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Browsing by master's degree program "Magisterprogrammet i genetik och molekylära biovetenskaper"

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  • Borgman, Vesa Petteri (2023)
    Intestinal stem cells maintain the regenerative potential of intestinal epithelium, which needs to be renewed constantly. Dysregulation of intestinal stem cell proliferation is associated with aging and intestinal diseases. The midgut of Drosophila melanogaster is a valuable model for studying intestinal stem cell driven tissue regeneration. It is similar in function to the mammalian small intestine but has a simpler cellular structure. Drosophila midgut is divided into five major regions with specialized physiological functions, characteristic morphological features and distinctive gene expression profiles. The midgut consists of a monolayer of absorptive enterocytes, small secreting enteroendocrine cells, intestinal stem cells and enteroblasts. Intestinal stem cells differentiate into enterocytes through a transient enteroblast phase. 5-hydroxytryptamine has been shown to activate proliferation of intestinal epithelium in mammals, but its mechanism of action is still unknown. Also, sex-specific differences in 5-hydroxytryptamine signalling have been recorded in mammals. 5-hydroxytryptamine signalling pathway has several downstream targets that have diverse downstream effect. Thus, 5-hydroxytryptamine signalling creates a complex and versatile regulatory network. The aim of my thesis is to study the effects of 5-hydroxytryptamine signalling on intestinal stem cell proliferation and cellular turnover in Drosophila midgut in both sexes. The effects of excessive amounts of 5-hydroxytryptamine are first studied by feeding Drosophila with 5-hydroxytryptophan, a product of the rate-limiting step in the 5-hydroxytryptamine synthesis pathway. The effects of 5-hydroxytryptamine signalling are further studied by knocking down and overexpressing a component of the 5-hydroxytryptamine signalling pathway in intestinal stem cells and enteroblasts. Dissected midguts are immunofluorescently stained, imaged and analysed both visually and with bioinformatics tools. The results indicate that 5-hydroxytryptamine signalling has both regional and sex-specific functions that affect intestinal stem cell proliferation and cellular turnover in Drosophila midgut. The most dramatic effects are seen in cellular turnover, which indicates that 5-hydroxytryptamine signalling plays a role in enteroblast differentiation. Furthermore, the results suggest that bidirectional signalling between enteroblasts and dying enterocytes facilitates cellular turnover in the midgut. As 5-hydroxytryptamine signalling is indicated in inflammatory bowel diseases such as Crohn’s disease, my results might help in the development of treatments for such conditions.
  • Aho, Niina (2022)
    Breast cancer is the most prevalent cancer in women worldwide and in 2020 it was the fifth deadliest. In Finland 2019 more than 5000 breast cancer cases were diagnosed, 94% in women and 6% in men. Until now, the high-risk breast cancer susceptibility genes have been identified including BRCA1, BRCA2 and TP53 as well as many of the moderate risk genes. Still, together all the identified genes explain only approximately half of the familial breast cancer cases. Furthermore, all the known breast cancer susceptibility genes are linked to the DNA repair mechanism. Serpina3 stands out as a non-DNA repair gene but as a gene that encodes a protease inhibitor which belongs to the serpin superfamily. Serpina3 has been associated with various diseases before and especially changes in its expression levels are linked to the tumor prognosis in many cancers including breast cancer. However, a previous study proposed that Serpina3 c.918-1G>C is a susceptibility variant for breast cancer in the Northern Finland population. This thesis a case-control study to investigate whether Serpina3 c.918-1G>C variant is associated with breast cancer in the Southern Finland population. In addition, the tumor histology and cellular markers of Serpina3 c.918-1G>C carriers were examined. This study utilized DNA collected from breast cancer patients as well as DNA from blood donors and healthy biobank controls. Breast cancer patients included both familial and unselected cases. The prevalence of Serpina3 c.918- 1G<C variant was studied by genotyping the cases and controls. Genotyping was done by TaqMan real-time PCR and carriers were further confirmed by Sanger sequencing. Moreover, statistical tests were used in the data analyses. The studied Serpina3 c.918-1G>C variant was not found to be significantly (p>0.05) enriched in the breast cancer cases. The variant was found in 0.23 % of familial and 0.36 % of unselected cases, altogether in 0.28 % of all studied breast cancer cases, the frequency in controls was 0.27 %. The tumor histology was found to be ductal in 73 % of the Serpina3 c.918- 1G>C variant carriers and only 9 % had lobular tumor. In other words, the tumor histology followed the usual distribution. All the carriers had a HER2 negative tumor and all except one case were both ER and PR positive. About half of the carriers expressed the cellular proliferation marker Ki67. As a conclusion, the results from this study do not suggest Serpina3 c.918-1G>C as a breast cancer risk variant at least in the Southern Finland population.
