Identification of Epigenetic Targets in Prostate Cancer for Therapeutic Development

Recurrent castration resistant prostate cancer remains a challenge for cancer therapies and novel treatment options in addition to current anti-androgen and mitosis inhibitors are needed. Aberrations in epigenetic enzymes and chromatin binding proteins have been linked to prostate cancer and they may form a novel class of drug targets in the future. In this thesis we systematically evaluated the epigenenome as a prostate cancer drug target. We functionally silenced 615 known and putative epigenetically active protein coding genes in prostate cancer cell lines using high throughput RNAi screening and evaluated the effects on cell proliferation, androgen receptor (AR) expression and histone patterns. Histone deacetylases (HDACs) were found to regulate AR expression. Furthermore, HDAC inhibitors reduced AR signaling and inhibited synergistically with androgen deprivation prostate cancer cell proliferation. In particular, TMPRSS2- EGR fusion gene positive prostate cancer cell lines were sensitive to combined HDAC and AR inhibition, which may partly be related to the dependency of a fusion gene induced epigenetic pathway. Histone demethylases (HDMs) were identified to regulate prostate cancer cell line proliferation. We discovered a novel histone JmjC-domain histone demethylase PHF8 to be highly expressed in high grade prostate cancers and mediate cell proliferation, migration and invasion in in vitro models. Additionally, we explored novel HDM inhibitor chemical structures using virtual screening methods. The structures best fitting to the active pocket of KDM4A were tested for enzyme inhibition and prostate cancer cell proliferation activity in vitro. In conclusion, our results show that prostate cancer may efficiently be targeted with combined AR and HDAC inhibition which is also currently being tested in clinical trials. HDMs were identified as another feasible novel drug target class. Future studies in representative animal models and development of specific inhibitors may reveal HDMs full potential in prostate cancer therapy

Transcriptional and Epigenetic Regulation of Human CD4+ T Helper Lineage Specification

Activated T helper (Th) cells have ability to differentiate into functionally distinct Th1, Th2 and Th17 subsets through a series of overlapping networks that include signaling and transcriptional control and the epigenetic mechanisms to direct immune responses. However, inappropriate execution in the differentiation process and abnormal function of these Th cells can lead to the development of several immune mediated diseases. Therefore, the thesis aimed at identifying genes and gene regulatory mechanisms responsible for Th17 differentiation and to study epigenetic changes associated with early stage of Th1/Th2 cell differentiation. Genome wide transcriptional profiling during early stages of human Th17 cell differentiation demonstrated differential regulation of several novel and currently known genes associated with Th17 differentiation. Selected candidate genes were further validated at protein level and their specificity for Th17 as compared to other T helper subsets was analyzed. Moreover, combination of RNA interference-mediated downregulation of gene expression, genome-wide transcriptome profiling and chromatin immunoprecipitation followed by massive parallel sequencing (ChIP-seq), combined with computational data integration lead to the identification of direct and indirect target genes of STAT3, which is a pivotal upstream transcription factor for Th17 cell polarization. Results indicated that STAT3 directly regulates the expression of several genes that are known to play a role in activation, differentiation, proliferation, and survival of Th17 cells. These results provide a basis for constructing a network regulating gene expression during early human Th17 differentiation. Th1 and Th2 lineage specific enhancers were identified from genome-wide maps of histone modifications generated from the cells differentiating towards Th1 and Th2 lineages at 72h. Further analysis of lineage-specific enhancers revealed known and novel transcription factors that potentially control lineage-specific gene expression. Finally, we found an overlap of a subset of enhancers with SNPs associated with autoimmune diseases through GWASs suggesting a potential role for enhancer elements in the disease development. In conclusion, the results obtained have extended our knowledge of Th differentiation and provided new mechanistic insights into dysregulation of Th cell differentiation in human immune mediated diseases.

Ulkomailla vahvistetut suomalaisten lasten adoptiot ja Suomen perintölainsäädäntö

English summary: Foreign adoptions of Finnish children and the Finnish law of inheritance (s. 1190-1191.)

Perheyrityksen sukupolvenvaihdoksen perintö- ja lahjaverotus

Tutkielman tavoitteena on selvittää perheyrityksen sukupolvenvaihdokseen liittyvä perintö- ja lahjaverotus eri tavoilla toteutetuissa sukupolvenvaihdoksissa. Tutkielma on kvalitatiivinen tutkimus, jossa menetelmien osalta pääpaino oli kirjallisuus- ja oikeustapaustutkimuksessa. Perheyrityksen sukupolvenvaihdoksen ja siihen liittyvien veroseuraamusten optimointi edellyttää suunnitelmallista prosessia, missä otetaan huomioon eri toteutusvaihtoehtojen verotuksellinen kohtelu sekä luopujan että jatkajan kannalta. Perheen sisällä tapahtuvat sukupolvenvaihdokset tapahtuvat useimmiten lahjana, lahjanluonteisena kauppana tai perintönä, jolloin perintö- ja lahjaverotuksessa osakkeiden arvon määrittely ja sukupolvenvaihdoksen yhteydessä saatavat verohuojennukset ja niiden huomioon ottaminen ovat tärkeitä tekijöitä. Yritysmuodon muutoksilla, yhtiön jakautumisella tai yhtiön omien osakkeiden lunastamisella voidaan myös vaikuttaa sukupolvenvaihdoksen verotukseen.

