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Browsing by study line "Solu- ja kehitysbiologia"

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  • Kuncheva, Ema (2022)
    Mutations in the KCNQ1 gene have been implicated in the onset of hypopituitarism. Regulating KCNQ1 expression would therefore enable future clinical research on the mechanism of the disease. CRISPR offers a flexible toolset for controlling genetic expression via knockout, knock-in, knockdown, and gene activation. Of these approaches, CRISPR activation (CRISPRa) is distinguished by its ability to induce gene overexpression in a cell’s native context, making it a valuable tool in the interrogation of genetic disorder pathogenesis. This thesis therefore tested the efficacy of a CRISPRa subsystem in increasing KCNQ1 expression. The CRISPRa subsystem, VPR, was chosen because of its high activation efficiency and the ease of controlling the activation system of its doxycycline-inducible mode of action. The cell line used for the experiment, HEK293, was similarly chosen because of its ease of culture and transfection. To validate the proper functioning of the activation system, expression rates of the related genes ASCL1 and GHRH were measured as positive controls. The activation system successfully upregulated the expression rates of the two genes. As the dCas9-VPR system is dependent on the Tet-ON operator for inducing activation in a controllable manner, a test for dCas9 leakage was conducted. RT-qPCR analysis showed the upregulation of ASCL1 expression in the uninduced state of the system, confirming the presence of dCas9-VPR leakage. The dCas9-VPR system finally aimed to test the expression rate of KCNQ1. Although one novel guide RNA successfully upregulated KCNQ1 expression, it did so inefficiently and its success was not shared by any of the other tested guide RNAs. Altogether, the dCas9-VPR system was successfully established in HEK293 cells, and the leakage of the inducible system was confirmed, however, KCNQ1 activation by CRISPRa requires further optimization.
  • Oshin, Afsana (2021)
    Tropomyosins (Tpm) are coiled-coil proteins, which wind around actin filaments to form head-to-tail oligomers. Tpms control actin filament growth, movement and interactions with other actin-binding proteins like myosins and cofilin. Tpms play essential role in the construction and stabilization of complex three-dimensional actomyosin contractile structures called stress fibers, because Tpms regulate structural and functional attributes of actin filament populations. In mammals, there are 4 TPM genes encoding above 40 TPM variants, giving rise to many functional Tpm protein isoforms. They are responsible for several physiological mechanisms in cell such as morphogenesis, cytokinesis, vesicle transportation, metabolism, motility, organ development, and signaling. Even though several studies have been conducted to determine structures and functions of various Tpms, many questions are still to be answered about Tpm2.1 and its significance in cells. So far, Tpm2.1 isoform has been a difficult protein to study due to poor success rate at achieving its complete depletion from the cell. Its involvement in cytokinesis, cell movement, cancer progression, and association with mechanosensing ability of cells were recently reported, and this raised the interest of researchers to focus on unveiling its precise cell biological function. Conditional deletion, degradation or inactivation of a protein helps to determine its function in cells. A new revised Auxin Inducible Degron version-2 (AID2) approach employs the cell´s own ubiquitin mediated protein degradation process, ensuring efficient and rapid depletion of target protein by the help of expressing OsTIR1(F74G) auxin-receptor mutant in presence of 5-phenyl-indole-3 acetic acid (5-Ph-IAA) ligand. In this study, we established a pipeline to identify Tpm2.1’s functions using AID2 technology by integrating OsTIR1(F74G) mutant at AAVS1 locus of the homozygous knock-in U2OS clones, containing mAID-msGFP2-TPM2.1 fusion insert at their endogenous TPM2.1 locus. We aimed to deplete Tpm2.1 from cells using this approach by inducing with 5-Ph-IAA and observe the direct, immediate phenotypes during Tpm2.1 degradation. We succeeded in achieving almost complete Tpm2.1 depletion. By this approach, we revealed that Tpm2.1 controls actin reorganization, stress fiber stability, and maturation of focal adhesions in cultured cells. To our knowledge, Tpm2.1 is the first actin-binding protein to be studied using AID2 approach, and the promising outcome brings hope to study other complicated actin-regulating proteins with this approach.
  • Butkovic, Rebeka (2020)
    Autophagy is a cellular recycling and quality control process that eliminates cellular material in a non-selective or selective fashion. Macroautophagy is non-selective, and degrades macromolecules or damaged organelles to sustain cellular homeostasis. The selective autophagy of dysfunctional or excess mitochondria is known as mitophagy. The clinical importance of functional degradation is exemplified by the lysosomal storage disorders (LSDs), where lysosomal hydrolytic enzymes are absent or dysfunctional. Previous investigations of a rare infantile LSD indicated a change in autophagy and decreased mitochondrial content. The aim of this MSc thesis was to quantitatively compare macroautophagy and mitophagy in a cellular model of this rare LSD, by generating fluorescent macroautophagy and mitophagy reporter-expressing cell lines from patient material. Fibroblasts derived from patients diagnosed with a rare infantile LSD were transduced with lentiviruses carrying either mCherry-GFP-LC3 or mito-QC reporters, for the microscopic analysis of autophagy and mitophagy, respectively. I also monitored autophagic flux by traditional biochemistry in untreated and starved cells, in the presence or absence of lysosomal inhibitors (bafilomycin A1). Basal and iron-depletion induced mitophagy was profiled using confocal microscopy, quantitative cell biology and biochemistry. My findings suggest differential autophagic turnover in LSD patient-derived fibroblasts, with a marked accumulation of non-acidified autophagic structures. Basal mitophagy was elevated in two out of three LSD patient cell lines compared to unaffected controls. LSD patient cells exhibited altered mitochondrial content and network architecture compared to controls. These phenotypes were accompanied by distinct changes in the endo-lysosomal system and increased cell size. The patient-derived cells exhibit a profound accumulation of lysosomes and autophagic structures. My findings are in accordance with previous research in the field, suggesting perturbed macroautophagy in this rare LSD. The observations of altered mitochondrial homeostasis in this LSD provide a basis for future investigation. The reporter-expressing cells, generated as part of this MSc thesis project, will enable future studies of mechanisms that underlie phenotypic changes, and will complement essential in vivo work in this area.
