Publications by Tuula Anneli Nyman

112 publications found

Publications 2019

  1. Mathiesen SB, Lunde M, Aronsen JM, Romaine A, Kaupang A, Martinsen M, de Souza GA, Nyman TA, Sjaastad I, Christensen G, Carlson CR (2019)
    The cardiac syndecan-4 interactome reveals a role for syndecan-4 in nuclear translocation of muscle LIM protein (MLP)
    J Biol Chem, 294 (22), 8717-8731
    DOI 10.1074/jbc.RA118.006423, PubMed 30967474
  2. Nassa G, Salvati A, Tarallo R, Gigantino V, Alexandrova E, Memoli D, Sellitto A, Rizzo F, Malanga D, Mirante T, Morelli E, Nees M, Åkerfelt M, Kangaspeska S, Nyman TA, Milanesi L, Giurato G, Weisz A (2019)
    Inhibition of histone methyltransferase DOT1L silences ERα gene and blocks proliferation of antiestrogen-resistant breast cancer cells
    Sci Adv, 5 (2), eaav5590
    DOI 10.1126/sciadv.aav5590, PubMed 30775443
  3. Richter U, Ng KY, Suomi F, Marttinen P, Turunen T, Jackson C, Suomalainen A, Vihinen H, Jokitalo E, Nyman TA, Isokallio MA, Stewart JB, Mancini C, Brusco A, Seneca S, Lombès A, Taylor RW, Battersby BJ (2019)
    Mitochondrial stress response triggered by defects in protein synthesis quality control
    Life Sci Alliance, 2 (1)
    DOI 10.26508/lsa.201800219, PubMed 30683687

Publications 2018

  1. Cypryk W, Nyman TA, Matikainen S (2018)
    From Inflammasome to Exosome-Does Extracellular Vesicle Secretion Constitute an Inflammasome-Dependent Immune Response?
    Front Immunol, 9, 2188
    DOI 10.3389/fimmu.2018.02188, PubMed 30319640
  2. Frohnmeyer E, Deptula P, Nyman TA, Laine PKS, Vihinen H, Paulin L, Auvinen P, Jokitalo E, Piironen V, Varmanen P, Savijoki K (2018)
    Secretome profiling of Propionibacterium freudenreichii reveals highly variable responses even among the closely related strains
    Microb Biotechnol, 11 (3), 510-526
    DOI 10.1111/1751-7915.13254, PubMed 29488359
  3. Giurato G, Nassa G, Salvati A, Alexandrova E, Rizzo F, Nyman TA, Weisz A, Tarallo R (2018)
    Quantitative mapping of RNA-mediated nuclear estrogen receptor β interactome in human breast cancer cells
    Sci Data, 5, 180031
    DOI 10.1038/sdata.2018.31, PubMed 29509190
  4. Nassa G, Giurato G, Cimmino G, Rizzo F, Ravo M, Salvati A, Nyman TA, Zhu Y, Vesterlund M, Lehtiö J, Golino P, Weisz A, Tarallo R (2018)
    Splicing of platelet resident pre-mRNAs upon activation by physiological stimuli results in functionally relevant proteome modifications
    Sci Rep, 8 (1), 498
    DOI 10.1038/s41598-017-18985-5, PubMed 29323256
  5. Sikorski K, Mehta A, Inngjerdingen M, Thakor F, Kling S, Kalina T, Nyman TA, Stensland ME, Zhou W, de Souza GA, Holden L, Stuchly J, Templin M, Lund-Johansen F (2018)
    A high-throughput pipeline for validation of antibodies
    Nat Methods, 15 (11), 909-912
    DOI 10.1038/s41592-018-0179-8, PubMed 30377371

Publications 2017

  1. Aittomäki S, Valanne S, Lehtinen T, Matikainen S, Nyman TA, Rämet M, Pesu M (2017)
    Proprotein convertase Furin1 expression in the Drosophila fat body is essential for a normal antimicrobial peptide response and bacterial host defense
    FASEB J, 31 (11), 4770-4782
    DOI 10.1096/fj.201700296R, PubMed 28705811
  2. Bulanova D, Ianevski A, Bugai A, Akimov Y, Kuivanen S, Paavilainen H, Kakkola L, Nandania J, Turunen L, Ohman T, Ala-Hongisto H, Pesonen HM, Kuisma MS, Honkimaa A, Walton EL, Oksenych V, Lorey MB, Guschin D, Shim J, Kim J, Than TT, Chang SY, Hukkanen V, Kulesskiy E, Marjomaki VS et al. (2017)
    Antiviral Properties of Chemical Inhibitors of Cellular Anti-Apoptotic Bcl-2 Proteins
    Viruses, 9 (10)
    DOI 10.3390/v9100271, PubMed 28946654
  3. Deptula P, Chamlagain B, Edelmann M, Sangsuwan P, Nyman TA, Savijoki K, Piironen V, Varmanen P (2017)
    Food-Like Growth Conditions Support Production of Active Vitamin B12 by Propionibacterium freudenreichii 2067 without DMBI, the Lower Ligand Base, or Cobalt Supplementation
    Front Microbiol, 8, 368
    DOI 10.3389/fmicb.2017.00368, PubMed 28337185
  4. Dumont V, Tolvanen TA, Kuusela S, Wang H, Nyman TA, Lindfors S, Tienari J, Nisen H, Suetsugu S, Plomann M, Kawachi H, Lehtonen S (2017)
    PACSIN2 accelerates nephrin trafficking and is up-regulated in diabetic kidney disease
    FASEB J, 31 (9), 3978-3990
    DOI 10.1096/fj.201601265R, PubMed 28550045
  5. Lorey MB, Rossi K, Eklund KK, Nyman TA, Matikainen S (2017)
    Global Characterization of Protein Secretion from Human Macrophages Following Non-canonical Caspase-4/5 Inflammasome Activation
    Mol Cell Proteomics, 16 (4 suppl 1), S187-S199
    DOI 10.1074/mcp.M116.064840, PubMed 28196878
  6. Nyman TA, Lorey MB, Cypryk W, Matikainen S (2017)
    Mass spectrometry-based proteomic exploration of the human immune system: focus on the inflammasome, global protein secretion, and T cells
    Expert Rev Proteomics, 14 (5), 395-407
    DOI 10.1080/14789450.2017.1319768, PubMed 28406322
  7. Nyman TA, Matikainen S (2017)
    Proteomics to study macrophage response to viral infection
    J Proteomics, 180, 99-107
    DOI 10.1016/j.jprot.2017.06.018, PubMed 28647517
  8. Tarallo R, Giurato G, Bruno G, Ravo M, Rizzo F, Salvati A, Ricciardi L, Marchese G, Cordella A, Rocco T, Gigantino V, Pierri B, Cimmino G, Milanesi L, Ambrosino C, Nyman TA, Nassa G, Weisz A (2017)
    The nuclear receptor ERβ engages AGO2 in regulation of gene transcription, RNA splicing and RISC loading
    Genome Biol, 18 (1), 189
    DOI 10.1186/s13059-017-1321-0, PubMed 29017520

