DOCSLIB.ORG

Effector Gene Expression Potential to Th17 Cells by Promoting Microrna

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Effector Gene Expression Potential to Th17 Cells by Promoting Microrna Downloaded from http://www.jimmunol.org/ by guest on September 26, 2021 is online at: average * The Journal of Immunology published online 17 May 2013 from submission to initial decision 4 weeks from acceptance to publication http://www.jimmunol.org/content/early/2013/05/17/jimmun ol.1300351 MicroRNA-155 Confers Encephalogenic Potential to Th17 Cells by Promoting Effector Gene Expression Ruozhen Hu, Thomas B. Huffaker, Dominique A. Kagele, Marah C. Runtsch, Erin Bake, Aadel A. Chaudhuri, June L. Round and Ryan M. O'Connell J Immunol Submit online. Every submission reviewed by practicing scientists ? is published twice each month by http://jimmunol.org/subscription 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://www.jimmunol.org/content/suppl/2013/05/17/jimmunol.130035 1.DC1 Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* Why • • • Material Permissions Email Alerts Subscription Supplementary The Journal of Immunology The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2013 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. This information is current as of September 26, 2021. Published May 17, 2013, doi:10.4049/jimmunol.1300351 The Journal of Immunology MicroRNA-155 Confers Encephalogenic Potential to Th17 Cells by Promoting Effector Gene Expression Ruozhen Hu,* Thomas B. Huffaker,* Dominique A. Kagele,* Marah C. Runtsch,* Erin Bake,* Aadel A. Chaudhuri,† June L. Round,* and Ryan M. O’Connell* Th17 cells are central to the pathogenesis of autoimmune disease, and recently specific noncoding microRNAs have been shown to regulate their development. However, it remains unclear whether microRNAs are also involved in modulating Th17 cell effector functions. Consequently, we examined the role of miR-155 in differentiated Th17 cells during their induction of experimental au- toimmune encephalomyelitis. Using adoptive transfer experiments, we found that highly purified, myelin oligodendrocyte glyco- protein Ag-specific Th17 cells lacking miR-155 were defective in their capacity to cause experimental autoimmune encephalomyelitis. Gene expression profiling of purified miR-1552/2IL-17F+ Th17 cells identified a subset of effector genes that are dependent on miR-155 for their proper expression through a mechanism involving repression of the transcription factor Ets1. Among the genes Downloaded from reduced in the absence of miR-155 was IL-23R, resulting in miR-1552/2 Th17 cells being hyporesponsive to IL-23. Taken together, our study demonstrates a critical role for miR-155 in Th17 cells as they unleash autoimmune inflammation and finds that this occurs through a signaling network involving miR-155, Ets1, and the clinically relevant IL-23–IL-23R pathway. The Journal of Immunology, 2013, 190: 000–000. utoimmunity occurs when dysregulated, autoreactive im- how miRNAs fit into the known regulatory circuits underlying http://www.jimmunol.org/ mune cells inappropriately respond to self-Ags and cause Th17 cell biology remains an important area of investigation. unwarranted inflammation that is destructive to sophis- miRNAs are small, ssRNA molecules that negatively regulate A + ticated tissue systems (1). Recently, Th17 cells, a subset of CD4 target gene expression posttranscriptionally. Specific miRNAs T cells defined by their expression of IL-17 cytokines, have emerged have been shown to support proper development of immune cells as key drivers of tissue inflammation. Th17 cells promote both the in mammals and have just recently been implicated in autoimmu- onset and persistence of inflammatory responses during autoimmune nity (20, 21). Among the miRNAs expressed in immune cells is disorders including multiple sclerosis, arthritis, psoriasis, lupus, and miR-155, which modulates the development of various inflam- inflammatory bowel disease (2, 3). matory T cell subsets, including Th1, Th17, and regulatory T cells by guest on September 26, 2021 Because of their central roles in driving disease, significant effort (18, 22–26). Demonstrating its importance during inflammation has gone into understanding the genes and pathways that regulate in vivo, we and others have recently shown that miR-1552/2 mice + Th17 cell development. Skewing of naive CD4 