Browsing by Subject " genetics"

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  • Weiss, Alexander; Baselmans, Bart M. L.; Hofer, Edith; Yang, Jingyun; Okbay, Aysu; Lind, Penelope A.; Miller, Mike B.; Nolte, Ilja M.; Zhao, Wei; Hagenaars, Saskia P.; Hottenga, Jouke-Jan; Matteson, Lindsay K.; Snieder, Harold; Faul, Jessica D.; Hartman, Catharina A.; Boyle, Patricia A.; Tiemeier, Henning; Mosing, Miriam A.; Pattie, Alison; Davies, Gail; Liewald, David C.; Schmidt, Reinhold; De Jager, Philip L.; Heath, Andrew C.; Jokela, Markus; Starr, John M.; Oldehinkel, Albertine J.; Johannesson, Magnus; Cesarini, David; Hofman, Albert; Harris, Sarah E.; Smith, Jennifer A.; Keltikangas-Järvinen, Liisa; Pulkki-Råback, Laura; Schmidt, Helena; Smith, Jacqui; Iacono, William G.; McGue, Matt; Bennett, David A.; Pedersen, Nancy L.; Magnusson, Patrik K. E.; Deary, Ian J.; Martin, Nicholas G.; Boomsma, Dorret I.; Bartels, Meike; Luciano, Michelle (2016)
    Approximately half of the variation in wellbeing measures overlaps with variation in personality traits. Studies of non-human primate pedigrees and human twins suggest that this is due to common genetic influences. We tested whether personality polygenic scores for the NEO Five-Factor Inventory (NEO-FFI) domains and for item response theory (IRT) derived extraversion and neuroticism scores predict variance in wellbeing measures. Polygenic scores were based on published genome-wide association (GWA) results in over 17,000 individuals for the NEO-FFI and in over 63,000 for the IRT extraversion and neuroticism traits. The NEO-FFI polygenic scores were used to predict life satisfaction in 7 cohorts, positive affect in 12 cohorts, and general wellbeing in 1 cohort (maximal N = 46,508). Meta-analysis of these results showed no significant association between NEO-FFI personality polygenic scores and the wellbeing measures. IRT extraversion and neuroticism polygenic scores were used to predict life satisfaction and positive affect in almost 37,000 individuals from UK Biobank. Significant positive associations (effect sizes
  • Service, S. K.; Verweij, K. J. H.; Lahti, J.; Congdon, E.; Ekelund, J.; Hintsanen, M.; Räikkönen, Katri; Lehtimaki, T.; Kahonen, M.; Widen, E.; Taanila, A.; Veijola, J.; Heath, A. C.; Madden, P. A. F.; Montgomery, G. W.; Sabatti, C.; Jarvelin, M-R; Palotie, A.; Raitakari, O.; Viikari, J.; Martin, N. G.; Eriksson, J. G.; Keltikangas-Järvinen, Liisa; Wray, N. R.; Freimer, N. B. (2012)
  • Liu, Xiaonan (Helsingin yliopisto, 2020)
    Cellular compartment organization, signaling transduction, and regulatory processes are governed by protein-protein interactions (PPIs). The affinity purification coupled mass spectrometry (AP-MS) and proximity-labeling methods such as BioID have been wildly applied to understand protein interaction networks. AP-MS methods are suited to identify and quantify protein interaction and protein complex stoichiometries, while the BioID method provides information regarding transient or close-proximity interactions. Both AP-MS and BioID can identify distinct interactions, and complementary provides a more comprehensive view of a protein's interactome. In this study, we developed an integrated approach utilizing 'multiple approaches combined' (MAC)-tag that utilizes both AP-MS and BioID in a single construct to parallel explore the protein interactive. First, we systematically applied the MAC-tag approach to 18 bona fide localization markers to generate a molecular context database for every cellular compartment. Using this molecular context as the reference, alignment interaction profile of other proteins of interest (POIs) on it can reveal the subcellular localization of the POIs. We named this reference database, mass spectrometry (MS)-microscopy. Similarly, we applied the MAC-tag approach on three sub-organelle localization markers of mitochondria to set up a sub-organelle molecular context proteome map. Using this sub-organelle reference proteome map, we could detect sub-mitochondrial localization of POIs by MS-microscopy system. Furthermore, by comparing interaction data from several MAC-tagged mitochondrial proteins, we could define the unique interactors of GrpE-like proteins (GRPEL1 and GRPEL2) to investigate their specific roles in mammalian mitochondria. Next, we utilized the MAC-tag approach to map the interactome of the mammalian Hedgehog signaling. We monitored the dynamic PPI network surrounding the core components in the absence and presence of Hh ligand. Our comparative PPI analysis showed that the interaction network recapitulates many known ciliary proteins, asserting the essential role of primary cilia in Hh signaling. Meanwhile, we characterized the interaction network at the level of cilium progression by monitoring the PPIs under cilia absence, ciliogenesis, and cilia absorption conditions. The significant overlap of the interaction between three states indicated that proteins could regulate the Hh signaling outside the primary cilia. Additionally, we expanded the coverage of MS-microscopy to the primary cilium, a transient organelle of the cell. Although what we present is just a glimpse of the Hh interaction network under ligand stimulation or specific growth conditions, these PPIs will extend our knowledge on the mammalian Hh signaling and help us to development of novel therapeutic strategies to inhibit abnormal Hh signaling in cancer. Collectively, the presented thesis introduces the MAC-tag approach that can be used for mapping local protein interactome, predicting subcellular localization of POIs, and reconstructing the interaction network of the signaling pathway.