Publications 2016

  1. Anastasina M, Le May N, Bugai A, Fu Y, Söderholm S, Gaelings L, Ohman T, Tynell J, Kyttänen S, Barboric M, Nyman TA, Matikainen S, Julkunen I, Butcher SJ, Egly JM, Kainov DE (2016)
    Influenza virus NS1 protein binds cellular DNA to block transcription of antiviral genes
    Biochim Biophys Acta, 1859 (11), 1440-1448
    DOI 10.1016/j.bbagrm.2016.09.005, PubMed 27664935
  2. Bæk KT, Bowman L, Millership C, Dupont Søgaard M, Kaever V, Siljamäki P, Savijoki K, Varmanen P, Nyman TA, Gründling A, Frees D (2016)
    The Cell Wall Polymer Lipoteichoic Acid Becomes Nonessential in Staphylococcus aureus Cells Lacking the ClpX Chaperone
    MBio, 7 (4)
    DOI 10.1128/mBio.01228-16, PubMed 27507828
  3. Christensen MH, Jensen SB, Miettinen JJ, Luecke S, Prabakaran T, Reinert LS, Mettenleiter T, Chen ZJ, Knipe DM, Sandri-Goldin RM, Enquist LW, Hartmann R, Mogensen TH, Rice SA, Nyman TA, Matikainen S, Paludan SR (2016)
    HSV-1 ICP27 targets the TBK1-activated STING signalsome to inhibit virus-induced type I IFN expression
    EMBO J, 35 (13), 1385-99
    DOI 10.15252/embj.201593458, PubMed 27234299
  4. Cypryk W, Lorey M, Puustinen A, Nyman TA, Matikainen S (2016)
    Proteomic and Bioinformatic Characterization of Extracellular Vesicles Released from Human Macrophages upon Influenza A Virus Infection
    J Proteome Res, 16 (1), 217-227
    DOI 10.1021/acs.jproteome.6b00596, PubMed 27723984
  5. Fu Y, Gaelings L, Söderholm S, Belanov S, Nandania J, Nyman TA, Matikainen S, Anders S, Velagapudi V, Kainov DE (2016)
    JNJ872 inhibits influenza A virus replication without altering cellular antiviral responses
    Antiviral Res, 133, 23-31
    DOI 10.1016/j.antiviral.2016.07.008, PubMed 27451344
  6. Gaelings L, Söderholm S, Bugai A, Fu Y, Nandania J, Schepens B, Lorey MB, Tynell J, Vande Ginste L, Le Goffic R, Miller MS, Kuisma M, Marjomäki V, De Brabander J, Matikainen S, Nyman TA, Bamford DH, Saelens X, Julkunen I, Paavilainen H, Hukkanen V, Velagapudi V, Kainov DE (2016)
    Regulation of kynurenine biosynthesis during influenza virus infection
    FEBS J, 284 (2), 222-236
    DOI 10.1111/febs.13966, PubMed 27860276
  7. Söderholm S, Fu Y, Gaelings L, Belanov S, Yetukuri L, Berlinkov M, Cheltsov AV, Anders S, Aittokallio T, Nyman TA, Matikainen S, Kainov DE (2016)
    Multi-Omics Studies towards Novel Modulators of Influenza A Virus-Host Interaction
    Viruses, 8 (10)
    DOI 10.3390/v8100269, PubMed 27690086
  8. Söderholm S, Kainov DE, Öhman T, Denisova OV, Schepens B, Kulesskiy E, Imanishi SY, Corthals G, Hintsanen P, Aittokallio T, Saelens X, Matikainen S, Nyman TA (2016)
    Phosphoproteomics to Characterize Host Response During Influenza A Virus Infection of Human Macrophages
    Mol Cell Proteomics, 15 (10), 3203-3219
    DOI 10.1074/mcp.M116.057984, PubMed 27486199
  9. Varghese FS, Thaa B, Amrun SN, Simarmata D, Rausalu K, Nyman TA, Merits A, McInerney GM, Ng LFP, Ahola T (2016)
    The Antiviral Alkaloid Berberine Reduces Chikungunya Virus-Induced Mitogen-Activated Protein Kinase Signaling
    J Virol, 90 (21), 9743-9757
    DOI 10.1128/JVI.01382-16, PubMed 27535052
  10. Välimäki E, Cypryk W, Virkanen J, Nurmi K, Turunen PM, Eklund KK, Åkerman KE, Nyman TA, Matikainen S (2016)
    Calpain Activity Is Essential for ATP-Driven Unconventional Vesicle-Mediated Protein Secretion and Inflammasome Activation in Human Macrophages
    J Immunol, 197 (8), 3315-3325
    DOI 10.4049/jimmunol.1501840, PubMed 27638862
  11. Wasik AA, Dumont V, Tienari J, Nyman TA, Fogarty CL, Forsblom C, Lehto M, Lehtonen E, Groop PH, Lehtonen S (2016)
    Septin 7 reduces nonmuscle myosin IIA activity in the SNAP23 complex and hinders GLUT4 storage vesicle docking and fusion
    Exp Cell Res, 350 (2), 336-348
    DOI 10.1016/j.yexcr.2016.12.010, PubMed 28011197

