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  • Mätzke, Sorjo (Helsingin yliopisto, 2004)
  • Hernandez Rios, Marcela (Helsingin yliopisto, 2012)
    Chronic periodontitis results from a complex aetiology, including the formation of a subgingival biofilm and the elicitation of the host s immune and inflammatory response. The hallmark of chronic periodontitis is alveolar bone loss and soft periodontal tissue destruction. Evidence supports that periodontitis progresses in dynamic states of exacerbation and remission or quiescence. The major clinical approach to identify disease progression is the tolerance method, based on sequential probing. Collagen degradation is one of the key events in periodontal destructive lesions. Matrix metalloproteinase (MMP)-8 and MMP-13 are the primary collagenolytic MMPs that are associated with the severity of periodontal inflammation and disease, either by a direct breakdown of the collagenised matrix or by the processing of non-matrix bioactive substrates. Despite the numerous host mediators that have been proposed as potential biomarkers for chronic periodontitis, they reflect inflammation rather than the loss of periodontal attachment. The aim of the present study was to determine the key molecular MMP-8 and -13 interactions in gingival crevicular fluid (GCF) and gingival tissue from progressive periodontitis lesions and MMP-8 null allele mouse model. In study (I), GCF and gingival biopsies from active and inactive sites of chronic periodontitis patients, which were determined clinically by the tolerance method, and healthy GCF were analysed for MMP-13 and tissue inhibitor of matrix metalloproteinases (TIMP)-1. Chronic periodontitis was characterised by increased MMP-13 levels and the active sites showed a tendency of decreased TIMP-1 levels associated with increments of MMP-13 and total protein concentration compared to inactive sites. In study (II), we investigated whether MMP-13 activity was associated with TIMP-1, bone collagen breakdown through ICTP levels, as well as the activation rate of MMP-9 in destructive lesions. The active sites demonstrated increased GCF ICTP levels as well as lowered TIMP-1 detection along with elevated MMP-13 activity. MMP-9 activation rate was enhanced by MMP-13 in diseased gingival tissue. In study (III), we analysed the potential association between the levels, molecular forms, isoenzyme distribution and degree of activation of MMP-8, MMP-14, MPO and the inhibitor TIMP-1 in GCF from periodontitis progressive patients at baseline and after periodontal therapy. A positive correlation was found for MPO/MMP-8 and their levels associated with progression episodes and treatment response. Because MMP-8 is activated by hypochlorous acid in vitro, our results suggested an interaction between the MPO oxidative pathway and MMP-8 activation in GCF. Finally, in study (IV), on the basis of the previous finding that MMP-8-deficient mice showed impaired neutrophil responses and severe alveolar bone loss, we aimed to characterise the detection patterns of LIX/CXCL5, SDF-1/CXCL12 and RANKL in P. gingivalis-induced experimental periodontitis and in the MMP-8-/- murine model. The detection of neutrophil-chemoattractant LIX/CXCL5 was restricted to the oral-periodontal interface and its levels were reduced in infected MMP-8 null mice vs. wild type mice, whereas the detection of SDF-1/CXCL12 and RANKL in periodontal tissues increased in experimentally-induced periodontitis, irrespectively from the genotype. Accordingly, MMP-8 might regulate LIX/CXCL5 levels by undetermined mechanisms, and SDF-1/CXCL12 and RANKL might promote the development and/or progression of periodontitis.
  • Pöyhönen, Rosanna (Helsingfors universitet, 2013)
    Charcot-Marie-Tooth (CMT) neuropathy is one of the most common forms of inherited peripheral neuropathies with the prevalence of one in 2500 individuals. CMT is phenotypically and genetically a very heterogeneous disease. It can be inherited as an autosomal recessive, dominant or X-linked trait. CMT is characterized by distal muscle weakness, atrophy and deformity of the feet as well as clumsiness of gait. The onset of CMT varies and also the symptoms of the disease can vary even among the members of a single family. So far more than 40 genes have been identified for CMT and the list is estimated to grow by 30-50 genes. Whole exome sequencing (WES) is a next generation sequencing technique, which targets the protein coding area of the genome. Through WES analysis it is possible to search for disease causing mutations with all kinds of inheritance patterns. Patients suffering from CMT are good candidates for WES analysis because of the genetic heterogeneity of their disease. WES can be used for diagnosing Mendelian disorders with atypical symptoms as well as diseases, which are difficult to confirm using clinical criteria alone and which require costly evaluation, e.g. CMT. In this master study new disease causing mutations for early-onset neuropathies are identified by whole exome sequencing. The aims of this study include using WES for the molecular diagnosis of four patients suffering from early-onset axonal neuropathies, the functional analysis of possible causative variants and improving and developing the process of analyzing variants from whole exome sequencing data, especially the analyzing steps of insertion and deletion variants. Finding causative variants among the insertion and deletion variants has previously been often left out from the WES analysis because of the lack of systematic analysis technique. As a result of the WES data analysis a new candidate disease gene, tripartite motif containing 2 (TRIM2) was identified. A missense mutation c.761T>A (p.E254V) and a deletion c.1779delA (p.K594Rfs7X) were found in patient 2, who suffers from severe CMT type 2. The carrier frequency was analysed to see whether the variants are present in the general population or not. The functional analysis of TRIM2 was started by preparing constructs carrying the missense mutation and the deletion and by setting up conditions for western blotting.
