Use of pyrosequencing to identify streptococci and to detect mutations causing antimicrobial resistance

Rapid identification and resistance determination of pathogens in clinical specimens is vital for accurate treatment and monitoring of infectious diseases. Antimicrobial drug resistance is increasing globally and healthcare settings are facing this cost-intensive and even life-threatening problem. The incidence of resistant pathogens in Finland has remained relatively steady and manageable at least for the time being. DNA sequencing is the gold standard method for genotyping, mutation analysis, and identification of bacteria. Due to significant cost decrease in recent years, this technique is available to many research and clinical laboratories. Pyrosequencing technique, a rapid real-time DNA sequencing method especially suitable for analyzing fairly short stretches of DNA, was used in this study. Due to its robustness and versatility, pyrosequencing was applied in this study for identification of streptococci and detection of certain mutations causing antimicrobial resistance in different bacteria. Certain streptococcal species such as S. pneumoniae and S. pyogenes are significantly important clinical pathogens. S. pneumoniae causes e.g. pneumonia and otitis media and is one of the most important community-acquired pathogens. S. pyogenes, also known as group A streptococcus, causes e.g. angina and erysipelas. In contrast, the socalled alpha-haemolytic streptococci, such as S. mitis and S. oralis, belong to the normal microbiota, which are regarded to be non-pathogenic and are nearly impossible to identify by phenotypic methods. In this thesis, a pyrosequencing method was developed for identification of streptococcal species based on the 16S rRNA sequences. Almost all streptococcal species could be differentiated from one another by the developed method, including S. pneumoniae from its close relatives S. mitis and S. oralis . New resistance genes and their variants are constantly discovered and reported. In this study, new methods for detecting certain mutations causing macrolide resistance or extended spectrum beta-lactamase (ESBL) phenotype were developed. These resistance detection approaches are not only suitable for surveillance of mechanisms causing antimicrobial resistance but also for routine analysis of clinical samples particularly in epidemic settings. In conclusion, pyrosequencing was found to be an accurate, versatile, cost-effective, and rapid DNA sequencing method that is especially suitable for mutation analysis of short DNA fragments and identification of certain bacteria.

The Role of an Oncoprotein CIP2A in Breast Cancer

Cancerous inhibitor of PP2A (CIP2A) is an oncoprotein expressed in several human cancer types. Previously, CIP2A has been shown to promote proliferation of cancer cells. Mechanistically, CIP2A is known to inhibit activity of a tumor suppressor protein phosphatase 2A (PP2A) towards an oncoprotein MYC, further stabilizing MYC in human cancer. However, the molecular mechanisms how CIP2A expression is induced during cellular transformation are not well known. Also, expression, functional role and clinical relevance of CIP2A in breast cancer had not been studied before. The results of this PhD thesis work demonstrate that CIP2A is highly expressed in human breast cancer, and that high expression of CIP2A in tumors is a poor prognostic factor in a subset of breast cancer patients. CIP2A expression correlates with inactivating mutations of tumor suppressor p53 in human cancer. Notably, we demonstrate that p53 inactivation up-regulates CIP2A expression via increased expression of an oncogenic transcription factor E2F1. Moreover, CIP2A promotes expression of E2F1, and this novel positive feedback loop between E2F1 and CIP2A is demonstrated to regulate sensitivity to both p53-dependent and -independent senescence induction in breast cancer cells. Importantly, in a CIP2A deficient breast cancer mouse model, abrogation of CIP2A attenuates mammary tumor formation and progression with features of E2F1 inhibition and induction of senescence. Furthermore, we demonstrate that CIP2A expression defines the cellular response to a senescence-inducing chemotherapy in breast cancer. Taken together, these results demonstrate that CIP2A is an essential promoter of breast cancer tumor growth by inhibiting senescence. Finally, this study implicates inhibition of CIP2A as a promising therapy target for breast cancer.

