Is the T-G-CT-G SNRNP70 Haplotype Another Proof That Mixed Connective

Total Page:16

File Type:pdf, Size:1020Kb

Is the T-G-CT-G SNRNP70 Haplotype Another Proof That Mixed Connective Is the T-G-CT-G SNRNP70 haplotype another proof that mixed connective tissue disease is distinct from systemic lupus erythematosus and systemic sclerosis? A novel gene variant in SNRNP70 gene A. Paradowska-Gorycka1, A. Wajda1, I. Stolarek2, A. Felis-Giemza3, M. Walczyk3, J. Nałecz-Janik3, M. Olesińska3 1Department of Molecular Biology, ABSTRACT Introduction National Institute of Geriatrics, Objective. U1-70K, encoded by the In 1990, Spritz et al. (1) introduced the Rheumatology and Rehabilitation, SNRNP70 gene, is a key early immu- sequence of SNRNP70 gene, which is Warsaw; nogen in connective tissue disease. The mapped on chromosome 19q13.33. SN- 2Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan; aim of the study was the genetic analy- RNP70 gene encoding the human U1- 3Department of Connective Tissue sis of the SNRNP70 gene in mixed con- 70K protein belonging to the U1 small Diseases, National Institute of Geriatrics, nective tissue disease (MCTD), sys- nuclear ribonucleoprotein (snRNP also Rheumatology and Rehabilitation, temic lupus erythematosus (SLE) and known as U1-RNP) complex, which is Warsaw, Poland. systemic sclerosis (SSc) patients. a key component of the spliceosome Agnieszka Paradowska-Gorycka, PhD Methods. SNRNP70 genetic vari- (2-4). U1-70K protein contains an N- Anna Wajda, PhD ants were detected using 3730 DNA terminal domain, an 80 amino acid Ireneusz Stolarek, PhD Analyzer. SNRNP70 rs560811128 G/A RNA binding domain (RBP) with two Anna Felis-Giemza, PhD (c.476-252 G/A), rs78616533delCT characteristics RNA recognition motifs Marcela Walczyk, MD Jolanta Nałecz-Janik, PhD (c.475+130_475+131delCT) and (RRMs) and a C-terminal domain with Marzena Olesińska, MD, PhD rs117167710 T/C (c.393+326 T/C) two Arg-rich domains. U1-70K protein Please address correspondence to: variants were genotyped using the tech- through RNP-80 motif directly binds Dr Agnieszka Paradowska-Gorycka, nique of sequence-specific hybridisa- to stem-loop I of U1-RNA as an indi- Department of Molecular Biology, tion probe binding assays. SNRNP70 vidual molecule (5-9). National Institute of Geriatrics, 393_47 G/A mutation was detected us- The U1-70K protein and U1-RNA in- Rheumatology and Rehabilitation, ing TaqMan SNP genotyping assay. volved immune cells, such as B and T Spartańska 1, Results. We found one novel cells, as well as their receptors in com- 02-637 Warszawa, Poland. c.393+47G>A and three, c.476-252 E-mail: [email protected]; plex interactions leading to the produc- agnieszka.paradowska-gorycka@ G/A, c.475+130_475+131delCT and tion of autoantibodies, inflammation spartanska.pl c.393+326 T/C, previously recorded and tissue damage (8, 10). Moreover, Received on April 3, 2019; accepted in variants. The present study revealed protein components of the U1-snRNP revised form on May 27, 2019. that T-G-CT-G haplotype demon- complex are targeted by autoantibodies Clin Exp Rheumatol 2019; 37 (Suppl. 119): strated significantly higher frequen- present in patients with systemic lupus S32-S40. cies in MCTD patients than in SLE erythematosus (SLE), systemic sclero- © Copyright CLINICAL AND and SSc patients. In MCTD patients sis (SSc) and mixed connective tissue EXPERIMENTAL RHEUMATOLOGY 2019. c.475+130_475+131delCT distribu- disease (MCTD) (11-14). Anti-U1- tion of genotype was gender-dependent snRNP antibodies are observed in 30– Key words: SNRNP70, anti-U1-70K, and showed association with thrombo-/ 35% of SLE patients, 2-14% of SSc pa- MCTD, phenotype, genetics leukocytopenia. Mutation at position tients and in nearly all, if not all, MCTD c.476-252G>A was predicted to pos- patients (8, 11, 12, 15). Antibodies sibly have an impact on splicing of the against U1-70K