  • Hebbar, Prashantha; Abubaker, Jehad Ahmed; Abu-Farha, Mohamed; Tuomilehto, Jaakko; Al-Mulla, Fahd; Thanaraj, Thangavel Alphonse (2019)
    Despite dedicated nation-wide efforts to raise awareness against the harmful effects of fast-food consumption and sedentary lifestyle, the Arab population continues to struggle with an increased risk for metabolic disorders. Unlike the European population, the Arab population lacks well-established genetic risk determinants for metabolic disorders, and the transferability of established risk loci to this population has not been satisfactorily demonstrated. The most recent findings have identified over 240 genetic risk loci (with similar to 400 independent association signals) for type 2 diabetes, but thus far only 25 risk loci (ADAMTS9, ALX4, BCL11A, CDKAL1, CDKN2A/B, COL8A1, DUSP9, FTO, GCK, GNPDA2, HMG20A, HNF1A, HNF1B, HNF4A, IGF2BP2, JAZF1, KCNJ11 , KCNQ1, MC4R, PPAR gamma, SLC30A8, TCF7L2, TFAP2B, TP53INP1, and WFS1) have been replicated in Arab populations. To our knowledge, large-scale population- or family-based association studies are non-existent in this region. Recently, we conducted genome-wide association studies on Arab individuals from Kuwait to delineate the genetic determinants for quantitative traits associated with anthropometry, lipid profile, insulin resistance, and blood pressure levels. Although these studies led to the identification of novel recessive variants, they failed to reproduce the established loci. However, they provided insights into the genetic architecture of the population, the applicability of genetic models based on recessive mode of inheritance, the presence of genetic signatures of inbreeding due to the practice of consanguinity, and the pleiotropic effects of rare disorders on complex metabolic disorders. This perspective presents analysis strategies and study designs for identifying genetic risk variants associated with diabetes and related traits in Arab populations.
  • Vattulainen, Sanna; Aho, Joonas; Salmenperä, Pertteli; Bruce, Siina; Tallila, Jonna; Gentile, Massimiliano; Sankelo, Marja; Laitinen, Tarja; Koskenvuo, Juha W.; Alastalo, Tero-Pekka; Myllykangas, Samuel (2015)
    The genetic basis of pulmonary arterial hypertension (PAH) among Finnish PAH patients is poorly understood. We adopted a novel-targeted next-generation sequencing (NGS) approach called Oligonucleotide-Selective Sequencing (OS-Seq) and developed a custom data analysis and interpretation pipeline to identify pathogenic base substitutions, insertions, and deletions in seven genes associated with PAH (BMPR2, BMPR1B, ACVRL1, ENG, SMAD9, CAV1, and KCNK3) from Finnish PAH patients. This study represents the first clinical study with OS-Seq technology on patients suffering from a rare genetic disorder. We analyzed DNA samples from 21 Finnish PAH patients, whose BMPR2 and ACVRL1 mutation status had been previously studied using Sanger sequencing. Our sequencing panel covered 100% of the targeted base pairs with >15× sequencing depth. Pathogenic base substitutions were identified in the BMPR2 gene in 29% of the Finnish PAH cases. Two of the pathogenic variant-positive patients had been previously tested negative using Sanger sequencing. No clinically significant variants were identified in the six other PAH genes. Our study validates the use of targeted OS-Seq for genetic diagnostics of PAH and revealed pathogenic variants that had been previously missed using Sanger sequencing.
  • Saari, Sini; Kemppainen, Esa; Tuomela, Tero; Oliveira, M.T.; Dufour, E.; Jacobs, H.T. (2019)
    The mitochondrial alternative oxidase, AOX, present in most eukaryotes apart from vertebrates and insects, catalyzes the direct oxidation of ubiquinol by oxygen, by-passing the terminal proton-motive steps of the respiratory chain. Its physiological role is not fully understood, but it is proposed to buffer stresses in the respiratory chain similar to those encountered in mitochondrial diseases in humans. Previously, we found that the ubiquitous expression of AOX from Ciona intestinalis in Drosophila perturbs the development of flies cultured under low-nutrient conditions (media containing only glucose and yeast). Here we tested the effects of a wide range of nutritional supplements on Drosophila development, to gain insight into the physiological mechanism underlying this developmental failure. On low-nutrient medium, larvae contained decreased amounts of triglycerides, lactate, and pyruvate, irrespective of AOX expression. Complex food supplements, including treacle (molasses), restored normal development to AOX-expressing flies, but many individual additives did not. Inhibition of AOX by treacle extract was excluded as a mechanism, since the supplement did not alter the enzymatic activity of AOX in vitro. Furthermore, antibiotics did not influence the organismal phenotype, indicating that commensal microbes were not involved. Fractionation of treacle identified a water-soluble fraction with low solubility in ethanol, rich in lactate and tricarboxylic acid cycle intermediates, which contained the critical activity. We propose that the partial activation of AOX during metamorphosis impairs the efficient use of stored metabolites, resulting in developmental failure. © 2019 The Authors. Journal of Experimental Zoology Part A: Ecological Genetics and Physiology Published by Wiley Periodicals, Inc.
