Group Leader

Tapio Lönnberg, PhD
Adjunct Professor in Genomics
tapio.lonnberg [at] utu.fi

Contact Information

Single-Cell Immunogenomics Group
Turku Bioscience
BioCity, Tykistökatu 6
20520 Turku, Finland
+358 (0)29 450 3738

About our research

Our research aims at gaining deeper understanding of cell fate decisions in the immune system. We leverage single-cell and spatial omics to explore phenotypic heterogeneity beyond the immune cell subsets defined by the expression of cell surface markers. Our current research encompasses arthritic, autoimmune, and cardiovascular diseases, aiming to identify core gene modules that are associated with disease state and can be exploited for more efficient diagnosis, patient stratification, and therapies.

We are affiliated with the InFLAMES flagship and the BioCity Turku MIST research program.

Selected publications

Huuhtanen L, Kasanen H, Peltola K, Lönnberg T, Glumoff V, Brück O, Dufva O, Peltonen K, Vikkula J, Jokinen E, Ilander M, Lee MH, Mäkelä S, Nyakas M, Li B, Hernberg M, Bono P, Lähdesmäki H, Kreutzman A & Mustjoki S:
Single-cell characterization of anti-LAG3+anti-PD1 treatment in melanoma patients.
Journal of Clinical Investigation 2023 e164809. PMID: 36719749

Rytkönen KT, Adossa N, Mahmoudian M, Lönnberg T, Poutanen M & Elo LL:
Cell type markers indicate distinct contributions of decidual stromal cells and natural killer cells in preeclampsia.
Reproduction 2022 1 64(5):V9-V13. PMID: 36111648

Huuhtanen J, Chen L, Jokinen E, Kasanen H, Lönnberg T, Kreutzman A, Peltola K, Hernberg M, Wang C, Yee C, Lähdesmäki H, Davis MM & Mustjoki S:
Evolution and modulation of antigen-specific T cell responses in melanoma patients.
Nature Communications 2022 13(1):5988. PMID: 36220826

Vandamme C, Rytkönen-Nissinen M, Lönnberg T, Randell J, Harvima RJ, Kinnunen T & Virtanen T:
Single-cell characterization of dog allergen-specific T cells reveals T _H 2 heterogeneity in allergic individuals.
J Allergy Clin Immunol. 2022 149(5):1732-1743. PMID: 34863852 

Huuhtanen J, Bhattacharya D, Lönnberg T, Kankainen M, Kerr C, Theodoropoulos J, Rajala H, Gurnari C, Kasanen T, Braun T, Teramo A, Zambello R, Herling M, Ishida F, Kawakami T, Salmi M, Loughran T, Maciejewski JP, Lähdesmäki H, Kelkka T, Mustjoki S:
Single-cell characterization of leukemic and non-leukemic immune repertoires in CD8 ⁺ T-cell large granular lymphocytic leukemia
Nature Communications 2022 13(1):1981. PMID: 35411050

Virtakoivu R, Rannikko JH, Viitala M, Vaura F, Takeda A, Lönnberg T, Koivunen J, Jaakkola P, Pasanen A, Shetty S, de Jonge MJA, Robbrecht D, Ma YT, Skyttä T, Minchom A, Jalkanen S, Karvonen MK, Mandelin J, Bono P & Hollmén M:
Systemic Blockade of Clever-1 Elicits Lymphocyte Activation Alongside Checkpoint Molecule Downregulation in Patients with Solid Tumors: Results from a Phase I/II Clinical Trial.
Clinical Cancer Research 2021 27(15):4205-4220. PMID: 34078651

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, Kaikkonen MU:
Single-Cell Epigenomics and Functional Fine-Mapping of Atherosclerosis GWAS Loci.
Circulation Research 2021 129(2):240-258. PMID: 34024118

Oliva-Olivera W, Castellano-Castillo D, von Meyenn F, Cardona F, Lönnberg T *& Tinahones FJ*:
Human adipose tissue-derived stem cell paracrine networks vary according metabolic risk and after TNFα-induced death: an analysis at the single-cell level.
Metabolism 2021; 116:154466. PMID: 33333081
*) Equal contribution

Kelkka T, Savola P, Bhattacharya D, Huuhtanen J, Lönnberg T, Kankainen M, Paalanen K, Tyster M, Lepistö M, Ellonen P, Smolander J, Eldfors S, Yadav B, Khan S, Koivuniemi R, Sjöwall C, Elo LL, Lähdesmäki H, Maeda Y, Nishikawa H, Leirisalo-Repo M, Sokka-Isler T, & Mustjoki S:
Adult-Onset Anti-Citrullinated Peptide Antibody-Negative Destructive Rheumatoid Arthritis Is

Characterized by a Disease-Specific CD8+ T Lymphocyte Signature.
Frontiers in Immunology 2021; 12:710831. PMID: 34135915

Mehtonen J, Teppo S, Lahnalampi M, Kokko A, Kaukonen R, Oksa L, Bouvy-Liivrand M, Malyukova A, Mäkinen A, Laukkanen S, Mäkinen PI, Rounioja S, Ruusuvuori P, Sangfelt O, Lund R, Lönnberg T, Lohi O & Heinäniemi M:
Single cell characterization of B-lymphoid differentiation and leukemic cell states during chemotherapy in ETV6-RUNX1-positive pediatric leukemia identifies drug-targetable transcription factor activities.
Genome Medicine 2020; 12(1):99. PMID: 33218352