Sukupolvenvaihdoksen toteuttaminen henkilöyhtiössä

Tutkielma on kvalitatiivinen tutkimus, jossa pääpaino perustuu kirjallisuus- ja oikeustapaustutkimukseen. Tutkielman tavoitteena on selvittää henkilöyhtiön sukupolvenvaihdoksen toteuttamisen vaihtoehdot sekä henkilöyhtiön yhtiöosuuksien luovutuksena että yhtiömuodon muutoksella, jolloin henkilöyhtiö muutetaan ensin osakeyhtiöksi ja sen jälkeen osakeyhtiö voi jakautua. Perheyrityksen sukupolvenvaihdoksen ja siihen liittyvien veroseuraamusten optimointi edellyttää suunnitelmallista prosessia, missä otetaan huomioon eri toteutusvaihtoehtojen verotuksellinen kohtelu sekä luopujien että jatkajien kannalta. Perheen sisällä tapahtuvat sukupolvenvaihdokset tapahtuvat useimmiten lahjana tai lahjanluonteisena kauppana, jolloin perintö- ja lahjaverotus on tarpeen ottaa huomioon jo suunnitteluvaiheessa. Yritysvarallisuuden arvostaminen perintö- ja lahjaverotuksessa sekä sukupolvenvaihdoksen yhteydessä saatavat verohuojennukset ja niiden huomioon ottaminen ovat tärkeitä tekijöitä. Tutkielman case- yrityksessä luopujien ja jatkajien tarpeet huomioiden yhtiömuodon muutos ja jakautuminen voitiin todeta kannattavimmaksi vaihtoehdoksi.

Health Related Quality of Life after Childhood Cancer - A Finnish Nationwide survey

The purpose of this Finnish epidemiological nationwide cross-sectional study was to evaluate the Health Related Quality of Life (HRQL) of young people that have survived childhood cancer at least four years after cancer diagnosis. The study aims were (1) to increase knowledge and understanding about the relationship between childhood cancer and its treatment and HRQL of childhood cancer survivors and (2) to identify survivors who need and could benefit from ongoing long-term follow-up, as well as (3) to identify what kind of aftercare the childhood cancer survivors will possibly need. HRQL and fatigue of currently still young survivors of extracranial childhood malignancies were evaluated with self-reports and parent proxy reports. HRQL was measured with age-appropriate generic instruments: PedsQL™, SF-36, 15D, 16D and 17D. Fatigue for children and adolescents aged below 18 years was measured with the PedsQL™ Multidimensional Fatigue Scale Finnish version. PedsQL™ parent-proxy and the PedsQL™ Multidimensional Fatigue Scale Parentproxy instruments were used to assess the perception of the parents on HRQL and fatigue of their children and adolescents. Postal-survey questionnaires were mailed to 852 childhood cancer survivors aged 11-27 years and their randomly selected gender-, age and living-place matched controls, as well as under 18-year-old children´s parents. A total of 474 survivors, 595 controls, 209 survivor’s parent and 253 control’s parent replied. The mean age of survivors at the time of the study was 18.4 years. The mean length of survival was 12.3 years, and the mean age at diagnosis 5.5 years. The most of the Finnish childhood cancer survivors evaluated that their HRQL as good. Survivors rated their HRQL equal or higher than their controls. The only dimension where the survivors scored poorer than the controls was the 15D mobility dimension. Survivors of childhood cancer did not suffer from significant fatigue. There were subgroups of childhood cancer survivors who had poorer level of HRQL, and suffered from fatigue more than the reference group. The demographic factors that associated with poorer HRQL were female gender, greater weight, living alone, need of remedial education, an additional non-cancer diagnosis, survivors with siblings, and self-reported unhappiness. Disease-related factors that associated with poorer HRQL were higher age at the time of diagnosis, the diagnosis of Wilms tumor, neuroblastoma, or osteosarcoma, and treatment with stem cell transplantation. The factors associated with more fatigue in survivors were male gender, older age at evaluation, the need of remedial education at school, lower overall average grade in the latest school marks report, length of survival more than 10 years, lower HRQL-scores, and a sarcoma diagnosis. However, all the used demographic and disease related factors explained only about one third of the variation in the HRQL scores. In open questions, the survivors were most worried about their physical health, but were also worried about their mental health, cancer inheritance, late-effects, and fertility and relapse issues. It seems that there are subgroups of survivors who need and could benefit from ongoing long-term follow-up. In the future, the survivors of childhood cancer need more information about their physical and mental health, as well as on their cancer inheritance, possible late-effects including fertility issues, and on the risk of relapse.