  • Pöyhönen, Julia Rosanna Hellin (Helsingfors universitet, 2013)
    Faculty of Medicine Subject: Translational medicine Author Rosanna Pöyhönen Title Identification of disease mutations in early-onset neuropathies by whole exome sequencing Supervisor Henna Tyynismaa Supervisor’s affiliation Research Programs Unit, Molecular Neurology and Department of Medical Genetics, University of Helsinki Abstract Charcot-Marie-Tooth (CMT) neuropathy is phenotypically and genetically a very heterogeneous disease. It can be inherited as an autosomal recessive, dominant or X-linked trait. CMT is characterized by distal muscle weakness, atrophy and deformity of the feet as well as clumsiness of gait. The onset of CMT varies and also the symptoms of the disease can vary even among the members of a single family. So far more than 40 genes have been identified for CMT and the list is estimated to grow by 30-50 genes. Whole exome sequencing (WES) is a new next generation sequencing technique, which targets the protein-coding area of the genome. Through WES analysis it is possible to search for disease causing mutations with all kinds of inheritance patterns. Patients suffering from CMT are good candidates for WES analysis because of the genetic heterogeneity of their disease. WES can be used for diagnosing Mendelian disorders with atypical symptoms as well as diseases, which are difficult to confirm using clinical criteria alone and which require costly evaluation, e.g. CMT. In this master study new disease causing mutations for early-onset neuropathies are identified by whole exome sequencing (WES). The aims of this study include using WES for the molecular diagnosis of four patients suffering from early-onset axonal neuropathies, the functional analysis of possible causative variants and improving and developing the process of analyzing variants from whole exome sequencing data, especially the analyzing steps of insertion and deletion variants. Finding causative variants among the insertion and deletion variants has previously been often left out from the WES analysis because of the lack of systematic analysis technique. As a result of the WES data analysis a new candidate disease gene, tripartite motif containing 2 (TRIM2) was identified. A missense mutation c.761T>A (p.E254V) and a deletion c.1779delA (p.K594Rfs7X) were found in patient 2, who suffers from severe CMT type 2. The carrier frequency was analysed to see whether the variants are present in the general population or not. The functional analysis of TRIM2 was started by preparing constructs carrying the missense mutation and the deletion and by setting up conditions for western blotting. Keywords Charcot-Marie-Tooth neuropathy, whole exome sequencing, disease gene, molecular diagnosis, functional analysis
  • Anttila, Timo Verneri (Helsingin yliopisto, 2010)
    Migraine is the common cause of chronic episodic headache, affecting 12%-15% of the Caucasian population (41 million Europeans and some half a million Finns), and causes considerable loss of quality of life to its sufferers, as well as being linked to increased risk for a wide range of conditions, from depression to stroke. Migraine is the 19th most severe disease in terms of disability-adjusted life years, and 9th among women. It is characterized by attacks of headache accompanied by sensitivity to external stimuli lasting 4-72 hours, and in a third of cases by neurological aura symptoms, such as loss of vision, speech or muscle function. The underlying pathophysiology, including what triggers migraine attacks and why they occur in the first place, is largely unknown. The aim of this study was to identify genetic factors associated with the hereditary susceptibility to migraine, in order to gain a better understanding of migraine mechanisms. In this thesis, we report the results of genetic linkage and association analyses on a Finnish migraine patient collection as well as migraineurs from Australia, Denmark, Germany, Iceland and the Netherlands. Altogether we studied genetic information of nearly 7,000 migraine patients and over 50,000 population-matched controls. We also developed a new migraine analysis method called the trait component analysis, which is based on individual patient responses instead of the clinical diagnosis. Using this method, we detected a number of new genetic loci for migraine, including on chromosome 17p13 (HLOD 4.65) and 10q22-q23 (female-specific HLOD 7.68) with significant evidence of linkage, along with five other loci (2p12, 8q12, 4q28-q31, 18q12-q22, and Xp22) detected with suggestive evidence of linkage. The 10q22-q23 locus was the first genetic finding in migraine to show linkage to the same locus and markers in multiple populations, with consistent detection in six different scans. Traditionally, ion channels have been thought to play a role in migraine susceptibility, but we were able to exclude any significant role for common variants in a candidate gene study of 155 ion transport genes. This was followed up by the first genome-wide association study in migraine, conducted on 2,748 migraine patients and 10,747 matched controls followed by a replication in 3,209 patients and 40,062 controls. In this study, we found interesting results with genome-wide significance, providing targets for future genetic and functional studies. Overall, we found several promising genetic loci for migraine providing a promising base for future studies in migraine.
