MINNA KAIKKONEN-MääTTä

Yhteystiedot

Avainsanat

Tutkimusryhmät - UEF

• 
  Itä-Suomen Genomikeskus
• 
  Kardiovaskulaarinen Genomiikka (Kaikkonen tutkimusryhmä)
• 
  Yksisolu-genomiikan keskus

Julkaisut

• Conklin, Austin C.; Nishi, Hitoo; Schlamp, Florencia; Örd, Tiit; Õunap, Kadri; Kaikkonen, Minna U.; Fisher, Edward A.; Romanoski, Casey E.. 2021. Meta-Analysis of Smooth Muscle Lineage Transcriptomes in Atherosclerosis and Their Relationships to In Vitro Models Immunometabolism 3 3: e210022. 2021
• Selvarajan, Ilakya; Toropainen, Anu; Garske, Kristina M.; López Rodríguez, Maykel; Ko, Arthur; Miao, Zong; Kaminska, Dorota; Õunap, Kadri; Örd, Tiit; Ravindran, Aarthi; Liu, Oscar H.; Moreau, Pierre R.; Jawahar Deen, Ashik; Männistö, Ville; Pan, Calvin; Levonen, Anna-Liisa; Lusis, Aldons J.; Heikkinen, Sami; Romanoski, Casey E.; Pihlajamäki, Jussi; Pajukanta, Päivi; Kaikkonen, Minna U.. 2021. Integrative analysis of liver-specific non-coding regulatory SNPs associated with the risk of coronary artery disease American journal of human genetics 108 3: 411-430. 2021
• Örd, Tiit; Õunap, Kadri; Stolze, Lindsey; Aherrahrou, Rédouane; Nurminen, Valtteri; Selvarajan, Ilakya; Toropainen, Anu; Lönnberg, Tapio; Aavik, Einari; Yla-Herttuala, Seppo; Civelek, Mete; Romanoski, Casey E; Kaikkonen, Minna U. 2021. Single-Cell Epigenomics and Functional Fine-Mapping of Atherosclerosis GWAS Loci Circulation research 129 2: 240-258. 2021
• Wu, CY; Borné, Y; Gao, R; Rodriguez, ML; Roell, WC; Wilson, JM; Regmi, A; Luan, C; Aly, DM; Peter, A; Machann, J; Staiger, H; Fritsche, A; Birkenfeld, AL; Tao, R; Wagner, R; Canouil, M; Hong, MG; Schwenk, JM [incl. Laakso, M]. 2021. Elevated circulating follistatin associates with an increased risk of type 2 diabetes Nature communications 12: 6486. 2021
• Mushimiyimana, Isidore; Tomas Bosch, Vanesa; Niskanen, Henri; Downes, Nicholas; Moreau, Pierre; Hartigan, Kiley; Ylä-Herttuala, Seppo; Laham-Karam, Nihay; Kaikkonen, Minna U.. 2021. Genomic landscapes of non-coding RNAs regulating VEGFA and VEGFC expression in endothelial cells Molecular and cellular biology 41 7: e00594-20. 2021
• Moreau, PR; Tomas Bosch, V; Bouvy-Liivrand,M; Õunap, K; Örd, T; Pulkkinen, HH; Pölönen, P; Heinäniemi, M; Ylä-Herttuala, S; Laakkonen, JP; Linna-Kuosmanen, S; Kaikkonen, MU. 2021. Profiling of Primary and Mature miRNA Expression in Atherosclerosis Associated Cell Types Arteriosclerosis, thrombosis, and vascular biology 41 7: 2149-2167. 2021
• Linna-Kuosmanen, Suvi; Bosch, Vanesa Tomas; Moreau, Pierre R; Bouvy-Liivrand, Maria; Niskanen, Henri; Kansanen, Emilia; Kivelä, Annukka; Hartikainen, Juha; Hippeläinen, Mikko; Kokki, Hannu; Tavi, Pasi; Levonen, Anna-Liisa; Kaikkonen, Minna U. 2021. NRF2 is a key regulator of endothelial microRNA expression under proatherogenic stimuli Cardiovascular research 117 5: 1339-1357. 2021
• Huang, Zhiqiang; Liang, Ning; Goñi, Saioa; Damdimopoulos, Anastasios; Wang, Cheng; Ballaire, Raphaelle; Jager, Jennifer; Niskanen, Henri; Han, Hongya; Jakobsson, Tomas; Bracken, Adrian P; Aouadi, Myriam; Venteclef, Nicolas; Kaikkonen, Minna U; Fan, Rongrong; Treuter, Eckardt. 2021. The corepressors GPS2 and SMRT control enhancer and silencer remodeling via eRNA transcription during inflammatory activation of macrophages Molecular cell 81 5: 953-968.e9. 2021
