Publications

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Publications in Tuhat

Last three years:

Toivonen S, Malinen MM, Küblbeck J, Petsalo A, Urtti A, Honkakoski P, Otonkoski T. Regulation of Human Pluripotent Stem Cell-Derived Hepatic Cell Phenotype by Three-Dimensional Hydrogel Models. Tissue Eng Part A. 2016 Jul;22(13-14):971-84.

Markmann JF, Bartlett ST, Johnson P, Korsgren O, Hering BJ, Scharp D, Kay TW, Bromberg J, Odorico JS, Weir GC, Bridges N, Kandaswamy R, Stock P, Friend P, Gotoh M, Cooper DK, Park CG, OʼConnell PJ, Stabler C, Matsumoto S, Ludwig B, Choudhary P, Khovatchev B, Rickels MR, Sykes M, Wood K, Kraemer K, Hwa A, Stanley E, Ricordi C, Zimmerman M, Greenstein J, Montanya E, Otonkoski T. Executive Summary of IPITA-TTS Opinion Leaders Report on the Future of β-Cell Replacement. Transplantation. 2016 Jul;100(7):e25-31.

Otonkoski T. New tools for experimental diabetes research: Cellular reprogramming and genome editing. Ups J Med Sci. 2016 May;121(2):146-50.

Bartlett ST, Markmann JF, Johnson P, Korsgren O, Hering BJ, Scharp D, Kay TW, Bromberg J, Odorico JS, Weir GC, Bridges N, Kandaswamy R, Stock P, Friend P,
Gotoh M, Cooper DK, Park CG, OʼConnell P, Stabler C, Matsumoto S, Ludwig B, Choudhary P, Kovatchev B, Rickels MR, Sykes M, Wood K, Kraemer K, Hwa A, Stanley
E, Ricordi C, Zimmerman M, Greenstein J, Montanya E, Otonkoski T. Report from IPITA-TTS Opinion Leaders Meeting on the Future of β-Cell Replacement. Transplantation. 2016 Feb;100 Suppl 2:S1-S44. doi: 10.1097/TP.0000000000001055. PubMed PMID: 26840096.

Kyttälä A, Moraghebi R, Valensisi C, Kettunen J, Andrus C, Pasumarthy KK, Nakanishi M, Nishimura K, Ohtaka M, Weltner J, Van Handel B, Parkkonen O,
Sinisalo J, Jalanko A, Hawkins RD, Woods NB, Otonkoski T, Trokovic R. Genetic Variability Overrides the Impact of Parental Cell Type and Determines iPSC
Differentiation Potential. Stem Cell Reports. 2016 Jan 12. pii: S2213-6711(15)00374-4. doi: 10.1016/j.stemcr.2015.12.009. [Epub ahead of print]PubMed PMID: 26777058.

Balboa D, Otonkoski T. Human pluripotent stem cell based islet models for diabetes research. Best Pract Res Clin Endocrinol Metab. 2015 Dec;29(6):899-909.
doi: 10.1016/j.beem.2015.10.012. Epub 2015 Oct 30. Review. PubMed PMID: 26696518.

Balboa D, Weltner J, Eurola S, Trokovic R, Wartiovaara K, Otonkoski T. Conditionally Stabilized dCas9 Activator for Controlling Gene Expression in Human Cell Reprogramming and Differentiation. Stem Cell Reports. 2015 Sep 8;5(3):448-59. 

Tamminen K, Balboa D, Toivonen S, Pakarinen MP, Wiener Z, Alitalo K, Otonkoski T. Intestinal Commitment and Maturation of Human Pluripotent Stem Cells Is Independent of Exogenous FGF4 and R-spondin1. PLoS One. 2015 Jul 31;10(7):e0134551. 

Trokovic R, Weltner J, Noisa P, Raivio T, Otonkoski T. Combined negative effect of donor age and time in culture on the reprogramming efficiency into induced pluripotent stem cells. Stem Cell Res. 2015 Jul;15(1):254-62.

Trokovic R, Weltner J, Otonkoski T. Generation of iPSC line HEL24.3 from human neonatal foreskin fibroblasts. Stem Cell Res. 2015 Jul;15(1):266-8.