  • Kozlova, Anastasia (2023)
    Chimeric antigen receptor (CAR) T cells are genetically modified usually autologous T cells expressing de novo designed CAR that binds a specific antigen on the surface of the cancer cells, inducing T cell receptor-independent activation and cytotoxic response against the targeted cancer cells. While CAR T cells have been shown to offer effective treatment in acute lymphoblastic leukemia, diffuse large B-cell lymphoma, and multiple myeloma, several resistance mechanisms can lead to CAR T cell exhaustion characterized by impaired functions and the expression of inhibitory receptors. The Finnish Red Cross Blood Service has developed novel CARs, differing in structure from the ones currently published. Since the evasion of CAR T cell exhaustion is considered one of the key objectives in the development of CAR T cell therapy, this Master’s thesis project aimed to create a working method to determine the exhaustion of CAR T cells in vitro after long-term repeated stimulation. In order to induce and measure exhaustion, CAR T cells were produced and activated ex vivo in the presence of IL-2 or IL-7/IL-15 cytokines, cultured long-term and repeatedly stimulated by exposure to target cells. CAR T cell cytotoxicity and expansion were determined and the expression of various inhibitory receptors was analyzed. The method enabled the comparison of the designed CAR T cell candidates and the positive control CD19-CD28ζ CAR T cells in long-term cytotoxic potency. In addition, it helped to reveal the surprising difference between IL-2 and IL-7/IL-15 cytokines and their impact on CAR T cell exhaustion. Although CAR T cells produced with IL-2 had poorer expansion during CAR T cell production than CAR T cells produced with IL-7/IL-15, they showed lower expression of exhaustion-related markers supported by better survival, proliferation and cytotoxic activity during long-term repeated stimulation assay.
  • Olgac, Ezgi (2022)
    Background– The BCL-2 protein family members are major regulators of apoptosis, and the anti-apoptotic (pro-survival) members of the family is commonly targeted with BH3 mimetic drugs in haematological cancers. However, these treatments have not been very impactful when administered as single agents and they have long been investigated for combination therapy with other agents. Acute myeloid leukaemia (AML) is one of the difficult-to-cure haematological malignancies. A recently approved therapy for AML consists of the combinatorial administration of venetoclax (a selective BCL-2 inhibitor) and a DNA methyltransferase (DNMT) inhibitor such as azacitidine or decitabine. Although this novel therapy has shown promising clinical results, the majority of the patients still relapse under this treatment. These relapsed patients typically become highly resistant to treatment and have poor prognosis, emphasising the need for new effective drug combinations. Apart from BCL-2, other family members like BCL-xL and MCL1 are also common targets of BH3-mimetic drugs. This project thus aims to understand and characterise the resistance against BH3-mimetics and investigate new therapeutic approaches to overcome the challenges of resistance. Aims– This study aims (i) to characterise BH3-resistant AML cell lines for uncovering the mechanisms of drug resistance, and (ii) to identify possible combination treatment options for overcoming drug-resistance. Methods– Viability assays with Cell Titer Glo® (CTG) and Drug Sensitivity and Resistance Testing (DSRT). The long-term effectiveness of venetoclax, azacitidine and talazoparib (a PARP inhibitor) as single agents, double combinations and triple combination were investigated with Time-to-Progression (TTP) assay. For the resistant cell line models, underlying resistance mechanisms were assessed by checking protein expression of pro- and/or anti-apoptotic members of the BCL-2 family members with western blot (WB). Real-time quantitative PCR (RT-qPCR) and WB were carried out for transcriptional and translational expression analyses of certain DNA damage-associated genes in PARP inhibitor-resistant cell lines. Results– Drug screening with DSRT has revealed promising results for two combination treatments of a BCL-xL inhibitor (A-1331852) (i) with an Aurora kinase A inhibitor (alisertib) and (ii) with an MCL1 inhibitor (S63845) for BCL-xL inhibitor-resistant cells. WB analyses of BCL-2 family members showed translational upregulation of un-inhibited members of the anti-apoptotic proteins in BH3-mimetic-resistant cell lines. A venetoclax-resistant AML cell line showed increased levels of the DNA damage marker P-γ-H2Ax upon treatments containing venetoclax, as well as increased levels of cleaved-PARP1, indicating induction of apoptosis. RT-qPCR analyses revealed increased mRNA expression of PARP1 in two resistant cell lines, whereas no significant expression changes in other DNA repair mechanism genes on the transcriptional level. Conclusions– In BH3-mimetic-resistant AML cell lines, apoptosis is avoided through translational upregulation of un-inhibited anti-apoptotic members of the BCL-2 family, and this resistance can be countered by combination treatment for additional inhibition of the compensatory anti-apoptotic proteins. Venetoclax is still effective on cells resistant to it, by inducing DNA damage and sensitising these cells against inhibitors of the members of DNA repair pathway. The transcriptional upregulation of PARP1 and the increase in its auto-catalytic activity suggests the DNA damage-inducing effects of the triple combination treatment [Ven + Aza + Tal].
  • Lamichane, Nicole (2019)
    Over the past years sugar consumption has seen great increases worldwide, together with a rise in the prevalence of metabolic diseases. There is a growing need for a comprehensive characterisation of the genes involved in sugar metabolism, yet the mechanisms by which cells sense and respond to sugars in vivo have remained incompletely understood. Here, I analyse members of a protein family best known for their regulation of differentiation during development with regards to their role in sugar metabolism. The Hairy and Enhancer of Split (HES) protein family are a group of basic helix-loop-helix (bHLH) transcription factors that function as major downstream effectors of the Notch signalling pathway. In mammals, the HES proteins have mostly been studied for their role in cell differentiation, but HES1 has been implicated in metabolic control. Drosophila has several transcription factors belonging to the HES family, including Hairy and seven bHLH transcription factors located in the Enhancer of split complex (E(spl)-C). The E(spl)-C bHLH transcription factors display high homology and are considered to be genetically redundant, and therefore little is known about their individual functions. The other HES family members in Drosophila have not previously been linked to metabolic regulation, but Hairy has been shown to repress the tricarboxylic acid cycle. In light of the findings implicating HES1 and Hairy in the regulation of metabolism, I systematically investigated the role of the HES transcription factors in sugar metabolism. By using the GAL4/UAS system in Drosophila melanogaster, I knocked down gene expression of each of the family members, and raised the flies on diets varying in sugar content to identify possible sugar intolerance phenotypes. Here, I show that knockdown of one of the E(spl)-C bHLH genes led to severe sugar intolerance that affected both survival and organismal growth, but did not alter the levels of circulating carbohydrates and storage lipids as measured with colorimetric assays and lipid staining. Furthermore, I identify the tissues in which this transcription factor functions to provide sugar tolerance. Using analysis of publically available chromatin-immunoprecipitation sequencing data coupled with quantitative RT-PCR, I uncover mTOR target Thor/4E-BP as a putative target gene. Additionally, I show that Hairy is similarly required for complete sugar tolerance, but that the mechanism differs from the E(spl)-C bHLH transcription factor. Hairy binds to and positively regulates expression of genes involved in glycolysis and the pentose phosphate pathway, suggestive of a cooperation with earlier known regulators of sugar sensing. In conclusion, I have shown that only two HES family members are involved in the regulation of sugar metabolism and that their regulatory mechanisms are distinct, implying that the HES family members have more diverse roles than previously assumed.