Publications 2015

  1. Anastasina M, Schepens B, Söderholm S, Nyman TA, Matikainen S, Saksela K, Saelens X, Kainov DE (2015)
    The C terminus of NS1 protein of influenza A/WSN/1933(H1N1) virus modulates antiviral responses in infected human macrophages and mice
    J Gen Virol, 96 (8), 2086-91
    DOI 10.1099/vir.0.000171, PubMed 25934792
  2. Cimmino G, Tarallo R, Nassa G, De Filippo MR, Giurato G, Ravo M, Rizzo F, Conte S, Pellegrino G, Cirillo P, Calabro P, Öhman T, Nyman TA, Weisz A, Golino P (2015)
    Activating stimuli induce platelet microRNA modulation and proteome reorganisation
    Thromb Haemost, 114 (1), 96-108
    DOI 10.1160/TH14-09-0726, PubMed 25903651
  3. Jokinen R, Lahtinen T, Marttinen P, Myöhänen M, Ruotsalainen P, Yeung N, Shvetsova A, Kastaniotis AJ, Hiltunen JK, Öhman T, Nyman TA, Weiler H, Battersby BJ (2015)
    Quantitative changes in Gimap3 and Gimap5 expression modify mitochondrial DNA segregation in mice
    Genetics, 200 (1), 221-35
    DOI 10.1534/genetics.115.175596, PubMed 25808953
  4. Savijoki K, Skogman M, Fallarero A, Nyman TA, Sukura A, Vuorela P, Varmanen P (2015)
    Penicillin G increases the synthesis of a suicidal marker (CidC) and virulence (HlgBC) proteins in Staphylococcus aureus biofilm cells
    Int J Med Microbiol, 306 (1), 69-74
    DOI 10.1016/j.ijmm.2015.11.006, PubMed 26725755
  5. Stellato C, Nassa G, Tarallo R, Giurato G, Ravo M, Rizzo F, Marchese G, Alexandrova E, Cordella A, Baumann M, Nyman TA, Weisz A, Ambrosino C (2015)
    Identification of cytoplasmic proteins interacting with unliganded estrogen receptor α and β in human breast cancer cells
    Proteomics, 15 (11), 1801-7
    DOI 10.1002/pmic.201400404, PubMed 25604459
  6. Söderholm S, Anastasina M, Islam MM, Tynell J, Poranen MM, Bamford DH, Stenman J, Julkunen I, Šaulienė I, De Brabander JK, Matikainen S, Nyman TA, Saelens X, Kainov D (2015)
    Immuno-modulating properties of saliphenylhalamide, SNS-032, obatoclax, and gemcitabine
    Antiviral Res, 126, 69-80
    DOI 10.1016/j.antiviral.2015.12.011, PubMed 26738783
  7. Yáñez-Mó M, Siljander PR, Andreu Z, Zavec AB, Borràs FE, Buzas EI, Buzas K, Casal E, Cappello F, Carvalho J, Colás E, Cordeiro-da Silva A, Fais S, Falcon-Perez JM, Ghobrial IM, Giebel B, Gimona M, Graner M, Gursel I, Gursel M, Heegaard NH, Hendrix A, Kierulf P, Kokubun K, Kosanovic M et al. (2015)
    Biological properties of extracellular vesicles and their physiological functions
    J Extracell Vesicles, 4, 27066
    DOI 10.3402/jev.v4.27066, PubMed 25979354
  8. Öhman T, Söderholm S, Paidikondala M, Lietzén N, Matikainen S, Nyman TA (2015)
    Phosphoproteome characterization reveals that Sendai virus infection activates mTOR signaling in human epithelial cells
    Proteomics, 15 (12), 2087-97
    DOI 10.1002/pmic.201400586, PubMed 25764225