develop as first, in the SNRNP70 transcript and it was present early immune response, and participate only in one MCTD patient. in the development of other antibodies. Conclusion. Our results demonstrated They are detected in 75–90% of MCTD that the T-G-CT-G SNRNP70 haplo- patients but in contrast, they have de- type is another proof that MCTD may tected only in 20–50% of SLE patients be distinct from SLE and SSc. The novel whose sera is anti-RNP positive (8, 12, Funding: this work was supported by c.476-252G>A mutation in SNRNP70 16, 17). A prerequisite for the diagnosis a grant from the Polpharma Scientific gene created a new acceptor splice site of MCTD is the presence of anti-U1- Foundation. and may potentially alert of splicing of RNP antibodies. In patients with high Competing interests: none declared. the SNRNP70 transcript. titres of these antibodies who do not S-32 Clinical and Experimental Rheumatology 2019 SNRNP70 gene in MCTD, SLE and SSc. / A. Paradowska-Gorycka et al. meet the criteria for MCTD diagnosis Table I. Patients’ characteristics. or any other connective tissue disease, Characteristics MCTD SLE SSc MCTD usually develops within 2 years. n=83 n=97 n=71 U1-70K is a major early immunogen mean values ± SD mean values ± SD mean values ± SD might be important for triggering of the immune response to U1-snRNP com- Age [years] 42.71 ± 13.40 40.58 ± 12.73 55.06 ± 13.47 Disease duration [years] 9.75 ± 8.52 3.85 ± 5.97 4.99 ± 7.50 plex (13, 16, 17). Gender 67 (81%) female 90 (93%) female 53 (75%) female However, the precise role of the U1- 16 (19%) male 7 (7%) male 18 (25%) male 70K protein and especially SNRNP70 Damage index MCTD-DI SLICC gene in the pathogenesis of MCTD, [median range (min-max)] 5 (0-68) 4 (0-17) 2 (0-15) SLE and/or SSc is unknown. To verify Activity index MCTD-AI SELENA_SLEDAI whether genetic variation located in [median range (min-max)] 9.4 (0-32) 4 (0-17) 0.5 (0-9) the SNRNP70 gene may be a factor ESR [mm/h] 27.58 ± 23 32.62 ± 26.89 19.37 ± 16.54 explaining phenotype or characteris- CRP [mg/L] 11.63 ± 14.80 25.7 ± 57.62 8.28 ± 11.21 tics above connective tissue diseases n** (%) (CTD), we used gene sequencing for anti-dsDNA 12 (14%) 58 (60) 1 (1%) anti-SSA Ro60 8 (10%) 37 (38%)-SSA 1 (1%) detection of all polymorphisms/muta- Ro52 23 (28%) 1 (1%) tion located in this gene. anti-SSB 1 (1%) 12 (12%) 0 (0%) anti-SM SmB 27 (33%) 14 (14%) 0 (0%) Materials and methods SmD 5 (6%) 0 (0%) anti-Rib 3 (4%) 10 (10%) 0 (0%) Study populations anti-Jo 2 (2%) 0 (0%) 0 (0%) A total of 504 individuals were selected anti-histon 12 (14%) 22 (23%) 1 (1%) to participate in this study. Peripheral anti-Scl-70 2 (2%) 1 (1%) 5 (7%) blood samples from 135 MCTD pa- anti-U1-RNP 82 (99%) 14 (14%) 0 anti-70K 60 (72%) - - tients, 135 SLE patients, 81 SSc pa- anti-A 68 (82%) - - tients, and 153 healthy subjects were anti-C 64 (77%) - - obtained. All patients were recruited Sjögren 18 (22%) 16 (16%) - from the Department of Connective Tis- Raynaud’s phenomenon 80 (96%) - 47 (66%) Facial erythema 36 (43%) 44 (45%) - sue Diseases of the National Institute of arthritis 78 (94%) 62 (64%) 24 (34%) Geriatrics, Rheumatology and Rehabili- Pulmonary fibrosis 28 (34%) 5 (5%) 21 (30%) tation. Healthy control participants were Leukopenia/trombocytopenia 51 (61%) 52 (50%) - recruited from the Regional Center for MCTD: mixed connective tissue disease; SLE: systemic lupus erythematosus; SSc: systemic sclero- Blood Donation and Blood Treatment in sis; SD: standard deviation; ESR: erythrocyte sedimentation rate; CRP: C-reactive protein; MCTD- Warsaw. Healthy subjects did not have -DI: MCTD damage index; SLICC: Systemic Lupus International Collaborating Clinics; MCTD-AI: a history of autoimmune and/or inflam- MCTD activity index; SELENA-SLEDAI: Systemic Lupus Erythematosus Disease Activity Index. matory disease at the time of sampling. MCTD patients, SLE