Background: Glioblastoma multiforme (GBM) is the most common and aggressive brain tumor with poor clinical outcome. Identification and development of new markers could be beneficial for the diagnosis and prognosis of GBM patients. Deregulation of microRNAs (miRNAs or miRs) is involved in GBM. Therefore, we attempted to identify and develop specific miRNAs as prognostic and predictive markers for GBM patient survival.Methods: Expression profiles of miRNAs and genes and the corresponding clinical information of 480 GBM samples from The Cancer Genome Atlas (TCGA) dataset were downloaded and interested miRNAs were identified. Patients' overall survival (OS) and progression-free survival (PFS) associated with interested miRNAs and miRNA-interactions were performed by Kaplan-Meier survival analysis. The impacts of miRNA expressions and miRNA-interactions on survival were evaluated by Cox proportional hazard regression model. Biological processes and network of putative and validated targets of miRNAs were analyzed by bioinformatics.Results: In this study, 6 interested miRNAs were identified. Survival analysis showed that high levels of miR-326/miR-130a and low levels of miR-323/miR-329/miR-155/miR-210 were significantly associated with long OS of GBM patients, and also showed that high miR-326/miR-130a and low miR-155/miR-210 were related with extended PFS. Moreover, miRNA-323 and miRNA-329 were found to be increased in patients with no-recurrence or long time to progression (TTP). More notably, our analysis revealed miRNA-interactions were more specific and accurate to discriminate and predict OS and PFS. This interaction stratified OS and PFS related with different miRNA levels more detailed, and could obtain longer span of mean survival in comparison to that of one single miRNA. Moreover, miR-326, miR-130a, miR-155, miR-210 and 4 miRNA-interactions were confirmed for the first time as independent predictors for survival by Cox regression model together with clinicopathological factors: Age, Gender and Recurrence. Plus, the availability and rationality of the miRNA-interaction as predictors for survival were further supported by analysis of network, biological processes, KEGG pathway and correlation analysis with gene markers.Conclusions: Our results demonstrates that miR-326, miR-130a, miR-155, miR-210 and the 4 miRNA-interactions could serve as prognostic and predictive markers for survival of GBM patients, suggesting a potential application in improvement of prognostic tools and treatments.

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第20607号 / 医博第4256号 / 新制||医||1023(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 山田 泰広, 教授 松田 道行, 教授 長船 健二 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

Background: Reduced temporal muscle thickness (TMT) has been discussed as a prognostic marker in IDH-wildtype glioblastoma. This retrospective multicenter study was designed to investigate whether TMT is an independent prognostic marker in newly diagnosed glioblastoma. Methods: TMT was retrospectively measured in 335 patients with newly diagnosed glioblastoma between 1 January 2014 and 31 December 2019 at the University Hospitals of Leipzig and Rostock. The cohort was dichotomized by TMT and tested for association with overall survival (OS) after 12 months by multivariate proportional hazard calculation. Results: TMT of 7.0 mm or more was associated with increased OS (46.3 ± 3.9% versus 36.6 ± 3.9%, p > 0.001). However, the sub-groups showed significant epidemiological differences. In multivariate proportional hazard calculation, patient age (HR 1.01; p = 0.004), MGMT promoter status (HR 0.76; p = 0.002), EOR (HR 0.61), adjuvant irradiation (HR 0.24) and adjuvant chemotherapy (HR 0.40; all p < 0.001) were independent prognostic markers for OS. However, KPS (HR 1.00, p = 0.31), BMI (HR 0.98, p = 0.11) and TMT (HR 1.06; p = 0.07) were not significantly associated with OS. Conclusion: TMT has not appeared as a statistically independent prognostic marker in this cohort of patients with newly diagnosed IDH-wildtype glioblastoma.