  • Avdonin, Savva (2021)
    Tiivistelmä – Referat – Abstract ROS or Reactive Oxygen Species can be found throughout all living organisms on the planet. Without ROS, processes, which are essential for the sustainment of most living organisms, such as respiration would not be possible. On the other hand, uncontrolled ROS generation can cause severe damage to the cellular structure. The family of ROS includes multiple compounds, which share a common trait of high chemical activity. ROS can be produced on demand by specific enzymes which are localized within cellular structures, such as membranes. One group of enzymes is called NADPH (Nicotinamide adenine dinucleotide phosphate) oxidases. These enzymes possess common structure which is composed of transmembrane region with multiple loop helixes and usually two or more terminal motifs, which are devised into regulatory EF-hand motifs and catalytic motifs. NADPH oxidases are essential ROS producers and can be found throughout most clades of living organism and are widely represented in different cellular compartments and distributed across different tissues in multicellular organisms. As an example, Nox family of NADPH oxidases can be found in human tissues and immune cells. Another common group of NADPH oxidases is respiratory burst oxidase homologues (RBOH) can be found in plants. Members of this group play important role in plant immune defense against pathogens. One example is AtRBOHD, which is expressed in Arabidopsis genus of plants. Upon activation, these enzymes are known to produce hydrogen peroxide (H2O2) as mean of antibacterial defense. These host defense mechanisms are known to be driven by different signaling molecules. It has been determined that in some examples of NADPH Oxidases, including Nox5 and RBOHD, the state of activation can be induced through the effects of Ca2+ ions. Moreover, it has been determined, that ROS-producing state of these NADPH oxidases is achieved through change of conformation. This change in conformation is attributed to the different modes of interaction of motifs of oxidases, which are dependent on concentration of bivalent cation Ca2+. Previous research regarding intramolecular interactions within specific NADPH oxidase- Nox5β has been performed by multiple research teams and different sources appear to contradict each other on the exact mode of interaction of Nox5β EF-hand upon presence of Ca2+. Therefore the exact interaction model of terminals of Nox5β is unclear. In addition, the effect of presence of Ca2+ on the interaction terminals in another representative of NADPH oxidases- AtRBOHD, which possess highly analogous molecular structure of catalytic C-terminus to Nox5β, has never been thoroughly studied, as well as interactive cross-compatibility of the C and N terminals from these two distinct species of NADPH oxidases. The objectives of this research are to analyze intramolecular interactions of N- and C- terminals in Arabidopsis RBOHD and Human Nox5β upon presence of ionic calcium, compare Ca2+-induced terminals interactions in said oxidases and to establish possible cross-compatibility of terminals in these two distinct NADPH oxidase species. Practical aspects of this research included cloning the C- and N- cytoplasmic regions of Nox5β and AtRBOHD into bacterial expression vectors utilizing the PIPE cloning method, heterologous production of epitope-tagged tails of NOX5β and RBOHD in E. Coli BL21 and finally in-vitro pull-down assays to analyse the interactions of the tails upon the presence of Ca2+ as well as interactive cross-compatibility of these tails. By utilizing methods mentioned above, this research has demonstrated that interactions of terminals motifs both in Nox5β and AtRBOHD are possible even in calcium-deprived environment, which was achieved through use calcium-binding agent (EDTA) and the effect of calcium on interactions of terminals both in RBOHD and Nox5β is very limited if not insignificant. This research has also demonstrated that the cross-compatible interactions between terminals of Nox5β and AtRBOHD are possible. Results of this research indicate a strong structural conservation within NADPH oxidases, which indicates similar intramolecular interaction mechanisms within two highly diverged species. These findings may prove to be useful as a background for the future research regarding ROS producing enzymes and evolutional conservation in structures of oxidases.