ERBB4 mutations in cancer and amyotrophic lateral sclerosis

ErbB receptor tyrosine kinases, epidermal growth factor receptor (EGFR, also known as ErbB1), ErbB2 (HER2 or NEU), ErbB3 (HER3), and ErbB4 (HER4), transduce signals borne by extracellular ligands into central cellular responses such as proliferation, survival, differentiation, and apoptosis. Mutations in ERBB genes are frequently detected in human malignant diseases of epithelial and neural origin, making ErbB receptors important drug targets. Targeting EGFR and ErbB2 has been successful in eg. lung and breast cancer, respectively, and mutations in these genes can be used to select patients that are responsive to the targeted treatment. Although somatic ERBB4 mutations have been found in many high-incidence cancers such as melanoma, lung cancer, and colorectal cancer and germ-line ERBB4 mutations have been linked to neuronal disorders and cancer, ErbB4 has generally been neglected as a potential drug target. Thus, the consequences of ERBB4 mutations on ErbB4 biology are largely unknown. This thesis aimed to elucidate the functional consequences and assess the clinical significance of somatic and germ-line ERBB4 mutations in the context of cancer and amyotrophic lateral sclerosis. The results of this study indicated that cancer-associated ERBB4 mutations can promote aberrant ErbB4 function by activating the receptor or inducing qualitative changes in ErbB4 signaling. ERBB4 mutations increased survival or decreased differentiation in vitro, suggesting that ERBB4 mutations can be oncogenic. Importantly, the potentially oncogenic mutations were located in various subdomains in ErbB4, possibly providing explanation for the characteristic scattered pattern of mutations in ERBB4. This study also demonstrated that hereditary variation in ERBB4 gene can have a significant effect on the prognosis of breast cancer. In addition, it was shown that hereditary or de novo germ-line ERBB4 mutations that predispose to amyotrophic lateral sclerosis inhibit ErbB4 activity. Together, these results suggest that ErbB4 should be considered as a novel drug target in cancer and amyotrophic lateral sclerosis.

EGFR, Her2, p53 ja ALDH1:n yhteys munasarjasyöpäpotilaiden ennusteeseen, ja tilastoja TYKSin vuosien 2001–2007 munasarjasyöpään sairastuneiden potilaiden aineistosta

Munasarjasyöpä on Suomessa tappavin ja toiseksi yleisin gynekologinen syöpä, lisäksi se on kymmenenneksi yleisin naisten syöpä. Yli 90% munasarjasyövistä on epiteeliperäisiä ja morfologisista alatyypeistä yleisin on seroosi syöpä. Serooseista syövistä yli 90 % on korkean riskin eli high grade –syöpää. Vaikka uudet hoidot ovat pidentäneet potilaan selviytymistä, niin kaiken kaikkiaan kokonaisennuste ei kuitenkaan ole parantunut viimeisen vuosikymmenen aikana. Aikaisin havaittu paikallinen epiteeliperäinen munasarjasyöpä on parannettavissa kirurgialla. Yli 2/3 epiteliaalisista munasarjasyövistä diagnosoidaan vasta levinneessä vaiheessa, jolloin viiden vuoden selviytyvyys potilailla on vain noin 30 %. Aiemmin munasarjasyöpien arveltiin olevan lähtöisin munasarjojen pintaepiteelistä, mutta uusimpien tutkimusten mukaan kyseessä on niin molekulaarisesti kuin etiologisesti ryhmä eri syöpiä, jotka ilmenevät samassa anatomisessa paikassa. Syventävässä työssäni tutkin munasarjasyövän käyttäytymistä ennustavia merkkiaineita Merkkiaineita tutkimalla pyritään tulevaisuudessa ennustamaan paremmin syöpien käyttäytymistä ja antamaan potilaille parempia täsmähoitoja. Syventävien opintojeni tarkoituksena oli tutkia munasarjasyöpää kirjallisuuteen tutustumalla ja tutkimalla retrospektiivistä vuosien 2001–2007 munasarjapotilasaineistoa. Keräsimme toisen tutkijan kanssa aineistoon 356 potilaan tiedot, joista 310 sisällytettiin tekemiini tilastoihin. Lisäksi tutkin kiinnostavia munasarjasyövän käyttäytymiseen mahdollisesti liittyviä merkkiaineita (EGFR, HER2, P53 JA ALDH1) uudessa 48 potilaan aineistossa ja selvitin proteiinien merkitystä taudin kulussa ja ennusteessa. 310 potilaan aineiston tulokset olivat sopusoinnussa aiempiin julkaisuihin. Aineistomme munasarjasyövistä 60 % on seroosia high grade –syöpää ja 67 % syövistä on levinneen vaiheen eli luokan III-IV tauteja. 48 potilaan immunohistokemiallisissa värjäyksissä mielenkiintoisin tulos on se, että Her2 :n värjäytymisintensiteetti korreloi kääntäen vahvaan ALDH1-värjäykseen eli se on korkea, kun ALDH1 on matala (korrelaatio -0.425; p=0.00994) Vastaavasti Her2 :n intensiteetin ollessa korkea ALDH1/heikko-soluja on paljon (p=0.00975). Tällaista tutkimus tulosta ei aiemmin ole esitetty. Tämä kiinnostava tulos tulee jatkossa varmistaa laajemmassa aineistossa.