Publications

Kaikkonen Lab publications

Publications on this page are generated from Minna Kaikkonen-Määttä’s ORCID record and the website citation database. For the complete and continuously updated publication record, use the external profile links below.

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Selected publications

Recent work from the group

Single-cell macrophage biomarkers for atherosclerosis publication figure

Cardiovascular Research · 2025

Single-cell to pre-clinical evaluation of Trem2, Folr2, and Slc7a7 as macrophage-associated biomarkers for atherosclerosis

Single-cell and pre-clinical evaluation of macrophage-associated biomarkers in atherosclerosis.

Dissecting the polygenic basis of atherosclerosis publication figure

American Journal of Human Genetics · 2023

Dissecting the polygenic basis of atherosclerosis via disease-associated cell states

Single-cell and bulk transcriptomic analysis connecting atherosclerosis cell states with CAD genetic risk.

NRF2 endothelial microRNA publication figure

Cardiovascular Research · 2021

NRF2 is a key regulator of endothelial microRNA expression under proatherogenic stimuli

Integrative regulatory analysis of NRF2, endothelial microRNAs, and proatherogenic stimulation.

Publication database

All publications

2026

Spatial mapping of stability in human atherosclerosis for the next generation of patient stratification

Gerard Pasterkamp, Minna U Kaikkonen, Michal Mokry

European Heart Journal · 18 Feb 2026 · doi:10.1093/eurheartj/ehag074

2025

Single-cell to pre-clinical evaluation of i Trem2 i , i Folr2 i , and i Slc7a7 i as macrophage-associated biomarkers for atherosclerosis

Single-cell to pre-clinical evaluation of Trem2 , Folr2 , and Slc7a7 as macrophage-associated biomarkers for atherosclerosis

Tiit Örd, Senthil Palani, Judith Giroud Gerbetant, Susanna Bodoy, Tapio Lönnberg, …, Ljubica Matic, Laurent Yvan-Charvet, Manuel Palacín, Anne Roivainen, Minna U Kaikkonen

Cardiovascular Research · 01 Nov 2025 · doi:10.1093/cvr/cvaf210

Investigating the Intracellular Compartmental Dynamics of miRNAs in Response to Hypoxia

Vanesa Tomas Bosch, Pierre R. Moreau, Pia Laitinen, Mari-Anna Väänänen, Tiia A. Turunen, Eloi Schmauch, Suvi Linna-Kuosmanen, Minna U Kaikkonen

openRxiv · 20 Sep 2025 · doi:10.1101/2025.09.18.676626

Nuclear Speckles are Regulatory Hubs for Viral and Host mRNA Expression During HSV-1 Infection

Shani Nadav-Eliyahu, Chaya Bohrer, Alon Boocholez, Noa Kinor, Vesa Aho, …, Sami Salminen, Henri Niskanen, Minna U Kaikkonen, Maija Vihinen-Ranta, Yaron Shav-Tal

openRxiv · 12 Sep 2025 · doi:10.1101/2025.09.11.675548

Mitochondrial ROS drive foam cell formation via STAT5 signaling in atherosclerosis

Laura Boccuni, Frieda Marka, Manuel Salzmann, Alessia Schirripa, Elisabeth Ableitner, …, Christian Hengstenberg, Bruno K. Podesser, Minna U. Kaikkonen, Johann Wojta, Philipp J. Hohensinner

Science Advances · 29 Aug 2025 · doi:10.1126/sciadv.adw9952

Alzheimer and cardiovascular genetic scores and cognition: the FINGER randomized controlled trial

Gazi Saadmaan, Maria Carolina Dalmasso, Maleeha Maria, Jenni Lehtisalo, Mikko Hiltunen, …, Alfredo Ramirez, Ruth Stephen, Tiia Ngandu, Miia Kivipelto, Alina Solomon

Brain · 06 Aug 2025 · doi:10.1093/brain/awaf277

Special issue: Decoding atherosclerosis: Epigenetics and functional genomics

Casey E. Romanoski, Minna U. Kaikkonen

Atherosclerosis · 01 Aug 2025 · doi:10.1016/j.atherosclerosis.2025.119230

Genome-wide Cross-multi-trait Analysis into Shared Genetic Architecture of Coronary Artery Disease and Aortic Aneurysms

Jimi Virkkala, Johannes Kettunen, Minna U. Kaikkonen

openRxiv · 28 Jun 2025 · doi:10.1101/2025.06.27.25330395

2024

Coronary Artery Disease Risk Variant Dampens the Expression of CALCRL by Reducing HSF Binding to Shear Stress Responsive Enhancer in Endothelial Cells In Vitro

Ilakya Selvarajan, Miika Kiema, Ru-Ting Huang, Jin Li, Jiayu Zhu, …, Casey E. Romanoski, Merja Heinäniemi, Johanna P. Laakkonen, Yun Fang, Minna U. Kaikkonen

Arteriosclerosis, Thrombosis, and Vascular Biology · 01 Jun 2024 · doi:10.1161/ATVBAHA.123.318964

Technological advancements in functional interpretation of genome wide association studies scp GWAS scp findings: bridging the gap to clinical translation

Technological advancements in functional interpretation of genome‐wide association studies ( GWAS ) findings: bridging the gap to clinical translation

Redouane Aherrahrou, Minna U Kaikkonen

FEBS Letters · 29 Apr 2024 · doi:10.1002/1873-3468.14884

Secreted Protein Profiling of Human Aortic Smooth Muscle Cells Identifies Vascular Disease Associations

Rédouane Aherrahrou, Ferheen Baig, Konstantinos Theofilatos, Dillon Lue, Alicia Beele, …, Aloke V. Finn, Gary K. Owens, Michael Joner, Manuel Mayr, Mete Civelek

Arteriosclerosis, Thrombosis, and Vascular Biology · 01 Apr 2024 · doi:10.1161/ATVBAHA.123.320274