  • Sagath, L.; Lehtokari, V.-L.; Välipakka, S.; Udd, B.; Wallgren-Pettersson, C.; Pelin, K.; Kiiski, K. (2018)
    Background: Our previous array, the Comparative Genomic Hybridisation design (CGH-array) for nemaline myopathy (NM), named the NM-CGH array, revealed pathogenic copy number variation (CNV) in the genes for nebulin (NEB) and tropomyosin 3 (TPM3), as well as recurrent CNVs in the segmental duplication (SD), i.e. triplicate, region of NEB (TRI, exons 82-89, 90-97, 98-105). In the light of this knowledge, we have designed and validated an extended CGH array, which includes a selection of 187 genes known to cause neuromuscular disorders (NMDs). Objective: Our aim was to develop a reliable method for CNV detection in genes related to neuromuscular disorders for routine mutation detection and analysis, as a much-needed complement to sequencing methods. Methods: We have developed a novel custom-made 4×180 k CGH array for the diagnostics of NMDs. It includes the same tiled ultra-high density coverage of the 12 known or putative NM genes as our 8×60 k NM-CGH-array but also comprises a selection of 175 additional genes associated with NMDs, including titin (TTN), at a high to very high coverage. The genes were divided into three coverage groups according to known and potential pathogenicity in neuromuscular disorders. Results: The array detected known and putative CNVs in all three gene coverage groups, including the repetitive regions of NEB and TTN. Conclusions: The targeted neuromuscular disorder 4×180 k array-CGH (NMD-CGH-array v1.0) design allows CNV detection for a broader spectrum of neuromuscular disorders at a high resolution. © 2018 - IOS Press and the authors. All rights reserved.
  • Räisänen, Maritta (Helsingin yliopisto, 2019)
    Uterine leiomyoma (also known as myoma) is the most common neoplasia in women during reproductive age and it represents a burden for public health care. Approximately 70% of Caucasian women develop myomas, although only 25% of cases are symptomatic. The genetic background of myomas varies significantly and the most common genetic causes are mutations in genes Mediator complex subunit 12 (MED12), Fumarate hydratase (FH) or YEATS Domain containing 4 (YEATS4) , rearrangements affecting the High Mobility Group AT-hook 2 (HMGA2), and deletions in COL4A5/6 locus. MED12 mutations represent the most common genetic alteration in myomas, being present in approximately 70% of cases. Genome organization comprises different levels of complexity, spanning from regulation of individual genes to changes in the architecture of large portions of chromosomes. Literature offers massive evidence of changes in genome organization among different cell types and between several tumor and related healthy cells, but information about these changes in myoma is lacking. The aim of this study is to determine the main features of genome organization in myomas belonging to the aforementioned five genetic subclasses, in order to identify which are the underlying common pathways that are dysregulated in the neoplasia. This is achieved by mapping regions of open chromatin in myomas and related my-ometrium samples with ATAC-seq. Sample’s clustering seems not to be individual-dependent, while tumors belonging to FH, YEATS4 and COL4A5/6 subclasses form distinct clusters, unlike MED12 and HMGA2 subclasses. Six open chromatin regions located within genes were identified in 19/25 tumors and not in myometrium. Seven myometrium-specific open chromatin regions were identified in 21/25 myometria and in less than 10 tumors. As expected, Gene Ontology enrichment analysis revealed that myomas belonging to FH subclass are characterized by deregulation of metabolic pathways. Many of the identified genes in the open chromatin regions have been linked to other tumors in previous studies. Tumor-specific open chromatin regions locate within oncogenes, while myometrium-specific ones are found in proximity of tumor suppressor genes, suggesting a biological role in myomagenesis for these genes. Further investigation on the identified genes (e.g. transcriptional regulation, gene expression and protein level) and addi-tional studies on chromatin architecture are needed to fully unravel the mechanism of myomagenesis.
