Browsing by master's degree program "Master's Programme in Genetics and Molecular Biosciences"

The composition and dynamics of the early life gut microbiota plays a major role in establishing neonatal immunity and is suggested to have multiple impacts on the child’s long-term health. Meanwhile, the composition of the infant gut microbiome has been shown to be affected by the birth mode, infant health and diet. However, the characterization of the infant gut microbiome and its impact on the host’s health is still challenging as the contribution and importance of multiple co-factors on the early microbiome during infant growth is still poorly understood and characterized. The Health and Early-life microbiota (HELMi) is a cohort of more than 1000 healthy Finnish infants currently followed from birth to 4-5 years old. By now, the HELMi dataset comprises more than 400 whole genome shotgun metagenomes obtained from stool samples from 80 infants and parents, but also an in-depth characterization of the families’ lifestyle, environment, health and nutrition, allowing for a precise and cutting-edge characterization of the early gut microbiota. Based on the datasets from the HELMi, this project used Metaphlan3, Kraken and Braken to determine the best computational approach for the taxonomic profiling of the metagenomic reads. Then a PERMANOVA test was performed to evaluate and determine the factors significantly associated with the compositional microbiota variation within the infant gut metagenomes. This study first identified technical factors introducing bias in taxonomic profiling (e.g., DNA extraction batch), which served as confounders in the analysis of environmental and host variables. The investigation of these biological factors indicates that pre-natal and peri-natal variables such as the mode of delivery significantly impact the infant gut microbiota, while we did not identify any significant impact of breastfeeding habits and medication exposures in this study.

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.

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.

Atherosclerosis is a cardiovascular disease characterized by the formation and growth of plaque within the arteries. Lipoproteins, especially LDL, initiate atherosclerosis by accumulating in the intima of arteries and becoming modified, e.g. oxidised. Oxidised LDL (OxLDL) is highly pro-atherogenic and promotes atherosclerosis in multiple ways. The role of platelets in the later stages of atherosclerosis is well-documented, but platelets may also be involved in earlier stages of atherosclerosis. Platelets release extracellular vesicles (PEVs) in the form of microvesicles (microparticles) and exosomes that participate in intercellular signalling and in similar pathophysiological processes as platelets. Lipoproteins are known to activate platelets but their effects on PEV formation have not yet been studied. The aim of this thesis was to investigate the effect of OxLDL on PEV formation and compare it to other potential agonists such as LDL, HDL, ATP, thrombin and collagen. Platelets were activated with these agonists separately or in combination with OxLDL. PEVs were studied from the platelet-depleted supernatant and the isolate, which was obtained by differential centrifugation. PEVs were quantified in terms of CD61+ PEVs and particle count by flow cytometry and nanoparticle tracking analysis, respectively. PEVs were characterized by the relative amounts of CD41 (platelet and PEV marker) and Hsp70 (general EV marker) detected by Western blotting. Lastly, the uptake of the differently induced PEVs by HepG2 hepatoma cells was compared by fluorescence microscopy as a characterization of the PEVs’ functionality. Among the lipoproteins, OxLDL was indicated to be a much more potent inducer of PEVs than LDL or HDL, as shown by flow cytometry of CD61+ PEVs, nanoparticle tracking analysis and CD41 and Hsp70 levels in the isolates. However, OxLDL was not as strong a PEV inducer as the co-stimulation with thrombin and collagen (T&C), which induced the highest PEV formation. Size distribution analysis showed that PEVs smaller than 100 nm in size comprised a larger proportion of the total PEVs in OxLDL-induced PEVs compared to LDL- and T&C-induced PEVs. OxLDL combined with weak PEV inducers such as HDL and ATP had an amplifying effect on the generation of CD61+ PEVs, while the highest PEV formation was observed when OxLDL was combined with thrombin and collagen. When OxLDL-induced PEV formation was tested against a range of HDL concentrations, the extent of PEV formation and relative Hsp70 levels both decreased in a HDL concentration-dependent manner up to 50 µg/mL HDL. Both LDL- and OxLDL-induced PEVs were taken up by HepG2 cells, but there was no statistically significant difference between the two. The results indicated the potency of OxLDL in inducing PEV formation, thereby suggesting a novel mechanism by which OxLDL could contribute to the progression of atherosclerosis. Further studies on OxLDL-induced PEVs are needed, but if significant lipoprotein-specific changes in PEV numbers and properties could be observed, PEVs could then be used as a biomarker to diagnose atherosclerosis already at the early stages.