  • Anttila, Timo Verneri (Helsingin yliopisto, 2010)
    Migraine is the common cause of chronic episodic headache, affecting 12%-15% of the Caucasian population (41 million Europeans and some half a million Finns), and causes considerable loss of quality of life to its sufferers, as well as being linked to increased risk for a wide range of conditions, from depression to stroke. Migraine is the 19th most severe disease in terms of disability-adjusted life years, and 9th among women. It is characterized by attacks of headache accompanied by sensitivity to external stimuli lasting 4-72 hours, and in a third of cases by neurological aura symptoms, such as loss of vision, speech or muscle function. The underlying pathophysiology, including what triggers migraine attacks and why they occur in the first place, is largely unknown. The aim of this study was to identify genetic factors associated with the hereditary susceptibility to migraine, in order to gain a better understanding of migraine mechanisms. In this thesis, we report the results of genetic linkage and association analyses on a Finnish migraine patient collection as well as migraineurs from Australia, Denmark, Germany, Iceland and the Netherlands. Altogether we studied genetic information of nearly 7,000 migraine patients and over 50,000 population-matched controls. We also developed a new migraine analysis method called the trait component analysis, which is based on individual patient responses instead of the clinical diagnosis. Using this method, we detected a number of new genetic loci for migraine, including on chromosome 17p13 (HLOD 4.65) and 10q22-q23 (female-specific HLOD 7.68) with significant evidence of linkage, along with five other loci (2p12, 8q12, 4q28-q31, 18q12-q22, and Xp22) detected with suggestive evidence of linkage. The 10q22-q23 locus was the first genetic finding in migraine to show linkage to the same locus and markers in multiple populations, with consistent detection in six different scans. Traditionally, ion channels have been thought to play a role in migraine susceptibility, but we were able to exclude any significant role for common variants in a candidate gene study of 155 ion transport genes. This was followed up by the first genome-wide association study in migraine, conducted on 2,748 migraine patients and 10,747 matched controls followed by a replication in 3,209 patients and 40,062 controls. In this study, we found interesting results with genome-wide significance, providing targets for future genetic and functional studies. Overall, we found several promising genetic loci for migraine providing a promising base for future studies in migraine.
  • Zhang, Teng (Helsingin yliopisto, 2015)
    The architecture of inflorescence refers to the spatio-temporal arrangement of flowers on the reproductive branches. Flowering plants have evolved great diversity in such branching systems. Among which, the showy capitulum type inflorescence in the large Compositae (Asteraceae) species is regarded as a prerequisite factor for their wide spreading around the world. Different from the simple raceme and cyme, capitulum compresses hundreds of individual florets on its receptacle, but overall resembles a single, solitary flower. The ontogeny of capitulum also bears resemblance to a single flower, with regard to the meristem determinacy, floral sequence and histological configurations. Recent molecular studies have revealed that a plant specific transcription factor LEAFY (LFY), is required for both the floral initiation and floral patterning, the two essential steps to form an inflorescence. The thesis elaborates Gerbera hybrida as a model to elucidate functions of the LFY ortholog during the development of inflorescence/flower in a capitulum background. In addition to the conserved functions in regulating floral meristem identity and floral patterning, three specified functions were revealed by transgenic Gerbera with down-regulated expression of GhLFY. Firstly, GhLFY is involved in the regulating the floral initiation of marginal ray florets. Down regulation of GhLFY resulted the marginal ray florets revert into a branching patterm that shown on the capitulum of Calyceraceae, the close relatives of Asteraceae. Secondly, the determinacy of IM is disrupted when GhLFY loses its functions, suggesting that GhLFY may function at both the flower and inflorescence interfaces. Thirdly, different flower types show specific responses to GhLFY down-regulation in floral patterning, indicating that there exist a potential genetic gradient among different flower types. At protein level, the LFY functions are specified by formation of versatile protein complexes with its transcriptional co-regulators. In Gerbera, GhLFY proteins tend to form homodimers and they were also capable to interact with a conserved transcriptional co-regulator, the UNUSUAL FLORAL ORGANS (UFO) ortholog GhUFO. Taken advantage of the forward Y2H library screening, 6 additional proteins were identified to interact with GhLFY, including several novel potential co-regulators of LFY that has not yet been identified in other species. Additionally, a bimolecular fluorescence complementation assay (BiFC) was optimized to verify the GhLFY self-interaction in planta.