Genetic variation drives differences in obesity-related gene regulation

Minna U. Kaikkonen

Trends in Genetics · 01 Apr 2024 · doi:10.1016/j.tig.2024.02.009

The critical role of isomiRs in accurate differential expression analysis of miRNA-seq data

Eloi Schmauch, Yassine Attia, Pia Laitinen, Tiia A. Turunen, Piia Bartos, …, Tarja Malm, Pasi Tavi, Manolis Kellis, Minna U Kaikkonen, Suvi Linna-Kuosmanen

openRxiv · 31 Mar 2024 · doi:10.1101/2024.03.28.587190

Translatome profiling reveals i Itih4 i as a novel smooth muscle cell specific gene in atherosclerosis

Translatome profiling reveals Itih4 as a novel smooth muscle cell–specific gene in atherosclerosis

Aarthi Ravindran, Lari Holappa, Henri Niskanen, Ilya Skovorodkin, Susanna Kaisto, …, Johanna P Laakkonen, Seppo Ylä-Herttuala, Seppo Vainio, Tiit Örd, Minna U Kaikkonen

Cardiovascular Research · 30 Jan 2024 · doi:10.1093/cvr/cvae028

Mechanosensitive super-enhancers regulate genes linked to atherosclerosis in endothelial cells

Jin Li, Jiayu Zhu, Olivia Gray, Débora R. Sobreira, David Wu, …, Matthew D. Krause, Minna U. Kaikkonen, Casey E. Romanoski, Marcelo A. Nobrega, Yun Fang

Journal of Cell Biology · 17 Jan 2024 · doi:10.1083/jcb.202211125

2023

Secreted protein profiling of human aortic smooth muscle cells identifies vascular disease associations

Rédouane Aherrahrou, Ferheen Baig, Konstantinos Theofilatos, Dillon Lue, Alicia Beele, …, Aloke Finn, Gary K. Owens, Michael Joner, Manuel Mayr, Mete Civelek

openRxiv · 11 Nov 2023 · doi:10.1101/2023.11.10.23298351

Exploring the genetic basis of coronary artery disease using functional genomics

Maykel López Rodríguez, Uma Thanigai Arasu, Minna U. Kaikkonen

Atherosclerosis · 01 Jun 2023 · doi:10.1016/j.atherosclerosis.2023.01.019

ApoA-I Nanotherapy Rescues Postischemic Vascular Maladaptation by Modulating Endothelial Cell and Macrophage Phenotypes in Type 2 Diabetic Mice

Mohan Babu, Durga Devi, Petri Mäkinen, Tiit Örd, Einari Aavik, Minna Kaikkonen, Seppo Ylä-Herttuala

Arteriosclerosis, Thrombosis, and Vascular Biology · 01 Jan 2023 · doi:10.1161/ATVBAHA.122.318196

2022

The Power of Single-Cell RNA Sequencing in eQTL Discovery

Maleeha Maria, Negar Pouyanfar, Tiit Örd, Minna U. Kaikkonen

Genes · 12 Mar 2022 · doi:10.3390/genes13030502

Functional noncoding SNPs in human endothelial cells fine-map vascular trait associations

Anu Toropainen, Lindsey K. Stolze, Tiit Örd, Michael B. Whalen, Paula Martí Torrell, Verena M. Link, Minna U. Kaikkonen, Casey E. Romanoski

Genome Research · 22 Feb 2022 · doi:10.1101/gr.276064.121

Single-Cell RNA-Seq Analysis of Olfactory Mucosal Cells of Alzheimer’s Disease Patients

Riikka Lampinen, Mohammad Feroze Fazaludeen, Simone Avesani, Tiit Örd, Elina Penttilä, …, Tarja Malm, Anthony R. White, Rosalba Giugno, Sweelin Chew, Katja M. Kanninen

Cells · 15 Feb 2022 · doi:10.3390/cells11040676

2021

isomiRs-specific differential expression is the rule, not the exception: Are we missing hundreds of species in microRNA analysis?

Eloi Schmauch, Pia Laitinen, Tiia A. Turunen, Mari-Anna Väänänen, Tarja Malm, Manolis Kellis, Minna U Kaikkonen, Suvi Linna-Kuosmanen

openRxiv · 17 Dec 2021 · doi:10.1101/2021.12.15.472814

Functional non-coding SNPs in human endothelial cells fine-map vascular trait associations

Anu Toropainen, Lindsey K. Stolze, Tiit Örd, Michael Whalen, Paula Martí Torrell, Verena M. Link, Minna U Kaikkonen, Casey Romanoski

openRxiv · 03 Aug 2021 · doi:10.1101/2021.08.03.454513

Characterization of a functional endothelial super-enhancer that regulates ADAMTS18 and angiogenesis

Isidore Mushimiyimana, Henri Niskanen, Mustafa Beter, Johanna P Laakkonen, Minna U Kaikkonen, Seppo Ylä-Herttuala, Nihay Laham-Karam

Nucleic Acids Research · 28 Jul 2021 · doi:10.1093/nar/gkab633

Single-Cell Epigenomics and Functional Fine-Mapping of Atherosclerosis GWAS Loci

Tiit Örd, Kadri Õunap, Lindsey K. Stolze, Redouane Aherrahrou, Valtteri Nurminen, …, Einari Aavik, Seppo Ylä-Herttuala, Mete Civelek, Casey E. Romanoski, Minna U. Kaikkonen

Circulation Research · 09 Jul 2021 · doi:10.1161/circresaha.121.318971

Profiling of Primary and Mature miRNA Expression in Atherosclerosis-Associated Cell Types

Pierre R. Moreau, Vanesa Tomas Bosch, Maria Bouvy-Liivrand, Kadri Õunap, Tiit Örd, …, Merja Heinäniemi, Seppo Ylä-Herttuala, Johanna P. Laakkonen, Suvi Linna-Kuosmanen, Minna U. Kaikkonen