• Mushimiyimana, I; Niskanen. H; Beter, M; Laakkonen, JP; Kaikkonen, MU; Ylä-Herttuala, S; Laham-Karam, N. 2021. Characterization of a functional endothelial super-enhancer that regulates ADAMTS18 and angiogenesis Nucleic acids research 49 14: 8078-8096. 2021
• Moisio, Olli; Palani, Senthil; Virta, Jenni; Elo, Petri; Liljenbäck, Heidi; Tolvanen, Tuula; Käkelä, Meeri; Miner, Maxwell G; Herre, Erika Atencio; Marjamäki, Päivi; Örd, Tiit; Heinäniemi, Merja; Kaikkonen, Minna U; Zhang, Fenghua; Srinivasarao, Madduri; Knuuti, Juhani; Low, Philip S; Saraste, Antti; Li, Xiang-Guo; Roivainen, Anne. 2020. Radiosynthesis and preclinical evaluation of [ 68 Ga]Ga-NOTA-folate for PET imaging of folate receptor ß-positive macrophages Scientific reports 10 1: 13593. 2020
• Stolze, Lindsey; Conklin, Austin; Whalen, Michael; López Rodríguez, Maykel; Õunap, Kadri; Selvarajan, Ilakya; Toropainen, Anu; Örd, Tiit; Li, Jin; Eshghi, Anna; Solomon, Alice; Fang, Yun; Kaikkonen, Minna; Romanoski, Casey. 2020. Systems Genetics in Human Endothelial Cells Identifies Non-coding Variants Modifying Enhancers, Expression, and Complex Disease Traits American journal of human genetics 106 6: P748-763. 2020
• Pulkkinen, H H; Kiema, M; Lappalainen, J P; Toropainen, A; Beter, M; Tirronen, A; Holappa, L; Niskanen, H; Kaikkonen, M U; Ylä-Herttuala, S; Laakkonen, Johanna P. 2020. BMP6/TAZ-Hippo signaling modulates angiogenesis and endothelial cell response to VEGF Angiogenesis 2021; 24 1: 12-144. 2020
• Aherrahrou, Rédouane; Guo, Liang; Nagraj, Vijay Peter; Aguhob, Aaron Andrew; Hinkle, Jameson; Chen, Lisa; Soh, Joon Yuhl; Lue, Dillon; Alencar, Gabriel F; Boltjes, Arjan; van der Laan, Sander W; Farber, Emily; Fuller, Daniela; Anane-Wae, Rita; Akingbesote, Ngozi D; Manichaikul, Ani W; Ma, Lijiang; Kaikkonen, Minna U; Björkegren, Johan LM; Önengüt-Gümüscu, Suna; et al.. 2020. Genetic Regulation of Atherosclerosis-Relevant Phenotypes in Human Vascular Smooth Muscle Cells Circulation research 127 12: 1552-1565. 2020
• Depuydt, Marie Ac; Prange, Koen Hm; Slenders, Lotte; Örd, Tiit; Elbersen, Danny; Boltjes, Arjan; de Jager, Saskia Ca; Asselbergs, Folkert W; de Borst, Gert J; Aavik, Einari; Lönnberg, Tapio; Lutgens, Esther; Glass, Christopher K; den Ruijter, Hester M; Kaikkonen, Minna U; Bot, Ilze; Slütter, Bram; van der Laan, Sander W; Ylä-Herttuala, Seppo; Mokry, Michal; et al. 2020. Microanatomy of the Human Atherosclerotic Plaque by Single-Cell Transcriptomics Circulation research 127 11: 1437-1455. 2020
• Hsin-Fu Liu, Oscar; Kiema, Miika; Beter, Mustafa; Ylä-Herttuala, Seppo; Laakkonen, Johanna P; Kaikkonen, Minna U. 2020. Hypoxia-Mediated Regulation of Histone Demethylases Affects Angiogenesis-Associated Functions in Endothelial Cells Arteriosclerosis thrombosis and vascular biology 40: 2665-2677. 2020
• 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
• 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 3 10: 1356-1372. 2019
• 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
• 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
• 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
• Kaikkonen, Minna U; Adelman, Karen. 2018. Emerging Roles of Non-Coding RNA Transcription Trends in biochemical sciences 43 9: 654-667. 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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