  • Kurtelius, Arttu; Väntti, Nelli; Jahromi, Behnam Rezai; Tähtinen, Olli; Manninen, Hannu; Koskenvuo, Juha; Tulamo, Riikka; Kotikoski, Satu; Nurmonen, Heidi; Kämäräinen, Olli-Pekka; Huttunen, Terhi; Huttunen, Jukka; Fraunberg, Mikael von Und Zu; Koivisto, Timo; Jääskeläinen, Juha E.; Lindgren, Antti E. (2019)
    Background-Varying degrees of co-occurrence of intracranial aneurysms (IA) and aortic aneurysms (AA) have been reported. We sought to compare the risk for AA in fusiform intracranial aneurysms (fIA) and saccular intracranial aneurysms (sIA) disease and evaluate possible genetic connection between the fIA disease and AAs. Additionally, the characteristics and aneurysms of the fIA and sIA patients were compared. Methods and Results-The Kuopio Intracranial Aneurysm Database includes all 4253 sIA and 125 fIA patients from its Eastern Finnish catchment population, and 13 009 matched population controls and 18 455 first-degree relatives to the IA patients were identified, and the Finnish national registers were used to identify the individuals with AA. A total of 33 fIA patients were studied using an exomic gene panel of 37 genes associated with AAs. Seventeen (14.4%) fIA patients and 48 (1.2%) sIA patients had a diagnosis of AA. Both fIA and sIA patients had AAs significantly more often than their controls (1.2% and 0.5%) or relatives (0.9% and 0.3%). In a competing risks Cox regression model, the presence of fIA was the strongest risk factor for AA (subdistribution hazard ratio 7.6, 95% CI 3.9-14.9, P Conclusions-The prevalence of AAs is increased slightly in sIA patients and significantly in fIA patients. fIA patients are older and have more comorbid diseases than sIA patients but this alone does not explain their clinically significant AA risk.
  • Hirvonen, Katariina; Korhonen, Tellervo; Salomaa, Veikko; Männistö, Satu; Kaprio, Jaakko (Helsingin yliopisto, 2017)
    DBH-geeni koodaa dopamiinia hajottavaa entsyymiä, joka on liitetty palkkiojärjestelmään vaikuttamisen kautta erilaisiin riippuvuuksiin. DBH:n variaatioiden on todistettu liittyvän tupakointikäytänteisiin ja –tapoihin monessa tutkimuksessa. Viimeisimpänä rs3025343 liitettiin tupakoinnin lopettamiseen suuressa GWAS meta-analyysissa. Tutkimuksemme tavoitteena olikin replikoida kyseinen löydös suuressa väestötutkimusnäytteessämme. Lisäksi halusimme tutkia, vaikuttaisiko rs3025343 jonkin muun ympäristötekijän kautta vai itsenäisesti tupakoinnin lopettamiseen. Tutkimusnäytteemme on peräisin suomalaisesta väestönäytteestä, FINRISK-tutkimuksesta. Siihen lukeutuu 26,582 genotyypattua henkilöä tupakointistatuksineen. Analyysit rajasimme 11,926 yksilöön, jotka olivat joko nykyisiä tupakoitsijoita (n=6,578) tai vähintään 6kk sitten tupakoinnin lopettaneita (n=5,348). Henkilöistä oli saatavilla myös kattavasti muita tietoja mukaan lukien sosioekonominen status, terveyteen liittyviä tapoja ja terveydentila, joita käytimme analyyseissä hyväksi. Yhteys rs3025343 ja tupakoinnin lopettamisen välillä (OR=1.12, p=0.094, 95%CI=0.98-1.30) osoittautui tutkimuksessamme identtiseksi GWAS-tutkimuksen kanssa (OR=1.12, 95%CI=1.08-1.18). Mikään testatuista fenotyypeistämme ei vaikuttanut tuohon yhteyteen merkitsevästi. Siviilisääty, koulutustaso, masennus, alkoholin käyttö, itseraportoitu terveys sekä COPD assosioituivat fenotyyppitekijöistä tupakoinnin lopettamiseen, mutta mikään edellämainituista assosiaatioista ei riippunut tutkimastamme genotyypistä. Vaikka tutkimustuloksemme ei ole tilastollisesti merkitsevä, efektikoko viittaa vahvasti siihen, että tutkimallamme polymorfismilla on jonkinasteinen yhteys tupakoinnin lopettamiseen. Merkitevyyden esiinsaamiseksi riittävällä voimalla (80%) otoskoon tulisi olla niinkin suuri kuin 36,092 tapausta ja 29,343 kontrollia, koska harvinaisemman alleelin kantajia on suhteellisen vähän (7,1%). DBH-geenin variaatiot ovat osoittautuneet monessa tutkimuksessa olevan yhteydessä nikotiiniriippuvuuteen tai tupakoinnin lopettamiseen. Jos näitä yhteyksiä saadaan tutkittua lisää, on mahdollista että tietoja voitaisiin käyttää hyväksi tulevaisuudessa esim. yksilöllisesti räätälöidyssä tupakoinnin lopettamisen hoidossa.