patients, SSc Collaborating Clinics/American Col- tigation was approved by the Research patients, and healthy subjects were of lege of Rheumatology (SLICC/ACR) Ethics Committee of the National In- Caucasian origin. Characteristics of all Damage Index (SLICC/ACR DI). Dam- stitute of Geriatrics, Rheumatology and participants were summarised in Ta- age most commonly affected skin, mus- Rehabilitation in Warsaw. All partici- ble I, where we presented only those culoskeletal and cardiovascular systems pants, patients, and healthy donors gave clinical parameters which are shared and lungs. Autoantibodies to Sm, Ro, informed written consent and research by the three diseases. Objective meth- La, RibP, PCNA, CENPB, Scl-70, Jo-1, was conducted in accordance with the ods were constructed based on the tools His, dsDNA were measured in sera us- Declaration of Helsinki. employed in SLE; an MCTD activity ing DOT-blot tests (recomLine ANA/ index (MCTD-AI) was modeled on the ENA, Mikrogen Diagnostik, Neuried, Mixed connective tissue disease Systemic Lupus Erythematosus Disease Germany). The identification of antinu- patients Activity Index (SLEDAI) score. The clear antibodies (ANA) was performed MCTD patients met Alarcon-Segovia most common symptoms of the active by indirect immunofluorescence (IF) and Villarreal classification criteria, disease were: decreased number of leu- on Hep2 cell lines (Euroimmun Pol- which were chosen due to their very kocytes and/or platelets, swelling of the ska, Wroclaw, Poland), with median a high specificity for MCTD. Patients hands, increased of erythrocyte sedi- titre of 1:5,840 (range 1:80 – 1:40,960). with MCTD, who met the classification mentation rate (ESR) and/or C-reactive The presence of anti-U1-RNP was de- criteria for two connective tissue diseas- protein (CRP) levels, hypergamma- termined by electrochemiluminescence es at the same time were excluded from globulinaemia and skin rashes. MCTD (ECLIA) using streptavidin-coated par- the study.
Recommended publications
  • Supplementary Materials
    Supplementary Materials COMPARATIVE ANALYSIS OF THE TRANSCRIPTOME, PROTEOME AND miRNA PROFILE OF KUPFFER CELLS AND MONOCYTES Andrey Elchaninov1,3*, Anastasiya Lokhonina1,3, Maria Nikitina2, Polina Vishnyakova1,3, Andrey Makarov1, Irina Arutyunyan1, Anastasiya Poltavets1, Evgeniya Kananykhina2, Sergey Kovalchuk4, Evgeny Karpulevich5,6, Galina Bolshakova2, Gennady Sukhikh1, Timur Fatkhudinov2,3 1 Laboratory of Regenerative Medicine, National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov of Ministry of Healthcare of Russian Federation, Moscow, Russia 2 Laboratory of Growth and Development, Scientific Research Institute of Human Morphology, Moscow, Russia 3 Histology Department, Medical Institute, Peoples' Friendship University of Russia, Moscow, Russia 4 Laboratory of Bioinformatic methods for Combinatorial Chemistry and Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia 5 Information Systems Department, Ivannikov Institute for System Programming of the Russian Academy of Sciences, Moscow, Russia 6 Genome Engineering Laboratory, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia Figure S1. Flow cytometry analysis of unsorted blood sample. Representative forward, side scattering and histogram are shown. The proportions of negative cells were determined in relation to the isotype controls. The percentages of positive cells are indicated. The blue curve corresponds to the isotype control. Figure S2. Flow cytometry analysis of unsorted liver stromal cells. Representative forward, side scattering and histogram are shown. The proportions of negative cells were determined in relation to the isotype controls. The percentages of positive cells are indicated. The blue curve corresponds to the isotype control. Figure S3. MiRNAs expression analysis in monocytes and Kupffer cells. Full-length of heatmaps are presented.
