic signature. We anticipate that these genes could serve as biomarkers or drug targets in personalised therapy of medulloblastoma. Keywords: Prognosis, medulloblastoma, mRNA expression, bayesian model averaging Introduction [9]. The ability of measuring mRNA expression levels of thousands of genes at one time has Medulloblastoma is the most common malig- made the microarray technology a promising nant brain tumour of childhood and accounts direction in cancer research. Based on microar- for 15%-20% of all paediatric primary brain ray data, many gene signatures have also been tumours [1]. Although there is approximately identified for the prediction of medulloblastoma 70% improvement in 5-year survival rates of prognosis [10, 11].
    [Show full text]
  • Activity in Primary Mammary Tumors Role for Wnt-Signaling in Mediating
    Downloaded from http://www.jimmunol.org/ by guest on October 2, 2021 is online at: average * The Journal of Immunology , 25 of which you can access for free at: 2010; 184:702-712; Prepublished online 16 from submission to initial decision 4 weeks from acceptance to publication December 2009; doi: 10.4049/jimmunol.0902360 http://www.jimmunol.org/content/184/2/702 Gene Expression Analysis of Macrophages That Facilitate Tumor Invasion Supports a Role for Wnt-Signaling in Mediating Their Activity in Primary Mammary Tumors Laureen S. Ojalvo, Charles A. Whittaker, John S. Condeelis and Jeffrey W. Pollard J Immunol cites 69 articles Submit online. Every submission reviewed by practicing scientists ? is published twice each month by Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://jimmunol.org/subscription http://www.jimmunol.org/content/suppl/2009/12/15/jimmunol.090236 0.DC1 This article http://www.jimmunol.org/content/184/2/702.full#ref-list-1 Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* Why • • • Material References Permissions Email Alerts Subscription Supplementary The Journal of Immunology The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2010 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. This information is current as of October 2, 2021. The Journal of Immunology Gene Expression Analysis of Macrophages That Facilitate Tumor Invasion Supports a Role for Wnt-Signaling in Mediating Their Activity in Primary Mammary Tumors Laureen S.
    [Show full text]
  • Utilizing Pacbio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in Oryza Sativa L
    International Journal of Molecular Sciences Article Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in Oryza sativa L. Stephanie Schaarschmidt 1,* , Axel Fischer 1, Lovely Mae F. Lawas 1,2 , Rejbana Alam 3, Endang M. Septiningsih 4 , Julia Bailey-Serres 3, S. V. Krishna Jagadish 5,6 , Bruno Huettel 7, 1, 1, Dirk K. Hincha y and Ellen Zuther * 1 Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; afi[email protected] (A.F.); lfl[email protected] (L.M.F.L.); [email protected] (D.K.H.) 2 Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA 3 Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA; [email protected] (R.A.); [email protected] (J.B.-S.) 4 Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA; [email protected] 5 International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines; [email protected] 6 Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA 7 Max Planck Genome Centre Cologne, Carl-von-Linné-Weg 10, 50829 Cologne, Germany; [email protected] * Correspondence: [email protected] (S.S.); [email protected] (E.Z.) We dedicate this paper to the memory of our colleague Dirk K. Hincha who passed away during the y preparation of this manuscript. Received: 28 September 2020; Accepted: 30 October 2020; Published: 31 October 2020 Abstract: The wide natural variation present in rice is an important source of genes to facilitate stress tolerance breeding.
    [Show full text]
  • Pituitary Cell Translation and Secretory Capacities Are Enhanced Cell Autonomously by the Transcription Factor Creb3l2
    ARTICLE https://doi.org/10.1038/s41467-019-11894-3 OPEN Pituitary cell translation and secretory capacities are enhanced cell autonomously by the transcription factor Creb3l2 Konstantin Khetchoumian1, Aurélio Balsalobre1, Alexandre Mayran1, Helen Christian2, Valérie Chénard3, Julie St-Pierre3 & Jacques Drouin1,3 1234567890():,; Translation is a basic cellular process and its capacity is adapted to cell function. In particular, secretory cells achieve high protein synthesis levels without triggering the protein stress response. It is unknown how and when translation capacity is increased during differentiation. Here, we show that the transcription factor Creb3l2 is a scaling factor for translation capacity in pituitary secretory cells and that it directly binds ~75% of regulatory and effector genes for translation. In parallel with this cell-autonomous mechanism, implementation of the phy- siological UPR pathway prevents triggering the protein stress response. Knockout mice for Tpit, a pituitary differentiation factor, show that Creb3l2 expression and its downstream regulatory network are dependent on Tpit. Further, Creb3l2 acts by direct targeting of translation effector genes in parallel with signaling pathways that otherwise regulate protein synthesis. Expression of Creb3l2 may be a useful means to enhance production of therapeutic proteins. 1 Laboratoire de génétique moléculaire, Institut de recherches cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada. 2 Departments of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX2 6HS, UK. 3 Department of Biochemistry, McGill University, Rosalind and Morris Goodman Research Centre, Montréal, QC H3A 1A3, Canada. Correspondence and requests for materials should be addressed to K.K. (email: [email protected]) or to J.D.