  • Saure, Emma (Helsingin yliopisto, 2018)
    Background and objectives: Autism spectrum disorders (ASD) are developmental neuropsychiatric disorders in which core symptoms are problems in communication and interaction as well as restrictive and repetitive behaviour and interests. ASD is 2-5 times more common in males than in females. In recent years, researchers have found, that there are differences between females and males in ASD symptoms, neuropsychological characteristics, comorbid problems, neurobiology and etiology. The purpose of this systematic review is to give a comprehensive picture about the role of female sex/gender in ASD. To establish this, the review covers symptoms of autism, neuropsychology, neurobiology, comorbidity, neurogenetics and neuroendocrinology. Research questions were the following: 1) Is there evidence of sex/gender differences in ASD symptoms and comorbidity disorders? 2) Are there sex/gender differences to be found in ASD etiology? 3) What kind of support different explanations about sex/gender bias have gotten in various research areas? The purpose of the study is also to integrate the existing theories into one model that takes account to different aspects of sex/gender differences in ASD. Methods: The protocol of this systematic review follows "The Preferred Reporting Items for Systematic Reviews and Meta-Analyses" (PRISMA) when applicable. Eligibly criteria and search terms were selected in a way that would offer the widest range of articles covering the subjects of this study. Literature search was conducted using the Medline and PsychINFO as search engines. The final sample consisted of a total of 129 articles. Data was extracted on all relevant variables of the study, that were the number of participants, age of participants, specific diagnoses, methods and results. Results: Sex/gender differences in ASD were found in all areas that were included in this systematic review. Females with high function ASD (HFASD) were found to have less problems in social communication and interaction and less repetitive and restricted behavior and interests than males with HFASD. In addition, HFASD were found to have better language skills than males with HFASD. However, females with ASD were found to have more sensory processing problems, mental health problems and epilepsy than males with ASD. Females with ASD were also found to have lower full-scale intelligence quotient than males with ASD. In the context of etiology, it has been found that there are sex/gender differences in neuroanatomy, susceptibility genes and hormone levels. Conclusions: Results from this systematic review suggest that females with HFASD are underdiagnosed. This results from etiological sex/gender differences that cause partially different clinical presentation of ASD between females and males. ASD research has also concentrated mostly on males with ASD while ignoring females with ASD. Underdiagnosing can have many unfavorable consequences for females with HFASD since if they do not have a diagnosis, they do not get support. In the future, it is crucial to pay attention to females with ASD in the clinical work and scientific research.
  • Gaultier, Simon; Blomberg, Anna; Ijäs, Asko; Vasko, Ville Veijo Wilhelm; Vesterinen, Eero; Brommer, Jon Egbert; Lilley, Thomas M. (2020)
    Although labeled as environmentally friendly, wind power can have negative impacts on the environment, such as habitat destruction or wildlife fatalities. Considering the distribution and migratory characteristics of European bats, the negative effects of wind power should be addressed on an appropriate scale. This review summarizes the current state of knowledge on interactions between wind farms and bats in Europe, and compares it with the situation in the countries of the European boreal biogeographic region. We analyzed data from papers published in international and national scientific journals, focusing on studies conducted in Europe. The issue of the impacts wind power has on bats is clearly overlooked in most of the countries of the European boreal region, with low volumes of research available on the topic. This is probably due to fewer wind farms in the area, making this recent issue a less-prioritized topic. However, the Baltic Sea, and the countries surrounding it, are of extreme importance with regards to bat migration, especially for the Pipistrellus nathusii. Therefore, more research on wind power and bats is needed in this region, as well as more cooperation between all the stakeholders.
  • Reuter, Enzio; Klingstedt, Holger; Karling, Tor G. (Societas pro Fauna et Flora Fennica, 1931)
    Acta Zoologica Fennica; 9
  • Dermadi Bebek, Denis (Helsingin yliopisto, 2014)
    Colorectal cancer (CRC) is one of the leading causes of death in developed countries. Although, a small fraction of cancers are caused by inherited genetic predisposition most of the CRCs are sporadic. In CRC, cancer risk is associated with lifestyle factors and aging. Even in dominantly inherited CRC predisposition such as in Lynch syndrome (LS), which is linked to germline mu- tations in the mismatch repair (MMR) genes MLH1, MSH2, MSH6 and PMS2, cancer develops as a result of accumulation of genetic and epigenetic changes. After diagnosing an LS family, to be able to offer contiguous pre-symptomatic surveillance and predictive gene counseling to mutation carriers in a family, the pathogenicity assessment of a mutation is needed. Dependent on the type and the site of a germline mutation, inherited cancer risk may vary from high to low and especially in the latter case cancer risk may be strongly affected by lifestyle factors such as diet. Epidemiological studies on humans and previous studies on mice have shown that especially a Western-style diet (WD) may predispose colon mucosa to CRC. However, the mechanisms, which mediate the effects of diet on tumorigenesis are largely unknown. Since both genetic and lifestyle factors have been shown to predispose to cancer, this the- sis analyzed biochemical defects caused by inherited MMR gene mutations and Western diet exposure. Different MMR gene mutations may compromise MMR function through various biochemical defects. Here, we studied 18 inherited non-truncating mutations in MSH2, the second most frequently mutated gene among Lynch syndrome patients. We assessed protein stability, DNA binding, and ATP mediated DNA release abilities of the MSH2 variants. The majority of variants in the amino terminal region including the connector and lever domains p.V161D, p.G162R, p.G164R, p.L173P, p.L187P, p.C333Y, p.D603N) affected protein stabil- ity. Variations in the ATPase domain (p.A636P, p.G674A, p.C697F, p.I745-I746del, p.E749K) totally abolished either mismatch binding or release. Four protein variants (p.T33P, p.A272 V, p.G322D, p.V923E) expressed slightly reduced mismatch binding and/or release efficiencies compared to wild-type (WT) MSH2 protein, while two variants (p.N127S, p.A834T) were in- distinguishable from WT. To define the effects of Western-style diet, we analyzed protein expression changes in histolog- ically normal colon mucosa of wild type (Mlh1+/+) and CRC predisposed mice (Mlh1+/-) after a long-term feeding experiment with WD and AIN-93G control diet. Using network analysis and data mining we also determined which of the affected proteins might be putative play- ers in early CRC development. Our results pinpoint changes in a complex protein interaction network involved in ATP synthesis coupled proton transport, oxidoreduction coenzyme and nicotinamide nucleotide metabolic processes, which are important in the generation of reactive oxygen species (ROS) and cellular protection against ROS toxicity. Additionally, we detected SELENBP1 and LGALS4, which are implied in neoplastic processes. Our studies show that mutations in the MMR gene affect the biochemistry of MMR, can have an effect on the phenotype of the mutation carriers and in the latest study suggest that the high sensitivity to Western diet may be linked to haplo-insufficiency caused by a loss of function mutation in the Mlh1+/- mice.