  • Sket, Tina (2020)
    Endoplasmic reticulum (ER) stress is caused by the accumulation of unfolded proteins in the ER, which leads to the activation of unfolded protein response (UPR) through three transmembrane protein sensors located in the ER membrane. The sensors correspond to three branches of the UPR, namely protein kinase RNA-like endoplasmic reticulum kinase (PERK), activating transcription factor 6 (ATF6), and inositol-requiring enzyme 1 (IRE1) branches. Upon ER stress, IRE1 dimerizes and oligomerizes, and its endonuclease domain is activated. It specifically targets X-box-binding protein 1 (XBP1) mRNA, from which a 26 nt intron is spliced. This allows a complete translation of spliced XBP1 mRNA into a functional protein that acts as a transcription factor. Together with the other pathways, the UPR leads to a decrease in the protein folding load by causing a reduction in the general level of protein translation, and by inducing the expression of protein folding machinery. However, if the UPR is activated continuously for a long time, the apoptotic pathway will be triggered, and the cell will die. ER stress and UPR are associated with various disorders, such as some types of cancer, diabetes, chronic inflammatory syndromes, and particularly neurodegeneration. For example, in Parkinson’s disease, it was suggested that prolonged ER stress induces the extensive apoptosis of dopaminergic neurons in substantia nigra pars compacta region of the midbrain. This hinders the normal functioning of the nigrostriatal pathway, and hence results in the progressive development of Parkinson’s motor symptoms. In order to study the regulation or IRE1 branch of the UPR, and to identify the ER-stress-modulating compounds, a human luciferase reporter cell line (XBP1-NLuc) was created in this work. The reporter was expressed when IRE1 splicing was activated, since the XBP1 intron fragment was fused to the Nano luciferase gene. The expression of the reporter was observed with luciferase assay at several time points during treatments. The treatments were done with ER stress inducers thapsigargin and tunicamycin, and with IRE1 inhibitors KIRA6 and 4μ8c, or the combination of those. Quantitative PCR (qPCR) was used to validate the expression of the reporter and to monitor the expression of the other branches of the UPR. Additionally, the oligomerization of IRE1 was observed with IRE1-GFP cell line that was treated identically to the XBP1-NLuc cell line, fixed, stained for nuclei, and imaged with fluorescent microscopy. After imaging, the IRE1-GFP clusters were analysed and quantified with CellProfiller and CellAnalyst softwares. Both cell lines were used to test the effect of neurotrophic factors CDNF, MANF, and MANF mutant isomers on the UPR with and without tunicamycin treatment. Collectively, the experiments confirmed that XBP1-NLuc cell line was created successfully and that it accurately reports IRE1 splicing activity. As expected, ER stress treatment increased the reporter expression, while IRE1 inhibitors decreased the expression of the reporter. qPCR revealed that the other observed UPR markers were activated as well upon thapsigargin treatment, however, they were not decreased with the treatment with IRE1 specific inhibitors. In line with XBP1-NLuc cell line, the IRE1-GFP cell line demonstrated an increased oligomerization of IRE1 upon ER stress induction. The KIRA6 inhibitor of IRE1, which prevents IRE1 oligomerization, decreased the formation of IRE1-GFP clusters. Additionally, the IRE1-endonuclease-activity inhibitor 4μ8c induced the formation of IRE1-GFP clusters. Curiously, the distribution of the intensity of IRE1-GFP clusters was bimodal and could point to two manners of IRE1 clustering and/or activation. Together, the experiments done with cells transfected with CDNF, MANF or MANF mutants, suggested that the tested neurotrophic factors decreased IRE1 oligomerization and its activation. However, there were substantial problems in the quantification of viable cells, which should be considered in the interpretation of these results. No significant difference among the tested neurotrophic factors was observed. In conclusion, the XBP1-NLuc reporter cell line provided a reliable reporter of IRE1 endonuclease activity, whose expression is increased during the ER stress. Together with IRE1-GFP cell line, it revealed the amount of IRE1 oligomerization and activation under various treatments and at different time points relative to treatments. Due to the effectiveness and accuracy, the XBP1-NLuc cell line can be further used in studying the regulation and activation of IRE1, as well as for the identification of ER-stress modulating molecules, which can be used for development of novel treatments for ER stress associated diseases, such as Parkinson’s disease.
  • Kari, Moisio (2023)
    Animals regulate their metabolism dynamically as a response to changes in nutritional landscape. Intestine is emerging as a key regulator of systemic metabolism. It possesses secretory enteroendocrine cells (EECs), which have a central role in intestinal nutrient sensing and signaling. However, how the number and function of EECs is regulated in response to nutrients remains poorly understood. Previous work in Hietakangas lab has shown that a transcriptional cofactor, C-terminal binding protein (CtBP), regulates the number of EECs in response to sugar feeding and loss of CtBP function in EECs causes sugar intolerance in Drosophila. CtBP’s transcriptional activity is modulated through homodimerization, which is controlled by redox coenzyme NAD+/NADH, whose levels are dependent on sugar metabolism. Therefore, I hypothesise that CtBP is a sugar- and redox-responsive regulator of EEC function. In this thesis, I aimed to understand how CtBP is regulated and what are its downstream effectors. My results show that the formation of CtBP homodimers is responsive to dietary sugars and cellular redox state. In addition, I observed that CtBP heterodimerizes with EEC fate determining transcription factor Prospero. Functional analysis of CtBP downstream effector genes shows significant overlap with those of Prospero. In conclusion, CtBP is a sugar- and redox-responsive cellular regulator of EEC function, which acts in cooperation with Prospero.
  • Lopez Cabezas, Rosa Maria (2022)
    In the past few years, there has been an increased consideration on the stem cell niche as a key factor to regulate stem cell maintenance and differentiation. Research on characterization of the stem cell microenvironment boosted after the determination of long-term three-dimensional (3D) tissue cultures, or so-called organoids. Organoids are derived from stem cells which self-organize in 3D multicellular structures upon embedding in an extracellular matrix mimic, such as Matrigel®. Their main advantage is these structures resemble the architectural distribution of the tissue of origin in vivo. Likewise, the cellular components of organoids vary depending on multiple variables as the tissue of origin and the growth factors they have access to. As a result of advances in this technique, some stem cell niches have been well characterized, as in the case of intestinal stem cells (ISCs), while others remain elusive as in case of the human gastric stem cells (hGSCs). Along with the remarkable development of 3D cultures, the interest of ECM proteins in stem cell regulation increased. Matrigel® is a rich matrix composed of several adhesive proteins such as laminins and collagens. Aside from providing structural support, the extracellular matrix (ECM) proteins forming this matrix contribute to cell adhesion and signalling. However, Matrigel® composition cannot be modified or even well-characterized due to its origin from Engelbreth-Holm-Swarm (EHS) mouse sarcoma cells. Additionally, it has been demonstrated that contains a high batch-to-batch variability. Other techniques to study the effects of individual ECM proteins have been used such as coating of tissue culture plates with ECM proteins. However, the biomechanical properties in this model are far from being physiological. Therefore, although preliminary results can be obtained using this technique, results extrapolation to an in vivo model can be questioned. To date, there is a lack of a reproducible, high-throughput and reliable technique to test the effect of ECM proteins on human gastric stem cells behavior. This Master’s thesis presents a novel transwell device containing a polyethylene glycol (PEG)-based hydrogel enriched with human ECM proteins to test their effect on human gastric stem cell regulation. Preliminary results showed that gastric organoid-derived epithelial cells (GODE) grown on hydrogels with ECM proteins that are localized at base of the gastric glands, such as Laminin-211, had a higher stem cell marker expression than the control grown on ECM proteins that are uniformly localized in vivo. Additionally, when GODE were grown on hydrogels containing ECM proteins that are localized at the surface of the native gastric epithelium, expression of surface gastric mucins markers was enhanced. These preliminary results highlight the utility of the optimized transwell device to further shed light on how the human gastric stem cells are regulated and what is the effect of the ECM proteins surrounding them.