  • Linna, Susanna (2022)
    While there is no current consensus on what characterizes a heathy gut microbiome, there are evidence supporting the association of high microbial diversity with health stability in the host species. A growing literature suggests that microbial communities can withstand short-term anthropogenic changes with resilience, however enduring long-term changes might have a negative impact on the natural composition of host microbiome. Parasitism and anthropogenic disturbances resulting in habitat degradation might represent two of such long-term challenges to the invisible diversity of microbial communities, with consequences for the fitness of their host species. In this study, I tested whether parasitism by a specialist parasitoid and ecological changes due to anthropogenic habitat degradation affected the microbial community associated with the diapausing larvae of the Glanville Fritillary butterfly (Melitaea cinxia). The larval samples were collected in September 2012 from seven different communes across the Åland islands, from two extreme types of habitat patches (i.e., highly human-impacted habitats versus natural meadows). The parasitoid wasp Hyposoter horticola naturally parasitize approximately a third of the M. cinxia larvae in Åland, giving an opportunity to further investigate how parasitism might affect the larvae-associated bacterial community in this system. The DNA from the gut of each larva was extracted, and the bacterial V5-V6 region of the 16S gene was amplified and sequenced at the Finnish Institute for Molecular Medicine. The sequencing data was prepared for analysis by processing it through Mothur and QIIME2 data cleaning protocols. According to alpha- and beta-diversity metrics analyses, anthropogenic degradation of the habitat did not cause significant changes in the bacterial composition of the microbiota associated with diapausing larvae of M. cinxia, however, parasitism with the parasitoid wasp has a significant negative effect on the beta diversity of the microbial communities associated with the diapausing larvae.
  • 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.
  • Juntunen, Valtteri (2021)
    Adeno-Associated Viruses (AAVs) are quickly becoming one of the most applied vectors for gene therapy applications. In the recent years three new AAV-based gene therapies have been approved by U.S. Food and Drug Administration (FDA) and European Medicines Agency (EMA). The regulatory bodies require accurate and reliable characterisation of the clinical grade viral vectors during and after production. Analytic methods measuring the purity, potency and safety of the product support the up-stream and down-stream processes during the production and are used for final-drug substance characterisation. Median Tissue Culture Infectious Dose (TCID50) is a well-established method for measuring the infectious titer of a virus. Here, an assay for determining the infectious titer of AAVs, which has previously been used to characterise the existing AAV2 Reference Standard Material (AAV2RSM) was set up and optimised for research use at Kuopio Center for Gene and Cell Therapy (KCT). The assay utilizes the HeRC32-cell line, a HeLa clone, that stably expresses AAV Rep and Cap -proteins and in presence of adenovirus, enables the replication of recombinant AAV-vectors. The cells were grown in 96-well plates and infected with 10-fold dilution series of AAV vectors (AAV2 and AAV6) using human adenovirus type 5 as the co-infector. 72 hours post infection the vector genome replication of AAV was detected with quantitative PCR (qPCR). Thresholds for qPCR determined copy number and cycle threshold (Ct) were set and used for the determination of infection-positive wells. The 50-percent endpoint was observed and used to calculate the infectious titer according to the Spearman-Kärber method. The assay was set up and optimised with the AAV2 Reference standard material (AAV2RSM) using two different primer-probe sets (targeted sequences were; SV40 polyadenylation signal and AAV inverted terminal repeats (ITRs)). Plates infected with AAV2RSM were analysed separately with both primers resulting in mean infectious titers of 8.07 ± 3.13 x 108 TCID50 Infectious Units (IU) / mL (n = 9) and 1.27 ± 0.464 x 109 TCID50 IU/mL (n = 9) for SV40 and ITR, respectively. After the assay was set up with the AAV2RSM, an in-house AAV6 product was analysed with the ITR primers yielding 6.09 ± 3.94 x 109 TCID50 (IU) / mL (n = 5). The assay protocol was successfully set up for research use at the KCT laboratory. Improvements were added to the original protocol to increase assay robustness, accuracy and precision as well as to minimize the possibility of over-estimation of the infectious titer. The assay can be further optimised for a particular therapeutic AAV product in the research laboratory or technology transferred to a production facility for optimisation and validation for the analytics needs of a production pipeline.