Publications 2014

  1. Cypryk W, Ohman T, Eskelinen EL, Matikainen S, Nyman TA (2014)
    Quantitative proteomics of extracellular vesicles released from human monocyte-derived macrophages upon β-glucan stimulation
    J Proteome Res, 13 (5), 2468-77
    DOI 10.1021/pr4012552, PubMed 24670152
  2. Denisova OV, Söderholm S, Virtanen S, Von Schantz C, Bychkov D, Vashchinkina E, Desloovere J, Tynell J, Ikonen N, Theisen LL, Nyman TA, Matikainen S, Kallioniemi O, Julkunen I, Muller CP, Saelens X, Verkhusha VV, Kainov DE (2014)
    Akt inhibitor MK2206 prevents influenza pH1N1 virus infection in vitro
    Antimicrob Agents Chemother, 58 (7), 3689-96
    DOI 10.1128/AAC.02798-13, PubMed 24752266
  3. Elo LL, Karjalainen R, Ohman T, Hintsanen P, Nyman TA, Heckman CA, Aittokallio T (2014)
    Statistical detection of quantitative protein biomarkers provides insights into signaling networks deregulated in acute myeloid leukemia
    Proteomics, 14 (21-22), 2443-53
    DOI 10.1002/pmic.201300460, PubMed 25211154
  4. Espino E, Koskenniemi K, Mato-Rodriguez L, Nyman TA, Reunanen J, Koponen J, Öhman T, Siljamäki P, Alatossava T, Varmanen P, Savijoki K (2014)
    Uncovering surface-exposed antigens of Lactobacillus rhamnosus by cell shaving proteomics and two-dimensional immunoblotting
    J Proteome Res, 14 (2), 1010-24
    DOI 10.1021/pr501041a, PubMed 25531588
  5. Marttila M, Lehtokari VL, Marston S, Nyman TA, Barnerias C, Beggs AH, Bertini E, Ceyhan-Birsoy O, Cintas P, Gerard M, Gilbert-Dussardier B, Hogue JS, Longman C, Eymard B, Frydman M, Kang PB, Klinge L, Kolski H, Lochmüller H, Magy L, Manel V, Mayer M, Mercuri E, North KN, Peudenier-Robert S et al. (2014)
    Mutation update and genotype-phenotype correlations of novel and previously described mutations in TPM2 and TPM3 causing congenital myopathies
    Hum Mutat, 35 (7), 779-90
    DOI 10.1002/humu.22554, PubMed 24692096
  6. Nassa G, Tarallo R, Giurato G, De Filippo MR, Ravo M, Rizzo F, Stellato C, Ambrosino C, Baumann M, Lietzèn N, Nyman TA, Weisz A (2014)
    Post-transcriptional regulation of human breast cancer cell proteome by unliganded estrogen receptor β via microRNAs
    Mol Cell Proteomics, 13 (4), 1076-90
    DOI 10.1074/mcp.M113.030403, PubMed 24525454
  7. Salomäki T, Karonen T, Siljamäki P, Savijoki K, Nyman TA, Varmanen P, Iivanainen A (2014)
    A Streptococcus uberis transposon mutant screen reveals a negative role for LiaR homologue in biofilm formation
    J Appl Microbiol, 118 (1), 1-10
    DOI 10.1111/jam.12664, PubMed 25308550
  8. Savijoki K, Iivanainen A, Siljamäki P, Laine PK, Paulin L, Karonen T, Pyörälä S, Kankainen M, Nyman TA, Salomäki T, Koskinen P, Holm L, Simojoki H, Taponen S, Sukura A, Kalkkinen N, Auvinen P, Varmanen P (2014)
    Genomics and Proteomics Provide New Insight into the Commensal and Pathogenic Lifestyles of Bovine- and Human-Associated Staphylococcus epidermidis Strains
    J Proteome Res, 13 (8), 3748-3762
    DOI 10.1021/pr500322d, PubMed 25014494
  9. Siljamäki P, Varmanen P, Kankainen M, Pyörälä S, Karonen T, Iivanainen A, Auvinen P, Paulin L, Laine PK, Taponen S, Simojoki H, Sukura A, Nyman TA, Savijoki K (2014)
    Comparative proteome profiling of bovine and human Staphylococcus epidermidis strains for screening specifically expressed virulence and adaptation proteins
    Proteomics, 14 (16), 1890-4
    DOI 10.1002/pmic.201300275, PubMed 24909406
  10. Siljamäki P, Varmanen P, Kankainen M, Sukura A, Savijoki K, Nyman TA (2014)
    Comparative exoprotein profiling of different Staphylococcus epidermidis strains reveals potential link between nonclassical protein export and virulence
    J Proteome Res, 13 (7), 3249-61
    DOI 10.1021/pr500075j, PubMed 24840314
  11. Söderholm S, Hintsanen P, Öhman T, Aittokallio T, Nyman TA (2014)
    PhosFox: a bioinformatics tool for peptide-level processing of LC-MS/MS-based phosphoproteomic data
    Proteome Sci, 12, 36
    DOI 10.1186/1477-5956-12-36, PubMed 25028575
  12. Wasik AA, Koskelainen S, Hyvönen ME, Musante L, Lehtonen E, Koskenniemi K, Tienari J, Vaheri A, Kerjaschki D, Szalay C, Révész C, Varmanen P, Nyman TA, Hamar P, Holthöfer H, Lehtonen S (2014)
    Ezrin is down-regulated in diabetic kidney glomeruli and regulates actin reorganization and glucose uptake via GLUT1 in cultured podocytes
    Am J Pathol, 184 (6), 1727-39
    DOI 10.1016/j.ajpath.2014.03.002, PubMed 24726496
  13. Weber-Boyvat M, Kentala H, Lilja J, Vihervaara T, Hanninen R, Zhou Y, Peränen J, Nyman TA, Ivaska J, Olkkonen VM (2014)
    OSBP-related protein 3 (ORP3) coupling with VAMP-associated protein A regulates R-Ras activity
    Exp Cell Res, 331 (2), 278-91
    DOI 10.1016/j.yexcr.2014.10.019, PubMed 25447204
  14. Öhman T, Söderholm S, Hintsanen P, Välimäki E, Lietzén N, MacKintosh C, Aittokallio T, Matikainen S, Nyman TA (2014)
    Phosphoproteomics combined with quantitative 14-3-3-affinity capture identifies SIRT1 and RAI as novel regulators of cytosolic double-stranded RNA recognition pathway
    Mol Cell Proteomics, 13 (10), 2604-17
    DOI 10.1074/mcp.M114.038968, PubMed 24997996
  15. Öhman T, Teirilä L, Lahesmaa-Korpinen AM, Cypryk W, Veckman V, Saijo S, Wolff H, Hautaniemi S, Nyman TA, Matikainen S (2014)
    Dectin-1 pathway activates robust autophagy-dependent unconventional protein secretion in human macrophages
    J Immunol, 192 (12), 5952-62
    DOI 10.4049/jimmunol.1303213, PubMed 24808366
  16. Aatonen MT, Ohman T, Nyman TA, Laitinen S, Grönholm M, Siljander PR (2014)
    Isolation and characterization of platelet-derived extracellular vesicles
    J Extracell Vesicles, 3
    DOI 10.3402/jev.v3.24692, PubMed 25147646