T cells toward the are highly resistant to distinct mouse models of autoimmunity, Th17 lineage is driven by the cytokines IL-6 and TGF-b,which including experimental autoimmune encephalomyelitis (EAE)— induce Th17 cell signature genes through such factors as Stat3, a model of human multiple sclerosis, T cell–dependent colitis, and RORgt, Ahr, Batf, and Irf4 (4-12). Furthermore, differentiated collagen-induced arthritis (18, 24, 27). Furthermore, dysregulated Th17 cells must receive additional signals from cytokines such as expression of miR-155 is also observed in mice and people with IL-23 to expand and achieve full inflammatory potential in vivo various types of autoimmune disorders (24, 28–30). Although (13–17). Recently, noncoding microRNAs (miRNAs) have also these reports reveal a prominent, clinically relevant role for miR- been found to regulate Th17 cell development (18, 19). However, 155 during autoimmunity, they have not determined whether this is a consequence of reduced inflammatory T cell numbers or compromised effector cell function. Furthermore, it remains un- *Division of Microbiology and Immunology, Department of Pathology, University of clear how miR-155 functions at the molecular level to instruct † Utah, Salt Lake City, UT, 84112; and Department of Radiation Oncology, Stanford Th17 cell biology. University School of Medicine, Stanford, CA, 94305 In the current study, we have investigated the role of miR-155 Received for publication February 6, 2013. Accepted for publication April 8, 2013. in differentiated Th17 cells. This was accomplished by generat- This work was supported by National Institutes of Health Grant 5R00HL102228-04. ing a novel mouse strain that allows for the isolation and analy- The microarray data presented in this article have been deposited in the National sis of viable, miR-1552/2 IL-17F–expressing CD4+ Tcellsthat Center for Biotechnology Information Gene Expression Omnibus database (http:// www.ncbi.nlm.nih.gov/geo/) under accession number GSE45122. specifically recognize the myelin oligodendrocyte glycoprotein 2/2 Address correspondence and reprint requests to Dr. Ryan M. O’Connell, Division (MOG)35–55 Ag. Our studies find that purified miR-155 Th17 of Microbiology and Immunology, Department of Pathology, University of Utah, 15 cells are extremely defective in causing EAE following adoptive North Medical Drive East, JMRB, Salt Lake City, UT, 84112. E-mail address: ryan. [email protected] transfer when compared with wild-type (Wt) controls. Further- The online version of this article contains supplemental material. more, we demonstrate that miR-155 directly targets the tran- scription factor Ets1 to regulate a subset of Th17 cell–effector Abbreviations used in this article: EAE, experimental autoimmune encephalomyeli- 2/2 tis; miRNA, microRNA; MOG, myelin oligodendrocyte glycoprotein; qPCR, quan- genes, which includes the IL-23R. Consequently, miR-155 titative real-time PCR; RFP, red fluorescent protein; shRNA, short hairpin RNA; 39- Th17 cells are hyporesponsive to IL-23, revealing a new link UTR, 39-untranslated region; Wt, wild-type. between miR-155 and the highly relevant IL-23–IL-23R pathway Copyright Ó 2013 by The American Association of Immunologists, Inc. 0022-1767/13/$16.00 (31–36). www.jimmunol.org/cgi/doi/10.4049/jimmunol.1300351 2 miR-155 PROMOTES Th17 CELL FUNCTION Materials and Methods bus database under accession number GSE45122 (http://www.ncbi.nlm. Mice nih.gov/geo/). All experiments were approved by the University of Utah Institutional ELISAs Animal Care and Use Committee. miR-155+/+, miR-1552/2, Rag12/2, IL- 2 ELISAs to detect expression of IL-17A and IFN-g were performed with 17F red fluorescent protein (RFP)+/ , 2D2 TCR Tg, and combinations of 2 2 cytokine-specific kits (eBioscience), according to the manufacturer’s these mice are all on a C57BL/6 genetic background. miR-155 / mice 2 2 instructions. were crossed with IL-17F RFP+/+ to create miR-155+/ IL-17F RFP+/ +/+ mice, which were crossed further to create both miR-155 and miR- Immunoblotting 1552/2IL-17F RFP+/2 mice. miR-155+/+IL-17F RFP+/+ and miR-1552/2 IL-17F RFP+/+ mice were crossed with Wt 2D2+ to create miR-155+/+IL- Cell pellets were lysed in 8 M urea buffer. Protein extracts were subjected 17F RFP+/22D2+ and miR-1552/2IL-17F RFP+/22D2+ mice, respectively. to gel electrophoresis and transferred onto a nitrocellulose membrane, Genotyping was performed as described previously (22, 37, 38). followed by Ab staining (Ets1 and b-actin; Santa Cruz Biotechnology) and detection as described previously (40). Expression levels were quantified Mouse models of EAE using National Institutes of Health ImageJ software. EAE was induced in mice as described previously (18). Briefly, MOG35–55 Luciferase reporter assays peptide (BD Biosciences) was emulsified in CFA (100 mg/ml) and injected s.c. into the base of the mouse’s tail. Pertussis toxin was injected i.p. into A region of the 39-untranslated region (39-UTR) of mouse Ets1 containing mice on days 0 and 2. Clinical symptoms of EAE were scored