Arteriosclerosis, Thrombosis, and Vascular Biology · 01 Jul 2021 · doi:10.1161/atvbaha.121.315579

Genomic Landscapes of Noncoding RNAs Regulating i VEGFA i and i VEGFC i Expression in Endothelial Cells

Genomic Landscapes of Noncoding RNAs Regulating VEGFA and VEGFC Expression in Endothelial Cells

Isidore Mushimiyimana, Vanesa Tomas Bosch, Henri Niskanen, Nicholas L. Downes, Pierre R. Moreau, Kiley Hartigan, Seppo Ylä-Herttuala, Nihay Laham-Karam, Minna U. Kaikkonen

Molecular and Cellular Biology · 01 Jul 2021 · doi:10.1128/MCB.00594-20

Cardiovascular disease causes proinflammatory microvascular changes in the human right atrium

Suvi Linna-Kuosmanen, Eloi Schmauch, Kyriakitsa Galani, Johannes Ojanen, Carles A. Boix, …, Minna U. Kaikkonen, Guillermo García-Cardeña, Pasi Tavi, Tuomas Kiviniemi, Manolis Kellis

openRxiv · 24 Jun 2021 · doi:10.1101/2021.06.23.449672

Meta-Analysis of Smooth Muscle Lineage Transcriptomes in Atherosclerosis and Their Relationships to In Vitro Models

Austin C. Conklin, Hitoo Nishi, Florencia Schlamp, Tiit Ord, Kadri Ounap, Minna U. Kaikkonen, Edward A. Fisher, Casey E. Romanoski

Immunometabolism · 21 May 2021 · doi:10.20900/immunometab20210022

Pharmacological or TRIB3-Mediated Suppression of ATF4 Transcriptional Activity Promotes Hepatoma Cell Resistance to Proteasome Inhibitor Bortezomib

Tiit Örd, Daima Örd, Minna U. Kaikkonen, Tõnis Örd

Cancers · 12 May 2021 · doi:10.3390/cancers13102341

The corepressors GPS2 and SMRT control enhancer and silencer remodeling via eRNA transcription during inflammatory activation of macrophages

Zhiqiang Huang, Ning Liang, Saioa Goñi, Anastasios Damdimopoulos, Cheng Wang, …, Myriam Aouadi, Nicolas Venteclef, Minna U. Kaikkonen, Rongrong Fan, Eckardt Treuter

Molecular Cell · 01 Mar 2021 · doi:10.1016/j.molcel.2020.12.040

Integrative analysis of liver-specific non-coding regulatory SNPs associated with the risk of coronary artery disease

Ilakya Selvarajan, Anu Toropainen, Kristina M. Garske, Maykel López Rodríguez, Arthur Ko, …, Sami Heikkinen, Casey E. Romanoski, Jussi Pihlajamäki, Päivi Pajukanta, Minna U. Kaikkonen

The American Journal of Human Genetics · 01 Mar 2021 · doi:10.1016/j.ajhg.2021.02.006

Polycomb Repressive Complex 2 Regulates Genes Necessary for Intestinal Microfold Cell (M Cell) Development

Joel Johnson George, Mikko Oittinen, Laura Martin-Diaz, Veronika Zapilko, Sharif Iqbal, …, Fábio Tadeu Arrojo Martins, Henri Niskanen, Pekka Katajisto, Minna U. Kaikkonen, Keijo Viiri

Cellular and Molecular Gastroenterology and Hepatology · 01 Jan 2021 · doi:10.1016/j.jcmgh.2021.05.014

2020

Peripheral inflammation preceeding ischemia impairs neuronal survival through mechanisms involving miR‐127 in aged animals

Sanna Loppi, Paula Korhonen, Maria Bouvy‐Liivrand, Simone Caligola, Tiia A. Turunen, …, Katja M. Kanninen, Minna U. Kaikkonen, Rosalba Giugno, Merja Heinäniemi, Tarja Malm

Aging Cell · 28 Dec 2020 · doi:10.1111/acel.13287

Genetic Regulation of Atherosclerosis-Relevant Phenotypes in Human Vascular Smooth Muscle Cells

Redouane Aherrahrou, Liang Guo, V. Peter Nagraj, Aaron Aguhob, Jameson Hinkle, …, Aloke Finn, Mohamad Navab, Alan M. Fogelman, Judith A. Berliner, Mete Civelek

Circulation Research · 04 Dec 2020 · doi:10.1161/circresaha.120.317415

Disease specific alterations in the olfactory mucosa of patients with Alzheimer’s disease

Riikka Lampinen, Mohammad Feroze Fazaludeen, Simone Avesani, Tiit Örd, Elina Penttilä, …, Anne M Koivisto, Anthony R White, Rosalba Giugno, Sweelin Chew, Katja M Kanninen

openRxiv · 24 Nov 2020 · doi:10.1101/2020.11.24.395947

Polycomb Repressive Complex 2-controlled Essrg regulates intestinal Microfold cell differentiation

Joel Johnson George, Mikko Oittinen, Laura Martin-Diaz, Veronika Zapilko, Sharif Iqbal, …, Fábio Tadeu Arrojo Martins, Henri Niskanen, Pekka Katajisto, Minna Kaikkonen, Keijo Viiri

openRxiv · 13 Nov 2020 · doi:10.1101/2020.11.13.379610

Microanatomy of the Human Atherosclerotic Plaque by Single-Cell Transcriptomics

Marie A.C. Depuydt, Koen H.M. Prange, Lotte Slenders, Tiit Örd, Danny Elbersen, …, Seppo Yla-Herttuala, Michal Mokry, Johan Kuiper, Menno P.J. de Winther, Gerard Pasterkamp

Circulation Research · 06 Nov 2020 · doi:10.1161/circresaha.120.316770

Hypoxia-Mediated Regulation of Histone Demethylases Affects Angiogenesis-Associated Functions in Endothelial Cells