Publications 2013

  1. Kankkunen P, Välimäki E, Rintahaka J, Palomäki J, Nyman T, Alenius H, Wolff H, Matikainen S (2013)
    Trichothecene mycotoxins activate NLRP3 inflammasome through a P2X7 receptor and Src tyrosine kinase dependent pathway
    Hum Immunol, 75 (2), 134-40
    DOI 10.1016/j.humimm.2013.11.010, PubMed 24269698
  2. Makarov A, Ylivinkka I, Nyman TA, Hyytiäinen M, Keski-Oja J (2013)
    Ephrin-As, Eph receptors and integrin α3 interact and colocalise at membrane protrusions of U251MG glioblastoma cells
    Cell Biol Int, 37 (10), 1080-8
    DOI 10.1002/cbin.10134, PubMed 23686814
  3. Richter U, Lahtinen T, Marttinen P, Myöhänen M, Greco D, Cannino G, Jacobs HT, Lietzén N, Nyman TA, Battersby BJ (2013)
    A mitochondrial ribosomal and RNA decay pathway blocks cell proliferation
    Curr Biol, 23 (6), 535-41
    DOI 10.1016/j.cub.2013.02.019, PubMed 23453957
  4. Turunen JJ, Verma B, Nyman TA, Frilander MJ (2013)
    HnRNPH1/H2, U1 snRNP, and U11 snRNP cooperate to regulate the stability of the U11-48K pre-mRNA
    RNA, 19 (3), 380-9
    DOI 10.1261/rna.036715.112, PubMed 23335637
  5. Välimäki E, Miettinen JJ, Lietzén N, Matikainen S, Nyman TA (2013)
    Monosodium urate activates Src/Pyk2/PI3 kinase and cathepsin dependent unconventional protein secretion from human primary macrophages
    Mol Cell Proteomics, 12 (3), 749-63
    DOI 10.1074/mcp.M112.024661, PubMed 23292187
  6. Ylivinkka I, Hu Y, Chen P, Rantanen V, Hautaniemi S, Nyman TA, Keski-Oja J, Hyytiäinen M (2013)
    Netrin-1-induced activation of Notch signaling mediates glioblastoma cell invasion
    J Cell Sci, 126 (Pt 11), 2459-69
    DOI 10.1242/jcs.120022, PubMed 23549787

Publications 2012

  1. Bien J, Näreaho A, Varmanen P, Gozdzik K, Moskwa B, Cabaj W, Nyman TA, Savijoki K (2012)
    Comparative analysis of excretory-secretory antigens of Trichinella spiralis and Trichinella britovi muscle larvae by two-dimensional difference gel electrophoresis and immunoblotting
    Proteome Sci, 10 (1), 10
    DOI 10.1186/1477-5956-10-10, PubMed 22325190
  2. Cirillo F, Nassa G, Tarallo R, Stellato C, De Filippo MR, Ambrosino C, Baumann M, Nyman TA, Weisz A (2012)
    Molecular mechanisms of selective estrogen receptor modulator activity in human breast cancer cells: identification of novel nuclear cofactors of antiestrogen-ERα complexes by interaction proteomics
    J Proteome Res, 12 (1), 421-31
    DOI 10.1021/pr300753u, PubMed 23170835
  3. Hu Y, Ylivinkka I, Chen P, Li L, Hautaniemi S, Nyman TA, Keski-Oja J, Hyytiäinen M (2012)
    Netrin-4 promotes glioblastoma cell proliferation through integrin β4 signaling
    Neoplasia, 14 (3), 219-27
    DOI 10.1593/neo.111396, PubMed 22496621
  4. Miettinen JJ, Matikainen S, Nyman TA (2012)
    Global secretome characterization of herpes simplex virus 1-infected human primary macrophages
    J Virol, 86 (23), 12770-8
    DOI 10.1128/JVI.01545-12, PubMed 22973042
  5. Rostila A, Puustinen A, Toljamo T, Vuopala K, Lindström I, Nyman TA, Oksa P, Vehmas T, Anttila SL (2012)
    Peroxiredoxins and tropomyosins as plasma biomarkers for lung cancer and asbestos exposure
    Lung Cancer, 77 (2), 450-9
    DOI 10.1016/j.lungcan.2012.03.024, PubMed 22537621
  6. Tammimies K, Vitezic M, Matsson H, Le Guyader S, Bürglin TR, Ohman T, Strömblad S, Daub CO, Nyman TA, Kere J, Tapia-Páez I (2012)
    Molecular networks of DYX1C1 gene show connection to neuronal migration genes and cytoskeletal proteins
    Biol Psychiatry, 73 (6), 583-90
    DOI 10.1016/j.biopsych.2012.08.012, PubMed 23036959