Load more

Recommended publications
  • Large-Scale Opening of Utrophints Tandem Calponin Homology (CH
    Large-scale opening of utrophin’s tandem calponin homology (CH) domains upon actin binding by an induced-fit mechanism Ava Y. Lin, Ewa Prochniewicz, Zachary M. James, Bengt Svensson, and David D. Thomas1 Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455 Edited by James A. Spudich, Stanford University School of Medicine, Stanford, CA, and approved June 20, 2011 (received for review April 21, 2011) We have used site-directed spin labeling and pulsed electron has prevented the development of a reliable structural model for paramagnetic resonance to resolve a controversy concerning the any of these complexes. A major unresolved question concerns structure of the utrophin–actin complex, with implications for the the relative disposition of the tandem CH domains (CH1 and pathophysiology of muscular dystrophy. Utrophin is a homolog of CH2) (9, 10). Crystal structures of the tandem CH domains dystrophin, the defective protein in Duchenne and Becker muscular showed a closed conformation for fimbrin (11) and α-actinin (12), dystrophies, and therapeutic utrophin derivatives are currently but an open conformation for both utrophin (Utr261) (Fig. 1A) being developed. Both proteins have a pair of N-terminal calponin and dystrophin (Dys246) (16). The crystal structure of Utr261 homology (CH) domains that are important for actin binding. suggests that the central helical region connecting CH1 and CH2 Although there is a crystal structure of the utrophin actin-binding is highly flexible. Even for α-actinin, which has a closed crystal domain, electron microscopy of the actin-bound complexes has structure, computational analysis suggests the potential for a high produced two very different structural models, in which the CH do- degree of dynamic flexibility that facilitates actin binding (17).
    [Show full text]
  • Keratin 19 Regulates Cell Shape and Cell-Cell Adhesion of MCF7 Cells While Maintaining E-Cadherin Localization at the Cell Surface
    Keratin 19 regulates cell shape and cell-cell adhesion of MCF7 cells while maintaining E-cadherin localization at the cell surface Welcome to my poster. This is Sarah Alsharif, a PhD student from the biology department. I am glad to present the work our lab has been doing in the breast cancer field. In fact, after lung cancer, breast cancer is the second cause of death in women worldwide (1). It is estimated that every 18 seconds, approximately one new case of breast cancer is documented (2). No one dies due to cancer itself. The death is because of metastasis which takes place when cancer cells leave a breast in which they are formed and reach other sites such as the brain or lung. Our lab is interested in investigating the mechanism behind metastasis of breast cancer. Metastasis is associated with what is called epithelial to mesenchymal transition (EMT), the process characterized by loss of cell to cell adhesion and expression of epithelial markers such as keratin intermediate filament proteins, as you can see in the first three images of cells. Those filaments are keratins and they are critical for the shape and for maintaining mechanical integrity of epithelial cells via cell to cell complexes called desmosomes. Among different keratins, keratin 19 (K19) is highly expressed in many types of cancer including breast cancer, and is correlated with a worse prognosis (3). Consistently, K19 expression has been reported to be significantly higher in metastatic breast cancer tumor cells compared to primary tumors (4). The role of K19 on mechanical properties of cancer cells for cell migration and possible impact on metastasis in breast cancer patients is still unknown.
