Scientific success stories based on Biocenter Finland technology services
Molecular modeling enhances our understanding on how lipase enzyme works, allowing better design of inhibitors
Molecular modeling and virtual screening combined with follow-up experimental validation are key services of the DDCB platform. Together they provide powerful tools to discover novel bioactive chemicals, and importantly, to understand mechanism of action of existing bioactive small molecules and to identify rational strategies for improving their activities.
Monoacylglycerol lipase has emerged as a promising and druggable target to treat cancer, neurodegenerative diseases, and metabolic disorders. The findings of this study (Laitinen T. et. al) may therefore allow for rational design of more potent and selective inhibitors of monoacylglycerol lipases that can be explored as safe and eff ective drugs to treat a range of different diseases.
- Laitinen T. et al. 2014. Mutation of Cys242 of human monoacylglycerol lipase disrupts balanced hydrolysis of 1- and 2-monoacylglycerols and selectively impairs inhibitor potency. Mol. Pharmacol. 85:510-519. (PubMed)
Placenta growth factor and CNS revascularization
Vascular bypass procedures in the central nervous system (CNS) remain technically challenging, hindered by complications and oft en failing to prevent adverse outcome such as stroke. Thus, there is an unmet clinical need for a safe andeff ective CNS revascularization. Vascular endothelial growth factors (VEGFs) are promising candidates for revascularization; however, their effects appear to be tissue-specific and their potential in the CNS has not been fully explored. (BF AAV facility)
- Gaal EI, Tammela T, Anisimov A, Marbacher S, Honkanen P, Zarkada G, Leppänen VM, Tatlisumak T, Hernesniemi J, Niemelä M, Alitalo K. Comparison of vascular growth factors in the murine brain reveals placenta growth factor as prime candidate for CNS revascularization. Blood 2013; 122:658-65, doi: 10.1182/blood-2012-07-441527. IF 9.060. (BIU-BCH) (PubMed)
Crystal structure of collagen prolyl 4-hydroxylase
Th e crystal structure has been solved of the DD-domain region of the α-chain human collagen prolyl 4-hydroxylase (C-P4H). (BCO Protein Crystallography Core Facility)
- Anantharajan J, Koski MK, Kursula P, Hieta R, Bergmann,U, Myllyharju J and Wierenga RK (2013) The unique structural motifs for substrate binding and dimerization of the alfa subunit of collagen prolyl 4-hydroxylase. Structure, 21,2107-2118. (PubMed)
MRI helps to estimate effi cacy of oncolytic adenovirus treatment
At present, it is not possible to reliably identify patients who will benefi t from oncolytic virus treatments. Conventional modalities such as computed tomography (CT), which measure tumor size, are unreliable owing to inflammation-induced tumor swelling. We hypothesized that magnetic resonance imaging (MRI) and spectroscopy (MRS) might be useful in this regard.
This study is an excellent demonstration of the basic idea of Biocenter Finland. Researchers in Helsinki needed sophisticated magnetic resonance spectroscopy techniques that are only available in Kuopio through Biocenter Finland. Animals were sent to Kuopio, the study was designed together, the protocols implemented and tested by a staff scientist in Kuopio, and measurements were carried out by a scientist from Helsinki. Results were analyzed and interpreted in collaboration and finally published in a high quality journal. (BCK MRI facility)
- Hemminki O, Immonen R, Närväinen J, Kipar A, Paasonen J, Jokivarsi KT, Yli-Ollila H, Soininen P, Partanen K, Joensuu T, Parvianen S, Pesonen SK, Koski A, Vähä-Koskela M, Cerullo V, Pesonen S, Gröhn OH, Hemminki A In vivo magnetic resonance imaging and spectroscopy identifi es oncolytic adenovirus responders. Int J Cancer. 2013 Nov 18, doi: 10.1002/ijc.28615. IF 6.2 (BIU- Kuopio) (PubMed)
Construction of novel database for data sharing and data analysis
One of the central challenges repeatedly encountered in projects utilizing novel high throughput methods is data storage and analysis. Data sharing when large and complicated data set should need to be seen by many scientists in a flexible manner is major target for research. In this interdisciplinary study a database was generated for stem cell research with advanced features enabling storing, sharing, integrating and analysing genome-wide data produced with Affymetrix and Illumina microarray platforms. Designing and building the database and its use to generate part of the data were performed in BioCity Turku by FMSC scientists.
