Minna Kaikkonen-Määttä

Benhammou, Jihane N; Ko, Arthur; Alvarez, Marcus; Kaikkonen, Minna U; Rankin, Carl; Garske, Kristina M; Padua, David; Bhagat, Yash; Kaminska, Dorota; Karja, Vesa; Pihlajamäki, Jussi; Pisegna, Joseph R; Pajukanta, Päivi. 2019. Novel Lipid Long Intervening Noncoding RNA, Oligodendrocyte Maturation-Associated Long Intergenic Noncoding RNA, Regulates the Liver Steatosis Gene Stearoyl-Coenzyme A Desaturase As an Enhancer RNA Hepatology communications [Epub ahead of print 14 Aug 2019]: 1-17. 2019

Viiri, LE; Rantapero, T; Kiamehr, M; Alexanova, A; Oittinen, M; Viiri, K; Niskanen, H; Nykter, M; Kaikkonen, MU; Aalto-Setälä, K. 2019. Extensive reprogramming of the nascent transcriptome during iPSC to hepatocyte differentiation Scientific reports 9 1: 3562. 2019

Jauhiainen, Suvi; Laakkonen, Johanna P; Ketola, Kirsi; Toivanen, Pyry, I; Nieminen, Tina; Ninchoji, Takeshi; Levonen, Anna-Liisa; Kaikkonen, Minna U; Ylä-Herttuala, Seppo. 2019. Axon Guidance-Related Factor FLRT3 Regulates VEGF-Signaling and Endothelial Cell Function Frontiers in physiology 10: 224. 2019

López Rodríguez, Maykel; Fernandes Silva, Lilian; Vangipurapu, Jagadish; Modi, Shalem; Kuusisto, Johanna; Kaikkonen, Minna U; Laakso, Markku. 2018. Functional Variant in the GCKR Gene Affects Lactate Levels Differentially in the Fasting State and During Hyperglycemia Scientific Reports 8 1: 15989. 2018

Samaranayake, Haritha Dhammika; Olsson, Venla; Kurkipuro, Jere Tuomas; Määttä, Ann-Marie; Stedt, Hanna; Kärkkäinen, Hanna-Riikka; Kaikkonen, Minna U; Taavitsainen, Miia; Vuorio, Taina; Parker, Nigel; Ylä-Herttuala, Seppo. 2018. Up-regulation of Mismatch Repair Pathway by Suicide Gene Therapy: Implications on the use of Temozolomide Treatment in Malignant Glioma Journal of Cancer Science & Therapy 10 8: 214-222. 2018

Moreau, Pierre R; Örd, Tiit; Downes, Nicholas L; Niskanen, Henri; Bouvy-Liivrand, Maria; Aavik, Einari; Ylä-Herttuala, Seppo; Kaikkonen, Minna U. 2018. Transcriptional Profiling of Hypoxia-Regulated Non-coding RNAs in Human Primary Endothelial Cells Frontiers in cardiovascular medicine 5 159: 12. 2018

Tirronen, Annakaisa; Vuorio, Taina; Kettunen, Sanna; Hokkanen, Krista; Ramms, Bastian; Niskanen, Henri; Laakso, Hanne; Kaikkonen, Minna U; Jauhiainen, Matti; Gordts, Philip LSM; Ylä-Herttuala, Seppo. 2018. Deletion of Lymphangiogenic and Angiogenic Growth Factor VEGF-D Leads to Severe Hyperlipidemia and Delayed Clearance of Chylomicron Remnants ARTERIOSCLEROSIS, THROMBOSIS AND VASCULAR BIOLOGY 38 10: 2327-2337. 2018

Kuosmanen, SM; Sihvola, V; Kansanen, E; Kaikkonen, MU; Levonen, AL. 2018. MicroRNAs mediate the senescence-associated decline of NRF2 in endothelial cells Redox Biology 18: 77-83. 2018

Kaikkonen, Minna U; Adelman, Karen. 2018. Emerging Roles of Non-Coding RNA Transcription Trends in biochemical sciences 43 9: 654-667. 2018