Publications 2011

  1. Frees D, Andersen JH, Hemmingsen L, Koskenniemi K, Bæk KT, Muhammed MK, Gudeta DD, Nyman TA, Sukura A, Varmanen P, Savijoki K (2011)
    New insights into Staphylococcus aureus stress tolerance and virulence regulation from an analysis of the role of the ClpP protease in the strains Newman, COL, and SA564
    J Proteome Res, 11 (1), 95-108
    DOI 10.1021/pr200956s, PubMed 22112206
  2. Koponen J, Laakso K, Koskenniemi K, Kankainen M, Savijoki K, Nyman TA, de Vos WM, Tynkkynen S, Kalkkinen N, Varmanen P (2011)
    Effect of acid stress on protein expression and phosphorylation in Lactobacillus rhamnosus GG
    J Proteomics, 75 (4), 1357-74
    DOI 10.1016/j.jprot.2011.11.009, PubMed 22119544
  3. Laulajainen M, Muranen T, Nyman TA, Carpén O, Grönholm M (2011)
    Multistep phosphorylation by oncogenic kinases enhances the degradation of the NF2 tumor suppressor merlin
    Neoplasia, 13 (7), 643-52
    DOI 10.1593/neo.11356, PubMed 21750658
  4. Lietzén N, Ohman T, Rintahaka J, Julkunen I, Aittokallio T, Matikainen S, Nyman TA (2011)
    Quantitative subcellular proteome and secretome profiling of influenza A virus-infected human primary macrophages
    PLoS Pathog, 7 (5), e1001340
    DOI 10.1371/journal.ppat.1001340, PubMed 21589892
  5. Laakso K, Koskenniemi K, Koponen J, Kankainen M, Surakka A, Salusjärvi T, Auvinen P, Savijoki K, Nyman TA, Kalkkinen N, Tynkkynen S, Varmanen P (2011)
    Growth phase-associated changes in the proteome and transcriptome of Lactobacillus rhamnosus GG in industrial-type whey medium
    Microb Biotechnol, 4 (6), 746-66
    DOI 10.1111/j.1751-7915.2011.00275.x, PubMed 21883975
  6. Rintahaka J, Lietzén N, Öhman T, Nyman TA, Matikainen S (2011)
    Recognition of cytoplasmic RNA results in cathepsin-dependent inflammasome activation and apoptosis in human macrophages
    J Immunol, 186 (5), 3085-92
    DOI 10.4049/jimmunol.1002051, PubMed 21257972
  7. Savijoki K, Lietzén N, Kankainen M, Alatossava T, Koskenniemi K, Varmanen P, Nyman TA (2011)
    Comparative proteome cataloging of Lactobacillus rhamnosus strains GG and Lc705
    J Proteome Res, 10 (8), 3460-73
    DOI 10.1021/pr2000896, PubMed 21615180

Publications 2010

  1. Ambrosino C, Tarallo R, Bamundo A, Cuomo D, Franci G, Nassa G, Paris O, Ravo M, Giovane A, Zambrano N, Lepikhova T, Jänne OA, Baumann M, Nyman TA, Cicatiello L, Weisz A (2010)
    Identification of a hormone-regulated dynamic nuclear actin network associated with estrogen receptor alpha in human breast cancer cell nuclei
    Mol Cell Proteomics, 9 (6), 1352-67
    DOI 10.1074/mcp.M900519-MCP200, PubMed 20308691
  2. Koskenniemi K, Laakso K, Koponen J, Kankainen M, Greco D, Auvinen P, Savijoki K, Nyman TA, Surakka A, Salusjärvi T, de Vos WM, Tynkkynen S, Kalkkinen N, Varmanen P (2010)
    Proteomics and transcriptomics characterization of bile stress response in probiotic Lactobacillus rhamnosus GG
    Mol Cell Proteomics, 10 (2), M110.002741
    DOI 10.1074/mcp.M110.002741, PubMed 21078892
  3. Lehtimäki S, Tillander S, Puustinen A, Matikainen S, Nyman T, Fyhrquist N, Savinko T, Majuri ML, Wolff H, Alenius H, Lauerma A (2010)
    Absence of CCR4 exacerbates skin inflammation in an oxazolone-induced contact hypersensitivity model
    J Invest Dermatol, 130 (12), 2743-51
    DOI 10.1038/jid.2010.208, PubMed 20631725
  4. Lehto M, Airaksinen L, Puustinen A, Tillander S, Hannula S, Nyman T, Toskala E, Alenius H, Lauerma A (2010)
    Thaumatin-like protein and baker's respiratory allergy
    Ann Allergy Asthma Immunol, 104 (2), 139-46
    DOI 10.1016/j.anai.2009.11.062, PubMed 20306817
  5. Lietzén N, Natri L, Nevalainen OS, Salmi J, Nyman TA (2010)
    Compid: a new software tool to integrate and compare MS/MS based protein identification results from Mascot and Paragon
    J Proteome Res, 9 (12), 6795-800
    DOI 10.1021/pr100824w, PubMed 20973569
  6. Moulder R, Lönnberg T, Elo LL, Filén JJ, Rainio E, Corthals G, Oresic M, Nyman TA, Aittokallio T, Lahesmaa R (2010)
    Quantitative proteomics analysis of the nuclear fraction of human CD4+ cells in the early phases of IL-4-induced Th2 differentiation
    Mol Cell Proteomics, 9 (9), 1937-53
    DOI 10.1074/mcp.M900483-MCP200, PubMed 20467038
  7. Nassa G, Tarallo R, Ambrosino C, Bamundo A, Ferraro L, Paris O, Ravo M, Guzzi PH, Cannataro M, Baumann M, Nyman TA, Nola E, Weisz A (2010)
    A large set of estrogen receptor β-interacting proteins identified by tandem affinity purification in hormone-responsive human breast cancer cell nuclei
    Proteomics, 11 (1), 159-65
    DOI 10.1002/pmic.201000344, PubMed 21182203
  8. Nassa G, Tarallo R, Guzzi PH, Ferraro L, Cirillo F, Ravo M, Nola E, Baumann M, Nyman TA, Cannataro M, Ambrosino C, Weisz A (2010)
    Comparative analysis of nuclear estrogen receptor alpha and beta interactomes in breast cancer cells
    Mol Biosyst, 7 (3), 667-76
    DOI 10.1039/c0mb00145g, PubMed 21173974
  9. Ohman T, Lietzén N, Välimäki E, Melchjorsen J, Matikainen S, Nyman TA (2010)
    Cytosolic RNA recognition pathway activates 14-3-3 protein mediated signaling and caspase-dependent disruption of cytokeratin network in human keratinocytes
    J Proteome Res, 9 (3), 1549-64
    DOI 10.1021/pr901040u, PubMed 20070120
  10. Piippo M, Lietzén N, Nevalainen OS, Salmi J, Nyman TA (2010)
    Pripper: prediction of caspase cleavage sites from whole proteomes
    BMC Bioinformatics, 11, 320
    DOI 10.1186/1471-2105-11-320, PubMed 20546630
  11. Sane P, Tuomisto F, Wiedmer SK, Nyman T, Vattulainen I, Holopainen JM (2010)
    Temperature-induced structural transition in-situ in porcine lens--changes observed in void size distribution
    Biochim Biophys Acta, 1798 (5), 958-65
    DOI 10.1016/j.bbamem.2010.01.011, PubMed 20122897
  12. Tarallo R, Bamundo A, Nassa G, Nola E, Paris O, Ambrosino C, Facchiano A, Baumann M, Nyman TA, Weisz A (2010)
    Identification of proteins associated with ligand-activated estrogen receptor α in human breast cancer cell nuclei by tandem affinity purification and nano LC-MS/MS
    Proteomics, 11 (1), 172-9
    DOI 10.1002/pmic.201000217, PubMed 21182205
  13. Weber-Boyvat M, Aro N, Chernov KG, Nyman T, Jäntti J (2010)
    Sec1p and Mso1p C-terminal tails cooperate with the SNAREs and Sec4p in polarized exocytosis
    Mol Biol Cell, 22 (2), 230-44
    DOI 10.1091/mbc.E10-07-0592, PubMed 21119007