    [Show full text]
  • U1 Snrnp Regulates Chromatin Retention of Noncoding Rnas
    bioRxiv preprint doi: https://doi.org/10.1101/310433; this version posted April 29, 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. U1 snRNP regulates chromatin retention of noncoding RNAs Yafei Yin,1,* J. Yuyang Lu,1 Xuechun Zhang,1 Wen Shao,1 Yanhui Xu,1 Pan Li,1,2 Yantao Hong,1 Qiangfeng Cliff Zhang,2 and Xiaohua Shen 1,3,* 1 Tsinghua-Peking Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing 100084, China 2 MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China 3 Lead Contact *Correspondence: [email protected] (Y.Y.), [email protected] (X.S.) Running title: U1 snRNP regulates ncRNA-chromatin retention Keywords: RNA-chromatin localization, U1 snRNA, lncRNA, PROMPTs and eRNA, splicing 1 bioRxiv preprint doi: https://doi.org/10.1101/310433; this version posted April 29, 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 Thousands of noncoding transcripts exist in mammalian genomes, and they preferentially localize to chromatin. Here, to identify cis-regulatory elements that control RNA-chromatin association, we developed a high-throughput method named RNA element for subcellular localization by sequencing (REL-seq). Coupling REL-seq with random mutagenesis (mutREL-seq), we discovered a key 7-nt U1 recognition motif in chromatin-enriched RNA elements.
    [Show full text]
  • U1 Snrnp Regulates Chromatin Retention of Noncoding Rnas
    Article U1 snRNP regulates chromatin retention of noncoding RNAs https://doi.org/10.1038/s41586-020-2105-3 Yafei Yin1 ✉, J. Yuyang Lu1, Xuechun Zhang1, Wen Shao1, Yanhui Xu1, Pan Li1,2, Yantao Hong1, Li Cui1, Ge Shan3, Bin Tian4, Qiangfeng Cliff Zhang1,2 & Xiaohua Shen1 ✉ Received: 26 November 2018 Accepted: 9 January 2020 Long noncoding RNAs (lncRNAs) and promoter- or enhancer-associated unstable Published online: xx xx xxxx transcripts locate preferentially to chromatin, where some regulate chromatin structure, Check for updates transcription and RNA processing1–13. Although several RNA sequences responsible for nuclear localization have been identifed—such as repeats in the lncRNA Xist and Alu-like elements in long RNAs14–16—how lncRNAs as a class are enriched at chromatin remains unknown. Here we describe a random, mutagenesis-coupled, high-throughput method that we name ‘RNA elements for subcellular localization by sequencing’ (mutREL-seq). Using this method, we discovered an RNA motif that recognizes the U1 small nuclear ribonucleoprotein (snRNP) and is essential for the localization of reporter RNAs to chromatin. Across the genome, chromatin-bound lncRNAs are enriched with 5′ splice sites and depleted of 3′ splice sites, and exhibit high levels of U1 snRNA binding compared with cytoplasm-localized messenger RNAs. Acute depletion of U1 snRNA or of the U1 snRNP protein component SNRNP70 markedly reduces the chromatin association of hundreds of lncRNAs and unstable transcripts, without altering the overall transcription rate in cells. In addition, rapid degradation of SNRNP70 reduces the localization of both nascent and polyadenylated lncRNA transcripts to chromatin, and disrupts the nuclear and genome-wide localization of the lncRNA Malat1.