Depuydt MAC, Prange KHM, Slenders L, Örd T, Elbersen D, Boltjes A, de Jager SCA, Asselbergs FW, de Borst GJ, Aavik E, Lönnberg T, Lutgens E, Glass CK, Kaikkonen MU, Bot I, Slütter B, van der Laan SW, Yla-Herttuala S, Mokry M, Kuiper J, de Winther MPJ & Pasterkamp G:
Microanatomy of the human atherosclerotic plaque by single-cell transcriptomics.
Circulation Research 2020 127(11):1437-1455. PMID: 32981416

Soon M, Lee HJ, Engel J, Straube J, Thomas B, Pernold C, Clarke L, Haldar R, Williams C, Lansink L, Kazakoff S, Koufariotis L, Wood S, Chen X, James K, Lönnberg T, Lane S, Belz G, Engwerda C, Khoury D, Davenport MP, Svensson V, Teichmann SA & Haque A:
Transcriptome Dynamics of CD4+ T cells during Malaria Maps Progressive Transition from Effector to Memory.
Nature Immunology 2020; 21(12):1597-1610. PMID: 33046889

Kim D*, Park G*, Huuhtanen J, Lundgren S, Khajuria RK, Hurtado AM, Muñoz-Calleja C, Cardeñoso L, Gómez-García de Soria V, Chen-Liang TH, Eldfors S, Ellonen P, Hannula S, Bruck O, Kreutzman A, Salmenniemi U, Lönnberg T, Jerez A, Itälä-Remes M, Myllymäki M, Keränen MAI & Mustjoki S:
Somatic Gain-of-Function mTOR mutation in Clonally Expanded T-lymphocytes Associated with Chronic Graft-Versus-Host Disease
Nature communications 2020; 11(1):2246. PMID: 32382059
*) Equal contribution

Takeda A, Hollmén M, Dermadi D, Pan J, Brulois KF, Kaukonen R, Lönnberg T, Boström P, Koskivuo I, Irjala H, Miyasaka M, Salmi M, Butcher EC & Jalkanen S:
Single-Cell Survey of Human Lymphatics Unveils Marked Endothelial Cell Heterogeneity and Mechanisms of Homing for Neutrophils.
Immunity 2019; 51(3):561-72. PMID: 31402260

Kallionpää H, Somani J, Tuomela S, Ullah U, de Albuquerque R, Lönnberg T, Komsi E, Siljander H, Honkanen J, Härkönen T, Peet A, Tillmann T, Chandra V, Anagandula MK, Frisk G, Otonkoski T, Rasool O, Lund R, Lähdesmäki H, Knip M & Lahesmaa R.
Early detection of peripheral blood cell signature in children developing beta-cell autoimmunity at a young age.
Diabetes 2019; 68(10), 2024-2034. PMID 31311800

Miragaia RJ, Zhang X, Gomes T, Svensson V, Ilicic T, Henriksson J, Kar G & Lönnberg T.
Single-cell RNA-sequencing resolves self-antigen expression during mTEC development.
Scientific Reports 2018; 8(1):685. PMID: 29330484

Haque A, Engel J, Teichmann SA & Lönnberg T:
A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications.
Genome Medicine 2017; 9(1):75. Review. PMID:28821273

Kolodziejczyk AA* & Lönnberg T*:
Global and targeted approaches to single-cell transcriptome characterization.
Briefings in Functional Genomics 2017; Review. PMID:29028866
*) Equal contribution

Lönnberg T*, Svensson V*, James KR*, Fernandez-Ruiz D, Sebina I, Montandon R, Soon MSF, Fogg LG, Nair AS, Liligeto UN, Stubbington MJT, Ly LH, Bagger FO, Zwiessele M, Lawrence ND, Souza-Fonseca-Guimaraes F, Bunn PT, Engwerda CR, Heath WR, Billker O, Stegle O, Haque A, & Teichmann SA:
Single-cell RNA-seq and computational analysis using temporal mixture modelling resolves TH1/TFH fate bifurcation in malaria.
Science Immunology 2017; 2:1-11. PMID 28345074
*) Equal contribution

Proserpio V, Piccolo A, Haim-Vilmovsky L, Kar G, Lönnberg T, Svensson V, Pramanik J, Natarajan KN, Zhai W, Zhang, X, Donati G, Kayikci M, Kotar J, McKenzie ANJ, Montandon R, Billker O, Woodhouse S, Cicuta P, Nicodemi M & Teichmann SA:
Single-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferation.
Genome Biology 2016; 17:103. PMID: 27176874

Proserpio V & Lönnberg T:
Single-cell technologies are revolutionizing the approach to rare cells.
Immunology and Cell Biology 2016; 94(3):225-9. Review. PMID: 26620630

Stubbington MJT*, Lönnberg T*, Proserpio V, Clare S, Speak AO, Dougan G & Teichmann SA:
T cell fate and clonality inference from single-cell transcriptomes.
Nature Methods 2016; 13(4):329-32. PMID: 26950746
*) Equal contribution

Hawkins RD, Larjo A, Tripathi SK, Wagner U, Luu Y, Lönnberg T, Raghav SK, Lee LK, Lund R, Ren B, Lähdesmäki H & Lahesmaa R:
Global chromatin state analysis reveals lineage-specific enhancers during the initiation of human T helper 1 and T helper 2 cell polarization.
Immunity 2013; 38(6):1271-84. PMID: 23791644

Chen Z, Lönnberg T & Lahesmaa R:
Holistic systems biology approaches to molecular mechanisms of human helper T cell differentiation to functionally distinct subsets.
Scandinavian Journal of Immunology 2013; 78(2):172-80. Review. PMID: 23679154

Lönnberg T, Chen Z & Lahesmaa R:
From a gene-centric to whole-proteome view of differentiation of T helper cell subsets.
Briefings in Functional Genomics 2013; 12(6):471-82. Review. PMID: 24106101