- 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. ESTOOLS Data@Hand: human stem cell gene expression resource. Nat Methods. 2013 Aug;10(9):814-5. (PubMed)
Activation of T lymphocytes
Activation of T lymphocytes is important in the response to pathogens and it has been unclear how immune cells increase their nutrition uptake to enhance metabolic activity in inflammatory responses. In this study the authors utilized genome-wide Affymetrix gene expression arrays to study the mechanisms regulating the process and highlight that activation of T lymphocytes in response to pathogens and infl ammatory cytokines involves System L amino acid transport activity through TCR mediated regulation of Slc7a5 expression, which enables immune-activated T cells to enhance nutrition uptake and metabolic activity and mediate adaptive immune responses (Sinclair et al., 2013). FMSC (BioCity Turku) services were used to define with Affymetrix gene expression arrays and functional assays the mechanisms involved in the process.
- Sinclair LV, Rolf J, Emslie E, Shi YB, Taylor PM, Cantrell DA. Control of amino-acid transport by antigen receptors coordinates the metabolic reprogramming essential for T cell differentiation. Nat Immunol. 2013 May;14(5):500-8. doi: 10.1038/ni.2556. (PubMed)
Three-dimensional structure of respiratory syncytial virus (RSV) solved
Respiratory syncytial virus (RSV) is a common cause of respiratory infection, but there is no vaccine available. It causes fl u-like symptoms in healthy adults, but becomes life-threatening in young children and the elderly. It is estimated to cause over 100 000 deaths yearly worldwide. BI-cryoEM in collaboration with Professor Ari Helenius (ETH Zurich) has now solved the three-dimensional structure of RSV.
- Liljeroos, L. Krzyzaniak, M., Helenius, A., Butcher, S.J. 2013. Architecture of respiratory syncytial virus revealed by electron cryotomography. Proc. Natl. Acad. Sci. (USA) 110:11133-11138. (PubMed)
Transcriptional response to stress
Lea Sistonen’s group was studying genome-wide transcriptional program that is rapidly provoked to counteract heat-induced stress and uncovered the broad range of molecular mechanisms that maintain cellular homeostasis under hostile conditions. Their results highlight the importance of the cell cycle phase in provoking cellular responses and identify molecular mechanisms that direct transcription during the progression of the cell cycle (Vihervaara et al., 2013). ChIP-seq for heat shock factors HSF1 and HSF2 was performed using next-generation sequencing services by FuGU.
- Vihervaara A, Sergelius C, Vasara J, Blom MA, Elsing AN, Roos-Mattjus P, Sistonen L. Transcriptional response to stress in the dynamic chromatin environment of cycling and mitotic cells. Proc Natl Acad Sci U S A. 2013 Sep 3;110(36):E3388-97. doi: 10.1073/pnas.1305275110. Epub 2013 Aug 19. (PubMed).