Gurzeler, Erika; Aavik, Einari; Laine, Anssi; Valkama, Teemu; Niskanen, Henri; Huusko, Jenni; Kaikkonen, Minna U; Ylä-Herttuala, Seppo. 2018. Therapeutic effects of rosuvastatin in hypercholesterolemic prediabetic mice in the absence of low density lipoprotein receptor BIOCHIMICA ET BIOPHYSICA ACTA - GENERAL SUBJECTS 2019; 1863 2: 481-490. 2018

Downes, Nicholas L; Laham-Karam, Nihay; Kaikkonen, Minna U; Ylä-Herttuala, Seppo. 2018. Differential but Complementary HIF1[alfa] and HIF2[alfa] Transcriptional Regulation MOLECULAR THERAPY 26 7: 1735-1745. 2018

Cuartero, Sergi; Weiss, Felix D; Dharmalingam, Gopuraja; Guo, Ya; Ing-Simmons, Elizabeth; Masella, Silvia; Robles-Rebollo, Irene; Xiao, Xiaolin; Wang, Yi-Fang; Barozzi, Iros; Djeghloul, Dounia; Amano, Mariane T; Niskanen, Henri; Petretto, Enrico; Dowell, Robin D; Tachibana, Kikue; Kaikkonen, Minna U; Nasmyth, Kim A; Lenhard, Boris; Natoli, Gioacchino; et al.. 2018. Control of inducible gene expression links cohesin to hematopoietic progenitor self-renewal and differentiation Nature immunology 19 9: 932-944. 2018

Belt, H; Koponen, JK; Kekarainen, T; Puttonen, KA; Mäkinen, PI; Niskanen, H;, Oja, J; Wirth, G; Koistinaho, J; Kaikkonen, MU; Ylä-Herttuala, S. 2018. Temporal Dynamics of Gene Expression During Endothelial Cell Differentiation From Human iPS Cells: A Comparison Study of Signalling Factors and Small Molecules. Frontiers in cardiovascular medicine 5: 16. 2018

Toivanen Pyry I, Nieminen Tiina, Laakkonen Johanna P, Heikura Tommi, Kaikkonen Minna U, Ylä-Herttuala Seppo. 2017. Snake venom VEGF Vammin induces a highly efficient angiogenic response in skeletal muscle via VEGFR-2/NRP specific signaling. Scientific Reports 7: 5525. 2017

Oishi Y, Spann NJ, Link VM, Muse ED, Strid T, Edillor C, Kolar MJ, Matsuzaka T, Hayakawa S, Tao J, Kaikkonen MU, Carlin AF, Lam MT, Manabe I, Shimano H, Saghatelian A, Glass CK. 2017. SREBP1 Contributes to Resolution of Pro-inflammatory TLR4 Signaling by Reprogramming Fatty Acid Metabolism. Cell Metabolism 25 2: 412-427. 2017

Niskanen, Henri; Tuszynska, Irina; Zaborowski, Rafal; Heinäniemi, Merja; Ylä-Herttuala, Seppo; Wilczynski, Bartek; Kaikkonen, Minna U. 2017. Endothelial cell differentiation is encompassed by changes in long range interactions between inactive chromatin regions NUCLEIC ACIDS RESEARCH 2018; 46 4: 1724-1740. 2017

López Rodríguez M, Kaminska D, Lappalainen K, Pihlajamäki J, Kaikkonen MU, Laakso M. 2017. Identification and characterization of a FOXA2-regulated transcriptional enhancer at a type 2 diabetes intronic locus that controls GCKR expression in liver cells. Genome Medicine 9: 63. 2017

Kuosmanen SM, Kansanen E, Kaikkonen MU, Sihvola V, Pulkkinen K, Jyrkkänen H-K, Tuoresmäki P, Hartikainen J, Hippeläinen M, Kokko H, Tavi P, Heikkinen S, Levonen A-M. 2017. NRF2 regulates endothelial glycolysis and proliferation with miR-93 and mediates the effects of oxidized phospholipids on endothelial activation. NUCLEIC ACIDS RESEARCH 2018; 46 3: 1124-1138. 2017