    [Show full text]
  • Whole-Genome Microarray Detects Deletions and Loss of Heterozygosity of Chromosome 3 Occurring Exclusively in Metastasizing Uveal Melanoma
    Anatomy and Pathology Whole-Genome Microarray Detects Deletions and Loss of Heterozygosity of Chromosome 3 Occurring Exclusively in Metastasizing Uveal Melanoma Sarah L. Lake,1 Sarah E. Coupland,1 Azzam F. G. Taktak,2 and Bertil E. Damato3 PURPOSE. To detect deletions and loss of heterozygosity of disease is fatal in 92% of patients within 2 years of diagnosis. chromosome 3 in a rare subset of fatal, disomy 3 uveal mela- Clinical and histopathologic risk factors for UM metastasis noma (UM), undetectable by fluorescence in situ hybridization include large basal tumor diameter (LBD), ciliary body involve- (FISH). ment, epithelioid cytomorphology, extracellular matrix peri- ϩ ETHODS odic acid-Schiff-positive (PAS ) loops, and high mitotic M . Multiplex ligation-dependent probe amplification 3,4 5 (MLPA) with the P027 UM assay was performed on formalin- count. Prescher et al. showed that a nonrandom genetic fixed, paraffin-embedded (FFPE) whole tumor sections from 19 change, monosomy 3, correlates strongly with metastatic death, and the correlation has since been confirmed by several disomy 3 metastasizing UMs. Whole-genome microarray analy- 3,6–10 ses using a single-nucleotide polymorphism microarray (aSNP) groups. Consequently, fluorescence in situ hybridization were performed on frozen tissue samples from four fatal dis- (FISH) detection of chromosome 3 using a centromeric probe omy 3 metastasizing UMs and three disomy 3 tumors with Ͼ5 became routine practice for UM prognostication; however, 5% years’ metastasis-free survival. to 20% of disomy 3 UM patients unexpectedly develop metas- tases.11 Attempts have therefore been made to identify the RESULTS. Two metastasizing UMs that had been classified as minimal region(s) of deletion on chromosome 3.12–15 Despite disomy 3 by FISH analysis of a small tumor sample were found these studies, little progress has been made in defining the key on MLPA analysis to show monosomy 3.
    [Show full text]
  • Table S1 the Four Gene Sets Derived from Gene Expression Profiles of Escs and Differentiated Cells
    Table S1 The four gene sets derived from gene expression profiles of ESCs and differentiated cells Uniform High Uniform Low ES Up ES Down EntrezID GeneSymbol EntrezID GeneSymbol EntrezID GeneSymbol EntrezID GeneSymbol 269261 Rpl12 11354 Abpa 68239 Krt42 15132 Hbb-bh1 67891 Rpl4 11537 Cfd 26380 Esrrb 15126 Hba-x 55949 Eef1b2 11698 Ambn 73703 Dppa2 15111 Hand2 18148 Npm1 11730 Ang3 67374 Jam2 65255 Asb4 67427 Rps20 11731 Ang2 22702 Zfp42 17292 Mesp1 15481 Hspa8 11807 Apoa2 58865 Tdh 19737 Rgs5 100041686 LOC100041686 11814 Apoc3 26388 Ifi202b 225518 Prdm6 11983 Atpif1 11945 Atp4b 11614 Nr0b1 20378 Frzb 19241 Tmsb4x 12007 Azgp1 76815 Calcoco2 12767 Cxcr4 20116 Rps8 12044 Bcl2a1a 219132 D14Ertd668e 103889 Hoxb2 20103 Rps5 12047 Bcl2a1d 381411 Gm1967 17701 Msx1 14694 Gnb2l1 12049 Bcl2l10 20899 Stra8 23796 Aplnr 19941 Rpl26 12096 Bglap1 78625 1700061G19Rik 12627 Cfc1 12070 Ngfrap1 12097 Bglap2 21816 Tgm1 12622 Cer1 19989 Rpl7 12267 C3ar1 67405 Nts 21385 Tbx2 19896 Rpl10a 12279 C9 435337 EG435337 56720 Tdo2 20044 Rps14 12391 Cav3 545913 Zscan4d 16869 Lhx1 19175 Psmb6 12409 Cbr2 244448 Triml1 22253 Unc5c 22627 Ywhae 12477 Ctla4 69134 2200001I15Rik 14174 Fgf3 19951 Rpl32 12523 Cd84 66065 Hsd17b14 16542 Kdr 66152 1110020P15Rik 12524 Cd86 81879 Tcfcp2l1 15122 Hba-a1 66489 Rpl35 12640 Cga 17907 Mylpf 15414 Hoxb6 15519 Hsp90aa1 12642 Ch25h 26424 Nr5a2 210530 Leprel1 66483 Rpl36al 12655 Chi3l3 83560 Tex14 12338 Capn6 27370 Rps26 12796 Camp 17450 Morc1 20671 Sox17 66576 Uqcrh 12869 Cox8b 79455 Pdcl2 20613 Snai1 22154 Tubb5 12959 Cryba4 231821 Centa1 17897