  • Hytti, Soile (2023)
    Depression and anxiety are the two most common mental disorders worldwide, and especially common among women of reproductive age. Hence, they are also common problems among pregnant women. Maternal depression and anxiety not only compromise the mother’s quality of life during pregnancy but increase the risk of perinatal complications and poor child neurodevelopment. The biological mechanisms that underpin this transmission remain largely unknown. The placenta, a transient fetal organ functioning as an interface between the mother and the fetus, plays a pivotal role, as the placenta transmits all environmental cues to the fetus. This thesis aims to investigate differential gene expression in the first-trimester chorionic villi and birth placenta samples from women with depression and/or anxiety and healthy controls. Samples are collected and processed as a part of the InTraUterine sampling in early pregnancy (ITU) study and both chorionic villus samples (CVS) collected during the early pregnancy and delivery placenta samples were studied. I defined three different phenotypes based on (i) maternal depression and anxiety disorder diagnosis, (ii) antidepressant and anxiolytic medication purchases, or (iii) self-reported depressive and anxiety symptoms during pregnancy. Genome-wide analysis of differential gene expression was conducted with DESeq2 R-package and further gene set enrichment analysis was performed with a web-based platform FUMA. When comparing mothers with depressive and anxiety symptoms to asymptotic controls, but not those with or without diagnoses or medication purchases, I found 478 genes differentially expressed. In the enrichment analysis these genes related to immune response and inflammation, such as leukocyte and T cell activation, defense response, and cytokine production. Together these results indicate that maternal depressive and anxiety symptoms during pregnancy change the immune system functions in the placenta which may partly explain the adverse effects of maternal depression and anxiety on the developing fetus. These findings may afford a target for timely targeted interventions to prevent perinatal complications and the transmission of maternal depression and anxiety to the next generation.
  • Arima, Tai (2022)
    Clathrin-mediated endocytosis is the most common pathway by which cells internalize cargoes from the membrane. It is a critical process in cell communication, development, and homeostasis. In order to study endocytic dynamics, it is critical that one can clearly distinguish receptors that have entered the cell from those which remain on the cell membrane. Current techniques for investigating endocytosis rely on removing membrane-bound components with harsh treatments which may interfere with cell physiology, and often depend on antibodies which are not widely available and - even when they are - may give unreliable signals and may affect receptor behavior and internalization rates. Additionally, a large portion of studies on clathrin-mediated endocytosis have been done on a single receptor, the transferrin receptor. Here we have developed a new assay which resolves the above issues through use of a novel protein probe. This fusion protein will allow us to resolve the issues with current endocytic assays mentioned above, and in theory can be used to study any membrane receptor which is endocytosed. Our preliminary results show that we can use our protein to effectively track endocytosed receptors without interference from signal of receptors remaining on the cell membrane. This shows that our protein may be a powerful tool for studying endocytosis across a wide variety of membrane-bound receptors.
  • Piki, Emilia (2021)
    Ovarian cancers (OCs) are gynecological malignancies that cause the most gynecological cancer related deaths due to asymptomatic early-stage development and late diagnosis. The treatment of OC has not improved significantly during the last decades, and challenges are often caused by chemoresistance and the heterogeneity of cancer cell populations. Therefore, there is an urgent need to improve OC treatment outcome and implement new targeted therapies that could address the subtype specific characteristics. The most common type of OC is epithelial ovarian cancer (EOC), that can be further divided into five subtypes with distinct molecular and histological characteristics. High-grade serous subtype represents majority of cases with up to 75% of EOC patients, while other subtypes such as low-grade serous, mucinous, clear cell and endometrioid OC being less common. Considerable progress has been made in cancer treatment via precision oncology, in which individual cancer biology and tumor molecular features are investigated and used to improve treatment decisions. For this purpose, the development of patient-derived cancer cells (PDCs) offers a good opportunity to study cancer biology in vitro and to build models for preclinical molecular profiling and functional testing. PDCs can be used to establish 2D and 3D models, and most recently, wide interest has been focused on patient-derived organoids (PDOs), that offer a better model of tumor and its microenvironment, while allowing long-term culture, cryopreservation, modification and high-throughput opportunities. In this study, the aim was to establish PDO cultures using tumor cells from low-grade serous OC patients for molecular profiling and functional drug testing. PDOs were generated from both fresh and frozen tumor tissue or ascitic samples resulting to successful development of long-term PDOs from three of the five models. In order to identify optimal culturing conditions for low-grade serous OC PDOs, two previously unpublished growth mediums were tested in parallel. The more complex of the mediums showed slightly better PDO growth in general. The immunohistochemistry staining with pan-cytokeratin and PAX8 was used to confirm the epithelial and ovarian origin of PDOs. In addition, cancer panel sequencing was performed to identify mutation profiles. Importantly, the small-scale drug testing, which was performed using conventional chemotherapeutics cisplatin and paclitaxel and targeted drugs gedatolisib and trametinib, showed sample-specific responses. In conclusion, the results from this project show that PDOs are good models for ex vivo precision medicine functional studies. Importantly, we managed to establish PDOs from frozen tumor cells, suggesting that PDOs could be initiated from living biobank samples. However, the challenges related to culturing of PDOs for functional assays included slower growth rate compared to 2D cancer cell cultures and technical challenges related to Matrigel, limiting the possibilities of high-throughput drug testing. By improving these factors, PDOs will offer an efficient 3D model for preclinical use.
