Geenit ja proteiinit kertovat lasten leukemian ennusteesta

publishedVersio

A Translational Approach Towards More Cost-Effective Lung Cancer Treatments

Lung cancer, globally the second most common cancer, causes 1.8 million deaths annually with 2 million new cases. It\u27s also one of Finland\u27s deadliest cancers. Chemotherapeutic agents, targeted drugs and radiation therapy have been the mainstay in oncologic treatment for lung cancer patients for decades. Checkpoint inhibitors (e.g. nivolumab, pembrolizumab, atezolizumab) have changed the landscape also in lung cancer. These drugs awake patients own immune system to attack cancer cells. These drugs are widely used in different cancers and they have efficacy also in lung cancer, but only in a minority of patients. Checkpoint inhibitors also induce autoimmune side effects. Majority are mild, but often irreversible, such as hypothyroidism or diabetes. Life-threatening and fatal adverse events are rare, but they also occur. Neither treatment response nor adverse effects can be predicted individually. In Finland, these drugs cost app. 10 000€ per month per one patient increasing the economic burden to our society. Thus, we need better understanding of lung cancer biology to be able to offer individual therapies in patient-centered manner, but also within the limits of the carrying capacity of our society. In 10-15% of lung adenocarcinomas there is a driver EGFR-mutation. Checkpoint inhibitor are ineffective in this type. However, EGFR pathway targeted agents, such as osimertinib, deliver often sustainable responses, but unfortunately resistance mechanism arise in this subtype as well. We need to better understand also the resistance mechanism in EGFR mutated subtypes to better tailor the best optimal treatment sequences to our patients. Translational research, that combines the basic science of lung cancer biology with patient characteristics and treatment outcomes, is a crucial tool in responding to these demands. Tumor microenvironment plays an important role in carcinogenesis, as well as in treatment response, especially acidic environment is immunosuppressive and promotes cancer cell survival. Mucins are a large family of transmembrane glycoproteins expressed on epithelial membranes, including airways. They form the protective immunogenic glycocalyx against microbes as well as pollutants, e.g., carcinogens in tobacco smoke. They are involved in lung cancer formation and in drug resistance forming an important compartment of the tumor microenvironment protecting cancer cells from immune system. Mucins function also as a signaling platform orchestrating cell proliferation, migration and metastasis. Our hypothesis is that dysfunctional regulation and expression of mucin 13, a member of mucin family, provides an immunosuppressive environment and associates with poor response to checkpoint inhibition and poor survival. Mucin 13 is also involved in EGFR signaling. Analyzing mucin 13 with advanced biomolecular techniques using tumor and serum samples of Finnish lung cancer patients combined with clinical characteristics and treatment outcomes will elucidate the biological mechanisms and improve patient selection for optimal treatments

The autonomic nerves around the vein of Marshall : a postmortem study with clinical implications

This study aims to analyze the vein of Marshall (VOM) in human autopsy hearts and its correlation with clinical data to elucidate the morphological substrates of atrial fibrillation (AF) and other cardiac diseases. Twenty-three adult autopsy hearts were studied, assessing autonomic nerves by immunohistochemistry with tyrosine hydroxylase (sympathetic nerves), choline acetyltransferase (parasympathetic nerves), growth-associated protein 43 (neural growth), and S100 (general neural marker) antibodies. Interstitial fibrosis was assessed by Masson trichrome staining. Measurements were conducted via morphometric software. The results were correlated with clinical data. Sympathetic innervation was abundant in all VOM-adjacent regions. Subjects with a history of AF, cardiovascular cause of death, and histologically verified myocardial infarction had increased sympathetic innervation and neural growth around the VOM at the mitral isthmus. Interstitial fibrosis increased with age and heart weight was associated with AF and cardiovascular cause of death. This study increases our understanding of the cardiac autonomic innervation in the VOM area in various diseases, offering implications for the development of new therapeutic approaches targeting the autonomic nervous system.Peer reviewe