  • 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.
  • Suonto, Lotta (2019)
    Amelogenesis Imperfecta (AI) is a group of hereditary diseases where tooth enamel is abnormally formed. This disease has been found in Lancashire Heeler dogs. However, none of the mutations known to cause AI in canine, explain the disease in the Lancashire Heeler population. A research study was initiated to investigate the genetic background of the disease in the breed. Based on the pedigree data the disease was suggested to be inherited as an autosomal recessive disease. Whole-exome sequencing of two affected dogs was performed which revealed a plausible candidate variant in a gene regulating intracellular calcium concentration. The aim of this study was to examine whether the mutation in the candidate gene causes AI. The DNA were extracted from blood samples of 249 Lancashire Heelers. A genome-wide SNP genotyping was conducted on four cases and a homozygosity mapping was performed. The candidate variant was genotyped in a large cohort of Lancashire Heelers (n=249) and dogs from related breeds (n=91) to confirm the association with the disease. The expression of the candidate gene in lymphocytes was studied with RT-PCR. Clinical studies were performed to evaluate the clinical features and serum calcium levels were measured. The segregation of genotypes and phenotypes of the dogs was complete. The identified variant is predicted to cause a premature STOP codon, which, if translated, leads to a truncated protein lacking protein transmembrane domains. According to the results acquired from RT-PCR, it is possible that the protein will complete the translation despite the mutation. Clinical studies did not reveal other clinical features than enamel defects and serum calcium levels were normal. According to the results, we suggest that the identified variant is causal for AI in Lancashire Heelers. The results have significant impact because no other genetic connection between the gene and AI has been found before. Consequently, the development of a gene test is possible, creating multiple opportunities for researchers and veterinary medicine. The results are applicable also to human medicine. However, we need more research to achieve a complete understanding of the mutation and its effects.
  • Kuitunen, Essi (2019)
    Glutamine, the conditionally essential amino acid, is a major carbon and nitrogen carrier required for a range of cell functions, such as protein synthesis and maintaining redox balance. While healthy cells adjust their activities in response to glutamine availability, tumor cells display deregulated glutamine uptake and metabolism allowing quick proliferation and survival in cellular stress conditions. Hence, further knowledge of the glutamine sensing network is of interest. Utilizing Drosophila melanogaster, the roles of formerly identified glutamine sensing regulator candidates, Forkhead box O (FoxO), Super sex combs (Sxc), Spalt major (Salm) and Spalt-related (Salr), were explored. Drosophila is an efficient model organism for analyzing gene regulatory mechanisms, with its simple genome but conserved genes and metabolic pathways. Loss-of function and gain-of-function mutants of the candidates were cultured with/without glutamine, and their physiological response and gene expression changes were analyzed. The results show the glutamine intolerant phenotype of FoxO and Sxc deficiency, not dependent on altered food intake levels of larvae. However, glutamine intolerance of Salr and Salm deficiency was not observed. Moreover, we aimed to gain further insight to the roles of FoxO and Sxc in glutamine metabolism. Since amino acid catabolism produces ammonia, and glutamine metabolism plays a vital role in ammonia detoxification, we performed a pH-based measurement of foxo and sxc mutant larvae hemolymph on food with/without glutamine. However, we could not associate FoxO or Sxc with regulation of glutamine-derived ammonia clearance. In addition, we explored FoxO downstream regulator candidates. Putative promoter areas of Paics, Uro, Sesn, salr, Prat2 and Gdh were cloned into reporter vectors and the luciferase activity was analyzed under the expression of foxo. The results indicate that FoxO is a regulator of all of the 6 genes. Next we could utilize the here constructed plasmids to see whether the FoxO-mediated regulation is affected by altered glutamine levels in cell culture.
  • 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.