  • Muranen, Sampo (2019)
    Tree shoot architecture research is important due to its significance in fields such as timber production, fruit and nut production and aesthetics of common areas. Also, research on genetic factors that regulate shoot and root system architecture might provide novel methods to store more carbon in forests and, hence, mitigate global warming in the future. LAZY1 is one of the major genes that affects branch and tiller angle in herbaceous and woody species such as Arabidopsis, rice and peach tree. LAZY1 has been under scrutiny over a decade but its molecular function remains unknown. However, it is known that lazy1 mutation affects polar auxin transport. Here it is studied how LAZY1 affects initial branch angle, fiber length and reaction wood development in silver birch (Betula pendula). Also, transcript levels of few shoot architecture related genes were analyzed. LAZY phylogenetic analysis provided evidence of a duplication of LAZY1 in three studied tree species (Betula pendula, Prunus persica, Populus trichocarpa), duplicated genes are here named LAZY1a and LAZY1b. Plant material employed in this study was a segregating population (50:50) of back-cross 1 of weeping birch (B. pendula ´Youngii´) which has a truncated lazy1a. Histological samples of branches were prepared by cryo-sectioning, stained with carbohydrate binding Alcian Blue and lignin binding Safranin dyes to reveal patterns of tension wood development. Due to the large size of branch sections, samples were imaged with a microscope and the images were merged together in a Photoshop application. Branch angles were measured manually with a protractor (angle) tool from stem to the middle of a branch. The data was analyzed using mixed linear models due to the nature of used plant material. We could not use clones because of major issues in in vitro propagation. Branch samples were macerated, fibers imaged and measured by ImageJ software. LAZY1a gene expression levels were analyzed by RT-qPCR method. RNA-sequence analysis indicated that the expression pattern of LAZY1a and LAZY1b is similar in B. pendula. However, one should construct a promoter-reporter line to study with better resolution if their expression is spatially analogous. Initial branch angle was significantly different in wild type compared to lazy1a mutant. For future, one could generate single and double knock out lines of lazy1a/b to study if they have cumulative effect on the branch angle, an important factor in timber quality. Tension wood formation was difficult to quantify with the employed method, due to issues in segregating G-layered tension wood from thick-walled reaction wood. A chemical analysis of cellulose content might provide a more objective method to observe tension wood in branches. RT-qPCR method indicated that LAZY1a transcript levels are higher in wild type compared to mutant. A complementation or knock down experiment would provide sound evidence that lazy1a induces the weeping phenotype. X-ray diffraction method could be employed to study the orientation of cellulose microfibril angle in branches of the wild type vs. mutant. Generation of effective tensional stress requires a cellulose microfibril angle less than 10 and this angle is affected by auxin concentration. It is possible, that this angle is larger in lazy1a due to defect in polar auxin transport.
  • Amin, Al (2021)
    Wood development is a significant process with both financial as well as natural perspectives. Trees and wood are of highly significance in Finland where a huge part of the gross national income devises from the forestry area. Ecologically and commercially the Norway spruce (Picea abies) is one of the most common tree species in Europe. It covers about 30% of Finland's forest area. Norway spruce is frequently used in research to study many phenomena related specifically to the wood formation and lignification. The principal objective of my thesis work was to reveal an unknown step in the lignification process in developing xylem of Norway spruce, i.e. the initiation site(s) for lignification. To achieve this goal, the aim was to investigate the chemical identity of possible lignification initiation sites in the middle lamellae and cell corners of developing Norway spruce xylem, and to answer the question where in the cell wall soluble monolignols first emerge and lead to the start of lignin formation (polymerization). I was approaching this goal with immunolabeling technique for confocal microscopy and Raman spectroscopy to unravel this initiation site of lignification by using specific monoclonal antibodies for cell wall compounds and comparing the results with the initial lignin deposition sites. To detect the location/distribution of some important polysaccharides and lignin substructure for lignification initiation, monoclonal antibodies i.e. LM10, LM11, LM15, LM24 and antibody Dibenzodioxocin or DBD were applied for confocal microscopy and some monolignol specific spectra were applied for Raman microscopy. The xylan was detected by LM10 in secondary cell wall abundantly and few are in primary cell wall of Norway spruce. The LM11 against arabinoxylan was determined more in primary cell walls but less in secondary cell wall. The location of xyloglucan was identified in the middle lamellae, primary and secondary cell wall of Norway spruce by LM15. The LM24 against glycosylated xyloglucan was found in secondary cell walls, abundantly in cell corners but few in primary cell wall. The primary antibody Dibenzodioxocin or DBD for the lignin substructure revealed that these were present in the mature cells of secondary cell walls (S2 and S3 layers). The lignin substructures DBD were not found in youngest cells where secondary cell walls are absent. The developing xylem of Norway spruce was subjected Raman microscopy and which revealed the locations of cinnamyl alcohol, coniferyl alcohol and coniferyl aldehyde. The cinnamyl alcohol was abundantly found at cell corner and middle lamellae in most developing part of xylem. The coniferyl alcohol was determined only in developing xylem cell corners. The coniferyl aldehyde was observed at cell corners, middle lamella and primary cell walls of developing xylem. The coniferyl aldehyde was located more in mature cells than younger cells. So, the Confocal and Raman microscopy images revealed the possible bindings of monolignols to polysaccharide in young cell corners, cell wall layers and middle lamellae.
  • Salciute, Martyna (2024)
    Lynch syndrome is the most common hereditary colorectal cancer (CRC) syndrome caused by inherited mutations in DNA mismatch repair genes. Of those, MLH1 is the most mutated predisposition gene and is best known for its involvement in the DNA mismatch repair (MMR) pathway. In addition to the MMR, MLH1 has proved to have a multifunctional role in assisting in the maintenance of genomic stability. Emerging evidence suggests, that reduced levels of MLH1 directly contribute to an increased number of DNA double-strand breaks (DSBs), leading to chromosomal instability (CIN) through impaired mitochondrial function and homologous recombination directed DSB repair. This study aimed to test this hypothesis by evaluating the DNA damage status and mitochondrial functionality in MLH1 knock-down (KD) fibroblast cell lines with varying expression levels of MLH1. DNA damage levels and repair kinetics were inspected by implementing the Comet assay. Moreover, mitochondrial homeostasis examination was done by utilizing functional mitochondrial staining and analysing mitochondrial DNA copy number. Although there was variability in the results, two KD cell lines exhibiting 30% (line 3A3) and 40% (line 2B7) MLH1 expression levels showed similar outcomes: decreased mitochondrial membrane potential, increased cellular reactive oxygen species (ROS) and stalled DNA damage repair as compared to control cell lines, suggesting the involvement of MLH1 deficiency. It is known, that MLH1 depletion predisposes to DNA damage due to impaired MMR. The findings of this thesis contribute to the growing body of evidence, suggesting that MLH1 deficiency may increase the propensity for DNA DSBs, possibly due to impaired mitochondrial function and subsequent elevation in cellular ROS. Furthermore, this increase in DNA breaks may result in CIN. However, given the limited sample size, the results warrant future studies with larger datasets.