Lymphatic vascular system consists of lymphatic capillaries and collectors existing alongside a circulatory system of blood vessels. The lymphatic system is responsible of draining tissue fluids, trafficking of immune cells and intestinal absorption of dietary lipids. Most of the lymphatic networks develop during embryogenesis, but lymphangiogenesis (the growth of new lymphatic vessel, LV) occurs also in adult tissues, for example, during inflammation. Exposure to vascular endothelial growth factor C (VEGF-C) initiates lymphatic endothelial cell (LEC) proliferation and sprouting of LVs. In lymphangiogenesis, leading tip cell migrates and samples the surrounding environment while stalk cells proliferate and are responsible of LV elongation and extension. Since polarity of dividing cells and subsequent daughter cell positioning possess a key role in morphogenesis of tubular organs, such as lungs, kidney or blood vessels, a regulation of daughter LEC positioning after cell division might determine how LVs elongate and widen. The aim of this study was to investigate the LV network enlargement and daughter LEC positioning during growth of LVs and to reveal potential contributing factors guiding the cell positioning (such as cell polarity). In this study, the LV network of mouse ear pinna was used as a model tissue to investigate LV network enlargement, daughter LEC positioning and LEC polarity in growing LVs. Characterization of mitotic cells in developing LV network revealed that LEC proliferation occurs throughout the entire length of LVs in the network. To investigate LEC polarity in developing and mature LVs, I analysed Golgi and nuclear polarity of tip and stalk LECs. I found that whereas LECs during development are polarized and oriented along the long axis of LV, there is more variation in the direction of LEC polarity in relation to LV long axis in mature LV. This observation raised a question whether changes in the cell polarity were reflected to cell positioning, hence I analysed the positioning of daughter LECs by forcing LECs to the cell cycle with VEGF-C. These results indicated cell-level mechanisms that may contribute to LEC positioning in lymphangiogenesis. My finding provides an efficient tool for further research due to its suitability for monitoring proliferating LECs and studying causative factors affecting LEC proliferation and positioning. Future experiments with real-time imaging will reveal more about lymphangiogenesis process and provide insights into the role of lymphatic vasculature in conditions such as inflammation-related lymphedema or anti-tumor immunity in cancer.

Breast cancer remains as the leading cause of cancer deaths among women. Triple-negative breast cancer (TNBC) is one of the most aggressive breast cancer subtypes and lacks targetable receptors, consequently, cannot be treated with current hormone of anti-HER2 targeting therapies. Thus, there is a need for discovering novel and well-tolerated therapies. MYC is a proto-oncogene and a transcription factor, that is frequently amplified and overexpressed in breast cancers. MYC is involved in many cellular processes promoting cell proliferation, however, overexpression of MYC can also sensitize cells to replicative stress and apoptotic cell death. In our previous studies we have shown that pharmacological activation of AMPK, a cellular energy sensor, synergises with Bcl-2 family inhibitors, such as navitoclax and venetoclax, and activates MYC-dependent apoptosis in breast cancer cell lines, transgenic mouse models of MYC-dependent mammary tumorigenesis and in MYC-high patient-derived explant cultures (PDECs). In subsequent study we observed, that indirect AMPK activator metformin alone inhibited tumor growth in vivo, but did not induce apoptosis in mouse tumors or in PDECs. Metformin, a type II diabetes mellitus drug, has shown anti-cancer effects in some population studies and is under investigation for a cancer therapies, however the whole mechanism of action in cancer is still not well-known. To elucidate metformin’s effects on MYC overexpressing triple-negative breast cancer cells, I will present, that metformin has anti-proliferative effects and show that long term metformin treatment induces senescence biomarkers in MYC-high TNBC breast cancer cell lines. To study metformin's short and long-term anti-proliferative activity, cell proliferation during and after drug treatment was investigated, which showed, that metformin’s effects do not seem to persist long after drug withdrawal. In conclusion, the key observation of this thesis was, that metformin does inhibit the proliferation of MYC overexpressing cancer cells and presents a senescence phenotype that possibly can be exploited to find new targeted therapies for triple-negative breast cancer patients.