Kaikkonen Minna U, Halonen Paavo, Liu Oscar Hsin-Fu, Turunen Tiia A, Pajula Juho, Moreau Pierre, Selvarajan Ilakya, Tuomainen Tomi, Aavik Einari, Tavi Pasi, Ylä-Herttuala Seppo. 2017. Genome-Wide Dynamics of Nascent Noncoding RNA Transcription in Porcine Heart After Myocardial Infarction Circulation: Cardiovascular Genetics 10 3: e001702. 2017

Bouvy-Liivrand Maria, Hernández de Sande Ana, Pölönen Petri, Mehtonen Juha, Vuorenmaa Tapio, Niskanen Henri, Sinkkonen Lasse, Unelma Kaikkonen Minna, Heinäniemi Merja. 2017. Analysis of primary microRNA loci from nascent transcriptomes reveals regulatory domains governed by chromatin architecture. NUCLEIC ACIDS RESEARCH 45 17: 9837-9849. 2017

Heinäniemi Merja, Vuorenmaa Tapio, Teppo Susanna, Kaikkonen Minna U, Bouvy-Liivrand Maria, Mehtonen Juha, Niskanen Henri, Zachariadis Vasilios, Laukkanen Saara, Liuksiala Thomas, Teittinen Kaisa, Lohi Olli. 2016. Transcription-coupled genetic instability marks acute lymphoblastic leukemia structural variation hotspots. Elife 5: e13087. 2016

Laakkonen Johanna P, Lappalainen Jari P, Theelen Thomas L, Toivanen Pyry I, Nieminen Tiina, Jauhiainen Suvi,Kaikkonen Minna U, Sluimer Judith C, Ylä-Herttuala Seppo. 2016. Differential regulation of angiogenic cellular processes and claudin-5 by histamine and VEGF via PI3K-signaling, transcription factor SNAI2 and interleukin-8. Angiogenesis [Epub ahead of print 21 Nov 2016]: 1-16. 2016

Malinen Marjo, Niskanen Einari A, Kaikkonen Minna U, Palvimo Jorma J. 2016. Crosstalk between androgen and pro-inflammatory signaling remodels androgen receptor and NF-kB cistrome to reprogram the prostate cancer cell transcriptome. NUCLEIC ACIDS RESEARCH 45 2: 619-630. 2016

Oittinen M, Popp A, Kurppa K, Lindfors K, Mäki M, Kaikkonen MU, Viiri K. 2016. Polycomb Repressive Complex 2 Enacts Wnt Signaling in Intestinal Homeostasis and Contributes to the Instigation of Stemness in Diseases Entailing Epithelial Hyperplasia or Neoplasia. STEM CELLS 2017; 35 2: 445-457. 2016

Toropainen Sari, Niskanen Einari A, Malinen Marjo, Sutinen Päivi, Kaikkonen Minna U, Palvimo Jorma J. 2016. Global analysis of transcription in castration-resistant prostate cancer cells uncovers active enhancers and direct androgen receptor targets. Scientific Reports 6: 33510. 2016

Shaked Iftach, Hanna Richard N, Shaked Helena, Chodaczek Grzegorz, Nowyhed Heba N, Tweet George, Tacke Robert, Basat Alp Bugra, Mikulski Zbigniew, Togher Susan, Miller Jacqueline, Blatchley Amy, Salek-Ardakani Shahram, Darvas Martin, Kaikkonen Minna U, Thomas Graham D, Lai-Wing-Sun Sonia, Rezk Ayman, Bar-Or Amit, Glass Christopher K, Bandukwala Hozefa, Hedrick Catherine C. 2015. Transcription factor Nr4a1 couples sympathetic and inflammatory cues in CNS-recruited macrophages to limit neuroinflammation. Nature Immunology 16 12: 1228-1234. 2015