  • Wendland, Lauri (Helsingin yliopisto, 2009)
    This thesis describes methods for the reliable identification of hadronically decaying tau leptons in the search for heavy Higgs bosons of the minimal supersymmetric standard model of particle physics (MSSM). The identification of the hadronic tau lepton decays, i.e. tau-jets, is applied to the gg->bbH, H->tautau and gg->tbH+, H+->taunu processes to be searched for in the CMS experiment at the CERN Large Hadron Collider. Of all the event selections applied in these final states, the tau-jet identification is the single most important event selection criterion to separate the tiny Higgs boson signal from a large number of background events. The tau-jet identification is studied with methods based on a signature of a low charged track multiplicity, the containment of the decay products within a narrow cone, an isolated electromagnetic energy deposition, a non-zero tau lepton flight path, the absence of electrons, muons, and neutral hadrons in the decay signature, and a relatively small tau lepton mass compared to the mass of most hadrons. Furthermore, in the H+->taunu channel, helicity correlations are exploited to separate the signal tau jets from those originating from the W->taunu decays. Since many of these identification methods rely on the reconstruction of charged particle tracks, the systematic uncertainties resulting from the mechanical tolerances of the tracking sensor positions are estimated with care. The tau-jet identification and other standard selection methods are applied to the search for the heavy neutral and charged Higgs bosons in the H->tautau and H+->taunu decay channels. For the H+->taunu channel, the tau-jet identification is redone and optimized with a recent and more detailed event simulation than previously in the CMS experiment. Both decay channels are found to be very promising for the discovery of the heavy MSSM Higgs bosons. The Higgs boson(s), whose existence has not yet been experimentally verified, are a part of the standard model and its most popular extensions. They are a manifestation of a mechanism which breaks the electroweak symmetry and generates masses for particles. Since the H->tautau and H+->taunu decay channels are important for the discovery of the Higgs bosons in a large region of the permitted parameter space, the analysis described in this thesis serves as a probe for finding out properties of the microcosm of particles and their interactions in the energy scales beyond the standard model of particle physics.
  • Heinonen, Satu-Maarit (Helsingin yliopisto, 2006)
    Epidemiological studies have associated high soy intake with a lowered risk for certain hormone-dependent diseases, such as breast and prostate cancers, osteoporosis, and cardiovascular disease. Soy is a rich source of isoflavones, diphenolic plant compounds that have been shown to possess several biological activities. Soy is not part of the traditional Western diet, but many dietary supplements are commercially available in order to provide the proposed beneficial health effects of isoflavones without changing the original diet. These supplements are usually manufactured from extracts of soy or red clover, which is another important source of isoflavones. However, until recently, detailed studies of the metabolism of these compounds in humans have been lacking. The aim of this study was to identify urinary metabolites of isoflavones originating from soy or red clover using gas chromatography - mass spectrometry (GC-MS). To examine metabolism, soy and red clover supplementation studies with human volunteers were carried out. In addition, the metabolism of isoflavones was investigated in vitro by identification of metabolites formed during a 24-h fermentation of pure isoflavones with a human fecal inoculum. Qualitative methods for identification and analysis of isoflavone metabolites in urine and fecal fermentation samples by GC-MS were developed. Moreover, a detailed investigation of fragmentation of isoflavonoids in electron ionization mass spectrometry (EIMS) was carried out by means of synthetic reference compounds and deuterated trimethylsilyl derivatives. After isoflavone supplementation, 18 new metabolites of isoflavones were identified in human urine samples. The most abundant urinary metabolites of soy isoflavones daidzein, genistein, and glycitein were found to be the reduced metabolites, i.e. analogous isoflavanones, a-methyldeoxybenzoins, and isoflavans. Metabolites having additional hydroxyl and/or methoxy substituents, or their reduced analogs, were also identified. The main metabolites of red clover isoflavones formononetin and biochanin A were identified as daidzein and genistein. In addition, reduced and hydroxylated metabolites of formononetin and biochanin A were identified; however, they occurred at much lower levels in urine samples than daidzein or genistein or their reduced metabolites. The results of this study show that the metabolism of isoflavones is diverse. More studies are needed to determine whether the new isoflavonoid metabolites identified here have biological activities that contribute to the proposed beneficial effects of isoflavones on human health. Another task is to develop validated quantitative methods to determine the actual levels of isoflavones and their metabolites in biological matrices in order to assess the role of isoflavones in prevention of chronic diseases.