Building object-oriented software with the D-Bus messaging system

Object-oriented programming is a widely adopted paradigm for desktop software development. This paradigm partitions software into separate entities, objects, which consist of data and related procedures used to modify and inspect it. The paradigm has evolved during the last few decades to emphasize decoupling between object implementations, via means such as explicit interface inheritance and event-based implicit invocation. Inter-process communication (IPC) technologies allow applications to interact with each other. This enables making software distributed across multiple processes, resulting in a modular architecture with benefits in resource sharing, robustness, code reuse and security. The support for object-oriented programming concepts varies between IPC systems. This thesis is focused on the D-Bus system, which has recently gained a lot of users, but is still scantily researched. D-Bus has support for asynchronous remote procedure calls with return values and a content-based publish/subscribe event delivery mechanism. In this thesis, several patterns for method invocation in D-Bus and similar systems are compared. The patterns that simulate synchronous local calls are shown to be dangerous. Later, we present a state-caching proxy construct, which avoids the complexity of properly asynchronous calls for object inspection. The proxy and certain supplementary constructs are presented conceptually as generic object-oriented design patterns. The e ect of these patterns on non-functional qualities of software, such as complexity, performance and power consumption, is reasoned about based on the properties of the D-Bus system. The use of the patterns reduces complexity, but maintains the other qualities at a good level. Finally, we present currently existing means of specifying D-Bus object interfaces for the purposes of code and documentation generation. The interface description language used by the Telepathy modular IM/VoIP framework is found to be an useful extension of the basic D-Bus introspection format.

Porin Kuudennen osan tarinoista rakennettu kulttuuriperintö

Tutkimus käsittelee viranomaisten ja asukkaiden välistä vuorovaikutusta kaavaprosessin aikana. Tutkimusalueena on valtakunnallisesti merkittäväksi kulttuuriympäristöksi luokiteltu Porin Kuudes osa, joka on yksi laajimmista yhtenäisenä säilyneistä 1800-luvun lopun puukaupunkialueista Suomessa. Hermeneuttis-fenomenologista otetta soveltava tutkimus perustuu muistitietoaineistoon, joka avaa näkökulman paikallisen kulttuuriperinnön syntymiseen, periytymiseen ja muutokseen. Kuudennen osan vuonna 2012 voimaan tulleessa asemakaavamuutoksessa suojeltiin 405 rakennusta. Sekä viranomaiset että asukkaat haluavat säilyttää arvokkaan ympäristön jälkipolville. Asukkaiden ja viranomaisten lähtökohdat arvottamiselle ovat kuitenkin erilaiset. Asiantuntijoiden näkemys kulttuuriympäristön arvoista perustuu eksplisiittiseen viralliseen tietoon, joka heijastaa positivistista käsitystä maailmasta mitattavista objekteista koostuvana kokonaisuutena. Asukkaiden arvostus asuinaluetta ja sen rakennuksia kohtaan puolestaan nousee sukupolvelta toiselle siirretyn aineettoman perinnön yhteisöllisestä merkityksestä. Heidän kokemuksensa kiteytyy kodin ja kotiseudun käsitteissä ja se tuodaan esiin rakennuksiin liittyvissä tarinoissa. Tulkinta on virallista tietoa haastavaa ja täydentävää. Kestäviä suojelupäätöksiä voidaan tehdä vain viranomaisten ja asukkaiden väliseen tasa-arvoiseen vuoropuheluun perustuen. Tutkimus nostaa asukkaiden kokemuksellisen, paikkaan sitoutuneen hiljaisen tiedon virallisen tiedon rinnalle, kulttuurisesti kestävän maankäytön suunnittelun perustaksi. Koska ihminen toimii sellaisten asioiden puolesta, jotka hän kokee arvokkaaksi, asukaslähtöinen rakennussuojelu on lähtökohtaisesti yhteisön omakseen kokeman aineettoman kulttuuriperinnön suojelua.

