Publications

Check our cardiovascular genomics page to read more of our publications

Selected Publications

  1. Örd T, Lönnberg T, Nurminen V, Ravindran A, Niskanen H, Kiema, M, Õunap K, Maria M, Moreau PR, Mishra PP, Palani S, Virta J, Liljenbäck H, Aaavik E, Roivainen A, Ylä-Herttuala S, LaakonenJP, Lehtimäki T, Kaikkonen MU. Dissecting the polygenic basis of atherosclerosis via disease-associated cell state signatures. Am J Hum Genet. 2023 May 4; 110(5):722-740.
  2. Aherrahrou R, Lue D Perry RN, Abbera YT, Khan MD, Soh JY, Örd T, Singha P, Yang K, Gilani H, Benavente ED,Wong D , Hinkle J , Ma L, Sheynkman GM, Ruijter HM , Miller CL, Bjorkegren JLM, Kaikkonen MU , Civelek M. Genetic Regulation of SMC Gene Expression and Splicing Predict Causal CAD Genes. Circ Res. 2023 Feb 3;132(3):323-338.
  3. Babu M, Devi D, Mäkinen P, Örd T, Aavik E, Kaikkonen MU, Ylä-Herttuala S. ApoA-I Nanotherapy Rescues Postischemic Vascular Maladaptation by Modulating Endothelial Cell and Macrophage Phenotypes in Type 2 Diabetic Mice. Arterioscler Thromb Vasc Biol. 2023 Jan;43(1):e46-e61.
  4. Maria M, Pouyanfar N, Örd T, Kaikkonen MU. The Power of Single-Cell RNA Sequencing in eQTL Discovery. Genes (Basel). 2022 Mar 12;13(3):502.
  5. Toropainen A, Stolze LK, Örd T, Whalen M, Torrell PM, Link VM, Kaikkonen MU, Romanoski C. Functional non-coding SNPs in human endothelial cells fine-map vascular trait associations. Genome Res. 2022 Mar; 32(3): 409–424.
  6. Moreau P, Bosch VT, Bouvy-Liivrand M, Õunap K , Örd T, Pulkkinen H, Pölönen P, Heinäniemi M, Ylä-Herttuala S, Laakkonen JP, Linna-Kuosmanen S, Kaikkonen MU . Profiling of Primary and Mature miRNA Expression in Atherosclerosis-Associated Cell Types. Arterioscler Thromb Vasc Biol. 2021 Jul; 41(7): 2149–2167. doi: 10.1161/ATVBAHA.121.315579.
  7. Örd T, Õunap K, Stolze LK, Aherrahrou R, Nurminen V, Toropainen A, Selvarajan I, Lönnberg T, Aavik E, Ylä-Herttuala S, Civelek M, Romanoski CE, and Kaikkonen MU. Single-Cell Epigenomics and Functional Fine-Mapping of Atherosclerosis GWAS Loci. Circ Res 2021 Jul 9;129(2): 240-258. doi: 10.1161/CIRCRESAHA.121.318971.
  8. Mushimiyimana I, Bosch VT, Niskanen H, Downes N, Moreau P, Hartigan K, Ylä-Herttuala S, Laham-Karam N, Kaikkonen MU. Genomic landscapes of non-coding RNAs regulating VEGFA and VEGFC expression in endothelial cells. Mol Cell Biol 2021 Jun 23;41(7):e0059420. doi: 10.1128/MCB.00594-20
  9. Selvarajan I, Toropainen A, Garske KM, López Rodríguez M, Ko A, Miao Z, Kaminska D, Õunap K, Örd T, Ravindran A, Liu OH, Moreau PR, Jawahar Deen A, Männistö V, Pan C, Levonen AL, Lusis AJ, Heikkinen S, Romanoski CE, Pihlajamäki J, Pajukanta P, Kaikkonen MU. Integrative analysis of liver-specific non-coding regulatory SNPs associated with the risk of coronary artery disease. Am J Hum Genet. 2021 Mar 4;108(3):411-430. doi: 10.1016/j.ajhg.2021.02.006.
  10. Huang Z, Liang N, Goñi S, Damdimopoulos A, Wang C, Ballaire R, Jager J, Niskanen H, Han H, Jakobsson T, Bracken AP, Aouadi M, Venteclef N, Kaikkonen MU, Fan R, Treuter E. The corepressors GPS2 and SMRT control enhancer and silencer remodeling via eRNA transcription during inflammatory activation of macrophages. Mol Cell. 2021 Mar 4;81(5):953-968.e9.
  11. Aherrahrou R, Guo L, Nagraj VP, Aguhob AA, Hinkle J, Chen L, Soh JY, Lue D, Alencar GF, Boltjes A, van der Laan SW, Farber E, Fuller D, Anane-Wae R, Akingbesote ND, Manichaikul AW, Ma L, Kaikkonen MU, Björkegren JL, Onengut-Gumuscu S, Pasterkamp G, Miller CL, Owens GK, Finn AV, Navab M, Fogelman AM, Berliner JA, Civelek M. Genetic Regulation of Atherosclerosis-Relevant Phenotypes in Human Vascular Smooth Muscle Cells.  Circ Res. 2020 Oct 12. doi: 10.1161/CIRCRESAHA.120.317415. (15.2)
  12. Depuydt MA, Prange KH, Slenders L, Örd T, Elbersen D, Boltjes A, de Jager SC, Asselbergs FW, de Borst GJ, Aavik E, Lönnberg T, Lutgens E, Glass CK, den Ruijter HM, Kaikkonen MU, Bot I, Slütter B, van der Laan SW, Yla-Herttuala S, Mokry M, Kuiper J, de Winther MP, Pasterkamp G. Microanatomy of the Human Atherosclerotic Plaque by Single-Cell Transcriptomics.  Circ Res. 2020 Sep 28. doi: 10.1161/CIRCRESAHA.120.316770 (15.2)
