Prof. Peppi Karppinen née Koivunen

2-Oxoglutarate-Dependent Enzymes as Novel Therapeutic Targets in Diseases
Karppinen Group June 2022

Research group information

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Research group leader

Research group description

2-oxoglutarate-dependent dioxygenases (2OGDDs) are an enzyme family of ~60 members in human that share the same reaction mechanism but act on different substrate varying from proteins to DNA, RNA and fatty acids. 2OGDDs require as cofactors Fe2+, 2-oxoglutarate (2OG) and O2. 2OGDDs include the collagen prolyl 4-hydroxylases (C-P4Hs), the hypoxia-inducible factor prolyl 4-hydroxylases (HIF-P4Hs / PHDs / EglNs), transmembrane P4H (P4H-TM) and the hypoxia-inducible factor (HIF) asparaginyl hydroxylase FIH. Many 2OGDDs act on chormatin structure as erasors, such as the DNA demethylating TETs and numerous histone lysine demethylases (KDMs). 2OGDDs can be targeted with small molecule compounds, such as the HIF-P4H inhibitors that have been accepted for the treatment of anemia. We hypothesize that these inhibitors can be used to treat ischemic, metabolic and inflammatory conditions. We also anticipate that other 2OGDDs can be targeted with small molecule inhibitors to for example to treat cancer.

Background and Significance

Oxygen homeostasis is essential for normal development and physiology, and many pathological processes are associated with hypoxia. The rescue response of cells to hypoxia is chiefly mediated by the hypoxia-inducible factor (HIF), which can initiate the transcription of hundreds of genes involved in hematopoiesis and iron metabolism, angiogenesis, glucose and lipid metabolism, inflammation and tumorigenesis. Activation of the HIF pathway aims to i) increase oxygen delivery to tissues and ii) decrease its usage e.g. in oxidative metabolism. The same physiologic pathway is activated at high altitude, which is exploited by endurance athletes. HIF is an αβ dimer. The HIFα subunit isoforms HIF1α and HIF2α are synthesized constitutively, and hydroxylation of two proline residues by the HIF prolyl 4-hydroxylases (HIF-P4Hs) targets them for proteasomal degradation via the von Hippel Lindau protein (VHL) in normoxia. Under hypoxia the hydroxylation is inhibited and the accumulated HIFα forms with HIFβ a transcriptionally active dimer. HIF-P4Hs have three isoenzymes HIF-P4Hs 1-3 (also known as PHDs 1-3, and EglNs 2, 1 and 3, respectively) in vertebrates, isoenzyme 2 being the most abundant and major form in most tissues. HIF-P4Hs belong to the enzyme family of 2-oxoglutarate-dependent dioxygenases (2OGDDs).

Epigenetic modifications to nucleic acid and protein components of the chromatin are central regulators of eukaryotic transcription. These modifications include the reversible methylation of DNA and histones. The epigenetic marks to chromatin are “written” or “erased” by enzymes. Several of these “erasers” are 2OGDDs, such as the leukemia associated DNA demethylating ten-eleven translocation (TET) enzymes and a number of JmjC-domain containing histone lysine demethylases (KDMs).

Our research group’s main interest are the HIF-P4Hs 1-3, FIH, P4H-TM, TETs and selected KDMs. The central role of HIF-P4Hs in oxygen sensing makes them promising candidates for the treatment pathologic hypoxia, such as ischemic conditions. HIF-P4Hs can be targeted with synthetic 2-oxoglutarate (2OG) analogue inhibitors which can be used to initiate the HIF response in normoxia and which can therefore be called hypoxiamimetics. We have shown recently that activating the endogenous HIF response genetically or pharmacologically by HIF-P4H inhibition protects mice from obesity, metabolic dysfunction, high-fat diet and aging-induced hepatic steatosis and atherosclerosis. It seems possible that HIF-P4H inhibition may have protective effects also in many other disease conditions, such as hepatic, inflammatory and immunological diseases. The KDMs are currently the least studied 2OGDD family members. KDMs regulate development, cellular differentiation, senescence and genomic stability, disruption of which can have profound effects, as evidenced by recent data indicating that several KDMs are linked to a number of cancers. We showed recently that KDMs become inhibited with low concentrations of cancer-associated 2OG analogues and treatment of cells with these compounds altered histone demethylation status. We also showed that catalytic activity of some KDMs is highly dependent on oxygen availability and similarly to the HIF-P4Hs, they act as nuclear oxygen sensors.