  • Raivio, Heini (2024)
    Immunopeptidomics research, focused on HLA-presented peptides, indicates that identifying neoantigens – unique peptides from cancer cell mutations – holds potential for personalized cancer treatment. PeptiCHIP, a compact microfluidic device from ValoTx, facilitates neoantigen identification in small tumor samples. This study evaluates PeptiCHIP against traditional immunopurification methods, assessing its advantages and commercial potential through stakeholder interviews guided by the double diamond model of design thinking. The aim is to establish PeptiCHIP’s unique advantages in immunopeptidomics research and precision oncology. Data for this research were gathered through semi-structured interviews and comparative laboratory analyses. The interviews revealed a positive reception among 19 stakeholders towards PeptiCHIP, highlighting a strong interest in its potential to accelerate workflows and enhance the personalization of cancer treatment. Laboratory comparisons confirmed that PeptiCHIP offers greater sensitivity than competitor products in detecting antigens, pinpointing the most immunogenic peptides from individual tumor samples. This suggests that the data could be effectively utilized as a targeted treatment approach in precision oncology therapies. The results indicate an eagerness to adopt PeptiCHIP, driven by its enhanced detection speed and accuracy. This research not only underscores the technological and commercial potential of PeptiCHIP in impacting precision oncology but also highlights the importance of aligning technological innovations with user needs and market demands. For ValoTx, a strategic commercial approach is needed to set a benchmark in precision oncology innovation.
  • Peltola, Sanni (2019)
    In recent decades, ancient DNA recovered from old and degraded samples, such as bones and fossils, has presented novel prospects in the fields of genetics, archaeology and anthropology. In Finland, ancient DNA research is constrained by the poor preservation of bones: they are quickly degraded by acidic soils, limiting the age of DNA that can be recovered from physical remains. However, some soil components can bind DNA and thus protect the molecules from degradation. Ancient DNA from soils and sediments has previously been used to reconstruct paleoenvironments, to study ancient parasites and diet and to demonstrate the presence of a species at a given site, even when there are no visible fossils present. In this pilot study, I explored the potential of archaeological sediments as an alternative source of ancient human DNA. I collected sediment samples from five Finnish Neolithic Stone Age (6,000–4,000 years ago) settlement sites, located in woodland. In addition, I analysed a lakebed sample from a submerged Mesolithic (10,000–7,000 years ago) settlement site, and a soil sample from an Iron Age burial with bones present to compare DNA yields between the two materials. Soil samples were converted into Illumina sequencing libraries and enriched for human mtDNA. I analysed the sequencing data with a customised metagenomics-based bioinformatic analysis workflow. I also tested program performance with simulated data. The results suggested that human DNA preservation in Finnish archaeological sediments may be poor or very localised. I detected small amounts of human mtDNA in three Stone Age woodland settlement sites and a submerged Mesolithic settlement site. One Stone Age sample exhibited terminal damage patterns suggestive of DNA decay, but the time of deposition is difficult to estimate. Interestingly, no human DNA was recovered from the Iron Age burial soil, suggesting that body decomposition may not serve as a significant source of sedimentary ancient DNA. Additional complications may arise from the high inhibitor content of the soil and the abundance of microbial and other non-human DNA present in environmental samples. In the future, a more refined sampling approach, such as targeting microscopic bone fragments, could be a strategy worth trialling.
  • Mitchell, Cristopher (2024)
    Coxsackievirus A9 (CVA9) is a member of the Picornaviridae family of viruses and Enterovirus genus. CVA9 is mostly associated with milder Enterovirus symptoms such as rashes, but there are also individual cases of more serious diseases caused by CVA9 infection, including hepatitis. The picornavirus capsid structure is largely conserved and composed of 3-4 viral proteins (VP). At the base of VP1 there is a hydrophobic pocket occupied by a lipid factor. The expulsion of that lipid factor leads to expansion of the capsid, viral uncoating and genome release into the cell. To prevent that expansion, an ongoing study has been screening and synthesizing hundreds of potential molecules to target the VP1 pocket and replace the pocket factor. One such molecule is CL300, an N-phenyl benzamide, which has an antiviral effect on CVA9. The purpose of this study was to validate the proposed mechanism of action of CL300 on CVA9 by confirming its binding location with cryogenic electron microscopy and single-particle processing methods. Through processing, 31,050 particles were narrowed down to 21,230 particles that were reconstructed into a 2.26 Å resolution density map of CVA9 with a heterogeneous density in the VP1 pocket. Due to features present in that density and the presence of multiple rotamer densities in a nearby residue, Y210, it was concluded that either CL300 or lipid factors were present in different VP1 pockets, resulting in an averaged density in the map. The final result of this study was a model of CVA9 with CL300 in the hydrophobic pocket. These results, in conjunction with the ongoing study into the antiviral effect of CL300, have implications for the potential future production of antivirals and vaccines to combat CVA9 and other Enterovirus infections where there is conservation of the binding pocket.