    [Show full text]
  • Large-Scale Analysis of Genome and Transcriptome Alterations in Multiple Tumors Unveils Novel Cancer-Relevant Splicing Networks
    Downloaded from genome.cshlp.org on October 2, 2021 - Published by Cold Spring Harbor Laboratory Press Large-scale analysis of genome and transcriptome alterations in multiple tumors unveils novel cancer-relevant splicing networks Endre Sebestyén1,*, Babita Singh1,*, Belén Miñana1,2, Amadís Pagès1, Francesca Mateo3, Miguel Angel Pujana3, Juan Valcárcel1,2,4, Eduardo Eyras1,4,5 1Universitat Pompeu Fabra, Dr. Aiguader 88, E08003 Barcelona, Spain 2Centre for Genomic Regulation, Dr. Aiguader 88, E08003 Barcelona, Spain 3Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), E08908 L’Hospitalet del Llobregat, Spain. 4Catalan Institution for Research and Advanced Studies, Passeig Lluís Companys 23, E08010 Barcelona, Spain *Equal contribution 5Correspondence to: [email protected] Keywords: alternative splicing, RNA binding proteins, splicing networks, cancer 1 Downloaded from genome.cshlp.org on October 2, 2021 - Published by Cold Spring Harbor Laboratory Press Abstract Alternative splicing is regulated by multiple RNA-binding proteins and influences the expression of most eukaryotic genes. However, the role of this process in human disease, and particularly in cancer, is only starting to be unveiled. We systematically analyzed mutation, copy number and gene expression patterns of 1348 RNA-binding protein (RBP) genes in 11 solid tumor types, together with alternative splicing changes in these tumors and the enrichment of binding motifs in the alternatively spliced sequences. Our comprehensive study reveals widespread alterations in the expression of RBP genes, as well as novel mutations and copy number variations in association with multiple alternative splicing changes in cancer drivers and oncogenic pathways. Remarkably, the altered splicing patterns in several tumor types recapitulate those of undifferentiated cells.
    [Show full text]
  • Ribosome Profiling Reveals an Important Role for Translational Control in Circadian Gene Expression
    Downloaded from genome.cshlp.org on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press Research Ribosome profiling reveals an important role for translational control in circadian gene expression Christopher Jang,1,4 Nicholas F. Lahens,2,4 John B. Hogenesch,2 and Amita Sehgal1,3 1Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA; 2Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA; 3Howard Hughes Medical Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA Physiological and behavioral circadian rhythms are driven by a conserved transcriptional/translational negative feedback loop in mammals. Although most core clock factors are transcription factors, post-transcriptional control introduces delays that are critical for circadian oscillations. Little work has been done on circadian regulation of translation, so to address this deficit we conducted ribosome profiling experiments in a human cell model for an autonomous clock. We found that most rhythmic gene expression occurs with little delay between transcription and translation, suggesting that the lag in the ac- cumulation of some clock proteins relative to their mRNAs does not arise from regulated translation. Nevertheless, we found that translation occurs in a circadian fashion for many genes, sometimes imposing an additional level of control on rhythmically expressed mRNAs and, in other cases, conferring rhythms on noncycling mRNAs. Most cyclically tran- scribed RNAs are translated at one of two major times in a 24-h day, while rhythmic translation of most noncyclic RNAs is phased to a single time of day.