Polinati PP, Ilmarinen T, Trokovic R, Hyotylainen T, Otonkoski T, Suomalainen A, Skottman H, Tyni T. Patient-Specific Induced Pluripotent Stem Cell-Derived RPE Cells: Understanding the Pathogenesis of Retinopathy in Long-Chain 3-Hydroxyacyl-CoA Dehydrogenase Deficiency. Invest Ophthalmol Vis Sci. 2015 May;56(5):3371-82.

Asikainen S, Heikkinen L, Juhila J, Holm F, Weltner J, Trokovic R, Mikkola M, Toivonen S, Balboa D, Lampela R, Icay K, Tuuri T, Otonkoski T, Wong G, Hovatta O. Selective microRNA-Offset RNA expression in human embryonic stem cells. PLoS One. 2015 Mar 30;10(3):e0116668. 

Andrews PW, Baker D, Benvinisty N, Miranda B, Bruce K, Brüstle O, Choi M, Choi YM, Crook JM, de Sousa PA, Dvorak P, Freund C, Firpo M, Furue MK, Gokhale P, Ha HY, Han E, Haupt S, Healy L, Hei DJ, Hovatta O, Hunt C, Hwang SM, Inamdar MS, Isasi RM, Jaconi M, Jekerle V, Kamthorn P, Kibbey MC, Knezevic I, Knowles BB, Koo SK, Laabi Y, Leopoldo L, Liu P, Lomax GP, Loring JF, Ludwig TE, Montgomery K, Mummery C, Nagy A, Nakamura Y, Nakatsuji N, Oh S, Oh SK, Otonkoski T, Pera M, Peschanski M, Pranke P, Rajala KM, Rao M, Ruttachuk R, Reubinoff B, Ricco L, Rooke H, Sipp D, Stacey GN, Suemori H, Takahashi TA, Takada K, Talib S, Tannenbaum S, Yuan BZ, Zeng F, Zhou Q. Points to consider in the development of seed stocks of pluripotent stem cells for clinical applications: International Stem Cell Banking Initiative (ISCBI). Regen Med. 2015;10(2 Suppl):1-44.

Laurila K, Autio R, Kong L, Närvä E, Hussein S, Otonkoski T, Lahesmaa R, Lähdesmäki H. Integrative genomics and transcriptomics analysis of human embryonic and induced pluripotent stem cells. BioData Min. 2014 Dec 13;7(1):32.  

Hakonen E, Toivonen S, Jalanko H, Otonkoski T. [Human stem cells in the treatment of pancreatic and hepatic diseases]. Duodecim. 2014;130(19):1973-80.

Trokovic R, Weltner J, Nishimura K, Ohtaka M, Nakanishi M, Salomaa V, Jalanko
A, Otonkoski T, Kyttälä A. Advanced Feeder-Free Generation of Induced Pluripotent Stem Cells Directly From Blood Cells. Stem Cells Transl Med. 2014 Oct 29.

Haapaniemi EM, Kaustio M, Rajala HL, van Adrichem AJ, Kainulainen L, Glumoff V, Doffinger R, Kuusanmäki H, Heiskanen-Kosma T, Trotta L, Chiang S, Kulmala P, Eldfors S, Katainen R, Siitonen S, Karjalainen-Lindsberg ML, Kovanen PE, Otonkoski T, Porkka K, Heiskanen K, Hänninen A, Bryceson YT, Uusitalo-Seppälä R, Saarela J, Seppänen M, Mustjoki S, Kere J. Autoimmunity, hypogammaglobulinemia, lymphoproliferation and mycobacterial disease in patients with dominant activating mutations in STAT3. Blood. 2014 Oct 27.

Flanagan SE, Haapaniemi E, Russell MA, Caswell R, Lango Allen H, De Franco E,  McDonald TJ, Rajala H, Ramelius A, Barton J, Heiskanen K, Heiskanen-Kosma T, Kajosaari M, Murphy NP, Milenkovic T, Seppänen M, Lernmark Å, Mustjoki S, Otonkoski T, Kere J, Morgan NG, Ellard S, Hattersley AT. Activating germline mutations in STAT3 cause early-onset multi-organ autoimmune disease. Nat Genet. 2014 Aug;46(8):812-4.