Figure. Regulation of the HIF pathway by oxygen levels and HIF-P4Hs and examples of HIF target genes. The shared catalytic reaction of 2OGDDs and conditions affecting it. Examples of 2OGDD associated diseases.

Future goals

Our objective is to investigate activation of the HIF pathway via HIF-P4H inhibition as a novel concept to treat metabolic, neurodegenerative and retinal diseases. Our second objective is to study the catalytic and inhibitory properties of KDMs, especially their potential to act as nuclear oxygen sensors and contribute to tumorigenesis. Our third objective is to unravel the role and function of P4H-TM.

The specific goals are:

  • To analyze the cross-talk between HIF hydroxylases and metabolism, inflammation and immunology

  • To characterize the kinetic and structural properties of selecetd KDMs and other less-studied 2OGDDs

  • To analyze the in vivo role of P4H-TM

Selected publications

Activation of the hypoxia response protects mice from amyloid-β accumulation. Ollonen T, Kurkela M, Laitakari A, Sakko S, Koivisto H, Myllyharju J, Tanila H, Serpi R, Koivunen P.Cell Mol Life Sci. 2022 Jul 19;79(8):432. doi: 10.1007/s00018-022-04460-6.PMID: 35852609

Contribution of HIF-P4H isoenzyme inhibition to metabolism indicates major beneficial effects being conveyed by HIF-P4H-2 antagonism. Tapio J, Halmetoja R, Dimova EY, Mäki JM, Laitala A, Walkinshaw G, Myllyharju J, Serpi R, Koivunen P.J Biol Chem. 2022 Aug;298(8):102222. doi: 10.1016/j.jbc.2022.102222. Epub 2022 Jul 1.PMID: 35787374

Systematic evaluation of the association between hemoglobin levels and metabolic profile implicates beneficial effects of hypoxia. Auvinen J, Tapio J, Karhunen V, Kettunen J, Serpi R, Dimova EY, Gill D, Soininen P, Tammelin T, Mykkänen J, Puukka K, Kähönen M, Raitoharju E, Lehtimäki T, Ala-Korpela M, Raitakari OT, Keinänen-Kiukaanniemi S, Järvelin MR, Koivunen P.Sci Adv. 2021 Jul 14;7(29):eabi4822. doi: 10.1126/sciadv.abi4822. Print 2021 Jul.PMID: 34261659

Genetic Ablation of Transmembrane Prolyl 4-Hydroxylase Reduces Atherosclerotic Plaques in Mice. Määttä J, Serpi R, Hörkkö S, Izzi V, Myllyharju J, Dimova EY, Koivunen P.Arterioscler Thromb Vasc Biol. 2021 Jul;41(7):2128-2140. doi: 10.1161/ATVBAHA.121.316034. Epub 2021 May 27.PMID: 34039020

Histone demethylase KDM6A directly senses oxygen to control chromatin and cell fate.Chakraborty AA, Laukka T, Myllykoski M, Ringel AE, Booker MA, Tolstorukov MY, Meng YJ, Meier SR, Jennings RB, Creech AL, Herbert ZT, McBrayer SK, Olenchock BA, Jaffe JD, Haigis MC, Beroukhim R, Signoretti S, Koivunen P, Kaelin WG Jr.Science. 2019 Mar 15;363(6432):1217-1222. doi: 10.1126/science.aaw1026. Epub 2019 Mar 14.PMID: 30872525

Key grants

1. Academy of Finland Flagship funding 2020-2024

2. Academy of Finland project grant 2021-2025

3. Jane and Aatos Erkko grant (shared with J. Myllyharju) 2020-2024

4. Sigrid Juselius 3-year grant 2022-2025

5. Finnish Cancer Organization 3-year grant 2022-2025

Key collaborators

1. Prof. Johanna Myllyharju, University of Oulu, Finland

2. Prof. William G. Kaelin Jr., Dana-Farber Cancer Institute, Harvard Medical School, USA

3. Dr. Gail Walkinshaw, FibroGen Inc., USA