  • Guo, Qi; Burgess, Stephen; Turman, Constance; Bolla, Manjeet K.; Wang, Qin; Lush, Michael; Abraham, Jean; Aittomäki, Kristiina; Andrulis, Irene L.; Apicella, Carmel; Arndt, Volker; Barrdahl, Myrto; Benitez, Javier; Berg, Christine D.; Blomqvist, Carl; Bojesen, Stig E.; Bonanni, Bernardo; Brand, Judith S.; Brenner, Hermann; Broeks, Annegien; Burwinkel, Barbara; Caldas, Carlos; Campa, Daniele; Canzian, Federico; Chang-Claude, Jenny; Chanock, Stephen J.; Chin, Suet-Feung; Couch, Fergus J.; Cox, Angela; Cross, Simon S.; Cybulski, Cezary; Czene, Kamila; Darabi, Hatef; Devilee, Peter; Diver, W. Ryan; Dunning, Alison M.; Earl, Helena M.; Eccles, Diana M.; Ekici, Arif B.; Eriksson, Mikael; Evans, D. Gareth; Fasching, Peter A.; Figueroa, Jonine; Flesch-Janys, Dieter; Flyger, Henrik; Gapstur, Susan M.; Gaudet, Mia M.; Giles, Graham G.; Muranen, Taru A.; Nevanlinna, Heli; kConFab AOCS Investigators (2017)
    There is increasing evidence that elevated body mass index (BMI) is associated with reduced survival for women with breast cancer. However, the underlying reasons remain unclear. We conducted a Mendelian randomization analysis to investigate a possible causal role of BMI in survival from breast cancer. We used individual-level data from six large breast cancer case-cohorts including a total of 36 210 individuals (2475 events) of European ancestry. We created a BMI genetic risk score (GRS) based on genotypes at 94 known BMI-associated genetic variants. Association between the BMI genetic score and breast cancer survival was analysed by Cox regression for each study separately. Study-specific hazard ratios were pooled using fixed-effect meta-analysis. BMI genetic score was found to be associated with reduced breast cancer-specific survival for estrogen receptor (ER)-positive cases [hazard ratio (HR) = 1.11, per one-unit increment of GRS, 95% confidence interval (CI) 1.01-1.22, P = 0.03). We observed no association for ER-negative cases (HR = 1.00, per one-unit increment of GRS, 95% CI 0.89-1.13,P = 0.95). Our findings suggest a causal effect of increased BMI on reduced breast cancer survival for ER-positive breast cancer. There is no evidence of a causal effect of higher BMI on survival for ER-negative breast cancer cases.
  • Reinikka, Siiri (Helsingin yliopisto, 2020)
    Endometrial polyps are one of the most common benign uterine lesions, affecting approximately 10% of all adult women. While endometrial polyps have a high prevalence, their molecular pathogenesis and genetic background are largely undefined. Accordingly, the aim of this thesis was to characterize the somatic mutational landscape of endometrial polyps – to identify mutations in cancer-associated genes, and to identify mutational signatures contributing towards the somatic mutational spectrum. The present study was conducted using whole exome sequencing of 23 endometrial polyps and 18 matching normal blood samples. Mutational signature analysis was conducted using MutationalPatterns and SigProfiler. Endometrial polyps were found to carry varying number of somatic mutations in their exomes, most of them present at a low allelic fraction. Moreover, 43% (10/23) of the polyps were identified to carry one to four cancer-associated mutations, including mutations in genes such as PIK3CA 17% (4/23), KRAS 13% (3/23) and ERBB1 9% (2/23), which are well-established cancer driver genes. Cancer-associated mutational signatures do not have a notable contribution towards the somatic mutational spectrum of endometrial polyps. However, a novel signature, ‘signature B’, characterized by T>G mutations, was found to affect a subset of polyp samples. To conclude, the whole exome sequencing of endometrial polyps revealed several mutations in cancer-associated genes and a novel mutational signature, which may contribute to the development of these benign tumours. However, further research is required to confirm and validate the novel signature, and to define the genetic alterations leading to the polyp pathogenesis.