Oscar Hsin-Fu Liu, Miika Kiema, Mustafa Beter, Seppo Ylä-Herttuala, Johanna P. Laakkonen, Minna U. Kaikkonen

Arteriosclerosis, Thrombosis, and Vascular Biology · 01 Nov 2020 · doi:10.1161/ATVBAHA.120.315214

BMP6/TAZ-Hippo signaling modulates angiogenesis and endothelial cell response to VEGF

H. H. Pulkkinen, M. Kiema, J. P. Lappalainen, A. Toropainen, M. Beter, …, L. Holappa, H. Niskanen, M. U. Kaikkonen, S. Ylä-Herttuala, Johanna P. Laakkonen

Angiogenesis · 06 Oct 2020 · doi:10.1007/s10456-020-09748-4

The proapoptotic gene interferon regulatory factor-1 mediates the antiproliferative outcome of paired box 2 gene and tamoxifen

Shixiong Wang, Venkata S. Somisetty, Baoyan Bai, Igor Chernukhin, Henri Niskanen, Minna U. Kaikkonen, Meritxell Bellet, Jason S. Carroll, Antoni Hurtado

Oncogene · 25 Aug 2020 · doi:10.1038/s41388-020-01435-4

Radiosynthesis and preclinical evaluation of [68Ga]Ga-NOTA-folate for PET imaging of folate receptor β-positive macrophages

Olli Moisio, Senthil Palani, Jenni Virta, Petri Elo, Heidi Liljenbäck, …, Juhani Knuuti, Philip S. Low, Antti Saraste, Xiang-Guo Li, Anne Roivainen

Scientific Reports · 12 Aug 2020 · doi:10.1038/s41598-020-70394-3

NRF2 is a key regulator of endothelial microRNA expression under proatherogenic stimuli

Suvi Linna-Kuosmanen, Vanesa Tomas Bosch, Pierre R Moreau, Maria Bouvy-Liivrand, Henri Niskanen, …, Mikko Hippeläinen, Hannu Kokki, Pasi Tavi, Anna-Liisa Levonen, Minna U Kaikkonen

Cardiovascular Research · 19 Jul 2020 · doi:10.1093/cvr/cvaa219

Systems Genetics in Human Endothelial Cells Identifies Non-coding Variants Modifying Enhancers, Expression, and Complex Disease Traits

Lindsey K. Stolze, Austin C. Conklin, Michael B. Whalen, Maykel López Rodríguez, Kadri Õunap, …, Anna Eshghi, Alice E. Solomon, Yun Fang, Minna U. Kaikkonen, Casey E. Romanoski

The American Journal of Human Genetics · 01 Jun 2020 · doi:10.1016/j.ajhg.2020.04.008

2019

Comparative transcriptome analysis of matched primary and distant metastatic ovarian carcinoma

H. Sallinen, S. Janhonen, P. Pölönen, H. Niskanen, O. H. Liu, …, J. M. Hartikainen, M. Anttila, M. Heinäniemi, S. Ylä-Herttuala, M. U. Kaikkonen

BMC Cancer · 19 Nov 2019 · doi:10.1186/s12885-019-6339-0

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

Jihane N. Benhammou, Arthur Ko, Marcus Alvarez, Minna U. Kaikkonen, Carl Rankin, …, Dorota Kaminska, Vesa Kärjä, Jussi Pihlajamäki, Joseph R. Pisegna, Päivi Pajukanta

Hepatology Communications · 14 Aug 2019 · doi:10.1002/hep4.1413

Axon Guidance-Related Factor FLRT3 Regulates VEGF-Signaling and Endothelial Cell Function

Suvi Jauhiainen, Johanna P. Laakkonen, Kirsi Ketola, Pyry I. Toivanen, Tiina Nieminen, Takeshi Ninchoji, Anna-Liisa Levonen, Minna U. Kaikkonen, Seppo Ylä-Herttuala

Frontiers in Physiology · 12 Mar 2019 · doi:10.3389/fphys.2019.00224

Extensive reprogramming of the nascent transcriptome during iPSC to hepatocyte differentiation

Leena E. Viiri, Tommi Rantapero, Mostafa Kiamehr, Anna Alexanova, Mikko Oittinen, Keijo Viiri, Henri Niskanen, Matti Nykter, Minna U. Kaikkonen, Katriina Aalto-Setälä

Scientific Reports · 05 Mar 2019 · doi:10.1038/s41598-019-39215-0

Therapeutic effects of rosuvastatin in hypercholesterolemic prediabetic mice in the absence of low density lipoprotein receptor

Erika Gurzeler, Einari Aavik, Anssi Laine, Teemu Valkama, Henri Niskanen, Jenni Huusko, Minna U. Kaikkonen, Seppo Ylä-Herttuala

Biochimica et Biophysica Acta (BBA) - General Subjects · 01 Feb 2019 · doi:10.1016/j.bbagen.2018.11.012

2018

Transcriptional Profiling of Hypoxia-Regulated Non-coding RNAs in Human Primary Endothelial Cells

Pierre R. Moreau, Tiit Örd, Nicholas L. Downes, Henri Niskanen, Maria Bouvy-Liivrand, Einari Aavik, Seppo Ylä-Herttuala, Minna U. Kaikkonen

Frontiers in Cardiovascular Medicine · 05 Nov 2018 · doi:10.3389/fcvm.2018.00159

Functional Variant in the GCKR Gene Affects Lactate Levels Differentially in the Fasting State and During Hyperglycemia

Maykel López Rodríguez, Lilian Fernandes Silva, Jagadish Vangipurapu, Shalem Modi, Johanna Kuusisto, Minna U. Kaikkonen, Markku Laakso

Scientific Reports · 30 Oct 2018 · doi:10.1038/s41598-018-34501-9

Deletion of Lymphangiogenic and Angiogenic Growth Factor VEGF-D Leads to Severe Hyperlipidemia and Delayed Clearance of Chylomicron Remnants