Arginine Methyltransferase PRMT7 Deregulates Expression of RUNX1 Target Genes in T-Cell Acute Lymphoblastic Leukemia

T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy with no well-established prognostic biomarkers. We examined the expression of protein arginine methyltransferases across hematological malignancies and discovered high levels of PRMT7 mRNA in T-ALL, particularly in the mature subtypes of T-ALL. The genetic deletion of PRMT7 by CRISPR-Cas9 reduced the colony formation of T-ALL cells and changed arginine monomethylation patterns in protein complexes associated with the RNA and DNA processing and the T-ALL pathogenesis. Among them was RUNX1, whose target gene expression was consequently deregulated. These results suggest that PRMT7 plays an active role in the pathogenesis of T-ALL.</p

Arginine Methyltransferase PRMT7 Deregulates Expression of RUNX1 Target Genes in T-Cell Acute Lymphoblastic Leukemia

T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy with no well-established prognostic biomarkers. We examined the expression of protein arginine methyltransferases across hematological malignancies and discovered high levels of PRMT7 mRNA in T-ALL, particularly in the mature subtypes of T-ALL. The genetic deletion of PRMT7 by CRISPR-Cas9 reduced the colony formation of T-ALL cells and changed arginine monomethylation patterns in protein complexes associated with the RNA and DNA processing and the T-ALL pathogenesis. Among them was RUNX1, whose target gene expression was consequently deregulated. These results suggest that PRMT7 plays an active role in the pathogenesis of T-ALL.publishedVersionPeer reviewe

Single cell characterization of B-lymphoid differentiation and leukemic cell states during chemotherapy in ETV6-RUNX1-positive pediatric leukemia identifies drug-targetable transcription factor activities

Background Tight regulatory loops orchestrate commitment to B cell fate within bone marrow. Genetic lesions in this gene regulatory network underlie the emergence of the most common childhood cancer, acute lymphoblastic leukemia (ALL). The initial genetic hits, including the common translocation that fuses ETV6 and RUNX1 genes, lead to arrested cell differentiation. Here, we aimed to characterize transcription factor activities along the B-lineage differentiation trajectory as a reference to characterize the aberrant cell states present in leukemic bone marrow, and to identify those transcription factors that maintain cancer-specific cell states for more precise therapeutic intervention. Methods We compared normal B-lineage differentiation and in vivo leukemic cell states using single cell RNA-sequencing (scRNA-seq) and several complementary genomics profiles. Based on statistical tools for scRNA-seq, we benchmarked a workflow to resolve transcription factor activities and gene expression distribution changes in healthy bone marrow lymphoid cell states. We compared these to ALL bone marrow at diagnosis and in vivo during chemotherapy, focusing on leukemias carrying the ETV6-RUNX1 fusion. Results We show that lymphoid cell transcription factor activities uncovered from bone marrow scRNA-seq have high correspondence with independent ATAC- and ChIP-seq data. Using this comprehensive reference for regulatory factors coordinating B-lineage differentiation, our analysis of ETV6-RUNX1-positive ALL cases revealed elevated activity of multiple ETS-transcription factors in leukemic cells states, including the leukemia genome-wide association study hit ELK3. The accompanying gene expression changes associated with natural killer cell inactivation and depletion in the leukemic immune microenvironment. Moreover, our results suggest that the abundance of G1 cell cycle state at diagnosis and lack of differentiation-associated regulatory network changes during induction chemotherapy represent features of chemoresistance. To target the leukemic regulatory program and thereby overcome treatment resistance, we show that inhibition of ETS-transcription factors reduced cell viability and resolved pathways contributing to this using scRNA-seq. Conclusions Our data provide a detailed picture of the transcription factor activities characterizing both normal B-lineage differentiation and those acquired in leukemic bone marrow and provide a rational basis for new treatment strategies targeting the immune microenvironment and the active regulatory network in leukemia