Polinati P, Ilmarinen T, Trokovic R, Hyötyläinen T, Otonkoski T, Suomalainen A, Skottman H, Tyni TA. Patient specific induced pluripotent stem cells derived
RPE cells: understanding the pathogenesis of retinopathy in LCHAD deficiency. Invest Ophthalmol Vis Sci. 2014 Jun 3.

Weltner J, Trokovic R, Otonkoski T. [Induced pluripotent stem cells (iPS) in medical research]. Duodecim. 2014;130(8):785-92.

Lindahl M, Danilova T, Palm E, Lindholm P, Võikar V, Hakonen E, Ustinov J, Andressoo JO, Harvey BK, Otonkoski T, Rossi J, Saarma M. MANF is indispensable for the proliferation and survival of pancreatic β cells. Cell Rep. 2014 Apr 24;7(2):366-75.

Hakonen E, Ustinov J, Palgi J, Miettinen PJ, Otonkoski T. EGFR signaling promotes β-cell proliferation and survivin expression during pregnancy. PLoS One. 2014 Apr 2;9(4):e93651. doi: 10.1371/journal.pone.0093651. eCollection 2014.

Noisa P, Lund C, Kanduri K, Lund R, Lähdesmäki H, Lahesmaa R, Lundin K, Chokechuwattanalert H, Otonkoski T, Tuuri T, Raivio T. Notch signaling regulates  the differentiation of neural crest from human pluripotent stem cells. J Cell Sci. 2014 May 1;127(Pt 9):2083-94.

Hakonen E, Ustinov J, Eizirik DL, Sariola H, Miettinen PJ, Otonkoski T. In vivo activation of the PI3K-Akt pathway in mouse beta cells by the EGFR mutation L858R protects against diabetes. Diabetologia. 2014 May;57(5):970-9. doi: 10.1007/s00125-014-3175-2.

Vuoristo S, Toivonen S, Weltner J, Mikkola M, Ustinov J, Trokovic R, Palgi J, Lund R, Tuuri T, Otonkoski T. A novel feeder-free culture system for human
pluripotent stem cell culture and induced pluripotent stem cell derivation. PLoS One. 2013 Oct 2;8(10):e76205.

Hämäläinen RH, Manninen T, Koivumäki H, Kislin M, Otonkoski T, Suomalainen A. Tissue- and cell-type-specific manifestations of heteroplasmic mtDNA 3243A>G mutation in human induced pluripotent stem cell-derived disease model. Proc Natl  Acad Sci U S A. 2013 Sep 17;110(38):E3622-30.

Toivonen S, Lundin K, Balboa D, Ustinov J, Tamminen K, Palgi J, Trokovic R, Tuuri T, Otonkoski T. Activin A and Wnt-dependent specification of human
definitive endoderm cells. Exp Cell Res. 2013 Oct 15;319(17):2535-44.

Shimomura K, Tusa M, Iberl M, Brereton MF, Kaizik S, Proks P, Lahmann C, Yaluri N, Modi S, Huopio H, Ustinov J, Otonkoski T, Laakso M, Ashcroft FM. A
mouse model of human hyperinsulinism produced by the E1506K mutation in the sulphonylurea receptor SUR1. Diabetes. 2013 Nov;62(11):3797-806.

Toivonen S, Ojala M, Hyysalo A, Ilmarinen T, Rajala K, Pekkanen-Mattila M, Äänismaa R, Lundin K, Palgi J, Weltner J, Trokovic R, Silvennoinen O, Skottman H, Narkilahti S, Aalto-Setälä K, Otonkoski T. Comparative analysis of targeted differentiation of human induced pluripotent stem cells (hiPSCs) and human embryonic stem cells reveals variability associated with incomplete transgene silencing in retrovirally derived hiPSC lines. Stem Cells Transl Med. 2013 Feb;2(2):83-93.

Mikkola M, Toivonen S, Tamminen K, Alfthan K, Tuuri T, Satomaa T, Natunen J,  Saarinen J, Tiittanen M, Lampinen M, Valmu L, Partanen J, Otonkoski T. Lectin from Erythrina cristagalli supports undifferentiated growth and differentiation of human pluripotent stem cells. Stem Cells Dev. 2013 Mar 1;22(5):707-16.