Annakaisa Tirronen, Taina Vuorio, Sanna Kettunen, Krista Hokkanen, Bastian Ramms, …, Hanne Laakso, Minna U. Kaikkonen, Matti Jauhiainen, Philip L.S.M. Gordts, Seppo Ylä-Herttuala

Arteriosclerosis, Thrombosis, and Vascular Biology · 01 Oct 2018 · doi:10.1161/atvbaha.118.311549

MicroRNAs mediate the senescence-associated decline of NRF2 in endothelial cells

Suvi M. Kuosmanen, Virve Sihvola, Emilia Kansanen, Minna U. Kaikkonen, Anna-Liisa Levonen

Redox Biology · 01 Sep 2018 · doi:10.1016/j.redox.2018.06.007

Emerging Roles of Non-Coding RNA Transcription

Minna U. Kaikkonen, Karen Adelman

Trends in Biochemical Sciences · 01 Sep 2018 · doi:10.1016/j.tibs.2018.06.002

Control of inducible gene expression links cohesin to hematopoietic progenitor self-renewal and differentiation

Sergi Cuartero, Felix D. Weiss, Gopuraja Dharmalingam, Ya Guo, Elizabeth Ing-Simmons, …, Kim A. Nasmyth, Boris Lenhard, Gioacchino Natoli, Amanda G. Fisher, Matthias Merkenschlager

Nature Immunology · 20 Aug 2018 · doi:10.1038/s41590-018-0184-1

Genetics instability of wtAAV2 genome and AAV promoter activities in the Baculovirus/Sf9 cells system

Adrien Savy, Minna U. Kaikkonen, Adrien Léger, Yohann Dickx, Lionel Galibert, Otto-Wilhelm Merten

PLOS ONE · 05 Jul 2018 · doi:10.1371/journal.pone.0199866

Differential but Complementary HIF1α and HIF2α Transcriptional Regulation

Nicholas L. Downes, Nihay Laham-Karam, Minna U. Kaikkonen, Seppo Ylä-Herttuala

Molecular Therapy · 01 Jul 2018 · doi:10.1016/j.ymthe.2018.05.004

Temporal Dynamics of Gene Expression During Endothelial Cell Differentiation From Human iPS Cells: A Comparison Study of Signalling Factors and Small Molecules

Heini Belt, Jonna K. Koponen, Tuija Kekarainen, Katja A. Puttonen, Petri I. Mäkinen, …, Joni Oja, Galina Wirth, Jari Koistinaho, Minna U. Kaikkonen, Seppo Ylä-Herttuala

Frontiers in Cardiovascular Medicine · 14 Mar 2018 · doi:10.3389/fcvm.2018.00016

2017

Endothelial cell differentiation is encompassed by changes in long range interactions between inactive chromatin regions

Henri Niskanen, Irina Tuszynska, Rafal Zaborowski, Merja Heinäniemi, Seppo Ylä-Herttuala, Bartek Wilczynski, Minna U Kaikkonen

Nucleic Acids Research · 04 Dec 2017 · doi:10.1093/nar/gkx1214

Aggravated Postinfarct Heart Failure in Type 2 Diabetes Is Associated with Impaired Mitophagy and Exaggerated Inflammasome Activation

Thota Durga Devi, Mohan Babu, Petri Mäkinen, Minna U. Kaikkonen, Merja Heinaniemi, …, Lassi Rieppo, Timo Liimatainen, Nikolay Naumenko, Pasi Tavi, Seppo Ylä-Herttuala

The American Journal of Pathology · 01 Dec 2017 · doi:10.1016/j.ajpath.2017.08.023

NRF2 regulates endothelial glycolysis and proliferation with miR-93 and mediates the effects of oxidized phospholipids on endothelial activation

Suvi M Kuosmanen, Emilia Kansanen, Minna U Kaikkonen, Virve Sihvola, Kati Pulkkinen, …, Mikko Hippeläinen, Hannu Kokki, Pasi Tavi, Sami Heikkinen, Anna-Liisa Levonen

Nucleic Acids Research · 17 Nov 2017 · doi:10.1093/nar/gkx1155

Analysis of primary microRNA loci from nascent transcriptomes reveals regulatory domains governed by chromatin architecture

Maria Bouvy-Liivrand, Ana Hernández de Sande, Petri Pölönen, Juha Mehtonen, Tapio Vuorenmaa, Henri Niskanen, Lasse Sinkkonen, Minna Unelma Kaikkonen, Merja Heinäniemi

Nucleic Acids Research · 03 Oct 2017 · doi:10.1093/nar/gkx909

Analysis of primary microRNA loci from nascent transcriptomes reveals regulatory domains governed by chromatin architecture

Maria Bouvy-Liivrand, Ana Hernández de Sande, Petri Pölönen, Juha Mehtonen, Tapio Vuorenmaa, Henri Niskanen, Lasse Sinkkonen, Minna Unelma Kaikkonen, Merja Heinäniemi

Nucleic Acids Research · 29 Jul 2017 · doi:10.1093/nar/gkx680

Snake venom VEGF Vammin induces a highly efficient angiogenic response in skeletal muscle via VEGFR-2/NRP specific signaling

Pyry I. Toivanen, Tiina Nieminen, Johanna P. Laakkonen, Tommi Heikura, Minna U. Kaikkonen, Seppo Ylä-Herttuala

Scientific Reports · 17 Jul 2017 · doi:10.1038/s41598-017-05876-y

Identification and characterization of a FOXA2-regulated transcriptional enhancer at a type 2 diabetes intronic locus that controls GCKR expression in liver cells

Maykel López Rodríguez, Dorota Kaminska, Kati Lappalainen, Jussi Pihlajamäki, Minna U. Kaikkonen, Markku Laakso

Genome Medicine · 06 Jul 2017 · doi:10.1186/s13073-017-0453-x

Genome-Wide Dynamics of Nascent Noncoding RNA Transcription in Porcine Heart After Myocardial Infarction