  • Leigh, Robert (Helsingin yliopisto, 2021)
    Disruption of chamber-specific gene regulatory networks underlies malformation of the heart and results in congenital heart disease. Re-activation of fetal gene regulatory networks in adults occurs during cardiac injury, and transcription factors composing these networks represent candidate therapeutic targets to impede heart failure progression. The identification of molecular markers and underlying regulators of cardiac chamber specification is thus an important step in understanding the aetiology of cardiovascular disease. Moreover, the examination of chemical modulation of molecular processes occurring during development allows for a more detailed understanding of the teratogenic effects of chemical compounds and could lead to the development of small molecule-based strategies for stimulating or impeding well-characterized developmental processes in the adult heart. To this end, this thesis is comprised of three studies related to the differentiation of atrial and ventricular cardiomyocytes and the selective modulation of this process. Study I led to the generation of an in vitro model of cardiomyocyte subtype specification of pluripotent stem cells for the use in studies II-III. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis of native embryonic atrial and ventricular tissue confirmed the robust ventricular-specific expression of myosin light chain 2 (Myl2) and also indicated the lack of an endogenous atrial-specific marker during early embryogenesis. Genome editing was used to integrate a fluorescent reporter into the endogenous Myl2 locus to mark cells of the ventricular lineage, whereas atrial cells were traced by an atrial-specific transgene driven by the slow myosin heavy chain 3 (SMyHC3) promoter. Atrial and ventricular reporter expression were confirmed in vivo by laser-assisted morula injection of reporter mouse embryonic stem cells (mESCs) and microscopy of chimeric embryos. In addition to this in vivo validation, spontaneous differentiation of reporter mESCs was characterized by qRT-PCR, indicating dynamic expression of retinoic acid signalling components. Differentiation assays were developed based on chemical perturbation of undifferentiated progenitor cells and differentiated cardiomyocytes, respectively. Members of the retinoid family, known teratogens and modulators of anterior-posterior patterning, were tested for effects on the activation of atrial and ventricular reporter genes. Additionally, a directed-differentiation assay was developed based on highly pure multipotent progenitor cells and differentiation assessment in a 384-well format. In this assay, chemical inhibitors of Wnt and Transforming growth factor β (Tgfβ) pathways led to promotion of ventricular reporter expression when added at the multipotent progenitor stage, but not after the onset of spontaneous beating. Additionally, exogenous all-trans retinoic acid added to undifferentiated progenitors led to an inhibition of ventricular differentiation, whereas addition following the onset of spontaneous beating led to activation of the ventricular reporter gene. In addition to chemical probes described in study I, novel compounds targeting the protein-protein interaction of core cardiac transcription factors Gata transcription factor 4 (Gata4) and NK2 homeobox 5 (Nkx2-5) were examined in study II. Specifically, the effects of GATA-targeted compounds on the differentiation of atrial and ventricular cardiomyoyctes were explored. Lead compound 3i-1000 increased the proportion of atrial and ventricular reporter cells after 10-day treatment in the spontaneous differentiation assay. Further exploration of the effects of GATA4 targeted compounds revealed that a shorter treatment (2-day) of cells prior to the onset of spontaneous beating led to an upregulation of ventricular reporter genes in a directed differentiation assay. An acetyl-lysine like domain among active compounds, in addition to analysis of the GATA4 interactome by Bio-ID revealed the potential association of bromodomain-containing proteins with chamber-specific gene expression. This was further investigated by combinatorial treatment with the Bromo- and Extra- Terminal domain family (BET) bromodomain inhibitor JQ1 and GATA-targeted compounds in reporter gene assays. Finally, the effects of GATA compounds on cardiomyocyte maturation were explored by compound treatment and global run-on sequencing (GRO-seq) in primary cardiomyocytes, revealing the upregulation of several targets previously identified as regulators of cell fate determination and regeneration. Study III detailed the embryonic/cardiac expression of proCholecystokinin (proCCK), a classical gut and neuropeptide. Analysis of mRNA-seq data suggested that proCCK is a transcriptional target of the TBX5 transcription factor in mESC-derived cardiomyocytes. Native, endogenous mRNA levels were characterized in embryonic hearts by whole mount in situ hybridization and optical projection tomography, revealing that proCck mRNA is present prior to the linear heart tube stage and that it is upregulated in the ventricles compared to the atria in the newly formed embryonic heart. Interestingly, mRNA of proCck and its receptors Cckar/Cckbr is mostly restricted to the atrial chambers in neonatal stages, in line with its potential role in regulating cardiac rhythm. In silico analysis implicated both TBX5 and MEF2C as regulators of proCck transcription, and this regulation was confirmed by conducting in vitro reporter gene assays. Additionally, proCCK was induced by endothelin-1 (ET-1), another peptide associated with maladaptive remodelling during heart failure. Furthermore, proCck mRNA levels declined in the left ventricles of rats following myocardial infarction (MI). Finally, exogenous cholecystokinin octapeptide (CCK-8) exerted no effects on the differentiation process of pluripotent stem cells (PSCs) to the cardiomyocyte fate. Collectively, these studies led to the generation of new methodology for the study of chamber-specific cardiac gene regulatory networks. Additionally, they led to an improved understanding of the dynamics of chamber-specific marker localization and upstream transcription factors governing their expression, potentially important to biomarker development. Finally, these studies have indicated that specific chemical compounds are capable of influencing chamber-specific gene regulatory networks. This knowledge might be utilized to develop novel therapeutic strategies for the treatment of heart failure.