Hemap: An nteractive online resource for characterizing molecular phenotypes across hematologic malignancies

Large collections of genome-wide data can facilitate the characterization of disease states and subtypes, permitting pan-cancer analysis of molecular phenotypes and evaluation of disease contexts for new therapeutic approaches. We analyzed 9,544 transcriptomes from over 30 hematologic malignancies, normal blood cell types and cell lines, and show that the disease types can be stratified in a data-driven manner. We utilized the obtained molecular clustering for discovery of cluster-specific pathway activity, new biomarkers and in silico drug target prioritization through integration with drug target databases. Using known vulnerabilities and available drug screens in benchmarking, we highlight the importance of integrating the molecular phenotype context and drug target expression for in silico prediction of drug responsiveness. Our analysis implicates BCL2 expression level as important indicator of venetoclax responsiveness and provides a rationale for its targeting in specific leukemia subtypes and multiple myeloma, links several polycomb group proteins that could be targeted by small molecules (SFMBT1, CBX7 and EZH1) with CLL, and supports CDK6 as disease-specific target in AML. Through integration with proteomics data, we characterized target protein expression for pre-B leukemia immunotherapy candidates, including DPEP1. These molecular data can be explored using our freely available interactive resource, Hemap, for expediting therapeutic innovations in hematologic malignancies