Minna U. Kaikkonen, Paavo Halonen, Oscar Hsin-Fu Liu, Tiia A. Turunen, Juho Pajula, …, Ilakya Selvarajan, Tomi Tuomainen, Einari Aavik, Pasi Tavi, Seppo Ylä-Herttuala

Circulation: Cardiovascular Genetics · 01 Jun 2017 · doi:10.1161/circgenetics.117.001702

SREBP1 Contributes to Resolution of Pro-inflammatory TLR4 Signaling by Reprogramming Fatty Acid Metabolism

Yumiko Oishi, Nathanael J. Spann, Verena M. Link, Evan D. Muse, Tobias Strid, …, Michael T. Lam, Ichiro Manabe, Hitoshi Shimano, Alan Saghatelian, Christopher K. Glass

Cell Metabolism · 01 Feb 2017 · doi:10.1016/j.cmet.2016.11.009

2016

Differential regulation of angiogenic cellular processes and claudin-5 by histamine and VEGF via PI3K-signaling, transcription factor SNAI2 and interleukin-8

Johanna P. Laakkonen, Jari P. Lappalainen, Thomas L. Theelen, Pyry I. Toivanen, Tiina Nieminen, Suvi Jauhiainen, Minna U. Kaikkonen, Judith C. Sluimer, Seppo Ylä-Herttuala

Angiogenesis · 21 Nov 2016 · doi:10.1007/s10456-016-9532-7

Crosstalk between androgen and pro-inflammatory signaling remodels androgen receptor and NF-κB cistrome to reprogram the prostate cancer cell transcriptome

Marjo Malinen, Einari A. Niskanen, Minna U. Kaikkonen, Jorma J. Palvimo

Nucleic Acids Research · 26 Sep 2016 · doi:10.1093/nar/gkw855

Global analysis of transcription in castration-resistant prostate cancer cells uncovers active enhancers and direct androgen receptor targets

Sari Toropainen, Einari A. Niskanen, Marjo Malinen, Päivi Sutinen, Minna U. Kaikkonen, Jorma J. Palvimo

Scientific Reports · 19 Sep 2016 · doi:10.1038/srep33510

Polycomb Repressive Complex 2 Enacts Wnt Signaling in Intestinal Homeostasis and Contributes to the Instigation of Stemness in Diseases Entailing Epithelial Hyperplasia or Neoplasia

Mikko Oittinen, Alina Popp, Kalle Kurppa, Katri Lindfors, Markku Mäki, Minna U. Kaikkonen, Keijo Viiri

Stem Cells · 13 Sep 2016 · doi:10.1002/stem.2479

Transcription-coupled genetic instability marks acute lymphoblastic leukemia structural variation hotspots

Merja Heinäniemi, Tapio Vuorenmaa, Susanna Teppo, Minna U Kaikkonen, Maria Bouvy-Liivrand, …, Vasilios Zachariadis, Saara Laukkanen, Thomas Liuksiala, Kaisa Teittinen, Olli Lohi

eLife · 19 Jul 2016 · doi:10.7554/elife.13087

2015

Transcription factor Nr4a1 couples sympathetic and inflammatory cues in CNS-recruited macrophages to limit neuroinflammation

Iftach Shaked, Richard N Hanna, Helena Shaked, Grzegorz Chodaczek, Heba N Nowyhed, …, Ayman Rezk, Amit Bar-Or, Christopher K Glass, Hozefa Bandukwala, Catherine C Hedrick

Nature Immunology · 01 Dec 2015 · doi:10.1038/ni.3321

Global SUMOylation on active chromatin is an acute heat stress response restricting transcription

Einari A. Niskanen, Marjo Malinen, Päivi Sutinen, Sari Toropainen, Ville Paakinaho, Anniina Vihervaara, Jenny Joutsen, Minna U. Kaikkonen, Lea Sistonen, Jorma J. Palvimo

Genome Biology · 28 Jul 2015 · doi:10.1186/s13059-015-0717-y

Differential Promoter Methylation of Macrophage Genes Is Associated With Impaired Vascular Growth in Ischemic Muscles of Hyperlipidemic and Type 2 Diabetic Mice

Mohan Babu, Thota Durga Devi, Petri Mäkinen, Minna Kaikkonen, Hanna P. Lesch, Sini Junttila, Asta Laiho, Bishwa Ghimire, Attila Gyenesei, Seppo Ylä-Herttuala

Circulation Research · 17 Jul 2015 · doi:10.1161/circresaha.115.306424

Quantification of nascent transcription by bromouridine immunocapture nuclear run-on RT-qPCR

Thomas C Roberts, Jonathan R Hart, Minna U Kaikkonen, Marc S Weinberg, Peter K Vogt, Kevin V Morris

Nature Protocols · 16 Jul 2015 · doi:10.1038/nprot.2015.076

Slit2 modifies VEGF-induced angiogenic responses in rabbit skeletal muscle via reduced eNOS activity

Tiina Nieminen, Pyry I. Toivanen, Johanna P. Laakkonen, Tommi Heikura, Minna U. Kaikkonen, Kari J. Airenne, Seppo Ylä-Herttuala

Cardiovascular Research · 22 May 2015 · doi:10.1093/cvr/cvv161

2014

Control of VEGF-A transcriptional programs by pausing and genomic compartmentalization

Minna U. Kaikkonen, Henri Niskanen, Casey E. Romanoski, Emilia Kansanen, Annukka M. Kivelä, Jarkko Laitalainen, Sven Heinz, Christopher Benner, Christopher K. Glass, Seppo Ylä-Herttuala

Nucleic Acids Research · 28 Oct 2014 · doi:10.1093/nar/gku1036

Clonal variation in interferon response determines the outcome of oncolytic virotherapy in mouse CT26 colon carcinoma model

J J Ruotsalainen, M U Kaikkonen, M Niittykoski, M W Martikainen, C G Lemay, …, F Le Boeuf, J C Bell, S Ylä-Herttuala, A E Hinkkanen, M J Vähä-Koskela

Gene Therapy · 18 Sep 2014 · doi:10.1038/gt.2014.83

Does mass balance between sense and antisense transcripts fine‐tune the outcome of gene expression?

