Biomedical Epigenomics

Group Leader

Riikka Lund, Ph.D., Senior Scientist, Adjunct Professor (Title of Docent)
Head of  Finnish Functional Genomics Centre 
riikka.lund@utu.fi

Contact Information

Biomedical Epigenomics Group
Turku Centre for Biotechnology
P.O. Box 123, BioCity
(Street adr. Tykistökatu 6 A)
FIN-20520 Turku, Finland
+358-2-333 7697 (Riikka Lund)
+358-41-517 1616 (Mobile)
+358-2-333 8015 (Laboratory)
+358-2-251 8808  (fax)

Group Members

https://www.btk.fi/functional-genomics/staff/

Description of Research

Our group explores, develops and implements the latest technologies and methods to study genomic and epigenomic regulation during early human development, aging and in diseases. By comparing and modelling epigenomes of healthy and diseased individuals with the latest cutting-edge methods our goal is to understand the mechanisms of the diseases, how they develop, find novel type of disease marker candidates and targets for drug development. By providing novel innovative approaches enabling prediction, early diagnosis and efficient precision treatment of diseases our ultimate goal is to promote lifelong health.

Current Projects

  • Regulation of stem cell state and transformation
  • Epigenetic mechanisms of childhood leukemia at single cell level
  • Epigenomics of childhood rhinovirus-induced wheezing and asthma
  • Epigenomic alterations in aging and Alzheimer’s disease
  • +several other collaborative projects

Funding

  • Wihuri Foundation (graduate student Mikko Konki)
  • Finnish Cultural Foundation (graduate student Mikko Konki)
  • Väreen Säätiö (postdoctoral researcher Riina Kaukonen)
  • Yrjö Jahnsson foundation
  • State Research Funding, Hospital District of Southwest Finland
  • Private donation

Current Key Collaborators

Hawkins David, University of Washington School of Medicine

Jartti Tuomas, Department of Pediatrics, Turku University Hospital

Kaprio Jaakko, University of Helsinki, FIMM

Lähdesmäki Harri, Turku Centre for Biotechnology and Aalto University

Ollikainen Miina, University of Helsinki, FIMM

Pedersen Nancy, Department of Medical Epidemiology and Biostatistics, Karolinska Institutet

Rinne Juha, Turku PET Centre, University of Turku and Turku University Hospital

Selected Publications

Methylome Analysis of Human Bone Marrow MSCs Reveals Extensive Age- and Culture-Induced Changes at Distal Regulatory Elements. Pasumarthy KP, Jayavelu ND, Kilpinen L, Andrus C, Battle SL, Korhonen M, Lehenkari P, Lund R, Laitinen S, Hawkins RD. Stem Cell Rep. 2017 Sept 12;9:1-17.

Epigenomic Landscapes of hESC-Derived Neural Rosettes: Modeling Neural Tube Formation and Diseases. Valensisi C, Andrus C, Buckberry S, Doni Jayavelu N, Lund RJ, Lister R, Hawkins RD. Cell Rep. 2017 Aug 8;20(6):1448-1462.

RNA Polymerase III Subunit POLR3G Regulates Specific Subsets of PolyA+ and SmallRNA Transcriptomes and Splicing in Human Pluripotent Stem Cells. Lund RJ, Rahkonen N, Malonzo M, Kauko L, Emani MR, Kivinen V, Närvä E, Kemppainen E, Laiho A, Skottman H, Hovatta O, Rasool O, Nykter M, Lähdesmäki H, Lahesmaa R. Stem Cell Rep. 2017 09 May;8(5):1442–1454.

DNA methylation and Transcriptome Changes Associated with Cisplatin Resistance in Ovarian Cancer. Lund RJ, Huhtinen K, Salmi J, Rantala J, Nguyen EV, Moulder R, Goodlett DR, Lahesmaa R, Carpén O. Sci Rep. 2017 May 4;7(1):1469.

Mature Let-7 miRNAs fine tune expression of LIN28B in pluripotent human embryonic stem cells. Rahkonen N, Stubb A, Malonzo M, Edelman S, Emani MR, Närvä E, Lähdesmäki H, Ruohola-Baker H, Lahesmaa R, Lund R. Stem Cell Res. 2016 Nov;17(3):498-503.

Epigenetic Silencing of the Key Antioxidant Enzyme Catalase in Karyotypically Abnormal Human Pluripotent Stem Cells. Konki M, Pasumarthy K, Malonzo M, Sainio A, Valensisi C, Söderström M, Emani MR, Stubb A, Närvä E, Ghimire B, Laiho A, Järveläinen H, Lahesmaa R, Lähdesmäki H, Hawkins RD, Lund RJ. Sci Rep. 2016 Feb 25;6:22190.

Decorin in Human Colon Cancer: Localization In Vivo and Effect on Cancer Cell Behavior In Vitro. Nyman MC, Sainio AO, Pennanen MM, Lund RJ, Vuorikoski S, Sundström JT, Järveläinen HT. J Histochem Cytochem. 2015 Sep;63(9):710-20.

