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Browsing by study line "Cell and Developmental Biology"

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  • Aung, July (2021)
    Epithelial cells line the surfaces of organs and tissues in a continuous and tightly packed manner, thereby functioning as a protective barrier between the tissue and the external environment known as the epithelium. During development, the epithelium undergoes a series of morphogenetic events which alters the shape and size of epithelial cells, enabling them to perform tissue specific functions in mature tissue. During morphogenesis, cells sense the mechanical forces and establish polarity through cell proliferation and rearrangement according to morphogenetic signalling pathways. This manoeuvre is achieved by the underlying actin cytoskeleton network which enables cells to resist the tension and stresses of morphogenesis via alteration of filament dynamics and network architecture. In vivo, numerous actin-regulatory proteins generate various polymerized forms of straight, branched, or contractile actin-myosin filaments, regulating dynamic actin filament turnover. The robust actin cytoskeleton provides the cell with protrusive and contractile forces that enable cells to migrate, maintain, and change its shape and form during morphogenetic events. Actin filament depolymerization is accomplished by ADF/cofilin (Drosophila homolog twinstar) binding to actin monomers (G-actin) and actin filaments. However, ADF/cofilin alone is not very efficient in promoting disassembly of actin monomers, especially in subcellular regions where ADF/cofilin is highly concentrated. AIP1 (Drosophila homolog flare) then enhances actin depolymerization via preferential binding to ADF/Cofilin rich regions in vitro. The aim of my thesis was to study the localization and roles of AIP1 and cofilin in follicular epithelium during Drosophila oogenesis. My results showed that Actin-Interacting-Protein-1 (AIP1) was expressed throughout oogenesis. AIP1 expression was increased in cell type-specific manner and AIP1 showed spatiotemporal localization in follicular epithelium during oogenesis. Silencing of AIP1 led to accumulation of ectopic F-actin aggregates, localization of which may reflect the cellular sites of dynamic actin reorganization in the follicular epithelium. My results also indicate that AIP1 may be indirectly responsible for maintaining epithelial integrity as its silencing resulted in formation of epithelial gaps throughout follicular epithelium. Also delays in border cell migration were observed. Considering the above, understanding how AIP1 functions in Drosophila morphogenetic events would therefore pave the way for a greater understanding of how this protein works in other organisms. The knowledge gained may also be used to extend the current understanding of the role of actin binding proteins in diseased states.
  • Sokka, Joonas (2019)
    Pluripotent stem cells (PSC) can exists in both primed and naïve states. The conventionally derived human PSCs represent the later primed state of pluripotency during embryo development, while the naïve state resembles the inner cell mass (ICM) of pre-implantation blastocyst. Primed human PSCs can be reverted chemically by transient histone deacetylase (HDAC) inhibition back to the naïve state in vitro. The reverted PSCs can then be characterized based on their morphology and expression of selected naïve markers using immunocytochemistry and RT-qPCR assays. Leucine twenty homeobox (LEUTX) is one of the genes expressed during the early stages of embryo development and is capable of activating the transcription of multiple genes, including pluripotency-associated genes, which are upregulated during the human embryonic genome activation (EGA). LEUTX expression could potentially improve the naïve reversion efficiency or the maintenance of naïve PSCs by driving the transcriptome of primed PSCs back towards the earlier cell stages of embryo development, potentially even to cell stages that precede the naïve state. The aim of this thesis was to setup the naïve reversion protocol and study the effects of LEUTX on the reversion by using the generated and tested H9 activator cell line for targeted activation of endogenous LEUTX expression. First, a conditionally stabilized CRISPRa activator cell line was generated for targeted activation of endogenous gene expression in H9 cells. Then sequence-specific guide RNAs (gRNA) targeting LEUTX for activation were introduced to the activator cell line. Using the generated activator cell line during the naïve reversions allows the targeted activation of specific genes, here LEUTX, and thus enables studying the effects of these genes on PSCs during the naïve reversion protocol. The induced activator cells expressing LEUTX managed to form four times as many naïve resembling colonies during the reversion compared to the controls, but most of these were lost after changing the medium conditions towards the end of the protocol. After the reversion was complete, the reverted PSCs were characterized as naïve PSCs based on their domed morphology and the high expression of naïve markers NANOG, KLF17, TFCP2L1 and DNMT3L when compared to the primed PSCs. The naïve reversion protocol was set up and optimized successfully and can now be used as a reliable way of obtaining human naïve PSCs for further experiments studying and modelling the earlier developmental stages during embryo development. Furthermore, the generated H9 activator cell line worked as intended and can be utilized for studying the effects of other targeted genes during the reversion or in the reverted naïve PSCs.