  • Tikka-Kleemola, Päivi (Helsingin yliopisto, 2009)
    Common migraine, i.e. migraine with (MA) or without aura (MO), is a chronic neurological disorder affecting about 10% of the Caucasian population. In MA, migraine headache is preceded by visual, sensoric and/or dysphasic reversible aura symptoms. Twin and family studies have suggested a multifactorial mode of inheritance for common migraine, and a stronger genetic component for MA than for MO. Since there is no biological or genetic marker to identify common migraine, aura symptoms provide a distinctive character to identify those suspected of suffering from migraine. The aim of this study was to identify MA susceptibility loci in well-phenotyped migraine samples with familial predisposition using different gene mapping methods. Genes coding for endothelin1 and its receptors EDNRA and ENDRB are potential candidate genes for cortical spreading depression (CSD), which is considered to be the underlying mechanism of migraine aura. The role of these genes in MA was studied in 850 Finnish migraine cases and 890 control individuals. Rare homozygous EDNRA SNPs showed nominal association with MA and with the age of onset trait (20 years). This result was also detected in the pooled analysis on 648 German MA cases and 651 control individuals when the test was adjusted for gender and sample origin. Evaluation of SNP genotyping reactions with two different DNA polymerase enzymes ensured that the genotype quality was high, and thus the discovered associations are considered reliable. The role of the 19p13 region was studied in a linkage analysis of 72 Finnish MA families. This region contains two migraine-associated genes: CACNA1A, which is associated with a predisposition to a rare Mendelian form of MA, familial hemiplegic migraine (FHM), and the insulin receptor gene (INSR) that is associated with common migraine. No evidence of linkage between the 19p13 and MA was detected. A novel visual aura locus was mapped to chromosome 9q21-q22 with significant evidence of linkage using a genome-wide linkage approach in 36 Finnish MA families. Five additional, potential loci were also detected. The 9q21-q22 region has previously been linked to occipitotemporal lobe epilepsy and MA, both of which involve prominent visual symptoms. Our result further supports a shared background for these episodic disorders.
  • Nummela, Pirjo (Helsingin yliopisto, 2011)
    Cancer is becoming the leading cause of deaths in the world. As 90% of all deaths from cancer are caused by metastasis, discovery of the mechanisms behind cancer cell invasion and metastasis is of utmost importance. Only new effective therapies targeting cancer progression can reduce cancer mortality rates. The aim of this study was to identify molecules that are relevant for tumor cell invasion and spreading in fibrosarcomas and melanomas, and to analyze their potential for cancer biomarkers or therapeutic targets. First, the gene expression changes of normal cells and transformed cells showing high invasiveness, S-adenosylmethionine decarboxylase (AdoMetDC)-transfected murine fibroblasts and human melanoma cells, were studied by microarray analyses. The function of the identified candidate molecules were then studied in detail in these cell lines. Finally, the physiological relevance of the identified changes was studied by immunohistochemical analyses of human sarcoma and melanoma specimens or by a mouse xenograft model. In fibrosarcoma cells, the most remarkable change detected was a dramatic up-regulation of the actin-sequestering molecule thymosin beta 4 (TB4), which was shown to be important for the transformed phenotype of the AdoMetDC-transfected cells (Amdc-s and -as). A sponge toxin latrunculin A, inhibiting the binding of TB4 to actin, was found to selectively inhibit the migration and invasion of these cells. Further, Amdc-s-induced mouse tumors and human high-grade sarcomas were found to show intense TB4 immunostaining. In addition to TB4, integrin subunits alfa 6 and beta 7 (ItgA6 and ItgB7) were found to be up-regulated in Amdc-s and -as cells. ItgA6 was shown to dimerize mainly with ItgB1 in Amdc-s. Inhibition of ItgA6 or ItgB1 function with neutralizing antibodies fully blocked the invasiveness of Amdc-s cells, and importantly also human HT-1080 fibrosarcoma cells, in three-dimensional (3D)-Matrigel mimicking tumor extracellular matrix (ECM). By immunohistochemical analyses, strong staining for ITGA6 was detected in human high-grade fibrosarcomas and other sarcomas, especially at the invasion fronts of the tumors. In the studied melanoma cell lines, the expression levels of the adhesion-related ECM proteins tenascin-C (TN-C), fibronectin (FN), and transforming growth factor beta-induced (TGFBI) were found to be highly up-regulated. By immunohistochemistry, intense TN-C and FN staining was detected in invasive and metastatic melanoma tumors, showing co-localization (together with procollagen-I) in tubular meshworks and channels around