Marquard J, Welters A, Buschmann T, Barthlen W, Vogelgesang S, Klee D, Krausch M, Raffel A, Otter S, Piemonti L, Mayatepek E, Otonkoski T, Lammert E, Meissner T. Association of exercise-induced hyperinsulinaemic hypoglycaemia with  MCT1-expressing insulinoma. Diabetologia. 2013 Jan;56(1):31-5.

Trokovic R, Weltner J, Manninen T, Mikkola M, Lundin K, Hämäläinen R, Suomalainen A, Otonkoski T. Small molecule inhibitors promote efficient generation of induced pluripotent stem cells from human skeletal myoblasts. Stem  Cells Dev. 2013 Jan 1;22(1):114-23.

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Relevant earlier publications:

Trokovic R, Weltner J, Manninen T, Mikkola M, Lundin K, Hämäläinen R, Suomalainen A, Otonkoski T. Small molecule inhibitors promote efficient generation of induced pluripotent stem cells from human skeletal myoblasts. Stem Cells Dev. 2013 Jan 1;22(1):114-23.

Weltner J, Anisimov A, Alitalo K, Otonkoski T, Trokovic R. Induced pluripotent stem cell clones reprogrammed via recombinant adeno-associated virus-mediated transduction contain integrated vector sequences. J Virol. 2012 Apr;86(8):4463-7. doi: 10.1128/JVI.06302-11. Epub 2012 Feb 1. PubMed PMID: 22301147.

International Stem Cell Initiative, Amps K, Andrews PW, Anyfantis G, Armstrong L, Avery S, Baharvand H, Baker J, Baker D, Munoz MB, Beil S, Benvenisty N, Ben-Yosef D, Biancotti JC, Bosman A, Brena RM, Brison D, Caisander G, Camarasa MV, Chen J, Chiao E, Choi YM, Choo AB, Collins D, Colman A, Crook JM, Daley GQ, Dalton A, De Sousa PA, Denning C, Downie J, Dvorak P, Montgomery KD, Feki A, Ford A, Fox V, Fraga AM, Frumkin T, Ge L, Gokhale PJ, Golan-Lev T, Gourabi H, Gropp M, Lu G, Hampl A, Harron K, Healy L, Herath W, Holm F, Hovatta O, Hyllner J, Inamdar MS, Irwanto AK, Ishii T, Jaconi M, Jin Y, Kimber S, Kiselev S, Knowles BB, Kopper O, Kukharenko V, Kuliev A, Lagarkova MA, Laird PW, Lako M, Laslett AL, Lavon N, Lee DR, Lee JE, Li C, Lim LS, Ludwig TE, Ma Y, Maltby E, Mateizel I, Mayshar Y, Mileikovsky M, Minger SL, Miyazaki T, Moon SY, Moore H, Mummery C, Nagy A, Nakatsuji N, Narwani K, Oh SK, Oh SK, Olson C, Otonkoski T, Pan F, Park IH, Pells S, Pera MF, Pereira LV, Qi O, Raj GS, Reubinoff B, Robins A, Robson P, Rossant J, Salekdeh GH, Schulz TC, Sermon K, Sheik Mohamed J, Shen H, Sherrer E, Sidhu K, Sivarajah S, Skottman H, Spits C, Stacey GN, Strehl R, Strelchenko N, Suemori H, Sun B, Suuronen R, Takahashi K, Tuuri T, Venu P, Verlinsky Y, Ward-van Oostwaard D, Weisenberger DJ, Wu Y, Yamanaka S, Young L, Zhou Q. Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage. Nat Biotechnol. 2011 Nov 27;29(12):1132-44.

Hongisto H, Vuoristo S, Mikhailova A, Suuronen R, Virtanen I, Otonkoski T, Skottman H. Laminin-511 expression is associated with the functionality of feeder cells in human embryonic stem cell culture. Stem Cell Res. 2012 Jan;8(1):97-108. doi: 10.1016/j.scr.2011.08.005.

Hakonen E, Ustinov J, Mathijs I, Palgi J, Bouwens L, Miettinen PJ, Otonkoski T. Epidermal growth factor (EGF)-receptor signalling is needed for murine beta cell mass expansion in response to high-fat diet and pregnancy but not after pancreatic duct ligation. Diabetologia. 2011 Jul;54(7):1735-43.