Publications 2009

  1. Korolainen MA, Nyman TA, Aittokallio T, Pirttilä T (2009)
    An update on clinical proteomics in Alzheimer's research
    J Neurochem, 112 (6), 1386-414
    DOI 10.1111/j.1471-4159.2009.06558.x, PubMed 20050976
  2. Ohman T, Rintahaka J, Kalkkinen N, Matikainen S, Nyman TA (2009)
    Actin and RIG-I/MAVS signaling components translocate to mitochondria upon influenza A virus infection of human primary macrophages
    J Immunol, 182 (9), 5682-92
    DOI 10.4049/jimmunol.0803093, PubMed 19380815
  3. Salmi J, Nyman TA, Nevalainen OS, Aittokallio T (2009)
    Filtering strategies for improving protein identification in high-throughput MS/MS studies
    Proteomics, 9 (4), 848-60
    DOI 10.1002/pmic.200800517, PubMed 19160393
  4. Tuomela S, Rautajoki KJ, Moulder R, Nyman TA, Lahesmaa R (2009)
    Identification of novel Stat6 regulated proteins in IL-4-treated mouse lymphocytes
    Proteomics, 9 (4), 1087-98
    DOI 10.1002/pmic.200800161, PubMed 19180534

Publications 2008

  1. Filén JJ, Filén S, Moulder R, Tuomela S, Ahlfors H, West A, Kouvonen P, Kantola S, Björkman M, Katajamaa M, Rasool O, Nyman TA, Lahesmaa R (2008)
    Quantitative proteomics reveals GIMAP family proteins 1 and 4 to be differentially regulated during human T helper cell differentiation
    Mol Cell Proteomics, 8 (1), 32-44
    DOI 10.1074/mcp.M800139-MCP200, PubMed 18701445
  2. Korolainen MA, Corthals GL, Kouvonen P, Kurkinen KM, Nyman TA (2008)
    3rd Annual FinnProt Meeting: from cells to systems
    Expert Rev Proteomics, 5 (3), 389-91
    DOI 10.1586/14789450.5.3.389, PubMed 18532906

Publications 2007

  1. Korolainen MA, Nyman TA, Nyyssönen P, Hartikainen ES, Pirttilä T (2007)
    Multiplexed proteomic analysis of oxidation and concentrations of cerebrospinal fluid proteins in Alzheimer disease
    Clin Chem, 53 (4), 657-65
    DOI 10.1373/clinchem.2006.078014, PubMed 17289803
  2. Rakkola R, Matikainen S, Nyman TA (2007)
    Proteome analysis of human macrophages reveals the upregulation of manganese-containing superoxide dismutase after toll-like receptor activation
    Proteomics, 7 (3), 378-84
    DOI 10.1002/pmic.200600582, PubMed 17211829

Publications 2006

  1. Rautajoki KJ, Marttila EM, Nyman TA, Lahesmaa R (2006)
    Interleukin-4 inhibits caspase-3 by regulating several proteins in the Fas pathway during initial stages of human T helper 2 cell differentiation
    Mol Cell Proteomics, 6 (2), 238-51
    DOI 10.1074/mcp.M600290-MCP200, PubMed 17114647
  2. Takatalo MS, Kouvonen P, Corthals G, Nyman TA, Rönnholm RH (2006)
    Identification of new Golgi complex specific proteins by direct organelle proteomic analysis
    Proteomics, 6 (12), 3502-8
    DOI 10.1002/pmic.200500516, PubMed 16691549

