Early Embryo Development and Complex Human Disorders
We focus on gene effects and networks in complex human phenotypes. We study early embryonic development and complex disorders, many with an inflammatory component, such as pre-eclampsia, psoriasis, and rare immune system-related diseases, as well as developmental dyslexia. In addition, our group has an interest in comparative studies between human and other species, such as the dog. There is a strong strategic synergy between the projects, even though they represent different physiological systems.
Our research group was established in 1994. We use modern genomics tools, including high-throughput DNA and RNA sequencing. We work in tight collaboration with clinical specialists as well as leading experts on special methods, such as proteomics, single-cell transcriptomics, and brain imaging, and are involved in a number of international consortia.
Our recent major breakthrough provided a detailed transcriptome of early embryos, and now our focus is to characterise the regulatory network of early embryonic development. Our recent work has highlighted the functions of DUX4, a gene that launches the activation of the embryo’s own genome. We have recently found that a central mechanism in pre-eclampsia involves an autoimmune-like process when the protection of placental cells by the expression of a gene called HLA-G is low and the mother’s immune system can more strongly attack the placenta. In psoriasis, we showed that innate immunity related signaling pathways are active also in non-immune cells of psoriatic skin. We have identified several susceptibility genes, e.g., for dyslexia, providing opportunities to study the pathogenetic mechanisms. We are currently studying the relationship between dyslexia susceptibility genes and brain activity. Our studies on immune deficiency disorders are focused on identifying genes behind the new and rare types of diseases. We have already identified several new genes with work ongoing on yet new genes.
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Senior Scientists
Sini Ezer
Shintaro Katayama
Satu Wedenoja, visiting scientist
Scientist
Jere Weltner
Doctoral Researchers
Gamze Yazgeldi Gunaydin
Katariina Kordemets
Tuuli Vallo
Nina Boskovic, visiting scientist
Akshara Urs, visiting scientist
Students
Viljami Wuollet
Staff
Eira Leinonen, Research Nurse
Auli Saarinen, Chief Laboratory Technician
Interaction network of human early embryonic transcription factors.
Gawriyski L, Tan Z, Liu X, Chowdhury I, Malaymar Pinar D, Zhang Q, Weltner J, Jouhilahti EM, Wei GH, Kere J, Varjosalo M. EMBO Reports. 2024.
Transcriptomic differences between human 8-cell-like cells reprogrammed with different methods.
Yoshihara M, Kere J. Stem Cell Reports. 2023.
Transient DUX4 expression induces blastomere-like expression program that is marked by SLC34A2.
Yoshihara M, Kirjanov I, Sokka J, Weltner J, Lundin K, Gawriyski L, Jouhilahti E-M, Varjosalo M, Tervaniemi MH, Otonkoski T, Trokovic R, Katayama S, Vuoristo S*, Kere J*. Stem Cell Reports. 2022.
Fetal HLA-G mediated immune tolerance and interferon response in preeclampsia.
Wedenoja S*, Yoshihara M, Teder H, Sariola H, Gissler M, Katayama S, Wedenoja J, Häkkinen IM, Ezer S, Linder N, Lundin J, Skoog T, Sahlin E, Iwarsson E, Pettersson K, Kajantie E, Mokkonen M, Heinonen S, Laivuori H, Krjutškov K, Kere J*. EBiomedicine. 2020.
Single cell map of the human ovarian cortex.
Wagner M, Yoshihara M, Douagi I, Damdimopoulos A, Panula S, Petropoulos S, Lu H, Pettersson K, Palm K, Katayama S, Hovatta O, Kere J, Lanner F, Damdimopoulou P. Nature Communications. 2020.
NET-CAGE characterizes the dynamics and topology of human transcribed cis-regulatory elements.
Hirabayashi S, Bhagat S, Matsuki Y, Takegami Y, Uehata T, Kanemaru A, Itoh M, Shirakawa K, Takaori-Kondo A, Takeuchi O, Carninci P, Katayama S, Hayashizaki Y, Kere J, Kawaji H, Murakawa Y. Nature Genetics. 2019.
Phylogenetic and mutational analyses of human LEUTX, a homeobox gene implicated in embryogenesis.
Katayama S, Ranga V, Jouhilahti E-M, Airenne TT, Johnson MS, Mukherjee K, Bürglin TR*, Kere J*. Scientific Reports. 2018.
Human pluripotent reprogramming with CRISPR dCas9 activators.
Weltner J, Balboa D, Katayama S, Bespalov M, Krjutškov K, Jouhilahti E-M, Trokovic R, Kere J*, Otonkoski T*. Nature Communications. 2018.
Novel PRD-like homeodomain transcription factors and retrotransposon elements in early human development.
Töhönen V, Katayama S, Vesterlund L, Jouhilahti E-M, Sheikhi M, Madissoon E, Filippini-Cattaneo G, Jaconi M, Johnsson A, Bürglin TR, Linnarsson S, Hovatta O, Kere J. Nature Communications. 2015.
Folkhälsan Research Foundation
Jane and Aatos Erkko Foundation
Päivikki and Sakari Sohlberg Foundation
Sigrid Juselius Stiftelse
Dyslexia consortium “DYSGEBRA”: Heikki Lyytinen, PhD, Professor, and Riitta Salmelin, DSc, Professor
Hannele Laivuori, MD, PhD, and the FINNPEC Consortium
Hannes Lohi, PhD, Professor, and the DoGA Consortium
Juha Grönholm MD, PhD
The FANTOM Consortium, RIKEN Yokohama Institute
Timo Otonkoski, MD, PhD, Professor
Mikko Seppänen, MD, PhD
Juha Tapanainen, MD, PhD, Professor