Studerande i början av sina akademiska studier har en varierande nivå av förhandskunskaper och det är väl rapporterat inom pedagogisk forskning att den tidigare kunskapen påverkar studerandens inlärning av olika koncept. Den konstruktivistiska inlärningsteorins grundprincip är att all ny kunskap byggs ovanpå den tidigare kunskapen och därför kan den tidigare kunskapen i stor mån förutspå hur väl inlärningen sker. Teorier kring konceptuell förändring bygger vidare på den konstruktivistiska inlärningsteorin och förklarar konceptuell förändring som den delen av inlärningen där mottagningen av den nya kunskapen leder till en omorganisering av den tidigare erfarna kunskapen, så att den tidigare kunskapen bearbetas och revideras så att den passar in med den nya kunskapen. De olika teorierna kring konceptuell förändring lyfter också fram att den tidigare kunskapen kan stå i strid med den nya kunskapen, och att det i dessa fall kan leda till att inlärningen av den nya kunskapen försvåras. I denna avhandling används begreppet missuppfattningar då man avser förståelse av koncept där tidigare kunskap står i strid med den nya kunskapen. Missuppfattningar kan delas in i faktuella och robusta missuppfattningar baserat på hur grova de är och i fyra olika kategorier enligt deras typ: felaktiga antaganden, bristfälliga mentala modeller, misskategorisering och avsaknad av schema. Denna studie undersökte utvecklingen av studerandes förståelse mellan det första, andra och tredje akademiska studieåret och förekomsten av missuppfattningar under det tredje akademiska studieåret. Studerandena som deltog i studien började studera i kandidatprogrammet i miljövetenskaper år 2019 och har besvarat studien under hösten i tre år i rad: år 2019 (N = 46) , 2020 (N = 37) och 2021 (N = 34). Studerandena besvarade ett frågeformulär med åtta öppna frågor som gällde centrala biologiska koncept: fotosyntesen, cellandningen, växternas roll ur näringskedjans perspektiv, växternas roll ur atmosfärens perspektiv och evolutionen. Svaren analyserades sedan kvantitativt för att undersöka utvecklingen av studerandenas förståelse mellan det första, andra och tredje akademiska studieåret. Dessutom analyserades svaren från det tredje (N = 34) akademiska studieåret kvalitativt för att undersöka vilka (miss)uppfattningar som förekom hos studerandena. Resultaten visar att studerandena klarade sig bättre i de uppgifter som mätte förmågan att ange fakta och sämre i de uppgifter som mätte förmågan att tillämpa kunskap. Det var en större variation mellan studerandenas svar i de faktabaserade uppgifterna, vilket överensstämmer med tidigare studiers resultat. I de tillämpade uppgifterna var studerandenas svar ganska korta och ytliga. Studerandenas prestationer under det tredje året varierade beroende på uppgift, och som förväntat baserat på tidigare studiers resultat hade den största utvecklingen skett i uppgiften som handlade om växternas roll ur näringskedjans perspektiv, medan studerandena i uppgiften om evolutionen presterat sämre under tredje året än under andra året. Evolutionen var också det koncept som hade flest grova missuppfattningar av typen avsaknad av schema, vilket indikerar att det finns en bristfällig förståelse för evolutionen. Då man känner till hur viktig roll den tidigare kunskapen har för inlärningen och hur väl kunskapen i början av de akademiska studierna kan förutspå studerandens inlärningsförmåga och prestationer i fortsatta akademiska studier förstår man hur viktigt det är att förstå sig på konceptuell förändring.