Novel Biomarkers of Pediatric B-cell Acute Lymphoblastic Leukemia

B-soluinen akuutti lymfoblastileukemia on yleisin lapsilla esiintyvä syöpä. Tälle klonaaliselle taudille on ominaista syöpäsolujen nopea jakaantuminen luuytimessä ja veressä. Ajoittain tautia voi esiintyä esimerkiksi imusolmukkeissa tai keskushermostossa. Vaikka taudin ennuste on parantunut merkittävästi viimeisten vuosikymmenten aikana taudin intensiivisemmän hoidon ja tarkemman hoitovasteseurannan avulla, aiheuttaa taudin uusiutuminen edelleen sairastavuutta ja kuolleisuutta. Tämän vuoksi tautia pyritään edelleen luokittelemaan tarkemmin, jotta hoitoa osataan kohdentaa paremmin. Taudin syntyyn liittyy olennaisella tavalla geenien ilmentymistä säätelevien transkriptiotekijöiden ilmentyminen normaalista poikkeavalla tavalla leukemiasoluissa, mikä voi johtaa leukemiasolujen kasvuun ja hallitsemattomaan jakaantumiseen. Tässä väitöskirjassa keskityttiin kahteen transkriptiotekijään: SOX11-nimiseen transkriptiotekijään, joka kytkeytyy hermoston kehitykseen sekä manttelisolulymfoomaan sekä itukeskuslähtöisissä lymfoomissa ilmentyvään BCL6- proto-onkogeeniin. Lisäksi tutkittiin RNA:ta sitovan IGF2BP3:n roolia leukemiassa. Tutkimuksissa hyödynnettiin olemassa olevia geeniekspressiotiedostoja sekä tutkimusta varten kerättyä väestöpohjaista immunohistokemian näytesarjaa. Ilmentymistuloksia verrattiin potilaiden kliinisiin tietoihin. BCL6:n ilmentyminen oli korkein TCF3-PBX1- sekä mm. uudessa MEF2D- alaryhmässä, ja se nivoutui myös pre-BCR-signalointireitin osien ilmentymiseen. Korkeampi mRNA-ekspressiotaso yhdistyi suotuisampaan ennusteeseen lapsipotilailla. Havaitsimme SOX11-ekspression yhteyden ETV6-RUNX1- ja TCF3- PBX1-alaryhmiin sekä suotuisampaan ennusteeseen B-ALL-potilailla. Lisäksi havaitsimme, että SOX11-geenin promoottorialueen korkea metylaatio liittyi geenin ilmentymisen säätelyyn, ja sitä voitiin muokata metylaatiota poistavalla lääkeaineella, desitabiinilla. IGF2BP3 ilmentyi laajalti eri B-ALL-alaryhmissä, ja korkeampi ilmentyminen mRNA-tasolla liittyi parempaan hoitovasteeseen korkean riskin potilailla. Väitöskirjatutkimuksessa tunnistettiin useita ennusteellisia biomarkkereita akuuttiin lymfoblastileukemiaan, ja löydökset viittaavat niiden mahdolliseen hyötyyn potilaiden ennustetta arvioitaessa. Tulokset tulisi kuitenkin jatkossa vahvistaa prospektiivisessa koeasetelmassa Ja nykyisissä hoitoprotokollissa ennen niiden mahdollista kliinistä käyttöä.B-cell acute lymphoblastic leukemia (B-ALL) is the most common pediatric malignancy. It is characterized by the fast proliferation of clonal white blood cells in the bone marrow and blood. Occasionally, B-ALL may infiltrate lymph nodes and other sites outside of bone marrow, such as the CNS. Although the prognosis has improved dramatically during the past decades through intensification of the treatment and monitoring of response to treatments, relapse of the disease is still a ma1or cause of morbidity and mortality. This prevalent hardship forces the continuous re-evaluation of disease classification and investigation for novel treatments. The pathogenesis of B-ALL includes the aberrant expression of different transcription factors that lead to uncontrolled proliferation and derailed migration of leukemic populations. This dissertation focused on two transcription factors, namely neurodevelopmental and mantle cell lymphoma-associated transcription factor SOX11 and the germinal center-originated lymphoma-associated proto- oncogene BCL6, along with the oncofetal post-transcriptional modifier protein IGF2BP3. We utilized pre-existing gene expression datasets, collected a population- based immunohistochemistry sample cohort, and correlated the findings to treatment response and patient survival. We found BCL6 was associated with the TCF3-PBX1 subtype and several novel subtypes, such as, MEF2D and components of the pre-BCR signaling pathway. At mRNA level, higher BCL6 levels indicated better prognosis. SOX11 was expressed particularly in ETV6-RUNX1 and TCF3-PBX1 subtypes of B-ALL, and high expression of SOX11 protein was associated with a favorable outcome. Low level of SOX11 promoter methylation was likely behind the high expression and high methylation levels could be overcome by treatment with demethylating agent decitabine. Finally, IGF2BP3 was discovered to be widely expressed in B-ALL at protein and mRNA levels and associated with a proliferative cell phenotype. High levels of IGFBP3 mRNA were associated with better treatment response in high-risk B-ALL cases. In summary, we found several potential novel biomarkers for B-ALL. Although the results suggest prognostic utility in patient care, they require further validation in prospective cohorts and with current treatment protocols before application in clinics