    [Show full text]
  • Defining Functional Interactions During Biogenesis of Epithelial Junctions
    ARTICLE Received 11 Dec 2015 | Accepted 13 Oct 2016 | Published 6 Dec 2016 | Updated 5 Jan 2017 DOI: 10.1038/ncomms13542 OPEN Defining functional interactions during biogenesis of epithelial junctions J.C. Erasmus1,*, S. Bruche1,*,w, L. Pizarro1,2,*, N. Maimari1,3,*, T. Poggioli1,w, C. Tomlinson4,J.Lees5, I. Zalivina1,w, A. Wheeler1,w, A. Alberts6, A. Russo2 & V.M.M. Braga1 In spite of extensive recent progress, a comprehensive understanding of how actin cytoskeleton remodelling supports stable junctions remains to be established. Here we design a platform that integrates actin functions with optimized phenotypic clustering and identify new cytoskeletal proteins, their functional hierarchy and pathways that modulate E-cadherin adhesion. Depletion of EEF1A, an actin bundling protein, increases E-cadherin levels at junctions without a corresponding reinforcement of cell–cell contacts. This unexpected result reflects a more dynamic and mobile junctional actin in EEF1A-depleted cells. A partner for EEF1A in cadherin contact maintenance is the formin DIAPH2, which interacts with EEF1A. In contrast, depletion of either the endocytic regulator TRIP10 or the Rho GTPase activator VAV2 reduces E-cadherin levels at junctions. TRIP10 binds to and requires VAV2 function for its junctional localization. Overall, we present new conceptual insights on junction stabilization, which integrate known and novel pathways with impact for epithelial morphogenesis, homeostasis and diseases. 1 National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK. 2 Computing Department, Imperial College London, London SW7 2AZ, UK. 3 Bioengineering Department, Faculty of Engineering, Imperial College London, London SW7 2AZ, UK. 4 Department of Surgery & Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK.
    [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]
  • Sirt1 Is Regulated by Mir-135A and Involved in DNA Damage Repair During Mouse Cellular Reprogramming
    www.aging-us.com AGING 2020, Vol. 12, No. 8 Research Paper Sirt1 is regulated by miR-135a and involved in DNA damage repair during mouse cellular reprogramming Andy Chun Hang Chen1,2,*, Qian Peng2,*, Sze Wan Fong1, William Shu Biu Yeung1,2, Yin Lau Lee1,2 1Department of Obstetrics and Gynaecology, The University of Hong Kong, Hong Kong SAR, China 2Shenzhen Key Laboratory of Fertility Regulation, The University of Hong Kong Shenzhen Hospital, Shenzhen, China *Co-first authors Correspondence to: Yin Lau Lee, William Shu Biu Yeung; email: [email protected], [email protected] Keywords: mouse induced pluripotent stem cells, cellular reprogramming, Sirt1, miR-135a, DNA damage repair Received: December 30, 2019 Accepted: March 30, 2020 Published: April 26, 2020 Copyright: Chen et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ABSTRACT Sirt1 facilitates the reprogramming of mouse somatic cells into induced pluripotent stem cells (iPSCs). It is regulated by micro-RNA and reported to be a target of miR-135a. However, their relationship and roles on cellular reprogramming remain unknown. In this study, we found negative correlations between miR-135a and Sirt1 during mouse embryonic stem cells differentiation and mouse embryonic fibroblasts reprogramming. We further found that the reprogramming efficiency was reduced by the overexpression of miR-135a precursor but induced by the miR-135a inhibitor. Co-immunoprecipitation followed by mass spectrometry identified 21 SIRT1 interacting proteins including KU70 and WRN, which were highly enriched for DNA damage repair.