Seppo Ylä‐Herttuala, Minna Kaikkonen

EMBO reports · 15 Jan 2014 · doi:10.1002/embr.201338030

Biodistribution and antitumor effect of Cetuximab-targeted lentivirus

Tuulia Huhtala, Minna U. Kaikkonen, Hanna P. Lesch, Sari Viitala, Seppo Ylä-Herttuala, Ale Närvänen

Nuclear Medicine and Biology · 01 Jan 2014 · doi:10.1016/j.nucmedbio.2013.10.005

2013

Vespucci: a system for building annotated databases of nascent transcripts

Karmel A. Allison, Minna U. Kaikkonen, Terry Gaasterland, Christopher K. Glass

Nucleic Acids Research · 04 Dec 2013 · doi:10.1093/nar/gkt1237

25-Hydroxycholesterol Activates the Integrated Stress Response to Reprogram Transcription and Translation in Macrophages

Norihito Shibata, Aaron F. Carlin, Nathanael J. Spann, Kaoru Saijo, Christopher S. Morello, …, Shankar Subramaniam, Douglas R. Cavener, Deborah H. Spector, David W. Russell, Christopher K. Glass

Journal of Biological Chemistry · 01 Dec 2013 · doi:10.1074/jbc.M113.519637

Effect of natural genetic variation on enhancer selection and function

S. Heinz, C. E. Romanoski, C. Benner, K. A. Allison, M. U. Kaikkonen, L. D. Orozco, C. K. Glass

Nature · 13 Oct 2013 · doi:10.1038/nature12615

NCoR Repression of LXRs Restricts Macrophage Biosynthesis of Insulin-Sensitizing Omega 3 Fatty Acids

Pingping Li, Nathanael J. Spann, Minna U. Kaikkonen, Min Lu, Da Young Oh, …, Edward A. Dennis, Steven M. Watkins, Johan Auwerx, Christopher K. Glass, Jerrold M. Olefsky

Cell · 01 Sep 2013 · doi:10.1016/j.cell.2013.08.054

Remodeling of the Enhancer Landscape during Macrophage Activation Is Coupled to Enhancer Transcription

Minna U. Kaikkonen, Nathanael J. Spann, Sven Heinz, Casey E. Romanoski, Karmel A. Allison, …, Hyun B. Chun, David F. Tough, Rab K. Prinjha, Christopher Benner, Christopher K. Glass

Molecular Cell · 01 Aug 2013 · doi:10.1016/j.molcel.2013.07.010

Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription

Michael T. Y. Lam, Han Cho, Hanna P. Lesch, David Gosselin, Sven Heinz, …, Andy Watt, Tamar R. Grossman, Michael G. Rosenfeld, Ronald M. Evans, Christopher K. Glass

Nature · 01 Jun 2013 · doi:10.1038/nature12209

2012

Distribution and Dynamics of Transcription-Associated Proteins during Parvovirus Infection

Teemu O. Ihalainen, Sami F. Willman, Einari A. Niskanen, Outi Paloheimo, Hanna Smolander, Juha P. Laurila, Minna U. Kaikkonen, Maija Vihinen-Ranta

Journal of Virology · 15 Dec 2012 · doi:10.1128/JVI.01625-12

Targeted delivery via avidin fusion protein: Intracellular fate of biotinylated doxorubicin derivative and cellular uptake kinetics and biodistribution of biotinylated liposomes

Suvi K. Soininen, Pauliina Lehtolainen-Dalkilic, Tanja Karppinen, Tiina Puustinen, Galina Dragneva, …, Hanna P. Lesch, Ann-Marie Määttä, Jukka Mönkkönen, Seppo Ylä-Herttuala, Marika Ruponen

European Journal of Pharmaceutical Sciences · 01 Dec 2012 · doi:10.1016/j.ejps.2012.09.001

Oxidative Stress-Regulated Lentiviral TK/GCV Gene Therapy for Lung Cancer Treatment

Hanna M. Leinonen, Anna-Kaisa Ruotsalainen, Ann-Marie Määttä, Heidi M. Laitinen, Suvi M. Kuosmanen, …, Haritha Samaranayake, Hanna P. Lesch, Minna U. Kaikkonen, Seppo Ylä-Herttuala, Anna-Liisa Levonen

Cancer Research · 29 Nov 2012 · doi:10.1158/0008-5472.CAN-12-1166

Control of Proinflammatory Gene Programs by Regulated Trimethylation and Demethylation of Histone H4K20

Joshua D. Stender, Gabriel Pascual, Wen Liu, Minna U. Kaikkonen, Kevin Do, Nathanael J. Spann, Michael Boutros, Norbert Perrimon, Michael G. Rosenfeld, Christopher K. Glass

Molecular Cell · 01 Oct 2012 · doi:10.1016/j.molcel.2012.07.020

In Vitro Targeting of Avidin-Expressing Glioma Cells with Biotinylated Persistent Luminescence Nanoparticles

Thomas Maldiney, Minna U. Kaikkonen, Johanne Seguin, Quentin le Masne de Chermont, Michel Bessodes, Kari J. Airenne, Seppo Ylä-Herttuala, Daniel Scherman, Cyrille Richard

Bioconjugate Chemistry · 07 Feb 2012 · doi:10.1021/bc200510z

Baculovirus mediated vascular endothelial growth factor D sup ΔNΔC sup gene transfer induces angiogenesis in rabbit skeletal muscle

Baculovirus‐mediated vascular endothelial growth factor‐D^ΔNΔC gene transfer induces angiogenesis in rabbit skeletal muscle