    [Show full text]
  • Autocrine IFN Signaling Inducing Profibrotic Fibroblast Responses By
    Downloaded from http://www.jimmunol.org/ by guest on September 23, 2021 Inducing is online at: average * The Journal of Immunology , 11 of which you can access for free at: 2013; 191:2956-2966; Prepublished online 16 from submission to initial decision 4 weeks from acceptance to publication August 2013; doi: 10.4049/jimmunol.1300376 http://www.jimmunol.org/content/191/6/2956 A Synthetic TLR3 Ligand Mitigates Profibrotic Fibroblast Responses by Autocrine IFN Signaling Feng Fang, Kohtaro Ooka, Xiaoyong Sun, Ruchi Shah, Swati Bhattacharyya, Jun Wei and John Varga J Immunol cites 49 articles Submit online. Every submission reviewed by practicing scientists ? is published twice each month by Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://jimmunol.org/subscription Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html http://www.jimmunol.org/content/suppl/2013/08/20/jimmunol.130037 6.DC1 This article http://www.jimmunol.org/content/191/6/2956.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 © 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 23, 2021. The Journal of Immunology A Synthetic TLR3 Ligand Mitigates Profibrotic Fibroblast Responses by Inducing Autocrine IFN Signaling Feng Fang,* Kohtaro Ooka,* Xiaoyong Sun,† Ruchi Shah,* Swati Bhattacharyya,* Jun Wei,* and John Varga* Activation of TLR3 by exogenous microbial ligands or endogenous injury-associated ligands leads to production of type I IFN.
    [Show full text]
  • Phylogenetic Comparison and Splice Site Conservation of Eukaryotic U1
    www.nature.com/scientificreports OPEN Phylogenetic comparison and splice site conservation of eukaryotic U1 snRNP‑specifc U1‑70K gene family Tao Fan1,3,4,8, Yu‑Zhen Zhao1,8, Jing‑Fang Yang5,8, Qin‑Lai Liu6,8, Yuan Tian3,4, Das Debatosh4, Ying‑Gao Liu3, Jianhua Zhang7, Chen Chen2*, Mo‑Xian Chen1* & Shao‑Ming Zhou1* Eukaryotic cells can expand their coding ability by using their splicing machinery, spliceosome, to process precursor mRNA (pre‑mRNA) into mature messenger RNA. The mega‑macromolecular spliceosome contains multiple subcomplexes, referred to as small nuclear ribonucleoproteins (snRNPs). Among these, U1 snRNP and its central component, U1‑70K, are crucial for splice site recognition during early spliceosome assembly. The human U1‑70K has been linked to several types of human autoimmune and neurodegenerative diseases. However, its phylogenetic relationship has been seldom reported. To this end, we carried out a systemic analysis of 95 animal U1-70K genes and compare these proteins to their yeast and plant counterparts. Analysis of their gene and protein structures, expression patterns and splicing conservation suggest that animal U1‑70Ks are conserved in their molecular function, and may play essential role in cancers and juvenile development. In particular, animal U1-70Ks display unique characteristics of single copy number and a splicing isoform with truncated C‑terminal, suggesting the specifc role of these U1‑70Ks in animal kingdom. In summary, our results provide phylogenetic overview of U1‑70K gene family in vertebrates. In silico analyses conducted in this work will act as a reference for future functional studies of this crucial U1 splicing factor in animal kingdom.
    [Show full text]
  • RNA-Binding Proteins with Mixed Charge Domains Self-Assemble and Aggregate in Alzheimer's Disease*
    bioRxiv preprint doi: https://doi.org/10.1101/243014; this version posted January 4, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Mixed Charge RNA binding proteins aggregate in AD RNA-binding proteins with mixed charge domains self-assemble and aggregate in Alzheimer's Disease* Isaac Bishof1,4, Eric B. Dammer1,4, Duc M. Duong1,4, Marla Gearing3,4, James J. Lah2,4, Allan I. Levey2,4, and Nicholas T. Seyfried1,2,4# 1Department of Biochemistry, 2Department of Neurology, 3Department of Pathology and Laboratory Medicine, 4Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA, 30322 #Address correspondence to: Nicholas T. Seyfried, Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, Georgia 30322, USA. Tel. 404.712.9783, Email: [email protected] *Running title: Mixed Charge RNA binding proteins aggregate in AD Keywords: protein-protein interaction, protein aggregation, systems biology, Tau protein, neurodegeneration, mass spectrometry, proteomics, RNA-binding protein, intrinsically disordered protein, RNA processing ABSTRACT on the U1-70K LC domain(s) for their U1 small nuclear ribonucleoprotein 70 kDa interaction. This included structurally similar (U1-70K) and other RNA binding proteins RBPs, such as LUC7L3 and RBM25, which (RBPs) are mislocalized to cytoplasmic require their respective mixed charge domains neurofibrillary Tau aggregates in Alzheimer’s for reciprocal interactions with U1-70K and disease (AD), yet understanding of the for participation in nuclear RNA granules.