    [Show full text]
  • Genome-Wide DNA Methylation Analysis of KRAS Mutant Cell Lines Ben Yi Tew1,5, Joel K
    www.nature.com/scientificreports OPEN Genome-wide DNA methylation analysis of KRAS mutant cell lines Ben Yi Tew1,5, Joel K. Durand2,5, Kirsten L. Bryant2, Tikvah K. Hayes2, Sen Peng3, Nhan L. Tran4, Gerald C. Gooden1, David N. Buckley1, Channing J. Der2, Albert S. Baldwin2 ✉ & Bodour Salhia1 ✉ Oncogenic RAS mutations are associated with DNA methylation changes that alter gene expression to drive cancer. Recent studies suggest that DNA methylation changes may be stochastic in nature, while other groups propose distinct signaling pathways responsible for aberrant methylation. Better understanding of DNA methylation events associated with oncogenic KRAS expression could enhance therapeutic approaches. Here we analyzed the basal CpG methylation of 11 KRAS-mutant and dependent pancreatic cancer cell lines and observed strikingly similar methylation patterns. KRAS knockdown resulted in unique methylation changes with limited overlap between each cell line. In KRAS-mutant Pa16C pancreatic cancer cells, while KRAS knockdown resulted in over 8,000 diferentially methylated (DM) CpGs, treatment with the ERK1/2-selective inhibitor SCH772984 showed less than 40 DM CpGs, suggesting that ERK is not a broadly active driver of KRAS-associated DNA methylation. KRAS G12V overexpression in an isogenic lung model reveals >50,600 DM CpGs compared to non-transformed controls. In lung and pancreatic cells, gene ontology analyses of DM promoters show an enrichment for genes involved in diferentiation and development. Taken all together, KRAS-mediated DNA methylation are stochastic and independent of canonical downstream efector signaling. These epigenetically altered genes associated with KRAS expression could represent potential therapeutic targets in KRAS-driven cancer. Activating KRAS mutations can be found in nearly 25 percent of all cancers1.
    [Show full text]
  • KIF1A-Related Autosomal Dominant Spastic Paraplegias (SPG30) in Russian Families G
    Rudenskaya et al. BMC Neurology (2020) 20:290 https://doi.org/10.1186/s12883-020-01872-4 RESEARCH ARTICLE Open Access KIF1A-related autosomal dominant spastic paraplegias (SPG30) in Russian families G. E. Rudenskaya1 , V. A. Kadnikova1* , O. P. Ryzhkova1 , L. A. Bessonova1, E. L. Dadali1 , D. S. Guseva1 , T. V. Markova1 , D. N. Khmelkova2 and A. V. Polyakov1 Abstract Background: Spastic paraplegia type 30 (SPG30) caused by KIF1A mutations was first reported in 2011 and was initially considered a very rare autosomal recessive (AR) form. In the last years, thanks to the development of massive parallel sequencing, SPG30 proved to be a rather common autosomal dominant (AD) form of familial or sporadic spastic paraplegia (SPG),, with a wide range of phenotypes: pure and complicated. The aim of our study is to detect AD SPG30 cases and to examine their molecular and clinical characteristics for the first time in the Russian population. Methods: Clinical, genealogical and molecular methods were used. Molecular methods included massive parallel sequencing (MPS) of custom panel ‘spastic paraplegias’ with 62 target genes complemented by familial Sanger sequencing. One case was detected by the whole -exome sequencing. Results: AD SPG30 was detected in 10 unrelated families, making it the 3rd (8.4%) most common SPG form in the cohort of 118 families. No AR SPG30 cases were detected. In total, 9 heterozygous KIF1A mutations were detected, with 4 novel and 5 known mutations. All the mutations were located within KIF1A motor domain. Six cases had pure phenotypes, of which 5 were familial, where 2 familial cases demonstrated incomplete penetrance, early onset and slow relatively benign SPG course.
    [Show full text]
  • CLIP-Seq and Massively Parallel Functional Analysis of the CELF6
    bioRxiv preprint doi: https://doi.org/10.1101/401604; this version posted August 27, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. CLIP-Seq and massively parallel functional analysis of the CELF6 RNA binding protein reveals a role in destabilizing synaptic gene mRNAs through interaction with 3’UTR elements in vivo Michael A. Rieger1,2, Dana M. King1, Barak A. Cohen1, Joseph D. Dougherty1,2 1Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA 2Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA Contact: Dr. Joseph D. Dougherty Washington University School of Medicine Department of Genetics Campus Box 8232 4566 Scott Ave. St. Louis, Mo. 63110-1093 (314) 286-0752 [email protected] bioRxiv preprint doi: https://doi.org/10.1101/401604; this version posted August 27, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract CELF6 is an RNA-binding protein in a family of proteins with roles in human health and disease, however little is known about the mRNA targets or in vivo function of this protein. We utilized HITS-CLIP/CLIP-Seq to identify, for the first time, in vivo targets of CELF6 and identify hundreds of transcripts bound by CELF6 in the brain. We found these are disproportionately mRNAs coding for synaptic proteins. We then conducted extensive functional validation of these targets, testing greater than 400 CELF6 bound sequence elements for their activity, applying a massively parallel reporter assay framework to evaluation of the CLIP data.