  • Veltman, Laurens (2024)
    Cell-based immunotherapies offer highly targeted treatment, potentially leading to higher response rates and reduced long-term side effects compared to chemotherapy. In the clinics, chimeric antigen receptor T-cell therapies are already being used as neo-adjuvant therapy for certain types of cancer, however, they can have significant drawbacks. Natural killer (NK) cells have emerged as a promising alternative option for targeting various hematological and solid tumors. Unlike T-cells, NK-cells do not need prior sensitization to the target and have the potential to be used as a allogeneic, ‘Off-the-shelf’, product. Acute myeloid leukemia (AML) is the most common type of acute leukemia in adults. Chemotherapy and small molecule drugs are typically used for the treatment of AML. However, the prognosis for relapsed or refractory AML patients remains unsatisfactory. Therefore, a collaborative project between the Helsinki Central Hospital and the Advanced Cell Therapy Center from the Finnish Red Cross, Blood Service was initiated to develop clinical-NK products targeting high-risk AML patients in Finland. A reliable and suitable in vitro cytotoxicity assay was required to assess the efficacy of NK cells before they could be given to AML patients. A luminescence-based method utilizing cellular ATP, was found to be the best performing method considering constraints such as the limited amount of patient material. AML blasts were successfully isolated from the whole blood of patients using CD33 microbeads and maintained in a composition of cytokines mix in RPMI media. The cytotoxicity assay paired with statistical analysis was able to identify significant differences in cytotoxic efficacy between NK cells from different donors. Additionally, results indicate improved cytotoxic efficacy in activated NK cells compared to non-activated NK cells, highlighting the usefulness of activated NK cells for use in the clinics.
  • Preussner, Annina (2021)
    The Y chromosome has an essential role in the genetic sex determination in humans and other mammals. It contains a male-specific region (MSY) which escapes recombination and is inherited exclusively through the male line. The genetic variations inherited together on the MSY can be used in classifying Y chromosomes into haplogroups. Y-chromosomal haplogroups are highly informative of genetic ancestry, thus Y chromosomes have been widely used in tracing human population history. However, given the peculiar biology and analytical challenges specific to the Y chromosome, the chromosome is routinely excluded from genetic association studies. Consequently, potential impacts of Y-chromosomal variation on complex disease remain largely uncharacterized. Lately the access to large-scale biobank data has enabled to extend the Y-chromosomal genetic association studies. A recent UK Biobank study suggested links between Y-chromosomal haplogroup I1 and coronary artery disease (CAD) in the British population, but this result has not been validated in other datasets. Since Finland harbours a notable frequency of Y-chromosomal haplogroup I1, the relationship between haplogroup I1 and CAD can further be inferred in the Finnish population using data from the FinnGen project. The first aim of this thesis was to determine the prevalence of Y-chromosomal haplogroups in Finland and characterize their geographical distributions using genotyping array data from the FinnGen project. The second aim was to assess the role between Finnish Y-chromosomal haplogroups and coronary artery disease (CAD) by logistic regression. This thesis characterized the Y-chromosomal haplogroups in Finland for 24 160 males and evaluated the association between Y-chromosomal haplogroups and CAD in Finland. The dataset used in this study was extensive, providing an opportunity to study the Y-chromosomal variation geographically in Finland and its role in complex disease more accurately compared to previous studies. The geographical distribution of the Y-chromosomal haplogroups was characterized on 20 birth regions, and between eastern and western areas of Finland. Consistent with previous studies, the results demonstrated that two major Finnish Y-chromosomal haplogroup lineages, N1c1 and I1, displayed differing distributions within regions, especially between eastern and western Finland. Results from logistic regression analysis between CAD and Y-chromosomal haplogroups suggested no significant association between haplogroup I1 and CAD. Instead, the major Finnish Y-chromosomal haplogroup N1c1 displayed a decreased risk for CAD in the association analysis when compared against other haplogroups. Moreover, this thesis also demonstrated that the association results were not straightforwardly comparable between populations. For instance, haplogroup I1 displayed a decreased risk for CAD in the FinnGen dataset when compared against haplogroup R1b, whereas the same association was reported as risk increasing for CAD in the UK Biobank. Overall, this thesis demonstrates the possibility to study the genetics of Y chromosome using data from the FinnGen project, and highlights the value of including this part of the genome in the future complex disease studies.