the invading melanoma cells. In vitro, TN-C and FN were further found to directly stimulate the migration of melanoma cells in 3D-collagen-I matrix. The third candidate protein, TGFBI, was found to be an anti-adhesive molecule for melanoma cells, and knockdown of its expression in metastatic melanoma cells (TGFBI-KD cells) led to dramatically impaired tumor growth in immunocompromized mice. Interestingly, the control tumors showed intense TGFBI immunostaining in the invasion fronts, showing partial co-localization with the fibrillar FN staining, whereas the small TGFBI-KD cell-induced tumors displayed amorphous, non-fibrillar FN staining. These data suggest an important role for TGFBI in FN fibrillogenesis and melanoma progression. In conclusion, we have identified several invasion-related molecules, which show potential for cancer diagnostic or prognostic markers, or therapeutic targets. Based on our previous and present fibrosarcoma studies, we propose the possibility of using ITGA6 antagonists (affecting tumor cell adhesion) in combination with TB4 inhibitors (affecting tumor cell migration) and cathepsin L inhibitors (affecting the degradation of basement membrane and ECM proteins) for the treatment of fibrosarcomas and other tumors overexpressing these molecules. With melanoma cells, in turn, we point to the importance of three secreted ECM proteins, TN-C, FN, and TGFBI, in melanoma progression. Of these, especially the potential of TN-C as a prognostic melanoma biomarker and TGFBI as a promising therapeutic target molecule are clearly worth additional studies.
  • Kyöstilä, Kaisa (Helsingin yliopisto, 2015)
    Inherited diseases occur across different species. This thesis work has provided insights into the molecular genetic background of three autosomal recessive diseases that affect specific dog breeds. The studied phenotypes comprised two neurodegenerative diseases and a type of skeletal dysplasia. Genome-wide methods, such as SNP chip genotyping, were used to identify disease-associated gene variants. In all three disease phenotypes, the likely causative variant was found in a gene that had not been previously associated with a monogenic disorder. The Norwegian Elkhound and Karelian Bear Dog breeds are affected with inherited chondrodysplasia that causes short-stature dwarfism of varying severity. A genome-wide association study in Norwegian Elkhounds revealed a disease-associated locus on canine chromosome 17 and a nonsense mutation in the ITGA10 gene. The identified mutation was homozygous in all affected dogs from both breeds, and may have been introduced to Karelian Bear Dogs from Norwegian Elkhounds. The ITGA10 gene encodes an α10-integrin protein that assembles into a collagen-binding α10β1 integrin. The α10β1 integrin is a cell surface receptor, found in growth plate chondrocytes, where it mediates the cell s attachments with the surrounding matrix. Due to the mutation, a full-length α10-protein is not produced, disturbing the growth of long bones. Early-onset cerebellar degeneration occurs in the Finnish Hound dog breed. Neurological examination of affected dogs revealed quickly progressing cerebellar ataxia and failure to thrive. Genome-wide association analyses mapped the disease to a 1.5-Mb locus on canine chromosome 8. Sequencing of the SEL1L gene from the locus identified a homozygous missense mutation in all affected dogs. The mutation causes a serine to proline amino acid change within a highly conserved functional domain of the encoded SEL1L protein. The SEL1L protein is found in the endoplasmic reticulum, where it functions within a protein quality control and degradation pathway. Cerebellar tissue samples from affected dogs showed signs of endoplasmic reticulum stress, which may be the cause of premature cell death. A novel neurological disease, characterized by juvenile to adult onset cerebellar ataxia, was recognized in the Lagotto Romagnolo breed. Through linkage analysis, homozygosity mapping and whole-genome sequencing, the disease was associated with a homozygous missense change in the autophagy-related ATG4D gene. Pathological examination of affected dogs revealed progressive cerebellar degeneration, and intracellular vacuolar changes both in neuronal and extraneuronal tissues. The ATG4D gene encodes a cysteine protease, which is thought to function in the macroautophagy pathway. The autophagy process degrades and recycles damaged or obsolete cellular materials via membrane-enclosed autophagosomes. In line with this, the neuronal tissues of affected dogs showed signs of altered autophagic flow. Overall, this study has revealed three new disease-linked genes in dogs, which may be associated to similar disorders in other species. On the basis of the results, DNA-tests have been developed for veterinary diagnostic and breeding purposes. Importantly, by shedding light into disease-causing pathways, the results of this study could prove beneficial not just for canine health but for human medicine as well.