LDL cholesterol recycling
Low-density lipoprotein (LDL) cholesterol recycles to the plasma membrane (PM) via a Rab8a-Myosin5b-actin-dependent membrane transport route, but the underlying mechanisms have remained obscure. LDL labeled with BODIPY cholesteryl linoleate was employed to identify this pathway in living cells. (Biomedicum Helsinki Imaging Unit)
- Kanerva et al. LDL cholesterol recycles to the plasma membrane via a Rab8a-Myosin5b-actin-dependent membrane transport route. Dev Cell 2013; 27:249–262. (PubMed)
Zebrafish models for tuberculosis
Many aspects of tuberculosis are still obscure. Especially the mechanisms leading to latency and reactivation of human tuberculosis are unclear, mainly due to the lack of standardized animal models of latent tuberculosis infection. Research utilizing the Tampere zebrafish core facility has shown that an intraperitoneal infection with a low dose (35 cfu) of M. marinum – a natural fi sh pathogen that is closely related to M. tuberculosis - a latent disease develops in most individuals. This latent infection can be then reactivated by immunosuppression (Parikka et al. (2012) PLoS Pathogens). Thus the adult zebrafish presents itself as a unique non-mammalian vertebrate model for studying the development of latency as well as reactivation of latent tuberculosis. The possibilities of screening for host and pathogen factors affecting the disease progression, as well as for novel therapeutic agents and vaccine targets make the established model especially attractive. During 2013 researchers at Tampere were able to show that new vaccine candidates against tuberculosis can be screened using this model (Oksanen et al. (2013) Vaccine). This will allow efficient identification of novel vaccine antigens guiding thus research efforts to create new - safe and effective - vaccine against tuberculosis.
- Oksanen KE, Halfpenny NJ, Sherwood E, Harjula SK, Hammarén MM, Ahava MJ, Pajula ET, Lahtinen MJ, Parikka M, Rämet M. An adult zebrafi sh model for preclinical tuberculosis vaccine development. Vaccine. 2013 Oct 25;31(45):5202-9. (PubMed)
- Parikka M, Vuoksio M, Harjula SK, Halfpenny N, Oksanen K, Lahtinen MJ, Pajula E, Iivanainen A, Pesu M & Rämet M. (2012) Mycobacterium marinum causes a latent infection that can be reactivated by gamma irradiation in adult zebrafi sh. PLoS Pathogens 8:e1002944.
Technology transfer: pre-clinical prostate cancer model
The validation of a pre-clinical cancer model (VCaP xenografts in castrated immuno defi cient mice) together with Orion Pharma was finalized at TCDM). The model has been successfully used in screening novel drugs developed against castration-resistant prostate cancer, and the model has been made available as a service at TCDM in 2013. Using xenograft models of human cells in mice TCDM has carried out 6 projects for Pharma industry. Furthermore, GM mouse models generated in the Oulu TG/GM unit have been used in preclinical screenings by Fibrogen Inc. (California, USA).
- Knuuttila M, Yatkin E, Kallio J, Savolainen S, Laajala TD, Aittokallio T, Oksala R, Häkkinen M, Keski-Rahkonen P, Auriola S, Poutanen M, Mäkelä S, Castration induces upregulation of intratumoral androgen synthesis and androgen receptor expression in orthotopic VCap human prostate cancer xenograft model. Am J Pathol. 2014 Aug;184(8):2163-73.
- Rahtu-Korpela L, Karsikas S, Hörkkö S, Sequeiros RB, Lammentausta E, Mäkelä KA, Herzig KH, Walkinshaw G, Kivirikko KI, Myllyharju J, Serpi R, Koivunen P. HIF prolyl 4-hydroxylase-2 inhibition improves glucose and lipid metabolism and protects against obesity and metabolic dysfunction. Diabetes. 2014 May 1. [Epub ahead of print]
Identification of chitosan-specifi c binders
BCO (bioinformatics) has contributed to a study where a combinationof calorimetry experiments, nuclear magnetic resonance (NMR), and theoretical protein ligand docking has led to the first identifi cation of carbohydrate binding modules specifi c to glucosamine (GlcN) polysaccharide chitosan.
- Shoko Shinya, Takayuki Ohnuma, Reina Yamashiro, Hisashi Kimoto, Hideo Kusaoke, Padmanabhan Anbazhagan, André H. Juffer and Tamo Fukamizo. The first identification of carbohydrate-binding modules specifi c to chitosan. J Biol Chem 2013 Oct 18;288(42):30042-53.