  • Lintala, Annika (2020)
    Bipotential gonads are precursor structures for testes and ovaries. Steroidogenic factor-1 (SF1) is one of the most important transcription factors in an embryo needed for the development and maintenance of bipotential gonads. If SF1 is not expressed, bipotential gonads fail to develop, and genitalia and kidneys are not formed. Later, SF1 expression persists high in testes, where it supports Sertoli and Leydig cell formation and development. If SF1 is not expressed enough in males, the bipotential gonads differentiate into ovaries. The factors activating and regulating SF1 are not currently fully known. By getting more knowledge of how SF1 is controlled, regulatory mechanisms behind normal fetal development of gonads and disorders of sex development (DSD) can be understood better. The aims of this thesis were to study whether growth factors, that naturally regulate differentiation of developing gonads, promote differentiation of human induced pluripotent stem cells (hiPSC) into Sertoli-like cells (SLCs) and whether SF1 expression is induced by the addition of these growth factors. For conducting the study, we used hiPSCs, which have an SF1 activation domain cassette previously introduced to the cells by clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9) (CRISPR/Cas9) method. SF1 could be activated by adding doxycycline (DOX) and trimethoprim (TMP). These hiPSCs were differentiated into intermediate mesoderm (IM) on the first four days according to the protocol published earlier by the group. After this, the differentiation to SLCs was guided by adding growth factors to the culture medium. Basic fibroblast growth factor (bFGF), fibroblast growth factor 9 (FGF9) and prostaglandin-2 (PGD2) were tested separately and in a combined cocktail also including follicle stimulating (FSH) and glial cell-derived neurotrophic factor (GDNF). In a control condition, cells were differentiated without additional growth factors. In all tested conditions, cells first differentiated into IM were further differentiated either in the presence or absence of DOX and TMP for 8 days. The differentiation medias were changed to the cells every day and lysis samples for quantitative PCR (qRT-PCR) were taken every other day. The relative gene expression levels of bipotential gonad, testis and steroidogenic gene markers from each condition were monitored with qRT-PCR and compared to the levels of the undifferentiated hiPSCs. Immunocytochemistry was performed to see the changes in protein production. Against our hypothesis and the previous studies by others, none of the tested growth factors induced the cells to differentiate into SLCs. However, SF1 expression was triggered by chemical induction with DOX and TMP. Also, the expression levels of bipotential gonadal and testicular gene markers increased in control conditions with/without chemical induction. PGD2 conditions were the only ones to resemble the gene expression and morphology of control conditions while the others differed. These results indicated that the addition of bFGF, FGF9, FSH and GDNF did not improve the differentiation of iPSCs into SLCs and in fact, bFGF and FGF9 hindered their differentiation into SLCs. As a future perspective the optimal concentrations for each growth factor and the duration of growth factor supplementation ought to be tested to refine the protocol.
  • Häkkänen, Iina (2022)
    Colorectal cancer (CRC) is one of the most common types of cancers, encompassing approximately 10 % of all cancer cases worldwide. Regulation of cell proliferation and cell fate decisions is crucial for maintaining cellular homeostasis and preventing CRC initiation, a process in which the Wingless (Wnt)/β-catenin signalling pathway is known to play an important role. For instance, somatic mutations occurring in the Apc gene lead to aberrant activation of the Wnt/β-catenin pathway, which further leads to the accumulation of β-catenin into the nucleus where the TCF/LEF transcription factors, including TCF1, TCF3, TCF4, and LEF1, bind β-catenin to activate downstream Wnt target genes and promote CRC development. TCF1 is encoded by the gene Tcf7 that can be alternatively spliced to produce long (p45) and short (p33) isoforms whose function in CRC development has remained poorly understood. Previously, deletion of Tcf7 has been found to increase intestinal adenoma formation in mice with one mutated Apc allele (ApcMin/+), which are predisposed to development of multiple intestinal adenomas. To study how heterozygous deletion of the p45 isoforms affects intestinal adenoma formation and the cellular transcriptome, we have studied ApcMin/+ mice, which have a heterozygous mutation of Tcf7 gene encoding only the p33 isoform (AmTp45∆/+). In our study, we used immunohistochemistry and RT-qPCR together with a single-cell RNA sequencing (scRNA-seq) analysis. Heterozygous deletion of the p45 isoforms in the ApcMin/+ mice dramatically increased the numbers of intestinal tumours, spleen size and its white pulp areas but it had no effect on cell proliferation or expression of the Wnt-target gene Prox1 in intestinal adenomas. In addition, ApcMin/+ mice with both heterozygous p45 and Lef1 deletions developed significantly more intestinal tumours. Without the Apc mutation, neither of these mouse models developed intestinal adenomas or spleen abnormalities. RT-qPCR analysis showed decreased expression of Tcf7 in the small intestine of the AmTp45∆/+ mice. scRNA-seq analysis revealed that the AmTp45∆/+ mice downregulated various Wnt antagonists and stem cell markers and upregulated several genes that function in different metabolic pathways. Overall, these results support the concept that Tcf7 functions in synergy with Apc to repress intestinal malignancy. Our results establish a basis for comparison of the relative importance and specific functions of the TCF/LEF1 family members in CRC development.