Roberts Thomas C, Hart Jonathan R, Kaikkonen Minna U, Weinberg Marc S, Vogt Peter K, Morris Kevin V. 2015. Quantification of nascent transcription by bromouridine immunocapture nuclear run-on RT-qPCR. Nature Protocols 10 8: 1198-1211. 2015

Niskanen Einari A, Malinen Marjo, Sutinen Päivi, Toropainen Sari, Paakinaho Ville, Vihervaara Anniina, Joutsen Jenny, Kaikkonen Minna U, Sistonen Lea, Palvimo Jorma J. 2015. Global SUMOylation on active chromatin is an acute heat stress response restricting transcription Genome biology 16: 153. 2015

Nieminen Tiina, Toivanen Pyry I, Laakkonen Johanna P, Heikura Tommi, Kaikkonen Minna U, Airenne Kari J, Ylä-Herttuala Seppo. 2015. Slit2 modifies VEGF-induced angiogenic responses in rabbit skeletal muscle via reduced eNOS activity. CARDIOVASCULAR RESEARCH 107 2: 267-276. 2015

Babu Mohan, Durga Devi Thota, Mäkinen Petri, Kaikkonen Minna, Lesch Hanna P, Junttila Sini, Laiho Asta, Ghimire Bishwa, Gyenesei Attila, Ylä-Herttuala Seppo. 2015. Differential Promoter Methylation of Macrophage Genes Is Associated With Impaired Vascular Growth in Ischemic Muscles of Hyperlipidemic and Type 2 Diabetic Mice: Genome-Wide Promoter Methylation Study. CIRCULATION RESEARCH [ONLINE: HTTP://CIRCRES.AHAJOURNALS.ORG/] 117: 289-299. 2015

Kaikkonen MU, Niskanen H, Romanoski CE, Kansanen E, Kivelä AM, Laitalainen J, Heinz S, Benner C, Glass CK, Ylä-Herttuala S. 2014. Control of VEGF-A transcriptional programs by pausing and genomic compartmentalization. NUCLEIC ACIDS RESEARCH 42 20: 12570-84. 2014

Ruotsalainen JJ, Kaikkonen MU, Niittykoski M, Martikainen MW, Lemay CG, Cox J, De Silva NS, Kus A, Falls TJ, Diallo JS, Le Boeuf F, Bell JC, Ylä-Herttuala S, Hinkkanen AE, Vähä-Koskela MJ. 2014. Clonal variation in interferon response determines the outcome of oncolytic virotherapy in mouse CT26 colon carcinoma model. GENE THERAPY 2014 Sep 18. [Epub ahead of print]: --. 2014

Ylä-Herttuala Seppo, Kaikkonen Minna. 2014. Does mass balance between sense and antisense transcripts fine-tune the outcome of gene expression?. EMBO REPORTS 2014 Feb;15(2): 125-126. 2014

Allison KA, Kaikkonen MU, Gaasterland T, Glass CK. 2013. Vespucci: a system for building annotated databases of nascent transcripts. NUCLEIC ACIDS RESEARCH 2013 Dec 4. [Epub ahead of print]: --. 2013

Heinz S, Romanoski CE, Benner C, Allison KA, Kaikkonen MU, Orozco LD, Glass CK. 2013. Effect of natural genetic variation on enhancer selection and function. NATURE (LONDON) 2013 Oct 13. [Epub ahead of print]: --. 2013

Huhtala Tuulia, Kaikkonen Minna U, Lesch Hanna P, Viitala Sari, Ylä-Herttuala Seppo, Närvänen Ale. 2013. Biodistribution and antitumor effect of Cetuximab-targeted lentivirus. NUCLEAR MEDICINE AND BIOLOGY 2014:41: 77-83. 2013

Kaikkonen MU, Spann NJ, Heinz S, Romanoski CE, Allison KA, Stender JD, Chun HB, Tough DF, Prinjha RK, Benner C, Glass CK. 2013. Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription. MOLECULAR CELL Volume 51, Issue 3: 310-325. 2013