SYLI - an external workflow system for DSpace

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Choosing the target loci : heat shock factors HSF1 and HSF2 as regulators of cell stress and development

Heat shock factors (HSFs) are an evolutionarily well conserved family of transcription factors that coordinate stress-induced gene expression and direct versatile physiological processes in eukaryote organisms. The essentiality of HSFs for cellular homeostasis has been well demonstrated, mainly through HSF1-induced transcription of heat shock protein (HSP) genes. HSFs are important regulators of many fundamental processes such as gametogenesis, metabolic control and aging, and are involved in pathological conditions including cancer progression and neurodegenerative diseases. In each of the HSF-mediated processes, however, the detailed mechanisms of HSF family members and their complete set of target genes have remained unknown. Recently, rapid advances in chromatin studies have enabled genome-wide characterization of protein binding sites in a high resolution and in an unbiased manner. In this PhD thesis, these novel methods that base on chromatin immunoprecipitation (ChIP) are utilized and the genome-wide target loci for HSF1 and HSF2 are identified in cellular stress responses and in developmental processes. The thesis and its original publications characterize the individual and shared target genes of HSF1 and HSF2, describe HSF1 as a potent transactivator, and discover HSF2 as an epigenetic regulator that coordinates gene expression throughout the cell cycle progression. In male gametogenesis, novel physiological functions for HSF1 and HSF2 are revealed and HSFs are demonstrated to control the expression of X- and Y-chromosomal multicopy genes in a silenced chromatin environment. In stressed human cells, HSF1 and HSF2 are shown to coordinate the expression of a wide variety of genes including genes for chaperone machinery, ubiquitin, regulators of cell cycle progression and signaling. These results highlight the importance of cell type and cell cycle phase in transcriptional responses, reveal the myriad of processes that are adjusted in a stressed cell and describe novel mechanisms that maintain transcriptional memory in mitotic cell division.

Yrittäjän poistuminen – yrittäjän yritystoiminnasta poistumisen suunnittelu

Tämän tutkimuksen tavoitteena oli laadullisia menetelmiä käyttäen lisätä ymmärrystä yrittäjän poistumisen ilmiöstä. Yrittäjän näkökulmasta tutkimuksessa tarkastellaan poistumiseen suhtautumista ja sen suunnitteluun ja toteutukseen vaikuttavia yrittäjän sisäisiä ja ulkoisia tekijöitä. Tutkimuksen aineisto kerättiin Lahden lähialueen yrittäjiltä käyttäen teemahaastattelun menetelmää. Aineiston analyysin menetelmänä oli teemoittelu. Psykologista omistajuutta sovellettiin tutkimuksen viitekehyksenä. Tutkimuksen tuloksena havaittiin yrittäjien suunnittelevan poistumistaan kahdessa vaiheessa, poistuen ensin yrittäjän roolista ja vasta määräämättömän ajan jälkeen kokonaan yrityksen toiminnasta ja sen tukijan roolista. Toimintatapa helpottaa yrittäjän psykologisesta omistajuudesta ja identiteetin muutoksesta johtuvaa luopumisen vaikeutta. Ulkoisista poistumiseen vaikuttavista tekijöistä tutkimuksessa nostetaan esille perheyritysten perintöveroon liitetyt ennakkokäsitykset, jotka voivat vaikuttaa poistumisen lykkäämiseen. Psykologisen omistajuuden käsite ja tutkimuksessa havaittu poistumiseen liitetty tabu selittävät osittain yrityksen ostajan löytämisen vaikeutta ja lopettavien yrittäjien määrää Suomessa. Tutkimuksen tulokset ovat merkittäviä yrittäjyyttä ja omistajanvaihdoksia edistävien toimijoiden kannalta.

Filopodia and stromal extracellular matrix as regulators of cancer cell invasion and growth

Bidirectional exchange of information between the cancer cells and their environment is essential for cancer to evolve. Cancer cells lose the ability to regulate their growth, gain the ability to detach from neighboring cells and finally some of the cells disseminate from the primary tumor and invade to the adjacent tissue. During cancer progression, cells acquire features that promote cancer motility and proliferation one of them being increased filopodia number. Filopodia are dynamic actin-rich structures extending from the leading edge of migrating cells and the main function of these structures is to serve as environmental sensors. It is nowadays widely appreciated, that not only the cancer cells, but also the surrounding of the tumor – the tumor microenvironment- contribute to cancer cell dissemination and tumor growth. Activated stromal fibroblasts, also known as cancer-associated fibroblasts (CAFs) actively participate on tumor progression. CAFs are the most abundant cell type surrounding the cancer cells and they are the main cell type producing the extracellular matrix (ECM) within tumor stroma. CAFs secrete growth factors to promote tumor growth, direct cancer cell invasion as well as modify the stromal ECM architecture. The aim of this thesis was to investigate the function of filopodia, particularly the role of filopodia-inducing protein Myosin-X (Myo10), in breast cancer cell invasion and metastasis. We found that Myo10 is an important regulator of basal type breast cancer spreading downstream of mutant p53. In addition, I investigated the role of CAFs and their secreted matrix on tumor growth. According to the results, CAF-derived matrix has altered organization and stiffness which induces the carcinoma cell proliferation via epigenetic mechanisms. I identified histone demethylase enzyme JMJD1a to be regulated by the stiffness and to participate in stiffness induced growth control.