Rapid systems medicine analysis for tumor samples
FIMM Technolocy Center (in a collaboration between the nodes of BF DDCB and BF-Bioinformatics networks as well as several research groups) has set up molecular profiling and drug sensitivity and resistant testing analyses allowing rapid identification of somatic mutations, CNVs and fusion transcripts by genome, exome and transcriptome sequencing as well as drug sensitivity profiling of individual cancer samples. This setup was used to analyse a cohort of patients with chemorefractory acute myeloid leukemia. (Pemovska et al, 2013).
- Pemovska T, Kontro M, Yadav B, Edgren H, Eldfors S, Szwajda A, Almusa H, Bespalov MM, Ellonen P, Elonen E, Gjertsen BT, Karjalainen R, Kulesskiy E, Lagström S, Lehto A, Lepistö M, Lundán T, Majumder MM, Marti JM, Mattila P, Murumägi A, Mustjoki S, Palva A, Parsons A, Pirttinen T, Rämet ME, Suvela M, Turunen L, Västrik I, Wolf M, Knowles J, Aittokallio T, Heckman CA, Porkka K, Kallioniemi O, Wennerberg K. Individualized systems medicine strategy to tailor treatments for patients with chemorefractory acute myeloid leukemia. Cancer Discov. 2013 Dec;3(12):1416-29. doi: 10.1158/2159-8290.CD-13-0350. (PubMed)
Metabolomics for bioavailability studies
An animal feeding trial was conducted at the BCK metabolite profiling facility. Differentially processed wheat bran fractions were included in the diet of the black mouse model in order to analyse the impact of technical processing on the bioavailability of the branbound phytochemicals. The non-targeted metabolite profiling revealed that the technical processing increased the bioavailability of certain phenolic acids as was evidenced by the different urinary metabolite profiles.
- Pekkinen J, Rosa NN, Savolainen OI, Keski-Rahkonen P, Mykkänen H, Poutanen K, Micard V, Hanhineva K. Disintegration of wheat aleurone structure has an impact on the bioavailability of phenolic compounds and other phytochemicals as evidenced by altered urinary metabolite profile of diet-induced obese mice. Nutr Metab (Lond). 2014 Jan 2;11(1):1. doi: 10.1186/1743-7075-11-1.
Imaging the traffi cking of 111In labeled lymphatic cells with SPECT/CT
OT-I lymphatic cells were radiolabeled with 111In in a scientifi c collaboration with Prof. A. Hemminki, Cancer Gene Th erapy Group and Academy research fellow Anu Airaksinen, Laboratory of Radiochemistry, University of Helsinki. Trafficking of the radiolabeled OT-I cells were followed by SPECT/CT in C57BL/6 mice bearing B16-OVA tumors. Influence of intratumoral adenovirus treatment on the OT-I tumor accumulation was evaluated. SPECT/CT imaging allowed follow up of the OT-I cell traffi cking in vivo at different time points and up to 7 days. Tumor accumulation of OT-I cells was quantified, which allowed comparison of the adenovirus-treated and non-treated groups, providing valuable information on the efficiency of the adenovirus treatment to infl uence the OT-I cell traffi cking into the treated tumor.
Gene transfer experiments elucidate VEGF-C action
Hennekam lymphangiectasia–lymphedema syndrome (OMIM 235510) is a rare autosomal recessive disease, which is associated with mutations in the collagenand calcium-binding EGF domains 1 (CCBE1) gene. Using AAV gene transfer, combined with various molecular biology approaches, the authors were able to identify ADAMTS3 as a VEGF-C activating protease and reveal a novel type of regulation of a vascular growth factor by a protein that enhances its proteolytic cleavage and activation. The results suggest CCBE1 is a potential therapeutic tool for the modulation of lymphangiogenesis and angiogenesis in a variety of diseases that involve the lymphatic system, such as lymphedema or lymphatic metastasis.