Lam MT, Cho H, Lesch HP, Gosselin D, Heinz S, Tanaka-Oishi Y, Benner C, Kaikkonen MU, Kim AS, Kosaka M, Lee CY, Watt A, Grossman TR, Rosenfeld MG, Evans RM, Glass CK. 2013. Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription. NATURE (LONDON) 2013 Jun 27;498(7455): 511-5. 2013

Li P, Spann NJ, Kaikkonen MU, Lu M, Oh da Y, Fox JN, Bandyopadhyay G, Talukdar S, Xu J, Lagakos WS, Patsouris D, Armando A, Quehenberger O, Dennis EA, Watkins SM, Auwerx J, Glass CK, Olefsky JM. 2013. NCoR Repression of LXRs Restricts Macrophage Biosynthesis of Insulin-Sensitizing Omega 3 Fatty Acids. CELL 2013 Sep 26;155(1): 200-14. 2013

Shibata N, Carlin AF, Spann NJ, Saijo K, Morello CS, McDonald JG, Romanoski CE, Maurya MR, Kaikkonen MU, Lam MT, Crotti A, Reichart D, Fox JN, Quehenberger O, Raetz CR, Sullards MC, Murphy RC, Merrill AH Jr, Brown HA, Dennis EA, Fahy E, Subramaniam S, Cavener DR, Spector DH, Russell DW, Glass CK. 2013. 25-hydroxycholesterol activates the integrated stress response to reprogram transcription and translation in macrophages. JOURNAL OF BIOLOGICAL CHEMISTRY 2013 Dec 13;288(50): 35812-23. 2013

Stender JD, Pascual G, Liu W, Kaikkonen MU, Do K, Spann NJ, Boutros M, Perrimon N, Rosenfeld MG, Glass CK. 2012. Control of Proinflammatory Gene Programs by Regulated Trimethylation and Demethylation of Histone H4K2 MOLECULAR CELL 48 1: 28-38. 2012

Soininen Suvi K, Lehtolainen-Dalkilic Pauliina, Karppinen Tanja, Puustinen Tiina, Dragneva Galina, Kaikkonen Minna U, Jauhiainen Marjo, Allart Brigitte, Selwood David L, Wirth Thomas, Lesch Hanna P, Määttä Ann-Marie, Mönkkönen Jukka, Ylä-Herttuala Seppo, Ruponen Marika. 2012. Targeted delivery via avidin fusion protein: Intracellular fate of biotinylated doxorubicin derivative and cellular uptake kinetics and biodistribution of biotinylated liposomes. EUROPEAN JOURNAL OF PHARMACEUTICAL SCIENCES 47: 848-856. 2012

Leinonen HM, Ruotsalainen AK, Määttä AM, Laitinen HM, Kuosmanen SM, Kansanen E, Pikkarainen JT, Lappalainen JP, Samaranayake H, Lesch HP, Kaikkonen MU, Ylä-Herttuala S, Levonen AL. 2012. Oxidative stress-regulated lentiviral TK/GCV gene therapy for lung cancer treatment. CANCER RESEARCH 2012 Oct 9. [Epub ahead of print]: - -. 2012

Maldiney T, Kaikkonen MU, Seguin J, le Masne de Chermont Q, Bessodes M, Airenne KJ, Ylä-Herttuala S, Scherman D, Richard C. 2012. In vitro targeting of avidin-expressing glioma cells with biotinylated persistent luminescence nanoparticles. BIOCONJUGATE CHEMISTRY 2012 Mar 21;23(3): 472-8. 2012

Ihalainen TO, Willman SF, Niskanen EA, Paloheimo O, Smolander H, Laurila JP, Kaikkonen MU, Vihinen-Ranta M.. 2012. Distribution and dynamics of transcription-associated proteins during parvovirus infection. JOURNAL OF VIROLOGY 2012 Oct 3. [Epub ahead of print]: --. 2012

Heikura T, Nieminen T, Roschier MM, Karvinen H, Kaikkonen MU, Mähönen AJ, Lesch HP, Rissanen TT, Laitinen OH, Airenne KJ, Ylä-Herttuala S.. 2012. Baculovirus-mediated vascular endothelial growth factor-D∆N∆C gene transfer induces angiogenesis in rabbit skeletal muscle. JOURNAL OF GENE MEDICINE 14 1: 35-43. 2012