  • Laukkanen, Ida (2024)
    Epigenetics is the study of changes in gene expression without alterations in the DNA sequence. Epigenetic modifications, of which DNA methylation (DNAm) is the most known, are crucial for many biological events, especially for normal development and genomic imprinting. In imprinted genes, only one of the parental alleles is consistently monoallelically expressed. The epigenome can be altered by various environmental factors such as diet and chemicals. Moreover, evidence indicates that assisted reproductive technology (ART) is associated with distinct DNAm patterns. Still, it is unclear whether these alterations are a consequence of ART procedures themselves or the underlying subfertility. This thesis aimed to study whether ART procedures and subfertility are associated with aberrant DNAm at the imprinted DLK1-DIO3 locus in the human placenta. The genes encoded from this paternally imprinted locus are essential in mammals' fetal and placental development. Moreover, recent evidence suggests that downregulation of the DLK1 gene is associated with ART and subfertility. Therefore, two gene regions, the IG-DMR and the DLK1 promoter, were chosen as study objects. The IG-DMR acts as the main regulator of gene expression at the whole DLK1-DIO3 locus, and promoter regions are considered important regulators of the expression of their corresponding genes. Eight ART, four subfertility, and six control samples of human placental DNA were studied. The subfertility group consisted of couples who were committed to initiating fertility treatments but eventually got pregnant spontaneously. The study was performed using traditional bisulfite sequencing, after which the differences in DNAm levels between study groups were statistically analyzed. As expected, significantly decreased DNAm level was observed in the placentas of subfertile couples compared to controls. Surprisingly, no significant differences were addressed between ART and control groups in either region. The partly unexpected results are explained by the fact that aberrant methylation at distinct imprinted DMRs, including the IG-DMR, is caused by the in vitro culture media. Moreover, the results indicate that the regulation of DLK1 expression is more complicated than that solely by the IG-DMR and the DLK1 promoter. Further research should be dedicated to differentiating the impacts of ART and subfertility on the epigenome and phenotype to better understand the health implications of ART.
  • Dhawan, Priyal (2024)
    The significance of adhesion to the basement membrane (BM) for the growth and survival of healthy mammary epithelial cells is well-established. In ductal carcinoma in situ (DCIS), a non-invasive form of breast cancer, luminal cells detach from the BM and proliferate within the ductal lumen of the mammary gland. This suggests that malignant cells are capable of evading detachment induced cell death, called anoikis during DCIS. The alterations that contribute to anoikis resistance may be essential for anchorage-independent survival, a phenomenon that remains largely unexplored in the context of BM. Hence, in this study, I aimed to investigate the association between anchorage-independent survival of breast cancer cells and the expression of BM components. I utilized a low-adhesion 3D suspension culture devoid of any matrix to evaluate the efficiency of mammosphere formation in luminal A and triple-negative breast cancer cell lines. To understand the ability of cancer cells to survive in an anchorage-independent environment, I investigated the expression profiles of BM components (including laminins and type IV collagen) across various breast cancer cell lines. Gene expression analysis of BM components was conducted in conventional 2D monolayer cultures, while immunofluorescence analysis was performed on mammospheres or single cell clusters derived from low-adhesion 3D cultures. Furthermore, to explore their functional significance, I examined the effect of laminin α5 (LAMA5) downregulation on the spheroid formation ability of luminal A cell line ZR75-1. The primary results of the study highlighted the ability of breast cancer cells to survive in low anchorage conditions by forming mammospheres or as single-cell clusters. Significant variations in the expression of BM components were observed across breast cancer cell lines and within the subtypes. Moreover, I observed the atypical expression and localization of BM components produced by the various breast cancer cell lines in the 3D culture. The potential functional relevance of BM was demonstrated by the decreased mammosphere-forming ability of the ZR75-1 with LAMA5 downregulation. Although further investigations are needed, these observations suggest a crucial role of BM produced by tumour cells in facilitating anoikis resistance and anchorage-independent survival of cancer cells.
  • Dong, Junru (2022)
    Formation of template switching mutation has previously been proposed as a mechanism of RNA evolution. TSM mechanism may contribute to the creation, maintenance, and modification of the RNA Hairpin. The finding of de novo TSM in RNA sequences will provide evidence for this hypothesis. Ribosomal RNAs (rRNAs) appear in multicopy clusters on different chromosomes and evolve through concerted evolution. To study the properties of de novo TSM and the dynamics of the concerted evolution of rRNA, we developed a computational tool to analyze pairwise differences and the phylogenetic relationship of rRNA genes on different chromosomes. The genome assemblies that are based on traditional short-read sequencing methods have limitations on studying long tandem repeat rDNA, because the reading length is shorter than on the rRNA gene. To overcome this limitation. PacBio Hifi long-read sequencing data for human rRNA 18S and 28S genes were studied. By analyzing the diversity of rRNA genes between individuals and families, single nucleotide mutations, multiple nucleotide insertions, and deletions were identified. As expected, genetic variations in ribosomal genes were detected both within and between individuals. A larger sample size may be required for TSM identification. The finding of this research that related to the dynamics and concerted evolution of human rRNA may contribute to a better understanding of rRNA mutation-related genetic disorders.