Pilvipalvelut ja pilvestä tarjottavat toimistosovellukset

Pilvipalveluilla tarkoitetaan verkon kautta käytettäviä palveluita. Näille palveluille on määritelty tiettyjä ominaisuuksia jotta niitä voidaan ajatella pilvipalveluiksi. Tässä työssä on tarkoitus tarkastella näitä omi-naisuuksia ja luokitteluja, jotka määrittävät pilvipalvelu – käsityksen. Selvennämme myös itse pilvipalvelu käsitettä ja mitä se pitää sisällään. Työssä tarkastellaan mitä mahdollisuuksia pilvet tuovat yrityksille, sekä yksityisille. Pilvipalvelut voivat olla sovelluksia palveluna (Software as a Service, SaaS), sovellusalusta palveluna (Platform as a Service, PaaS) tai infrastruktuuri palveluna (Infrastructure as a Service). Tarkastelemme näitä palveluiden luokitteluja ja katsomme niistä esimerkkejä. Käymme läpi pilvityypit, jotka ovat yksityinen, julkinen, hybridi ja yhteisöllinen pilvi. Tietoturva on yksi pilvipalveluiden suurimpia kysymyksiä. Paneudumme pilvipalveluiden tietoturvauh-kiin ja niiden ehkäisyyn. Katsomme myös pilvipalveluiden tulevaisuuden näkymiä, onko odotettavissa palveluiden yleistymistä pilvessä, vai ovatko pilvipalvelut tämän hetkinen ohimenevä hitti. Käytännön puolella vertailemme kolmea SaaS – pilvipalvelun tarjoajaa, jotka tarjoavat toimistosovelluksia pilvipalveluna. Nämä palveluntarjoajat ovat Microsoftin Office 365, Googlen Apps, sekä Zohon Docs – palvelu. Tarkoitus on testata palveluiden käytettävyyttä ja ominaisuuksia. Työn tarkoituksena on toimia yleisenä opastuksena pilvipalveluista ja niiden ominaisuuksista.By Cloud Services we mean services used via network. These services have some specific properties, so that they can be called Cloud Services. The purpose of this thesis is to examine those qualities. We also clarify the meaning of Cloud Services and what it contains. In this work we go over the possibilities that Cloud Services bring to companies and civilians. Cloud Services can be Software as a Service (SaaS), Platform as a Service (PaaS) or Infrastructure as a Service (Iaas). We study these Services and examine them with examples. We review Cloud types, private cloud, public cloud, hybrid cloud and Intercloud. Data security is one of the biggest question-marks in Cloud Services. We go into Cloud Services security threats and examine the techniques how to prevent them. We also examine the possible future of Cloud Services, are they going to grow or does it just have temporary success. In practice we test three SaaS - Cloud service providers that offer office applications as a cloud service. These services are Microsoft 365, Google Apps and Zoho Docs. Purpose is to test their usability and features. The purpose of this thesis is to be a guide to Cloud Servises and their features

Kansainvälisen virtuaalisen oppimista tukevan aineiston hyödyntäminen ongelmalähtöisen oppimisen tukena lääketieteen alkuvaiheen opinnoissa

Virtuaalisen aineiston jakamisen ajoittamista on tutkittu vähän. Tällä tutkimuksella pyrittiin selvittämään, miten virtuaalisen aineiston jakaminen ja tarjoaminen tulisi ajoittaa ongelmalähtöistä oppimista tukemaan. Tutkimukseen osallistui ensimmäisen vuoden lääketieteen opiskelijoita Hapen saanti-jaksolla vuosina 2007 ja 2008. Vuonna 2007 opiskelijoita oli 118 ja 100 vuonna 2008. Vuonna 2007 opiskelijoille tarjottiin sydän- ja verenkiertoelimistöä käsittelevä aineisto kerralla Moodle-oppimisympäristön avulla. Vuonna 2008 aineisto tarjottiin osissa. Molemmilta kursseilta tiedusteltiin jakson lopuksi kokemuksia ja mielipiteitä IVIMEDS-aineistosta kyselylomakkeella. Vuonna 2007 kahden tutorryhmän tutoreita kehotettiin painottamaan aineiston käyttämistä. Osaa opiskelijoista haastateltiin pienryhmissä vuonna 2007. Kyselylomakkeiden ja haastatteluiden tulokset taulukoitiin ja analysoitiin. Vuonna 2007 vastanneita oli 107 (90,7 %) ja 68 vuonna 2008 (68 %). Vuonna 2007 aineisto koettiin oppimisen kannalta hyödyllisemmäksi kuin vuonna 2008. Vaihtelevat käyttöliittymät osoittautuivat ongelmaksi. Tutkimuksen perusteella aineisto tulisi tarjota opiskelijoille kerralla ja opettaa aineiston käyttöä. Avainsanat: sähköinen oppiminen, elinikäinen lääketieteen oppiminen, pienryhmähaastattel