Neurodevelopmental disorders (NDDs) are disabilities in which the formation and development of the central nervous system is altered. NDDs severely impact the quality of life of the individuals that are affected by them, however little is known about the causes or the molecular mechanisms that are behind their onset. For this reason, being able to model them is pivotal to our society since, by understanding the mechanisms underlying such disorders, we could develop possible treatments. Previous research has suggested that disturbances in the early neuronal development could be at the basis of NDDs onset. Therefore, in this work, I have modeled neuronal differentiation in Kabuki syndrome (KS), a known NDD, assaying the expression of key early neurodevelopmental markers at four specific timepoints, using induced pluripotent stem cell (iPSC) technology. By concurrently differentiating three KS patient-derived and three control iPSC lines to neural precursor cells (NPCs) and profiling them with immunocytochemistry (ICC) and quantitative real-time PCR (RT-qPCR), I was able to identify differences in the early developmental trajectories of NPCs between the two conditions. The ICC data suggested that differentiating KS cell lines incur in precocious differentiation when compared to control cell lines, suggesting that the disease-causing mutations could lead to accelerated neuronal maturation of early NPCs. However, RT-qPCR analysis of the expression patterns of key neurogenesis markers was unable to statistically confirm the observed trend between the two phenotypes, likely due to limitations in statistical power. Despite this, the expression of four out of seven NPC markers was higher in early KS cells than in control cell lines, supporting the hypothesis of accelerated neuronal maturation. Taken together, this work highlighted some of the challenges related to iPSC-based disease modelling studies, and the need to further confirm the inferred mechanisms of asynchronous neuronal development observed in this work.

Human induced pluripotent stem cells (iPSCs) are an important in vitro model of disease and development. iPSCs can be differentiated in culture into cell types which are difficult to access from patients, such as neurons. Applying iPSC-derived cellular models to disease studies requires a thorough characterization of the derived cell types, as well as assessing reproducibility across cell lines or differentiation batches. With the aim of providing such a comprehensive molecular characterization at an early stage of cortical neuronal differentiation in vitro, six iPSC lines from four donors were differentiated to cortical neural progenitors using a modification of an established protocol (Shi et al., 2012a). The protocol successfully produced neural progenitors, with over 75% of the differentiated cells aligning with a cortical identity, as confirmed via qPCR and immunocytochemistry of established markers such as PAX6, NES and SOX1. To further classify the cell types produced as well as identify potential differences between cell lines, gene expression of the obtained cells was profiled with single cell RNA sequencing of ~22,000 cells, which uncovered the heterogeneity of neural progenitors produced. Further, although two differentiation batches produced similar cell-type compositions on a whole, a fraction of the lines showed inter-individual differences in cell type composition, which correlated with expression variability of known marker genes. Additionally, the cell types produced in vitro were compared to those produced in vivo by mapping our dataset to a reference fetal brain dataset (Polioudakis et al., 2019). It was observed that the in vitro dataset represented a subset of the cell types present at mid-gestation. Overall, the single cell characterization of differentiated cells allowed greater resolution in understanding cell-type heterogeneity of cortical neurogenesis, which is of key relevance for future applications such as disease modeling.

Anthocyanins are pigment molecules responsible for the majority of flower colors existing in nature. Emerging from the flavonoid biosynthetic pathway, anthocyanin biosynthetic pathway branches into orange pelargonidin derivates, red cyanidin derivates and blue delphinidin derivates. Dihydroflavonol 4-reductase (DFR), a NADPH-dependent oxidoreductase, catalyzes the first anthocyanin specific step after the branching point for all three branches. In some cases, DFR exhibits substrate specificity leading to some flowering plant species’ inability to produce certain colors; like petunias lacking orange colors. Ornamental plant industry thrives on breeding of novel colors and color patterns, and thus understanding of the capabilities of anthocyanin biosynthesis is of key importance. The aim of this study is to gain insight into the amino acid residues causing substrate specificities in Petunia hybrida. The study focused on an amino acid region that has been previously identified as affecting substrate specificities in Gerbera hybrida. To examine the effects of three different mutations in this region, enzyme activity was examined both in vitro and in vivo. Experiments consisted of kinetic assays with protein extracts from infiltrated Nicotiana benthamiana and determination of anthocyanin content from stable transformations of Petunia hybrida. Anthocyanin content was determined from transformed petunia flowers with high performance liquid chromatography. Kinetic assays show distinct substrate specificity profiles for all three mutations, indicating a correlation between the studied residues and substrate specificity. The transformed petunias also exhibited altered anthocyanin content, with two of the three mutant transformants exhibiting increased pelargonidin production. The observed effects of these mutations support the previous results indicating that this region has a role in determining substrate specificities of DFR enzymes.