Representative Publications & Projects

    Representative Publications

    J1. Saarela U, Akram SU, Desgrange A, Rak-Raszewska A, Shan J, Cereghini S, Ronkainen VP, Heikkilä J, Skovorodkin I, Vainio SJ. Novel fixed z-direction (FiZD) kidney primordia and an organoid culture system for time-lapse confocal imaging. Development. 2017 144(6), pp1113-1117

    Tissue, organ and organoid cultures provide suitable models for developmental studies, but our understanding of how the organs are assembled at the single-cell level still remains unclear. We describe here a novel fixed z-direction (FiZD) culture setup that permits high-resolution confocal imaging of organoids and embryonic tissues. In a FiZD culture a permeable membrane compresses the tissues onto a glass coverslip and the spacers adjust the thickness, enabling the tissue to grow for up to 12 days. Thus, the kidney rudiment and the organoids can adjust to the limited z-directional space and yet advance the process of kidney morphogenesis, enabling long-term time-lapse and high-resolution confocal imaging. As the data quality achieved was sufficient for computer-assisted cell segmentation and analysis, the method can be used for studying morphogenesis ex vivo at the level of the single constituent cells of a complex mammalian organogenesis model system.

    J2. Krause M, Samoylenko A, Vainio SJ. Exosomes as renal inductive signals in health and disease, and their application as diagnostic markers and therapeutic agents. Front Cell Dev Biol. 2015;3:65.

    Cells secrete around 30-1000 nm membrane-enclosed vesicles, of which members of the subgroup between 30 and 100 nm are termed exosomes (EXs). EXs are released into the extracellular space and are widely present in body fluids and incorporated mRNA, miRNA, proteins, and signaling molecules. Increasing amounts of evidence suggest that EXs play an important role not only in cell-to-cell communication but also in various physiological and disease processes. EXs secreted by kidney cells control nephron function and are involved in kidney diseases and cancers. This makes them potential targets for diagnostic and therapeutic applications such as non-invasive biomarkers and cell-free vaccines and for use as drug delivery vehicles. This review provides an overview on the known roles of EXs in kidney development and diseases, including renal cancer. Additionally, it covers recent findings on their significance as diagnostic markers and on therapeutic applications to renal diseases and cancers. The intention is to promote an awareness of how many questions still remain open but are certainly worth investigating.

    J3. Junttila S, Saarela U, Halt K, Manninen A, Pärssinen H, Lecca MR, Brändli AW,  Sims-Lucas S, Skovorodkin I, Vainio SJ. Functional genetic targeting of embryonic kidney progenitor cells ex vivo. J Am Soc Nephrol. 2015;26(5):pp1126-37.

    The embryonic mammalian metanephric mesenchyme (MM) is a unique tissue because it is competent to generate the nephrons in response to Wnt signaling. An ex vivo culture in which the MM is separated from the ureteric bud (UB), the natural inducer, can be used as a classic tubule induction model for studying nephrogenesis. However, technological restrictions currently prevent using this model to study the molecular genetic details before or during tubule induction. Using nephron segment-specific markers, we now show that tubule induction in the MM ex vivo also leads to the assembly of highly segmented nephrons. This induction capacity was reconstituted when MM tissue was dissociated into a cell suspension and then reaggregated (drMM) in the presence of human recombinant bone morphogenetic protein 7/human recombinant fibroblast growth factor 2 for 24 hours before induction. Growth factor–treated drMM also recovered the capacity for organogenesis when recombined with the UB. Cell tracking and time-lapse imaging of chimeric drMM cultures indicated that the nephron is not derived from a single progenitor cell. Furthermore, viral vector-mediated transduction of green fluorescent protein was much more efficient in dissociated MM cells than in intact mesenchyme, and the nephrogenic competence of transduced drMM progenitor cells was preserved. Moreover, drMM cells transduced with viral vectors mediating Lhx1 knockdown were excluded from the nephric tubules, whereas cells transduced with control vectors were incorporated. In summary, these techniques allow reproducible cellular and molecular examinations of the mechanisms behind nephrogenesis and kidney organogenesis in an ex vivo organ culture/organoid setting.

    J4. Andersson ER, Saltó C, Villaescusa JC, Cajanek L, Yang S, Bryjova L, Nagy II, Vainio SJ, Ramirez C, Bryja V, Arenas E. Wnt5a cooperates with canonical Wnts to  generate midbrain dopaminergic neurons in vivo and in stem cells. Proc Natl Acad  Sci U S A. 2013;110(7):E602-10.