    [Show full text]
  • Targeting the Deregulated Spliceosome Core Machinery in Cancer Cells Triggers Mtor Blockade and Autophagy
    Published OnlineFirst January 28, 2013; DOI: 10.1158/0008-5472.CAN-12-2501 Cancer Therapeutics, Targets, and Chemical Biology Research Targeting the Deregulated Spliceosome Core Machinery in Cancer Cells Triggers mTOR Blockade and Autophagy Virginie Quidville1,2,3, Samar Alsafadi1,2,3, Aïcha Goubar1,2,3,Fred eric Commo1,2,3,Veronique Scott1,2,3, Catherine Pioche-Durieu2,3, Isabelle Girault1,2,3, Sonia Baconnais2,3, Eric Le Cam2,3, Vladimir Lazar2,3, Suzette Delaloge1,2, Mahasti Saghatchian1,2, Patricia Pautier2, Philippe Morice2,3, Philippe Dessen2,3, Stephan Vagner1,2,3, and Fabrice Andre1,2,3 Abstract The spliceosome is a large ribonucleoprotein complex that guides pre-mRNA splicing in eukaryotic cells. Here, we determine whether the spliceosome could constitute an attractive therapeutic target in cancer. Analysis of gene expression arrays from lung, breast, and ovarian cancers datasets revealed that several genes encoding components of the core spliceosome composed of a heteroheptameric Sm complex were overexpressed in malignant disease as compared with benign lesions and could also define a subset of highly aggressive breast cancers. siRNA-mediated depletion of SmE (SNRPE) or SmD1 (SNRPD1) led to a marked reduction of cell viability in breast, lung, and melanoma cancer cell lines, whereas it had little effect on the survival of the nonmalignant MCF-10A breast epithelial cells. SNRPE or SNRPD1 depletion did not lead to apoptotic cell death but autophagy, another form of cell death. Indeed, induction of autophagy was revealed by cytoplasmic accumulation of autophagic vacuoles and by an increase in both LC3 (MAP1LC3A) protein conversion and the amount of acidic autophagic vacuoles.
    [Show full text]
  • Interaction of Tau with the RNA-Binding Protein TIA1 Regulates Tau Pathophysiology and Toxicity Tara Vanderweyde Boston University
    University of Kentucky UKnowledge Sanders-Brown Center on Aging Faculty Aging Publications 5-17-2016 Interaction of tau with the RNA-Binding Protein TIA1 Regulates tau Pathophysiology and Toxicity Tara Vanderweyde Boston University Daniel J. Apicco Boston University Katherine Youmans-Kidder Boston University Peter E. A. Ash Boston University Casey Cook Mayo Clinic See next page for additional authors Right click to open a feedback form in a new tab to let us know how this document benefits oy u. Follow this and additional works at: https://uknowledge.uky.edu/sbcoa_facpub Part of the Cell and Developmental Biology Commons, Family, Life Course, and Society Commons, Geriatrics Commons, and the Molecular and Cellular Neuroscience Commons Repository Citation Vanderweyde, Tara; Apicco, Daniel J.; Youmans-Kidder, Katherine; Ash, Peter E. A.; Cook, Casey; Lummertz da Rocha, Edroaldo; Jansen-West, Karen; Frame, Alissa A.; Citro, Allison; Leszyk, John D.; Ivanov, Pavel; Abisambra, Jose F.; Steffen, Martin; Li, Hu; Petrucelli, Leonard; and Wolozin, Benjamin, "Interaction of tau with the RNA-Binding Protein TIA1 Regulates tau Pathophysiology and Toxicity" (2016). Sanders-Brown Center on Aging Faculty Publications. 65. https://uknowledge.uky.edu/sbcoa_facpub/65 This Article is brought to you for free and open access by the Aging at UKnowledge. It has been accepted for inclusion in Sanders-Brown Center on Aging Faculty Publications by an authorized administrator of UKnowledge. For more information, please contact [email protected]. Authors Tara Vanderweyde, Daniel J. Apicco, Katherine Youmans-Kidder, Peter E. A. Ash, Casey Cook, Edroaldo Lummertz da Rocha, Karen Jansen-West, Alissa A. Frame, Allison Citro, John D.