    [Show full text]
  • Dimerization of Mammalian Kinesin-3 Motors Results in Superprocessive Motion
    Dimerization of mammalian kinesin-3 motors results in superprocessive motion Virupakshi Soppinaa,1, Stephen R. Norrisa,b, Aslan S. Dizajia, Matt Kortusa, Sarah Veatchb, Michelle Peckhamc, and Kristen J. Verheya,1 aDepartment of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109; bDepartment of Biophysics, University of Michigan, Ann Arbor, MI 48109; and cSchool of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom Edited by J. Richard McIntosh, University of Colorado, Boulder, CO, and approved March 7, 2014 (received for review January 15, 2014) The kinesin-3 family is one of the largest among the kinesin Defects in kinesin-3 transport have been implicated in a wide superfamily and its members play important roles in a wide range variety of neurodegenerative, developmental, and cancer dis- of cellular transport activities, yet the molecular mechanisms of eases (22). However, a mechanistic understanding of this im- kinesin-3 regulation and cargo transport are largely unknown. portant class of cellular transporters is currently limited. We performed a comprehensive analysis of mammalian kinesin-3 To date, mechanistic studies have focused on truncated ver- motors from three different subfamilies (KIF1, KIF13, and KIF16). sions of mammalian KIF1A and its homolog CeUNC-104, and Using Forster resonance energy transfer microscopy in live cells, these studies have yielded contradictory results (23). For exam- we show for the first time to our knowledge that KIF16B motors ple, murine KIF1A has been proposed to function as a monomer undergo cargo-mediated dimerization. The molecular mechanisms that diffuses along the microtubule surface or as a processive dimer.
    [Show full text]
  • Quantigene Flowrna Probe Sets Currently Available
    QuantiGene FlowRNA Probe Sets Currently Available Accession No. Species Symbol Gene Name Catalog No. NM_003452 Human ZNF189 zinc finger protein 189 VA1-10009 NM_000057 Human BLM Bloom syndrome VA1-10010 NM_005269 Human GLI glioma-associated oncogene homolog (zinc finger protein) VA1-10011 NM_002614 Human PDZK1 PDZ domain containing 1 VA1-10015 NM_003225 Human TFF1 Trefoil factor 1 (breast cancer, estrogen-inducible sequence expressed in) VA1-10016 NM_002276 Human KRT19 keratin 19 VA1-10022 NM_002659 Human PLAUR plasminogen activator, urokinase receptor VA1-10025 NM_017669 Human ERCC6L excision repair cross-complementing rodent repair deficiency, complementation group 6-like VA1-10029 NM_017699 Human SIDT1 SID1 transmembrane family, member 1 VA1-10032 NM_000077 Human CDKN2A cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4) VA1-10040 NM_003150 Human STAT3 signal transducer and activator of transcripton 3 (acute-phase response factor) VA1-10046 NM_004707 Human ATG12 ATG12 autophagy related 12 homolog (S. cerevisiae) VA1-10047 NM_000737 Human CGB chorionic gonadotropin, beta polypeptide VA1-10048 NM_001017420 Human ESCO2 establishment of cohesion 1 homolog 2 (S. cerevisiae) VA1-10050 NM_197978 Human HEMGN hemogen VA1-10051 NM_001738 Human CA1 Carbonic anhydrase I VA1-10052 NM_000184 Human HBG2 Hemoglobin, gamma G VA1-10053 NM_005330 Human HBE1 Hemoglobin, epsilon 1 VA1-10054 NR_003367 Human PVT1 Pvt1 oncogene homolog (mouse) VA1-10061 NM_000454 Human SOD1 Superoxide dismutase 1, soluble (amyotrophic lateral sclerosis 1 (adult))
    [Show full text]