  • Hahtola, Sonja (Helsingin yliopisto, 2008)
    Cutaneous T-cell lymphomas (CTCL) represent a group of non-Hodgkin lymphomas showing a growing incidence especially in the Western world. The mechanisms leading to the disease are largely unknown, diagnosis is difficult and therefore often delayed, and no curative therapy exists. CTCL presents with skin symptoms although the malignant cells are not derived of human skin but of human immune system instead. The malignant cells are mature T helper memory cells, and preferentially express cytokines characteristic to T-helper 2 (Th2) type immune response. Chromosomal instability is a typical feature of CTCL. Some secondary cancers occur in CTCL patients more often than in general population, the most common of which are lung cancers and non-Hodgkin lymphomas. The aim of the study was to identify genes relevant to CTCL pathogenesis to clarify the poorly understood pathomechanisms behind the disease group. The two most common subgroups of CTCL, mycosis fungoides (MF) and Sezary syndrome (SS), as well as the difficult to diagnose subcutaneous panniculitis like T-cell lymphoma (SPTL), were studied. To reveal the molecular pathogenesis underlying CTCL-associated lung cancer, CTCL-associated lung cancer samples were analysed and compared to primary / reference lung cancer samples. Identification of potential novel diagnostic markers as well as target molecules for therapy was a special focus of the study. To achieve this, patient derived material was studied with molecular cytogenetic techniques, microarrays and gene expression analyses. This study identified the first specific, recurrent gene-level aberration in CTCL, namely the deletion / translocation of neuron navigator 3 (NAV3) gene, characteristic to many different CTCL subgroups, namely MF, SS, and SPTL. NAV3 is a putative haploinsufficient tumor suppressor influencing the differentiation of T-helper cells. The pathways affected by its aberrant function, are currently being studied. Novel insights to CTCL pathogenesis were achieved through the observation that several genes specific for Th1 type immune response (e.g. T-bet, RANTES, and NKG7) were downregulated in CTCL. For the first time, CTCL-associated lung cancers were observed to show chromosomal aberrations differing from primary lung cancers. This finding warrants further prospective studies to identify the common underlying factors between CTCL and CTCL-associated lung cancer. Demonstration of NAV3 deletion by FISH provides a novel diagnostic tool, and overexpression of certain membrane antigens (e.g. MS4A4A, LIR9 and CD52) will provide the basis for developing novel antibody-based therapeutic means.
  • Aavikko, Mervi (Helsingin yliopisto, 2014)
    Identification of tumor susceptibility genes has contributed significantly to our understanding on molecular basis of cancer. Over one hundred high risk tumor susceptibility genes have been identified during past few decades, but some remain still to be characterized, including those that do not cause other clinically recognizable syndromic features, and present with incomplete penetrance. The aim of this study was to assess the familial aggregation of cancers in Finland and to identify novel tumor predisposition families and genes in families with Kaposi sarcoma (KS), nodular lymphocyte predominant Hodgkin lymphoma (NLPHL), and intracranial meningioma. First, to assess the familial aggregation of cancers in Finland, we conducted a computerized clustering of 878 593 patients in FCR, based on family name at birth, municipality of birth, and tumor type. Additional clustering, based on family name at birth and tumor type, was also conducted. We calculated a cluster score to assess the frequency of familial aggregation of different tumor types. The top scoring types included those with well-established genetic background, but also those with unknown genetic etiology such as KS. We performed genealogy analysis from the clustered KS cases, and identified a family with five affected individuals and several smaller KS families. Furthermore, we showed that KS incidence is unevenly distributed in Finland, with more cases in the western and northeastern than other parts of the country. Second, we examined the genetic susceptibility in the KS family with five affected cases. We mapped the shared genomic regions and performed whole genome and exome sequencing. We identified 14 candidate variants, among them a missense variant (c.1337C>T, p.Thr446Ile) in the DNA binding domain of STAT4. We showed that healthy variant carriers had decreased IFN-γ production in the activated T-cells. We studied STAT4 in a large number of familial and sporadic KS cases, but detected no additional mutation carriers. Our results suggest STAT4 as a KS predisposing gene. However, further genetic and functional validation is needed to claim causality. Third, a family of four cousins with a rare subtype of Hodgkin lymphoma, namely NLPHL, was studied for genetic predisposition. Linkage analysis and exome sequencing revealed a frameshift mutation (c.2437-2438_delAG) in NPAT segregating with NLPHL in the family. We sequenced NPAT from a large number of HL patients, and detected an in-frame deletion (c.2171-2173delCTT, p.Ser725del) that was more prevalent in cases than in population matched controls (odds ratio 4.11, P=0.018), supporting the role of NPAT as a candidate predisposition gene. Fourth, we studied a family with five affected siblings with intracranial meningiomas, four of whom had multiple meningiomas. We identified a c.367C>T (p.Arg123Cys) mutation in SUFU that segregated with the meningiomas in the family. The tumors from the affected individuals showed loss of heterozygosity of the wild-type allele at the site of the mutation. We showed that the mutation led to lowered SUFU activity and dysregulated Hedgehog signaling. Our genetic and functional analyses indicate that germline SUFU mutations predispose to meningiomas, particularly multiple meningiomas.