    Wnts are a family of secreted proteins that regulate multiple steps of neural development and stem cell differentiation. Two of them, Wnt1 and Wnt5a, activate distinct branches of Wnt signaling and individually regulate different aspects of midbrain dopaminergic (DA) neuron development. However, several of their functions and interactions remain to be elucidated. Here, we report that loss of Wnt1 results in loss of Lmx1a and Ngn2 expression, as well as agenesis of DA neurons in the midbrain floor plate. Remarkably, a few ectopic DA neurons still emerge in the basal plate of Wnt1(-/-) mice, where Lmx1a is ectopically expressed. These results indicate that Wnt1 orchestrates DA specification and neurogenesis in vivo. Analysis of Wnt1(-/-);Wnt5a(-/-) mice revealed a greater loss of Nurr1(+) cells and DA neurons than in single mutants, indicating that Wnt1 and Wnt5a interact genetically and cooperate to promote midbrain DA neuron development in vivo. Our results unravel a functional interaction between Wnt1 and Wnt5a resulting in enhanced DA neurogenesis. Taking advantage of these findings, we have developed an application of Wnts to improve the generation of midbrain DA neurons from neural and embryonic stem cells. We thus show that coordinated Wnt actions promote DA neuron development in vivo and in stem cells and suggest that coordinated Wnt administration can be used to improve DA differentiation of stem cells and the development of stem cell-based therapies for Parkinson's disease.

    J5. Patent Strategy to engineering the mammalian skin stem cells to serve as novel biosensors, PCT-application, Ref: 013226_TISA and Ref: 2150199PC.

    The present invention relates to a field of genetically edited cells and furthermore determining indicator signals of genetically edited cells. The invention relates to a method for obtaining indicator signals from a cell, and more particularly to a method for determining a biological state of a cell. Furthermore, the present invention relates to a regenerative cell and use of a regenerative cell or a specific indicator poly-nucleotide for monitoring purposes. Also, a system for carrying out the method of the present invention is included.

    Representative Projects

    P1. RENALTRACT has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement N°642937. RENALTRACT acknowledges that to make significant advances, an interdisciplinary approach is required where experts and technologies of the physical sciences (imaging technology), chemistry (medicinal chemistry, metabolomics), biological sciences (developmental, cell biology, organ culture, physiology, genetics, “Omics”), systems biology and clinicians work in concert.

    P2. EURenOmics consortium is devoted to improving the lives of patients affected by rare kidney diseases. In line with the objectives of the International Rare Disease Research Consortium (IRDiRC), we aim to develop novel tools that will allow to make more accurate  diagnoses, predict the disease course and the efficacy of available treatments, and help  developing new and better therapies for rare kidney diseases. The project is receiving funding as part of the European Community’s commitment to the IRDiRC initiative. In this quest we are joining forces with our FP7 partner project Neuromics (for neuromuscular disorders) and the RD-CONNECT infrastructure platform. The research efforts of EURenOmics are focused on the following 5 groups of kidney diseases. Our Consortium comprises 17 European academic institutions, 9 SMEs and 1 academic partner from the United States. We have access to the largest rare renal disease cohorts assembled to date (collectively >12,000 patients) with detailed clinical information and comprehensive biorepositories containing DNA, blood, urine, amniotic fluid and kidney tissue.

    P3. The Centre of Excellence in Cell-Extracellular Matrix (ECM) Research granted by the Academy of Finland for years 2012 - 2017 is an integrated consortium of six research groups. The Centre of Excellence in Cell-Extracellular Matrix (ECM) Research granted by the Academy of Finland for years 2012 - 2017 is an integrated consortium of six research groups led by Drs. Taina Pihlajaniemi, Johanna Myllyharju, Seppo Vainio, Robert Winqvist, Aki Manninen, and Lauri Eklund. The consortium aims to understand how cell‐ECM interplay and the ECM microenvironments contribute to tissue development and homeostasis as well as how disruption of these essential conditions and interactions influence the integrity of tissues and malignancy development. The consortium integrates expertise in research on cell-ECM interplay, collagens, ECM synthesis and hypoxia response, embryonic induction and organogenesis, cancer genetics and tumor biology, epithelial cell polarity, and vascular morphogenesis. New understanding gained from the studies of the CoE will lead to improved diagnostics and treatments. The CoE in Cell-ECM Research strenghtens the Oulu profile as one of the leading centres in ECM biology wordwide and provides well-organized and tightly internationally linked training opportunities for at least 35 PhD and MD-PhD students.The current number of personnel working for the CoE is about 100 and about 20 % of research staff is recruited from abroad. The laboratories of the CoE operate at the Medical Campus of the University of Oulu, Finland, and the groups are part of Biocenter Oulu. The Coe allows a strategic change in the focus of the research.

    P4. Tekes project, BioRealHealth. This is a consortia project that is directed by Prof Seppo Vainio. The consortia integrates Oulu university and VTT research aiming to develop novel skin related diagnostics and biosensor technologies. The project runs 2017-2019 and is integrated to 10 joining  companies.

    P5. BioFuture 2023, a project NanoBioMass. This is a research consortia between Oulu and Helsinki university and als the Finnish Natural resource Research center (Luke). The project runs 2016-2020 and targets the nano- and microlevel vesicles in Nature.

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