  • Fischbach, Lea (2022)
    Establishing and maintaining cell polarity is critical to all multicellular organisms. Apicobasal polarity is a type of cell polarity specific to epithelial cells, which is established and maintained by three distinct protein complexes. Among them, the Scribble (Scrib) complex plays a role as a basolateral determinant. Scrib is a scaffold protein with multiple functions, including maintenance of the basolateral polarity of epithelial cells and a tumor suppressor, acting as a regulator of the Hippo signalling, an evolutionarily conserved pathway which controls organ size through regulation of cell proliferation and apoptosis by inhibiting the transcriptional co-activator protein Yorkie (Yki). A recent experiment proposed that Scrib is involved in maintaining tissue homeostasis through relaying apicobasal polarity regulation across the tissue. This mechanism can be used both by normal cells to rescue hypomorphic scrib cells and by loss of scrib cells to spread loss of polarity. The signal is likely related by cell-cell contact and the junctions present in epithelial cells may be involved in this communication. This project aims to identify the genes involved in tissue homeostasis through intercellular alignment of apicobasal polarity together with Scrib. First, a screening protocol was established by studying genetic interactions and tissue structure. Second, a systematic screening was carried out by using deficiency lines of left arm of the third chromosome in Drosophila. Fly stock expressing spatially and temporally controlled scrib RNAi was established and crossed with deficiency lines to identify genes that have synergy with Scrib. The wing discs of the offspring were dissected, imaged, and the phenotypes were sorted into categories according to the degree of overgrowth. Five strong candidates and four candidates with milder phenotype were identified. The results show the screening method is robust and suitable to carry out a finer, single gene level screen of the candidates, as well as screening for additional candidates in the rest of the Drosophila genome. The identified candidates provide new leads to develop the theorical model of intercellular alignment of apicobasal polarity. Understanding how apicobasal polarity is maintained in the dynamic environment of a living organism is important for physiological and pathological conditions. This study provides an important insight into further understanding tissue development and homeostasis.
  • Metso, Saana (2023)
    Lethal congenital contracture syndrome 1 (LCCS1) is a severe developmental disorder that is part of the Finnish disease heritage. The affected foetuses die in utero and show a lack of motor neurons accompanied by severe atrophy of the ventral spinal cord and muscles and severe contracture of joints, which result in a lack of involuntary movements. Other associated symptoms include hydrops, micrognatia (small jaw), pulmonary hypodysplasia and small size. The syndrome leads to prenatal death before 32nd gestational week, but the cause remains elusive. LCCS1 is caused by a homozygous mutation, FINmajor, in GLE1 RNA export mediator (GLE1) -gene. The mutation is a c.432- 10A > G substitution at the border of intron three and exon four, resulting in a new splice acceptor site 10 nucleotides upstream of the intron-exon junction. This results in aberrant splicing and nine extra nucleotides in the mRNA, corresponding to three extra amino acids in the GLE1 protein of the affected individuals. GLE1 is an important player in RNA biology in cells. In humans it has two isoforms, GLE1A and GLE1B, that have distinct roles. While GLE1A plays a role in cells’ stress response by mediating the formation and disassembly of stress granules in the cytoplasm, GLE1B is found at the nuclear envelope where it mediates mRNA transport from the nucleus to the cytoplasm. Earlier studies using HeLa cells and zebrafish have demonstrated that FINmajor in GLE1 knock-down background disrupts the mRNA export from nucleus to cytoplasm and leads to apoptosis in neural precursors and abnormal arborization of motor neurons, thus mimicking some of the phenotypic features observed in human patients. Kuure group has generated a mouse model with endogenous FINmajor, but it fails to morphologically phenocopy the human disorder (unpublished data). Importantly, human-origin non-cancerous models with endogenous FINmajor mutation have not yet been used in the studies of GLE1 and LCCS1. My aim in the thesis was to create a human embryonic stem (hES) cell line carrying homozygous FINmajor mutation in its genome. A relatively new tool, CRISPR/CAS -system allows for precise genetic engineering in a variety of model organisms. By optimizing the system to efficiently edit the GLE1 gene, I was able to introduce FINmajor mutation in hES cells, creating a new model system to study this disorder. While previous models had relied on temporary silencing of the gene with morpholinos or siRNAs, the hES cell line with GLE1 FINmajor mutation will for the first time give insights on how the mutation affects cellular functions, mRNA biology and cell differentiation in LCCS1. This way the hES cell line I have generated will yield new information on the development, progression and manifestation of the syndrome to better understand its mechanisms.