Publications 2005

  1. Aittokallio T, Salmi J, Nyman TA, Nevalainen OS (2005)
    Geometrical distortions in two-dimensional gels: applicable correction methods
    J Chromatogr B Analyt Technol Biomed Life Sci, 815 (1-2), 25-37
    DOI 10.1016/j.jchromb.2004.07.037, PubMed 15652796
  2. Björkblom B, Ostman N, Hongisto V, Komarovski V, Filén JJ, Nyman TA, Kallunki T, Courtney MJ, Coffey ET (2005)
    Constitutively active cytoplasmic c-Jun N-terminal kinase 1 is a dominant regulator of dendritic architecture: role of microtubule-associated protein 2 as an effector
    J Neurosci, 25 (27), 6350-61
    DOI 10.1523/JNEUROSCI.1517-05.2005, PubMed 16000625
  3. Filén JJ, Nyman TA, Korhonen J, Goodlett DR, Lahesmaa R (2005)
    Characterization of microsomal fraction proteome in human lymphoblasts reveals the down-regulation of galectin-1 by interleukin-12
    Proteomics, 5 (18), 4719-32
    DOI 10.1002/pmic.200402016, PubMed 16247730
  4. Korolainen MA, Auriola S, Nyman TA, Alafuzoff I, Pirttilä T (2005)
    Proteomic analysis of glial fibrillary acidic protein in Alzheimer's disease and aging brain
    Neurobiol Dis, 20 (3), 858-70
    DOI 10.1016/j.nbd.2005.05.021, PubMed 15979880
  5. Korolainen MA, Goldsteins G, Nyman TA, Alafuzoff I, Koistinaho J, Pirttilä T (2005)
    Oxidative modification of proteins in the frontal cortex of Alzheimer's disease brain
    Neurobiol Aging, 27 (1), 42-53
    DOI 10.1016/j.neurobiolaging.2004.11.010, PubMed 16298240
  6. Moulder R, Filén JJ, Salmi J, Katajamaa M, Nevalainen OS, Oresic M, Aittokallio T, Lahesmaa R, Nyman TA (2005)
    A comparative evaluation of software for the analysis of liquid chromatography-tandem mass spectrometry data from isotope coded affinity tag experiments
    Proteomics, 5 (11), 2748-60
    DOI 10.1002/pmic.200401187, PubMed 15952233
  7. Rakkola R, Matikainen S, Nyman TA (2005)
    Proteome characterization of human NK-92 cells identifies novel IFN-alpha and IL-15 target genes
    J Proteome Res, 4 (1), 75-82
    DOI 10.1021/pr049857b, PubMed 15707360
  8. Rosengren AT, Nyman TA, Lahesmaa R (2005)
    Proteome profiling of interleukin-12 treated human T helper cells
    Proteomics, 5 (12), 3137-41
    DOI 10.1002/pmic.200401151, PubMed 16038020
  9. Rosengren AT, Nyman TA, Syyrakki S, Matikainen S, Lahesmaa R (2005)
    Proteomic and transcriptomic characterization of interferon-alpha-induced human primary T helper cells
    Proteomics, 5 (2), 371-9
    DOI 10.1002/pmic.200400967, PubMed 15700245
  10. Salmi J, Moulder R, Filén JJ, Nevalainen OS, Nyman TA, Lahesmaa R, Aittokallio T (2005)
    Quality classification of tandem mass spectrometry data
    Bioinformatics, 22 (4), 400-6
    DOI 10.1093/bioinformatics/bti829, PubMed 16352652

Publications 2004

  1. Rautajoki K, Nyman TA, Lahesmaa R (2004)
    Proteome characterization of human T helper 1 and 2 cells
    Proteomics, 4 (1), 84-92
    DOI 10.1002/pmic.200300510, PubMed 14730674

Publications 2003

  1. Rosengren AT, Salmi JM, Aittokallio T, Westerholm J, Lahesmaa R, Nyman TA, Nevalainen OS (2003)
    Comparison of PDQuest and Progenesis software packages in the analysis of two-dimensional electrophoresis gels
    Proteomics, 3 (10), 1936-46
    DOI 10.1002/pmic.200300544, PubMed 14625856

Publications 2002

  1. Salmi J, Aittokallio T, Westerholm J, Griese M, Rosengren A, Nyman TA, Lahesmaa R, Nevalainen O (2002)
    Hierarchical grid transformation for image warping in the analysis of two-dimensional electrophoresis gels
    Proteomics, 2 (11), 1504-15
    DOI 10.1002/1615-9861(200211)2:11<1504::AID-PROT1504>3.0.CO;2-B, PubMed 12442250

Publications 2001

  1. Nyman TA (2001)
    The role of mass spectrometry in proteome studies
    Biomol Eng, 18 (5), 221-7
    PubMed 11911089
  2. Nyman TA, Rosengren A, Syyrakki S, Pellinen TP, Rautajoki K, Lahesmaa R (2001)
    A proteome database of human primary T helper cells
    Electrophoresis, 22 (20), 4375-82
    DOI 10.1002/1522-2683(200112)22:20<4375::AID-ELPS4375>3.0.CO;2-P, PubMed 11824605
  3. Tarkka MT, Nyman TA, Kalkkinen N, Raudaskoski M (2001)
    Scots pine expresses short-root-specific peroxidases during development
    Eur J Biochem, 268 (1), 86-92
    PubMed 11121106

Publications 2000

  1. Nyman TA, Matikainen S, Sareneva T, Julkunen I, Kalkkinen N (2000)
    Proteome analysis reveals ubiquitin-conjugating enzymes to be a new family of interferon-alpha-regulated genes
    Eur J Biochem, 267 (13), 4011-9
    PubMed 10866800

Publications 1998

  1. Nyman TA, Kalkkinen N, Tölö H, Helin J (1998)
    Structural characterisation of N-linked and O-linked oligosaccharides derived from interferon-alpha2b and interferon-alpha14c produced by Sendai-virus-induced human peripheral blood leukocytes
    Eur J Biochem, 253 (2), 485-93
    PubMed 9654101
  2. Nyman TA, Tölö H, Parkkinen J, Kalkkinen N (1998)
    Identification of nine interferon-alpha subtypes produced by Sendai virus-induced human peripheral blood leucocytes
    Biochem J, 329 ( Pt 2), 295-302
    DOI 10.1042/bj3290295, PubMed 9425112

 
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