    [Show full text]
  • Identification of RNA-Binding Protein SNRPA1 for Prognosis in Prostate Cancer
    www.aging-us.com AGING 2021, Vol. 13, No. 2 Research Paper Identification of RNA-binding protein SNRPA1 for prognosis in prostate cancer Penghui Yuan1, Le Ling1, Xintao Gao1, Taotao Sun1, Jianping Miao2, Xianglin Yuan3, Jihong Liu1, Zhihua Wang1, Bo Liu3 1Department of Urology Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China 2Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China 3Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China Correspondence to: Bo Liu, Zhihua Wang; email: [email protected], https://orcid.org/0000-0001-5118-1890; [email protected], https://orcid.org/0000-0002-5155-1457 Keywords: prostate cancer, prognosis, RNA-binding protein, SNRPA1 Received: June 3, 2020 Accepted: October 20, 2020 Published: January 15, 2021 Copyright: © 2021 Yuan 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 Prostate cancer is one of the deadliest cancers in men. RNA-binding proteins play a critical role in human cancers; however, whether they have a significant effect on the prognosis of prostate cancer has yet to be elucidated. In the present study, we performed a comprehensive analysis of RNA sequencing and clinical data from the Cancer Genome Atlas dataset and obtained differentially expressed RNA-binding proteins between prostate cancer and benign tissues. We constructed a protein-protein interaction network and Cox regression analyses were conducted to identify prognostic hub RNA-binding proteins.
    [Show full text]
  • Proteins Identified by Proteomics
    Supplementary table 1: Proteins identified by proteomics Protein Accession Gene Symbol Ratio Protein Name mitogen-activated protein kinase-activated protein kinase 2 gi|32481209 MAPKAPK2 0.04 isoform 2 gi114155133 DNAH9 0.05 dynein, axonemal, heavy chain 9 isoform 2 gi|4506145 PRSS1 0.09 protease, serine, 1 preproprotein gi|4507823 UGT2B11 0.10 UDP glucuronosyltransferase 2 family, polypeptide B11 gi|31377593 RANBP3L 0.10 RAN binding protein 3-like gi|45827809 MAP3K6 0.10 mitogen-activated protein kinase kinase kinase 6 gi|31795544 ORC1L 0.19 origin recognition complex, subunit 1 gi|4504191 MSH6 0.23 mutS homolog 6 gi|4503971 GDI1 0.26 GDP dissociation inhibitor 1 gi|4502197 TRIM23 0.27 ADP-ribosylation factor domain protein 1 isoform alpha gi|30410794 PSME3 0.28 proteasome activator subunit 3 isoform 1 gi|4506703 RPS24 0.29 ribosomal protein S24 isoform c gi|8923415 MARCH5 0.30 membrane-associated ring finger (C3HC4) 5 gi|39725634 LARP1 0.30 la related protein isoform 1 RBM14/RBM4 NP_002887 fusion 0.31 Transcriptional coactivator CoAZ gi|4506891 SET 0.33 SET translocation (myeloid leukemia-associated) gi|57863257 TCP1 0.33 T-complex protein 1 isoform a gi|25777612 PSMD3 0.35 proteasome 26S non-ATPase subunit 3 gi|22748937 XPO5 0.35 exportin 5 gi68303565 PSMA8 0.36 proteasome alpha 8 subunit isoform 3 gi|29789090 RCC2 0.37 regulator of chromosome condensation 2 gi113412226 LOC642098 0.38 similar to ribosomal protein L31 gi|4506189 PSMA7 0.38 proteasome alpha 7 subunit gi|38201619 EIF4G1 0.38 eukaryotic translation initiation factor 4 gamma,
    [Show full text]