  • Vaahtomeri, Kari (Helsingin yliopisto, 2011)
    Tumorigenesis is a consequence of inactivating mutations of tumor suppressor genes and activating mutations of proto-oncogenes. Most of the mutations compromise cell autonomous and non-autonomous restrains on cell proliferation by modulating kinase signal transduction pathways. LKB1 is a tumor suppressor kinase whose sporadic mutations are frequently found in non-small cell lung cancer and cervical cancer. Germ-line mutations in the LKB1 gene lead to Peutz-Jeghers syndrome with an increased risk of cancer and development of benign gastrointestinal hamartomatous polyps consisting of hyperproliferative epithelia and prominent stromal stalk composed of smooth muscle cell lineage cells. The tumor suppressive function of LKB1 is possibly mediated by 14 identified LKB1 substrate kinases, whose activation is dependent on the LKB1 kinase complex. The aim of my thesis was to identify cell signaling pathways crucial for tumor suppression by LKB1. Re-introduction of LKB1 expression in the melanoma cell line G361 induces cell cycle arrest. Here we demonstrated that restoring the cytoplasmic LKB1 was sufficient to induce the cell cycle arrest in a tumor suppressor p53 dependent manner. To address the role of LKB1 in gastrointestinal tumor suppression, Lkb1 was deleted specifically in SMC lineage in vivo, which was sufficient to cause Peutz-Jeghers syndrome type polyposis. Studies on primary myofibroblasts lacking Lkb1 suggest that the regulation of TGFβ signaling, actin stress fibers and smooth muscle cell lineage differentiation are candidate mechanisms for tumor suppression by LKB1 in the gastrointestinal stroma. Further studies with LKB1 substrate kinase NUAK2 in HeLa cells indicate that NUAK2 is part of a positive feedback loop by which NUAK2 expression promotes actin stress fiber formation and, reciprocally the induction of actin stress fibers promote NUAK2 expression. Findings in this thesis suggest that p53 and TGFβ signaling pathways are potential mediators of tumor suppression by LKB1. An indication of NUAK2 in the promotion of actin stress fibers suggests that NUAK2 is one possible mediator of LKB1 dependent TGFβ signaling and smooth muscle cell lineage differentiation.
  • Hilditch, Satu (Helsingin yliopisto, 2010)
    Pectin is a natural polymer consisting mainly of D-galacturonic acid monomers. Microorganisms living on decaying plant material can use D-galacturonic acid for growth. Although bacterial pathways for D-galacturonate catabolism had been described previously, no eukaryotic pathway for D-galacturonate catabolism was known at the beginning of this work. The aim of this work was to identify such a pathway. In this thesis the pathway for D-galacturonate catabolism was identified in the filamentous fungus Trichoderma reesei. The pathway consisted of four enzymes: NADPH-dependent D-galacturonate reductase (GAR1), L-galactonate dehydratase (LGD1), L-threo-3-deoxy-hexulosonate aldolase (LGA1) and NADPH-dependent glyceraldehyde reductase (GLD1). In this pathway D-galacturonate was converted to pyruvate and glycerol via L-galactonate, L-threo-3-deoxy-hexulosonate and L-glyceraldehyde. The enzyme activities of GAR1, LGD1 and LGA1 were present in crude mycelial extract only when T. reesei was grown on D-galacturonate. The activity of GLD1 was equally present on all the tested carbon sources. The corresponding genes were identified either by purifying and sequencing the enzyme or by expressing genes with homology to other similar enzymes in a heterologous host and testing the activities. The new genes that were identified were expressed in Saccharomyces cerevisiae and resulted in active enzymes. The GAR1, LGA1 and GLD1 were also produced in S. cerevisiae as active enzymes with a polyhistidine-tag, and purified and characterised. GAR1 and LGA1 catalysed reversible reactions, whereas only the forward reactions were observed for LGD1 and GLD1. When gar1, lgd1 or lga1 was deleted in T. reesei the deletion strain was unable to grow with D-galacturonate as the only carbon source, demonstrating that all the corresponding enzymes were essential for D-galacturonate catabolism and that no alternative D-galacturonate pathway exists in T. reesei. A challenge for biotechnology is to convert cheap raw materials to useful and more valuable products. Filamentous fungi are especially useful for the conversion of pectin, since they are efficient producers of pectinases. Identification of the fungal D-galacturonate pathway is of fundamental importance for the utilisation of pectin and its conversion to useful products.