  13. Hsin-Fu Liu O, Kiema M, Beter M, Ylä-Herttuala S, Laakkonen JP, Kaikkonen MU. Hypoxia-Mediated Regulation of Histone Demethylases Affects Angiogenesis-Associated Functions in Endothelial Cells.  Arterioscler Thromb Vasc Biol. 2020 Nov;40(11):2665-2677. (6.6) 
  14. Linna-Kuosmanen S, Bosch VT, Moreau PR, Bouvy-Liivrand M, Niskanen H, Kansanen E, Kivelä A, Hartikainen J, Hippeläinen M, Kokki H, Tavi P, Levonen AL, Kaikkonen MU. NRF2 is a key regulator of endothelial microRNA expression under proatherogenic stimuli.  Cardiovasc Res. 2020 Jul 19:cvaa219. doi: 10.1093/cvr/cvaa219 (8.2)
  15. Stolze LK, Conklin A, Whalen MB, López Rodríguez M, Õunap K, Selvarajan I, Toropainen A, Tiit Örd, Li J, Solomon A, Fang Y, Kaikkonen MU, Romanoski CE. Molecular Quantitative Trait Locus Mapping In Human Endothelial Cells Identifies Regulatory SNPs Underlying Gene Expression and Complex Disease Traits. Am J Hum Genet. 2020 Jun 4;106(6):748-763. (10.5)
  16. Benhammou JN, Ko A, Alvarez M, Kaikkonen MU, Rankin C, Garske KM, Padua D, Bhagat Y, Kaminska D, Kärjä V, Pihlajamäki J, Pisegna JR and Pajukanta P. Novel lipid lincRNA OLMALINC regulates the liver steatosis gene, SCD, as an enhancer RNA. Hepatology Communications 2019 Aug 14;3(10):1356-1372 (NA)
  17. Kaikkonen MU, Adelman K. Emerging Roles of Non-Coding RNA Transcription. Trends Biochem Sci. 2018 Sep;43(9):654-667. (15.7)
  18. Moreau PR, Örd T, Downes NL, Niskanen H, Bouvy-Liivrand M, Aavik E, Ylä-Herttuala S, Kaikkonen MU. Transcriptional Profiling of Hypoxia-Regulated Non-coding RNAs in Human Primary Endothelial Cells. Front Cardiovasc Med. 2018 Nov 5;5:159. (3.9)
  19. Downes NL, Laham-Karam N, Ylä-Herttuala S*, Kaikkonen MU*. Differential but Complementary HIF1α and HIF2α Transcriptional Regulation. Mol Ther. 2018 Jul 5;26(7):1735-1745. (7.0) 
  20. Niskanen H, Tuszynska I, Zaborowski R, Heinäniemi M, Ylä-Herttuala S, Wilczynski B, Kaikkonen MU. Endothelial cell differentiation is encompassed by changes in long range interactions between inactive chromatin regions. Nucleic Acids Res. 2018 Feb 28;46(4):1724-1740. (11.6) 
  21. Bouvy-Liivrand M, Hernández de Sande A, Pölönen P, Mehtonen J, Niskanen H, Sinkkonen L, Heinäniemi M* and Kaikkonen MU*. Analysis of primary miRNA loci from nascent transcriptomes across cell types reveals regulatory domains governed by chromatin architecture. Nucleic Acids Research, 2017 Sep 29;45(17):9837-9849 (11.6) 
  22. López Rodríguez M, Kaminska D, Lappalainen K, Pihlajamäki J, Laakso M*, Kaikkonen MU*. 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 2017 Jul 6;9(1):63. (10.5)
  23. Kaikkonen MU, Halonen O, Liu OH, Turunen T, Pajula J, Moreau P, Tuomainen T, Aavik E, Tavi P, Ylä-Herttuala S. Genome-wide dynamics of nascent non-coding RNA transcription in porcine heart after myocardial infarction. Circulation: Cardiovascular Genetics 2017 Jun;10(3) (5.7)
  24. Kaikkonen MU, Niskanen H, Romanoski CE, Kansanen E, Kivelä AM, Laitalainen J, Heinz S, Benner C, Glass CK, Ylä-Herttuala S. Control of VEGF-A transcriptional programs by pausing and genomic compartmentalization. Nucleic Acids Research 2014 Nov 10;42(20):12570-84 (11.6)         
  25. Heinz S*, Romanoski CE* , Benner C, Allison KA, Kaikkonen MU, Orozco LD, Glass CK. Effect of natural genetic variation on enhancer selection and function. Nature 2013;503(7477):487-92. (41.6)    
  26. Kaikkonen MU*, Spann N*, Heinz S, Romanoski CE, Allison KA, Stender JD, Chun HB, Tough DF, Prinjha RK, BennerC and Glass CK. Remodeling of the enhancer landscape during macrophage activation is linked to enhancer transcription. Molecular Cell, 2013, Aug ;51(3): 310-325. (14.2)
  27. Lam MTY, Cho H, Lesch HP, Heinz S, Tanaka-Oishi Y, Benner C, Kaikkonen MU, Salim A, Kosaka M, Lee CY, Watt A, Grossman T, Rosenfeld MG, Evans RM, Glass CK. Rev-Erbs negatively regulate macrophage gene expression by repressing enhancer-directed transcription. Nature, 2013 Jun;498 (7455):511-5.  (41.6)                   
  28. Wang D, Garcia-Bassets I, Benner C, Li W, Su X, Zhou Y, Qiu J, Liu W, Kaikkonen MU, Ohgi KA, Glass CK, Rosenfeld MG, Fu XD. Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature. 2011 May 15;474(7351):390-4.  (41.6)