    [Show full text]
  • Rab Gtpases: Switching to Human Diseases
    cells Review Rab GTPases: Switching to Human Diseases Noemi Antonella Guadagno and Cinzia Progida * Department of Biosciences, University of Oslo, 0316 Oslo, Norway * Correspondence: [email protected]; Tel.: +47-22-85-44-41 Received: 30 June 2019; Accepted: 14 August 2019; Published: 16 August 2019 Abstract: Rab proteins compose the largest family of small GTPases and control the different steps of intracellular membrane traffic. More recently, they have been shown to also regulate cell signaling, division, survival, and migration. The regulation of these processes generally occurs through recruitment of effectors and regulatory proteins, which control the association of Rab proteins to membranes and their activation state. Alterations in Rab proteins and their effectors are associated with multiple human diseases, including neurodegeneration, cancer, and infections. This review provides an overview of how the dysregulation of Rab-mediated functions and membrane trafficking contributes to these disorders. Understanding the altered dynamics of Rabs and intracellular transport defects might thus shed new light on potential therapeutic strategies. Keywords: GTPases; Rab proteins; membrane trafficking; neurodegeneration; cancer; intracellular pathogens 1. Introduction Intracellular membrane trafficking is essential for the transport of membranes and cargoes between the different compartments in eukaryotic cells. It uses vesicular or tubular carriers that travel along the endocytic and exocytic pathways and it is regulated by complex protein machineries [1]. Rab GTPases are evolutionarily conserved regulators of vesicular transport, with more than 60 members described in humans [2,3]. They are localized to different membrane compartments in order to control both the specificity and the directionality of membrane trafficking.
    [Show full text]
  • APPL1 Regulates Basal NF-Kb Activity by Stabilizing
    4090 Research Article APPL1 regulates basal NF-kB activity by stabilizing NIK Anna Hupalowska, Beata Pyrzynska and Marta Miaczynska* International Institute of Molecular and Cell Biology, 4 Ks. Trojdena Street, 02-109 Warsaw, Poland *Author for correspondence ([email protected]) Accepted 3 May 2012 Journal of Cell Science 125, 4090–4102 ß 2012. Published by The Company of Biologists Ltd doi: 10.1242/jcs.105171 Summary APPL1 is a multifunctional adaptor protein that binds membrane receptors, signaling proteins and nuclear factors, thereby acting in endosomal trafficking and in different signaling pathways. Here, we uncover a novel role of APPL1 as a positive regulator of transcriptional activity of NF-kB under basal but not TNFa-stimulated conditions. APPL1 was found to directly interact with TRAF2, an adaptor protein known to activate canonical NF-kB signaling. APPL1 synergized with TRAF2 to induce NF-kB activation, and both proteins were necessary for this process and function upstream of the IKK complex. Although TRAF2 was not detectable on APPL endosomes, endosomal recruitment of APPL1 was required for its function in the NF-kB pathway. Importantly, in the canonical pathway, APPL1 appeared to regulate the proper spatial distribution of the p65 subunit of NF-kB in the absence of cytokine stimulation, since its overexpression enhanced and its depletion reduced the nuclear accumulation of p65. By analyzing the patterns of gene transcription upon APPL1 overproduction or depletion we found altered expression of NF-kB target genes that encode cytokines. At the molecular level, overexpressed APPL1 markedly increased the level of NIK, the key component of the noncanonical NF-kB pathway, by reducing its association with the degradative complex containing TRAF2, TRAF3 and cIAP1.
    [Show full text]
  • Chromosome 12, Frequently Deleted in Human Pancreatic Cancer, May Encode a Tumor-Suppressor Gene That Suppresses Angiogenesis
    Laboratory Investigation (2004) 84, 1339–1351 & 2004 USCAP, Inc All rights reserved 0023-6837/04 $30.00 www.laboratoryinvestigation.org Chromosome 12, frequently deleted in human pancreatic cancer, may encode a tumor-suppressor gene that suppresses angiogenesis Sumitaka Yamanaka1,2,*, Makoto Sunamura3,*, Toru Furukawa1, Libo Sun3, Liviu P Lefter1,3, Tadayoshi Abe1,3, Toshimasa Yatsuoka1,3, Hiroko Fujimura3, Emiko Shibuya3, Noriko Kotobuki4, Mitsuo Oshimura4, Akira Sakurada2, Masami Sato2, Takashi Kondo2, Seiki Matsuno3 and Akira Horii1 1Department of Molecular Pathology, Tohoku University School of Medicine, Sendai, Japan; 2Department of Thoracic Surgery, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan; 3Department of Gastroenterological Surgery, Tohoku University School of Medicine, Sendai, Japan and 4Department of Cell Technology, Tottori University School of Medicine, Yonago, Japan Several lines of evidence have suggested that the long arm of chromosome 12 may carry a tumor-suppressor gene(s) that plays a role in pancreatic ductal carcinogenesis. We have previously found a significant association between loss of heterozygosity of the 12q arm and a poor prognosis in pancreatic cancer patients. In this study, we introduced a normal copy of chromosome 12 into some pancreatic ductal carcinoma cells. Both anchorage-dependent and -independent proliferations as well as invasiveness were similar throughout the hybrid clones when compared with their corresponding parental cells. In sharp contrast, significant suppression of tumorigenesis was observed after inoculation of the hybrid clones into nude mice. Measurements made up to 1 month later showed that there was a significant delay in the growth of tumors into which the introduced normal copy of chromosome 12 had been restored.
    [Show full text]