  • Michalowski, Piotr (2019)
    The TrkB signaling pathway plays an important role in synaptic transmission and plasticity. Synaptic plasticity is disrupted in many neurological disorders, such as major depression and dementia. A number of studies indicate that TrkB (tropomyosin-related kinase B) signaling is required for the therapeutic effects of antidepressants. Both conventional and rapid-acting antidepressants encompass the TrkB pathway but the underlying mechanism of this remains unknown. Recent studies have, however, revealed an intriguing link between emergence of slow wave EEG activity (SWA) or sedation and the TrkB pathway. Notably, various anesthetics and sedatives (e.g. isoflurane and medetomidine) that increase SWA concomitantly induce TrkB signalling, and this seems to happen independently of BDNF (brain-derived neurotrophic factor), the primary ligand of TrkB. Given the ability of Src kinase to transactivate TrkB in vitro, we have examined the acute effects of medetomidine and isoflurane on SrcY416 and TrkBY816 phosphorylation in the adult rodent cortex and hippocampus by using Western blotting. Pyrazolopyrimidine 2 (PP2), a Src kinase inhibitor, was implemented in order to inhibit TrkB signalling pathway induced by medetomidine. The study was further extended to sleep deprivation experiments to investigate the effects of deep sleep on the Src and TrkB protein phosphorylation. Phosphorylation of GSK3βS9, another important molecular event coupled with antidepressant effects, was also investigated. The results indicate that both isoflurane and medetomidine activate Src kinase and TrkB signalling pathway. Such an effect was not, however, seen in the PP2 study and thus we failed to confirm the mechanistic connection between Src and TrkB. A trend in the phosphorylation of TrkB, Src and GSK3β was found in the brain samples collected after 15 minutes of recovery sleep, suggesting that TrkB signalling is also facilitated during physiological SWA. In conclusion, these results reinforce the hypothesis that SWA occurs simultaneously with TrkB signaling. Future studies are required to test the involvement of Src kinase in this phenomenon.
  • Prajapati, Biplu (2021)
    Transfer RNA (tRNA) is one of the most extensively modified RNA molecules. The role of tRNA modifications become apparent during physiological condition such as oxidative stress, where it serves as an adaptive response to the changing environment. These modifications are upregulated mainly at the wobble position of the tRNA to enhance the translational efficiency of the stress response genes through enhanced decoding rate and tRNA–mRNA interaction. Hence, tRNA modification has a crucial role in regulating translational fidelity, and such modifications can be utilized to fine-tune the translation for improved production of heterologous protein. Therefore, this study aimed to analyze the tRNA modification changes in two laboratory-significant E. coli strains (BL21 (DE3) and K12) during oxidative stress and utilize these modifications to enhance the production of heterologous protein using a defined cell-free protein synthesis system. Ultra-performance liquid chromatography-mass spectrometry was used to detect and quantify the tRNA modification changes in the hydrogen peroxide-treated E. coli cells. The results showed unique tRNA modification patterns and intensities between the two bacterial strains in response to oxidative stress. Modifications such as ac4c and m2,2G were upregulated in E. coli BL21 (DE3) following hydrogen peroxide treatment, whereas k2C and chm5U were increased in E. coli K12. Further analysis of the dataset revealed that most of the upregulated ribonucleoside modifications were predominant at the anticodon loop of the tRNAs, indicating the potentiality of these tRNA pools to impact on translation. Likewise, I optimized an E. coli-based cell-free protein synthesis system to investigate the effect of modified tRNA pools on translation. Hence, this study serves as a stepping stone to understand the tRNA modification landscape of E. coli and provides a platform to depict the function of post-transcriptional tRNA modifications in translation with the CFPS system.