Heikura T, Nieminen T, Roschier M, Karvinen H, Kaikkonen M, Mähönen A, Lesch H, Rissanen T, Laitinen O, Airenne K, Ylä-Herttuala S. 2011. Baculovirus-mediated VEGF-D(ΔNΔC) Gene Transfer Induces Angiogenesis In Rabbit Skeletal Muscle. JOURNAL OF GENE MEDICINE 2011 Dec 12: --. 2011

Kaikkonen Minna U, Lam Michael TY, Glass Christopher K. 2011. Non-coding RNAs as regulators of gene expression and epigenetics. CARDIOVASCULAR RESEARCH 90: 430-440. 2011

Kaikkonen Minna U, Ylä-Herttuala Seppo, Airenne Kari J. 2011. How to avoid complement attack in baculovirus-mediated gene delivery JOURNAL OF INVERTEBRATE PATHOLOGY 107: S71-S79. 2011

Kaikkonen MU, Lesch HP, Pikkarainen J, Räty JK, Vuorio T, Huhtala T, Taavitsainen M, Laitinen T, Tuunanen P, Gröhn O, Närvänen A, Airenne KJ, Ylä-Herttuala S. 2009. (Strept)avidin-displaying lentiviruses as versatile tools for targeting and dual imaging of gene delivery. GENE THERAPY 16: 894-904. 2009

Lesch HP, Pikkarainen JT, Kaikkonen MU, Taavitsainen M, Samaranayake H, Lehtolainen-Dalkilic P, Vuorio T, Määttä A-M, Wirth T, Airenne KJ, Ylä-Herttuala S. 2009. Avidin fusion protein-expressing lentiviral vector for targeted drug delivery. HUMAN GENE THERAPY 20: 871-882. 2009

Kaikkonen M. 2008. Engineering Baculo- and Lentiviral Vectors for Enhanced and Targeted Gene Delivery. Kuopion yliopiston julkaisuja G.- A.I. Virtanen -instituutti. 2008

Kaikkonen MU, Viholainen JI, Närvänen A, Ylä-Herttuala S, Airenne KJ. 2008. Targeting and purification of metabolically biotinylated baculovirus. HUMAN GENE THERAPY 19 6: 589-600. 2008

Laakkonen JP, Kaikkonen MU, Ronkainen PHA, Ihalainen TO, Niskanen EA, Häkkinen M, Salminen M, Kulomaa MS, Ylä-Herttuala S, Airenne KJ, Vihinen-Ranta M. 2008. Baculovirus-mediated immediate-early gene expression and nuclear reorganization in human cells. CELLULAR MICROBIOLOGY 10 3: 667-681. 2008

Mähönen AJ, Airenne KJ, Purola S, Peltomaa E, Kaikkonen MU, Riekkinen MS, Heikura T, Kinnunen K, Roschier MM, Wirth T, Ylä-Herttuala S. 2007. Post-transcriptional regulatory element boosts baculovirus-mediated gene expression in vertebrate cells. JOURNAL OF BIOTECHNOLOGY 131 1: 1-8. 2007

Räty JK, Liimatainen T, Huhtala T, Kaikkonen MU, Airenne KJ, Hakumäki JM, Närvänen A, Ylä-Herttuala S. 2007. SPECT/CT imaging of baculovirus biodistribution in rat. GENE THERAPY 14: 930-938. 2007

Räty JK, Liimatainen T, Kaikkonen MU, Gröhn O, Airenne KJ, Ylä-Herttuala S. 2007. Non-invasive imaging in gene therapy. MOLECULAR THERAPY 15 9: 1579-1586. 2007

Kaikkonen MU, Räty JK, Airenne KJ, Wirth T, Heikura T, Ylä-Herttuala S. 2006. Truncated vesicular stomatitis virus G protein improves baculovirus transduction efficiency in vitro and in vivo. GENE THERAPY 13: 304-312. 2006

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