  • Vähäkangas, Eliisa (2020)
    The intestinal epithelium is one of the fastest renewing tissues in mammals. Intestinal stem cells (ISC) are responsible for producing all differentiated cell types of the intestinal epithelium, through transit amplifying generations. ISCs reside in the crypt domain of the intestine which are pit like structures located between villi protrusions. The ISCs are interspersed between Paneth cells, which along with cells of the surrounding mesenchyme act as the stem cell niche. ISCs have been reported to divide symmetrically to produce two identical daughter cells. However, the symmetry of these divisions has been concluded based on mathematical modelling which do not account for the possibility that a very small population of ISCs would divide asymmetrically or for qualitative asymmetry occurring in these divisions. Asymmetric cell division is a process by which daughter cells gain different amounts or different qualities of certain factors which lead to their differing fates. Asymmetric division can include asymmetric segregation of organelles such as mitochondria or peroxisomes, which have both been shown to be asymmetrically apportioned in yeast mitosis. Peroxisomes are single membrane enclosed organelles which function in many metabolic processes, most importantly in lipid and reactive oxygen species (ROS) metabolism. Mitochondria have been reported to be age selectively apportioned during cell division of mammary epithelial stem like cell. The same has been shown to occur for peroxisomes based on unpublished data from my host lab. This prior research of the lab also indicates that selective peroxisomal apportioning would require peroxisomes to be specifically gathered at the centrosomes from metaphase onwards to control their inheritance. In this thesis I will look into peroxisomal dynamics in the intestinal crypt. The first aim is to verify the Lgr5-EGFP-creERT2 x LSL-SNAP-tag-PTS1 mouse model, by checking that the SNAP-tag-PTS1 fusion protein properly localizes to peroxisomes. Secondly, I aim to look into the ages of peroxisomes in ISCs compared to differentiated cells, concentrating on Paneth cells. The third and final aim is to look into the apportioning of old and young peroxisomes during stem cell division. This aim includes looking into the peroxisomal localization at metaphase and checking how peroxisomes are expected to be inherited in later mitotic cells. The SNAP-tag-PTS1 construct adequately co-localizes with the peroxisomal membrane protein 70, also at the old SNAP labelling time point chosen for the following experiments. The SNAP-tag-PTS1 old labelling does not co-localize with the lysosomal associated protein Lamp1 to a high extent, indicating that the peroxisomes with the labelling are not in autolysosomes in amounts that would hamper with the results of the following experiments. There is no noticeable difference between the age contents of peroxisomes in stem cells versus Paneth cells. However, when moving up from base of the crypt to the transit amplifying zone there seems to be an increasing number of peroxisomes, as would be expected based on previous reports of peroxisomes in the intestinal epithelium. At metaphase it seems that approximately half of the cells have a tendency to gather peroxisomes at one centrosome to a higher extent than elsewhere in the cell. Interestingly this condensation was rarely seen at both centrosomes in a given cell. A large heterogeneity was observed when looking into the apportioning of old and young peroxisomes in anaphase or later on in mitosis. A majority of the dividing cells apportioned approximately equal amount of young and old peroxisomes to both daughter cells. Some divisions apportioned inequal amounts of peroxisomes to the daughter cells, with one daughter getting more peroxisomes overall. The daughter cell getting more peroxisomes was more likely to get significantly more of the old label than its pair. This indicates that there could be a small subpopulation of intestinal stem cells that divide their peroxisomes asymmetrically qualitatively as well as quantitatively, however, to definitively conclude this further research is required.
  • Neiro, Jakke (2019)
    In recent years, the two-spotted field cricket Gryllus bimaculatus has emerged as a central model for studies on insect development, regeneration and physiology. At the moment, G.bimaculatus has the most extensive molecular toolkit within the Exopterygota, making it the foremost model for evolutionary developmental biology and comparative physiology within the field of entomology. However, the postembryonic development of G. bimaculatus has received considerably less attention than embryonic development. In this thesis, I have studied the postembryonic development of G. bimaculatus to better understand the evolution and physiology of the understudied Exopterygota. My thesis encompasses five parts: postembryonic morphology, wing development, appendage regeneration, allometry, and growth. The postembryonic stages, the nymphal stages, have never been properly characterised in G. bimaculatus. By following postembryonic development daily at 30 C, 8 nymphal stages (instars) were identified. Size, coloration, sclerotisation of the thorax, and morphology of the wings, the hind tibia and the ovipositor were useful characters in distinguishing the stages. The Dpp/BMP signalling pathway patterns the wing venation in the endopterygotan insects Drosophila melanogaster and Athaliae rosae, but nothing is virtually known about wing development in exopterygotan insects. The wings and the wing venation pattern in different nymphal stages of G. bimaculatus were studied using the hydrogen peroxide clearing protocol along with both brightfield and fluorescence microscopy, while the role of the Dpp/BMP signalling pathway was studied using immunohistochemistry (IHC), in situ hybridisation (ISH), and RNA interference (RNAi). The longitudinal veins are patterned in the 3rd and 4th nymphal stages, while the secondary veins in the 8th stage. The IHC and ISH experiments displayed only non-specific staining, while the RNAi experiments did not produce any change in the phenotype, possibly because of molecular redundancy. The nymphal legs of G. bimaculatus are known to be highly regenerative, and the Dpp/BMP signalling pathway has been shown to provide positional information in leg regeneration. However, nothing is known about the regeneration of the other appendages in G. bimaculatus. Antennae and cerci were amputated in different nymphal stages, and the degree of final regeneration depended on the nymphal stage. RNAi experiments did not produce any change in the phenotype, possibly because of molecular redundancy. The interrelationship between static, ontogenetic and evolutionary allometry in insects is poorly understood. The allometry of hind femur length with respect to body length has been shown to be negative in Orthoptera (i.e. evolutionary allometry), but nothing is known about corresponding ontogenetic and static allometry. By measuring hind femur length and body length in G. bimaculatus in different nymphal stages, the ontogenetic allometry was determined to be slightly positive or isometric, while the static allometries of different stages tended to be negative but highly variable. This may indicate that allometric relationships constrain development in the microevolutionary perspective, but are nevertheless evolvable in a macroevolutionary perspective of millions of years. The growth conditions and rearing of crickets and other insects have been widely reported, but the shape of the growth curve itself has been less investigated. The exponential, the von Bertalanffy (VBGF), the West, Brown and Enquist (WBE), and the dynamic energy budget (DBE) models have been proposed as continuous models for insect growth. These models were t to growth data from G. bimaculatus and the DBE and was shown to be optimal with parameter values α=0 and pAm = 0.69. The insects have been thought to follow Dyar's law, i.e. that the growth ratio or moulting increment (MI) is constant throughout development, although numerous other competing moulting models have been devised for the crustaceans. By fitting different moulting models to head width data from G. bimaculatus, the log-linear model (Mauchline's model) turned out to explain the MI the best. Lastly, the oxygen-dependent induction of moulting (ODIM) model has been proposed to explain moulting patterns in insects, but the model has never been applied to exopterygotan taxa. By fitting the ODIM model to growth data from G. bimaculatus, the model could predict moulting mass but not instar durations, probably because of high postembryonic plasticity in G. bimaculatus.