Hussein SM, Batada NN, Vuoristo S, Ching RW, Autio R, Närvä E, Ng S, Sourour M, Hämäläinen R, Olsson C, Lundin K, Mikkola M, Trokovic R, Peitz M, Brüstle O, Bazett-Jones DP, Alitalo K, Lahesmaa R, Nagy A, Otonkoski T. Copy number variation and selection during reprogramming to pluripotency. Nature. 2011 Mar 3;471(7336):58-62.

Närvä E, Autio R, Rahkonen N, Kong L, Harrison N, Kitsberg D, Borghese L, Itskovitz-Eldor J, Rasool O, Dvorak P, Hovatta O, Otonkoski T, Tuuri T, Cui W, Brüstle O, Baker D, Maltby E, Moore HD, Benvenisty N, Andrews PW, Yli-Harja O, Lahesmaa R. High-resolution DNA analysis of human embryonic stem cell lines reveals culture-induced copy number changes and loss of heterozygosity. Nat Biotechnol. 2010 Apr;28(4):371-7.

Laurent LC, Nievergelt CM, Lynch C, Fakunle E, Harness JV, Schmidt U, Galat V, Laslett AL, Otonkoski T, Keirstead HS, Schork A, Park HS, Loring JF. Restricted ethnic diversity in human embryonic stem cell lines. Nat Methods. 2010 Jan;7(1):6-7.

Satomaa T, Heiskanen A, Mikkola M, Olsson C, Blomqvist M, Tiittanen M, Jaatinen T, Aitio O, Olonen A, Helin J, Hiltunen J, Natunen J, Tuuri T, Otonkoski T, Saarinen J, Laine J. The N-glycome of human embryonic stem cells. BMC Cell Biol. 2009 Jun 2;10:42.

Vuoristo S, Virtanen I, Takkunen M, Palgi J, Kikkawa Y, Rousselle P, Sekiguchi K, Tuuri T, Otonkoski T. Laminin isoforms in human embryonic stem cells: synthesis, receptor usage and growth support. J Cell Mol Med. 2009 Aug;13(8B):2622-33.

Banerjee M, Otonkoski T. A simple two-step protocol for the purification of human pancreatic beta cells. Diabetologia. 2009 Apr;52(4):621-5.

Otonkoski T, Jiao H, Kaminen-Ahola N, Tapia-Paez I, Ullah MS, Parton LE, Schuit F, Quintens R, Sipilä I, Mayatepek E, Meissner T, Halestrap AP, Rutter GA, Kere J. Physical exercise-induced hypoglycemia caused by failed silencing of monocarboxylate transporter 1 in pancreatic beta cells. Am J Hum Genet. 2007 Sep;81(3):467-74.

International Stem Cell Initiative, Adewumi O, Aflatoonian B, Ahrlund-Richter L, Amit M, Andrews PW, Beighton G, Bello PA, Benvenisty N, Berry LS, Bevan S, Blum B, Brooking J, Chen KG, Choo AB, Churchill GA, Corbel M, Damjanov I, Draper JS, Dvorak P, Emanuelsson K, Fleck RA, Ford A, Gertow K, Gertsenstein M, Gokhale PJ, Hamilton RS, Hampl A, Healy LE, Hovatta O, Hyllner J, Imreh MP, Itskovitz-Eldor J, Jackson J, Johnson JL, Jones M, Kee K, King BL, Knowles BB, Lako M, Lebrin F, Mallon BS, Manning D, Mayshar Y, McKay RD, Michalska AE, Mikkola M, Mileikovsky M, Minger SL, Moore HD, Mummery CL, Nagy A, Nakatsuji N, O'Brien CM, Oh SK, Olsson C, Otonkoski T, Park KY, Passier R, Patel H, Patel M, Pedersen R, Pera MF, Piekarczyk MS, Pera RA, Reubinoff BE, Robins AJ, Rossant J, Rugg-Gunn P, Schulz TC, Semb H, Sherrer ES, Siemen H, Stacey GN, Stojkovic M, Suemori H, Szatkiewicz J, Turetsky T, Tuuri T, van den Brink S, Vintersten K, Vuoristo S, Ward D, Weaver TA, Young LA, Zhang W. Characterization of human embryonic stem cell lines by the International Stem Cell Initiative. Nat Biotechnol. 2007 Jul;25(7):803-16.