  • Mantela, Fanni (2021)
    There are no comprehensive research data on Finnish matriculation examinations in biology. This type of data is needed, because evaluation guides what and how students learn and what they consider important. Genetics is one the most challenging topics in biology, and in the opinion of teachers it will continue to be an important discipline in the future. The importance of studying genetics can also be justified with philosophical, social and health reasons. This is why the present study focused on the genetics component of the matriculation exam in biology. The aim of the study was to provide information on the challenges and contents of past matriculation examinations in biology and how they have aligned with high school curricula. The results of the study could be used to evaluate this alignment in relation to genetics questions in the biology exam, and could help in designing new matriculation examinations that align better with the existing high or new high school curricula and their aims. The research questions were: 1. What knowledge and cognitive dimensions are measured with the genetics-related questions in matriculation examinations in biology? 2. How do knowledge and cognitive dimensions in genetics-related questions in biology matriculation examinations relate to high school curriculum aims? The data comprised matriculation examination papers in biology from spring 2011 to autumn 2020 (20 exams) and the aims of the Finnish national High School Curriculum in 2003 and in 2015. Qualitative content analysis was performed on the knowledge dimensions (factual, conceptual or procedural knowledge) and the cognitive process dimensions (remembering, understanding, applying, analyzing, evaluating or creating). The basis of this qualitative content analysis was Bloom’s revised taxonomy. The analysis was conducted on genetics-related matriculation examination questions and on the aims of the high school curriculum. The test questions and the aims were compared to determine whether they aligned. Classified questions were divided into two subcategories depending on which high school curricula they corresponded to. Genetics-related questions from spring 2011 to autumn 2017 corresponded to the High School Curriculum in 2003 and questions from spring 2018 to autumn 2020 corresponded to the High School Curriculum in 2015. Questions from the previous period were divided into all knowledge dimensions. All questions, except one, incorporated lower cognitive dimensions (remembering, understanding and applying). The main combined class was understanding conceptual knowledge. Questions from the later time period were also divided into all knowledge dimensions. Mostly lower cognitive dimensions were incorporated into the questions, but a few subquestions addressed higher cognitive dimensions (analyzing, evaluating and creating). The main combined class was understanding conceptual knowledge. All the aims were classified into conceptual or procedural knowledge classes. The aims were also divided between all cognitive dimensions, except remembering. Using constructive alignment as the basis for matching aims with questions, two aims in the High School Curriculum of 2003 and six aims in the High School Curriculum of 2015 had no questions that matched them. These aims mostly measured the cognitive dimension of creating. Several aims appeared to incorporate higher cognitive dimensions, but the questions were less well aligned with the aims than with those incorporating lower cognitive dimensions. The results concerning knowledge and cognitive dimensions were mostly as expected. Lower cognitive dimensions were highlighted in genetics-related matriculation examination questions in biology. The challenge of interpretation brought ambiguity to the aims and cumulative levels of cognitive dimensions when aligning questions with aims, as some of the questions aligned with aims did not assess such high cognitive dimensions as would be expected based on the aims, but were nonetheless aligned with them. Furthermore, there may be several reasons behind the absence of the creating dimension in matriculation examination questions. The alignment of questions and aims would be important to consider in the future, because evaluation has a considerable impact on studying.