The L1TD1 protein interactome reveals the importance of post-transcriptional regulation in human pluripotency. Emani MR, Närvä E, Stubb A, Chakroborty D, Viitala M, Rokka A, Rahkonen N, Moulder R, Denessiouk K, Trokovic R, Lund R, Elo LL, Lahesmaa R. Stem Cell Reports. 2015 Mar 10;4(3):519-28.

Gut microbiota as an epigenetic regulator: pilot study based on whole-genome methylation analysis. Kumar H, Lund R, Laiho A, Lundelin K, Ley RE, Isolauri E, Salminen S. MBio. 2014 Dec 16;5(6). pii: e02113-14.

Expression profiles of long non-coding RNAs located in autoimmune disease-associated regions reveal immune cell-type specificity. Hrdlickova B, Kumar V, Kanduri K, Zhernakova DV, Tripathi S, Karjalainen J, Lund RJ, Li Y, Ullah U, Modderman R, Abdulahad W, Lähdesmäki H, Franke L, Lahesmaa R, Wijmenga C, Withoff S. Genome Med. 2014 Oct 28;6(10):88.

Notch signaling regulates the differentiation of neural crest from human pluripotent stem cells. Noisa P, Lund C, Kanduri K, Lund R, Lähdesmäki H, Lahesmaa R, Lundin K, Chokechuwattanalert H, Otonkoski T, Tuuri T, Raivio T. J Cell Sci. 2014 May 1;127(Pt 9):2083-94.

Continuous hypoxic culturing of human embryonic stem cells enhances SSEA-3 and MYC levels. Närvä E, Pursiheimo JP, Laiho A, Rahkonen N, Emani MR, Viitala M, Laurila K, Sahla R, Lund R, Lähdesmäki H, Jaakkola P, Lahesmaa R. PLoS One. 2013 Nov 13;8(11):e78847.

Lack of decorin expression by human bladder cancer cells offers new tools in the therapy of urothelial malignancies. Sainio A, Nyman M, Lund R, Vuorikoski S, Boström P, Laato M, Boström PJ, Järveläinen H. PLoS One. 2013 Oct 11;8(10):e76190.

A novel feeder-free culture system for human pluripotent stem cell culture and induced pluripotent stem cell derivation. Vuoristo S, Toivonen S, Weltner J, Mikkola M, Ustinov J, Trokovic R, Palgi J, Lund R, Tuuri T, Otonkoski T. PLoS One. 2013 Oct 2;8(10):e76205.

ESTOOLS Data@Hand: human stem cell gene expression resource. Kong L, Aho KL, Granberg K, Lund R, Järvenpää L, Seppälä J, Gokhale P, Leinonen K, Hahne L, Mäkelä J, Laurila K, Pukkila H, Närvä E, Yli-Harja O, Andrews PW, Nykter M, Lahesmaa R, Roos C, Autio R. Nat Methods. 2013 Sep;10(9):814-5.

Karyotypically abnormal human ESCs are sensitive to HDAC inhibitors and show altered regulation of genes linked to cancers and neurological diseases. Lund RJ, Emani MR, Barbaric I, Kivinen V, Jones M, Baker D, Gokhale P, Nykter M, Lahesmaa R, Andrews PW. Stem Cell Res. 2013 Nov;11(3):1022-36.

Global chromatin state analysis reveals lineage-specific enhancers during the initiation of human T helper 1 and T helper 2 cell polarization. Hawkins RD, Larjo A, Tripathi SK, Wagner U, Luu Y, Lönnberg T, Raghav SK, Lee LK, Lund R, Ren B, Lähdesmäki H, Lahesmaa R. Immunity. 2013 Jun 27;38(6):1271-84.

Genetic and epigenetic stability of human pluripotent stem cells. Lund RJ, Närvä E, Lahesmaa R. Nat Rev Genet. 2012 Oct;13(10):732-44. Review.

High-throughput karyotyping of human pluripotent stem cells. Lund RJ, Nikula T, Rahkonen N, Närvä E, Baker D, Harrison N, Andrews P, Otonkoski T, Lahesmaa R. Stem Cell Res. 2012 Nov;9(3):192-5.

RNA-binding protein L1TD1 interacts with LIN28 via RNA and is required for human embryonic stem cell self-renewal and cancer cell proliferation. Närvä E, Rahkonen N, Emani MR, Lund R, Pursiheimo JP, Nästi J, Autio R, Rasool O, Denessiouk K, Lähdesmäki H, Rao A, Lahesmaa R. Stem Cells. 2012 Mar;30(3):452-60.

Genome-wide profiling of interleukin-4 and STAT6 transcription factor regulation of human Th2 cell programming. Elo LL, Järvenpää H, Tuomela S, Raghav S, Ahlfors H, Laurila K, Gupta B, Lund RJ, Tahvanainen J, Hawkins RD, Oresic M, Lähdesmäki H, Rasool O, Rao KV, Aittokallio T, Lahesmaa R. Immunity. 2010 Jun 25;32(6):852-62.