Tommi Heikura, Tiina Nieminen, Miia M. Roschier, Henna Karvinen, Minna U. Kaikkonen, …, Hanna P. Lesch, Tuomas T. Rissanen, Olli H. Laitinen, Kari J. Airenne, Seppo Ylä‐Herttuala

The Journal of Gene Medicine · 01 Jan 2012 · doi:10.1002/jgm.1637

2011

Mechanisms Establishing TLR4-Responsive Activation States of Inflammatory Response Genes

Laure Escoubet-Lozach, Christopher Benner, Minna U. Kaikkonen, Jean Lozach, Sven Heinz, …, Alexander Hoffmann, Shankar Subramaniam, Gary Hardiman, Michael G. Rosenfeld, Christopher K. Glass

PLoS Genetics · 08 Dec 2011 · doi:10.1371/journal.pgen.1002401

How to avoid complement attack in baculovirus-mediated gene delivery

Minna U. Kaikkonen, Seppo Ylä-Herttuala, Kari J. Airenne

Journal of Invertebrate Pathology · 01 Jul 2011 · doi:10.1016/j.jip.2011.05.007

Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA

Dong Wang, Ivan Garcia-Bassets, Chris Benner, Wenbo Li, Xue Su, …, Minna U. Kaikkonen, Kenneth A. Ohgi, Christopher K. Glass, Michael G. Rosenfeld, Xiang-Dong Fu

Nature · 15 May 2011 · doi:10.1038/nature10006

Non-coding RNAs as regulators of gene expression and epigenetics

M. U. Kaikkonen, M. T. Y. Lam, C. K. Glass

Cardiovascular Research · 09 May 2011 · doi:10.1093/cvr/cvr097

2010

Screening of Complement Inhibitors: Shielded Baculoviruses Increase the Safety and Efficacy of Gene Delivery

Minna U Kaikkonen, Antti I Maatta, Seppo Ylä-Herttuala, Kari J Airenne

Molecular Therapy · 01 May 2010 · doi:10.1038/mt.2010.25

Avidin-biotin technology in targeted therapy

Hanna P Lesch, Minna U Kaikkonen, Jere T Pikkarainen, Seppo Ylä-Herttuala

Expert Opinion on Drug Delivery · 16 Mar 2010 · doi:10.1517/17425241003677749

Culture medium induced vimentin reorganization associates with enhanced baculovirus-mediated gene delivery

Anssi J. Mähönen, Kaisa-Emilia Makkonen, Johanna P. Laakkonen, Teemu O. Ihalainen, Sari P. Kukkonen, Minna U. Kaikkonen, Maija Vihinen-Ranta, Seppo Ylä-Herttuala, Kari J. Airenne

Journal of Biotechnology · 01 Jan 2010 · doi:10.1016/j.jbiotec.2009.11.003

2009

Avidin Fusion Protein-Expressing Lentiviral Vector for Targeted Drug Delivery

Hanna P. Lesch, Jere T. Pikkarainen, Minna U. Kaikkonen, Miia Taavitsainen, Haritha Samaranayake, …, Taina Vuorio, Ann-Marie Määttä, Thomas Wirth, Kari J. Airenne, Seppo Ylä-Herttuala

Human Gene Therapy · 01 Aug 2009 · doi:10.1089/hum.2009.007

(Strept)avidin-displaying lentiviruses as versatile tools for targeting and dual imaging of gene delivery

M U Kaikkonen, H P Lesch, J Pikkarainen, J K Räty, T Vuorio, …, P Tuunanen, O Gröhn, A Närvänen, K J Airenne, S Ylä-Herttuala

Gene Therapy · 14 May 2009 · doi:10.1038/gt.2009.47

2008

Targeting and Purification of Metabolically Biotinylated Baculovirus

Minna U. Kaikkonen, Jenni I. Viholainen, Ale Närvänen, Seppo Ylä-Herttuala, Kari J. Airenne

Human Gene Therapy · 01 Jun 2008 · doi:10.1089/hum.2007.177

Baculovirus-mediated immediate-early gene expression and nuclear reorganization in human cells

Johanna P. Laakkonen, Minna U. Kaikkonen, Paula H.A. Ronkainen, Teemu O. Ihalainen, Einari A. Niskanen, …, Mirka Salminen, Markku S. Kulomaa, Seppo Ylä-Herttuala, Kari J. Airenne, Maija Vihinen-Ranta

Cellular Microbiology · 01 Mar 2008 · doi:10.1111/j.1462-5822.2007.01074.x

2007

Non-invasive Imaging in Gene Therapy

Jani Kristian Räty, Timo Liimatainen, Minna Unelma Kaikkonen, Olli Gröhn, Kari Jumani Airenne, Seppo Ylä-Herttuala

Molecular Therapy · 01 Sep 2007 · doi:10.1038/sj.mt.6300233

Post-transcriptional regulatory element boosts baculovirus-mediated gene expression in vertebrate cells

Anssi J. Mähönen, Kari J. Airenne, Sanna Purola, Erik Peltomaa, Minna U. Kaikkonen, …, Tommi Heikura, Kati Kinnunen, Miia M. Roschier, Thomas Wirth, Seppo Ylä-Herttuala

Journal of Biotechnology · 01 Aug 2007 · doi:10.1016/j.jbiotec.2007.05.022

SPECT/CT imaging of baculovirus biodistribution in rat

J K Räty, T Liimatainen, T Huhtala, M U Kaikkonen, K J Airenne, J M Hakumäki, A Närvänen, S Ylä-Herttuala

Gene Therapy · 05 Apr 2007 · doi:10.1038/sj.gt.3302934

2005

Truncated vesicular stomatitis virus G protein improves baculovirus transduction efficiency in vitro and in vivo

M U Kaikkonen, J K Räty, K J Airenne, T Wirth, T Heikura, S Ylä-Herttuala

Gene Therapy · 03 Nov 2005 · doi:10.1038/sj.gt.3302657