  • Jäntti, Maija (2020)
    Uterine leiomyomas are benign tumors originating in the smooth muscle cells of the uterine wall. Leiomyomas represent one of the most common tumor types in women affecting up to 80% of pre-menopausal women. Besides having extensive implications on women´s health through the numerous symptoms they cause, leiomyomas are a cause of remarkable financial burden worldwide. Bivalent promoters are defined by the co-occurrence of two histone modifications with opposite functions: trimethylation of lysine 4 on histone 3 (H3K4me3) and trimethylation of lysine 27 on histone 3 (H3K27me3). H3K4me3 is associated with promoters of actively expressed genes, whereas H3K27me3 is frequently found at promoters of silenced genes. The genes controlled by the bivalent promoters are reversibly silenced or expressed at low levels and remain poised for fast activation or full repression as a response to external cues. Bivalent chromatin is gaining more and more importance as new roles are identified in tumorigenesis and cell differentiation. Despite this, the vast majority of data available was obtained from cell lines, and not from human tissue. The aim of this thesis work was to map the genomic location of bivalent promoters in uterine leiomyoma and myometrium tissue, and to characterize the functions of bivalently-controlled genes in differentiated tissue. This would provide novel information about bivalent promoters’ distribution in human tissues and also their potential role in myomagenesis. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) against H3K4me3 and H3K27me3 was performed on fresh frozen tissue samples of uterine leiomyomas and corresponding myometrium. A promoter was defined as bivalent, if it showed overlap between H3K4me3 and H3K27me3 peaks within a 2 kb region of a gene’s transcription start site in all samples. Altogether 951 bivalent promoters were found in myometrium and leiomyoma. Strikingly, only 231 (24.3%) promoters were present in both tissue types, most bivalent promoters being tissue-specific. These findings indicated bivalent promoters regulating a substantial number of genes also in differentiated tissue and the presence of extensive alterations in bivalent promoter distribution during myomagenesis. Gene ontology analyses of the bivalently-controlled genes in myometrium revealed the highest score for developmental processes. Instead, for leiomyomas, the highest enrichment was detected in stem cell fate specification-related processes. The data presented in this thesis suggests that bivalent chromatin plays an important role during myomagenesis, as it undergoes a significant reorganization during the process. Future experiments will provide novel insights about the role for these changes, i.e.: if they underlie the process.
  • Sirjala, Janika (2023)
    Human induced pluripotent stem cells (hiPSCs) are derived from adult differentiated somatic cells and reprogrammed to an embryonic-like state. Pluripotent stem cells can be differentiated into almost any somatic cell type by using directed differentiation methods, but the differentiation efficiency often varies depending on the cell type. hiPSCs and cells differentiated from them can be used as a disease model carrying the patient’s phenotype and genotype. Amyotrophic lateral sclerosis (ALS) is a progressive motor neuron disease where both upper and lower motor neurons degenerate, leading to paralysis. There is no curative treatment for ALS, and it leads to the death of the patient in 3 to 5 years on average from the first symptoms. The most common genetic cause of familial ALS is a hexanucleotide repeat expansion in C9orf72-gene. ALS pathology is strongly linked to endoplasmic reticulum (ER) stress, which affects cell homeostasis and proteostasis, and leads to apoptosis when prolonged. The primary aim of this research is to characterize the differentiation of four hiPSCs lines towards lower motor neurons and to study the neuroprotective effects of cerebral dopamine neurotrophic factor (CDNF) and CDNF-derived peptide on ER stress and cell viability. This experiment used two control cell lines from two healthy donors and two patient cell lines from two different ALS patients carrying the C9orf72-mutation. To evaluate the efficiency of the differentiation towards motor neurons, molecular markers for pluripotent and neural progenitor cells as well as for maturated motor neurons were analyzed. Relative gene expression levels were measured from weekly time points with qPCR. Immunocytochemical (ICC) antibody staining was performed during differentiation. Endogenic CDNF levels were analyzed from differentiating cells at weekly time points and the effect of CDNF on Thapsigargin (TG) -induced ER stress in motor neurons was analyzed. In addition, cell viability was analyzed in TG-CDNF treatment. All pluripotent and progenitor markers were downregulated in differentiated cells, and the expression of the mature motor neuron markers was upregulated. Mature motor neuron markers were also expressed at the protein level. The endogenous CDNF levels were highest at the progenitor cell stage. The ER stress response was upregulated in TG-treated cells, and there were no differences between treatments against ER stress. Furthermore, TG and growth factor treatments differentially affected the viability of the control and patient cell lines. Treatment decreased viability in control cell lines and increased viability in patient cell lines. Pluripotent stem cells were successfully differentiated toward motor neurons. The differentiation was performed twice, and the results were similar on both individual biological repeats. Analysis of endogenous CDNF expression levels was performed for the first time on hiPSCs lines. In this study, CDNF or its derivate didn’t reduce ER stress but it influenced cell viability, especially in patient cell lines with growth factor treatment. In the future, TG-treatment could be optimized regarding timing and growth factor treatment, or the toxin could be changed to another ER-stress inducing toxin. In addition, the C9orf72 pathology should be identified in order to use differentiated motor neurons as a pre-clinical disease model.