  • Jokinen, Vilja (Helsingin yliopisto, 2021)
    Uterine leiomyomas are benign smooth muscle tumors arising in myometrium. They are very common, and the incidence in women is up to 70% by the age of 50. Usually, leiomyomas are asymptomatic, but some patients suffer from various symptoms, including abnormal uterine bleeding, pelvic pain, urinary frequency, and constipation. Uterine leiomyomas may also cause subfertility. Genetic alterations in the known driver genes MED12, HMGA2, FH, and COL4A5-6 account for about 90 % of all leiomyomas. These initiator mutations result in distinct molecular subtypes of leiomyomas. The majority of whole-genome sequencing (WGS) studies analyzing chromosomal rearrangements have been performed using fresh frozen tissues. One aim of this study was to examine the feasibility of detecting chromosomal rearrangements from WGS data of formalin-fixed paraffin embedded (FFPE) tissue samples. Previous results from 3’RNA-sequencing data revealed a subset of uterine leiomyoma samples that displayed similar gene expression patterns with HMGA2-positive leiomyomas but were previously classified as HMGA2-negative by immunohistochemistry. According to 3’RNA-sequencing, all these tumors overexpressed PLAG1, and some of them overexpressed HMGA2 or HMGA1. Thus, the second aim of this study was to identify driver mutations in these leiomyoma samples using WGS. In this study, WGS was performed for 16 leiomyoma and 4 normal myometrium FFPE samples. The following bioinformatic tools were used to detect somatic alterations at multiple levels: Delly for chromosomal rearrangements, CNVkit for copy-number alterations, and Mutect for point mutations and small insertions and deletions. Sanger sequencing was used to validate findings. The quality of WGS data obtained from FFPE samples was sufficient for detecting chromosomal rearrangements, although the number of calls were quite high. We identified recurrent chromosomal rearrangements affecting HMGA2, HMGA1, and PLAG1, mutually exclusively. One sample did not harbor any of these rearrangements, but a deletion in COL4A5-6 was found. Biallelic loss of DEPDC5 was seen in one sample with an HMGA2 rearrangement and in another sample with an HMGA1 rearrangement. HMGA2 and HMGA1 encode architectural chromatin proteins regulating several transcription factors. It is well-known that HMGA2 upregulates PLAG1 expression. The structure and functionality of HMGA2 and HMGA1 are very similar and conserved, so it might be that HMGA1 may also regulate PLAG1 expression. The results of this study suggest that HMGA2 and HMGA1 drive tumorigenesis by regulating PLAG1, and thus, PLAG1 rearrangements resulting in PLAG1 overexpression can also drive tumorigenesis. A few samples, previously classified as HMGA2-negative by immunohistochemistry, revealed to harbor HMGA2 rearrangements, suggesting that the proportion of HMGA2-positive leiomyomas might be underestimated in previous studies using immunohistochemistry. Only one study has previously reported biallelic inactivation of DEPDC5 in leiomyomas, and the results of this study support the idea that biallelic loss of DEPDC5 is a secondary driver event in uterine leiomyomas.
  • Männistö, Jonna M. E.; Maria, Maleeha; Raivo, Joose; Kuulasmaa, Teemu; Otonkoski, Timo; Huopio, Hanna; Laakso, Markku (2020)
    Context: Major advances have been made in the genetics and classification of congenital hyperinsulinism (CHI). Objective: To examine the genetics and clinical characteristics of patients with persistent and transient CHI. Design: A cross-sectional study with the register data and targeted sequencing of 104 genes affecting glucose metabolism. Patients: Genetic and phenotypic data were collected from 153 patients with persistent (n = 95) and transient (n = 58) CHI diagnosed between 1972 and 2015. Of these, 86 patients with persistent and 58 with transient CHI participated in the analysis of the selected 104 genes affecting glucose metabolism, including 10 CHI-associated genes, and 9 patients with persistent CHI were included because of their previously confirmed genetic diagnosis. Main outcome measures: Targeted next-generation sequencing results and genotype-phenotype associations. Results: Five novel and 21 previously reported pathogenic or likely pathogenic variants in ABCC8, KCNJ11, GLUD1, GCK, HNF4A, and SLC16A1 genes were found in 68% (n = 65) and 0% of the patients with persistent and transient CHI, respectively. K-ATP channel mutations explained 82% of the mutation positive cases. Conclusions: The genetic variants found in this nationwide CHI cohort are in agreement with previous studies, mutations in the KATP channel genes being the major causes of the disease. Pathogenic CHI-associated variants were not identified in patients who were both diazoxide responsive and able to discontinue medication within the first 4 months. Therefore, our results support the notion that genetic testing should be focused on patients with inadequate response or prolonged need for medication.