Cirka 300 000 individer drabbas årligen i världen av oral cancer och mer än nittio procent av alla orala cancerformer utgörs av skivepitelcancer. Den femåriga prognosen är generellt 50 % och den 5-åriga relativa överlevnaden har under en tioårsperiod förblivit densamma. Detta motiverar utvecklingen av bättre prognostiska markörer och diagnostiska metoder för att tidigt identifiera de patienter som har risk att utveckla oral skivepitelcancer för att förbättra prognosen och minska lidandet genom tidig insatt behandling. β-catenin är en adhesionsmolekyl som är viktig för bibehållandet av cellulär integration och avvikelser i celladhesionsmolekyler tros spela en central roll när tumörceller invaderar närliggande vävnad det vill säga metastaserar till andra organ.Syftet med studien är att med hjälp av immunohistokemi undersöka om β-catenin kan fungera som en prognostisk markör för utvecklingen av oral skivepitelcancer. Detta görs genom att jämföra förekomsten av β-catenin med hjälp av monoklonala antikroppar i normalt skivepitel, dysplasi och cancer från 18 patienter som har diagnostiserats med oral skivepitelcancer. Infärgningen av Beta catenin jämfördes i normalt oralt skivepitel med cancer och dysplasi för alla biopsier för att undersöka om det förekommer någon skillnad av infärgningen. Förutom detta skedde även en jämförelse av normalt skivepitel med dysplasi och cancer inom varje enskild biopsi.Resultaten visade att det finns en skillnad i uttrycket av β-catenin i normalt skivepitel jämfört med dysplasi och cancer i denna patientgrupp. I denna studie visade mer än 70 % av biopsierna en stark eller måttlig och stark infärgning av β-catenin i normalt skivepitel, mer än 60 % av biopsierna visade en måttlig eller måttlig och svag infärgning av dysplasi och 58,8 % av alla biopsier visade svag infärgning eller ingen och svag infärgning av skivepitelcancer. Då studien visar att mängden av β-catenin är starkast i normalt oralt skivepitel, måttligt i dysplasi och svagast i cancer tyder detta på att β-catenin skulle kunna vara en viktig faktor i utvecklingen av skivepitelcancer i munhålan vilket stämmer väl överens med resultat från andra studier. / Approximately 300,000 individuals are affected every year in the world of oral cancer and more than ninety percent of all oral cancers consists of squamous cell carcinoma. The five-year prognosis is generally 50 % and the 5-year relative survival has over ten years remained the same. This motivates the development of better prognostic markers and diagnostic methods for the early identification of patients at risk of developing oral squamous cell carcinoma to improve prognosis and reduce the suffering of these patients with early treatment.β-catenin is an adhesion molecule that is important for the maintenance of cellular integration and abnormalities of cell adhesion molecules is thought to play a central role in tumorigenesis. The abnormalites is though to enhance tumour cells to break loose from neighbouring cells and invade nearby tissues and organs, however the exact mechanisms are unknown. The purpose of the study is that using immunohistochemistry to examine whether β-catenin may serve as a prognostic marker for the development of oral squamous cell carcinoma. This is done by examining the presence of β-catenin with monoclonal antibodies in 18 biopsies with normal squamous epithelia, dysplasia and cancer from 18 patients diagnosed with oral squamous cell carcinoma from the department of Oral Pathology at Malmö Högskola, Malmö. The staining of beta catenin was compared in normal oral squamous cancer and dysplasia for all biopsies to see whether there is any difference of dyeing. Besides this, there was also a comparison of normal squamous epithelium with dysplasia and cancer in each biopsy.The results showed that there is a difference in the expression of β-catenin in normal squamous epithelium, dysplasia and cancer in this population. In this study, more than 70 % of the biopsies expressed a strong or moderate and strong staining of β -catenin in normal oral squamous epithelium, more than 60 % of the biopsies showed a moderate or moderate and weak staining of dysplasia and 58.8 % of all biopsies showed weak or no staining and weak staining of squamous cell carcinoma.As the study shows that the amount of β -catenin is strongest in normal oral squamous epithelium, moderate in dysplasia and weakest in cancer, this suggests that β -catenin could be an important factor in the development of squamous cell carcinoma of the oral cavity which is in line with results from other studies.

Les protéoglycanes à héparane-sulfates (HSPGs) sont des macromolécules ubiquitaires situées à la surface des cellules et au sein des matrices extracellulaires jouant un rôle clé dans le contrôle des interactions cellules-matrice et du micro-environnement tumoral. Leur biosynthèse est assurée par une machinerie enzymatique complexe impliquant des glycosyltransférases et sulfotransférases, lesquelles ajoutent des motifs sulfatés en différentes positions des résidus de la chaîne glucidique. Ces modifications confèrent aux HSPGs la capacité d’interagir avec de nombreux ligands comme les facteurs de croissance et leurs récepteurs permettant de réguler divers processus physiopathologiques tels que la prolifération et la survie cellulaires, l’angiogenèse et le développement tumoral. J’ai focalisé mon étude sur une famille de sulfotransférases, les 3-O-sulfotransférases (3-OSTs) responsables d’une modification rare et terminale des chaînes de HS et en particulier sur l’isoforme 3A (3-OST3A) dont le rôle dans le développement tumoral a été précédemment mis en évidence par notre équipe. L’objectif de ce travail de thèse est d’explorer le rôle de la 3-OST3A dans la régulation du développement du cancer du sein. Ces travaux mettent en évidence que le gène 3-OST3A est régulé épigénétiquement dans un panel de lignées cellulaires cancéreuses mammaires. Les tests cellulaires de prolifération et d’apoptose montrent que la 3-OST3A exerce une action oncogénique ou suppresseur de tumeur dépendante de la signature moléculaire des cellules cancéreuses mammaires. Au niveau clinique, un fort taux d’expression de la 3-OST3A dans les tumeurs est corrélé négativement avec la survie des patientes atteintes d’un cancer du sein de sous-type HER2+. Ces travaux sont les premiers à mettre en évidence un rôle fonctionnel de la 3-OST3A en tant que régulateur du comportement tumoral des cellules cancéreuses mammaires et permettent de l’envisager comme marqueur pronostique de l’évolution du sous-type de tumeur mammaire HER2. La poursuite de cette étude a pour objectif de comprendre les mécanismes qui expliquent les conséquences délétères de la forte expression de la 3-OST3A sur l’agressivité du cancer du sein HER2+. Mes résultats suggèrent que la 3-OST3A induirait l’activation du récepteur HER2 par une voie dépendante de la formation du complexe ternaire HS 3-O-sulfatés/FGF-7/FGFR2IIIb dans les cellules SKBR3, un modèle de cellules cancéreuses mammaires surexprimant le récepteur HER2 responsable du caractère agressif du cancer du sein HER2+ / Heparan sulfate proteoglycans (HSPG) are ubiquitous macromolecules located at the cell plasma membrane and in extracellular matrices playing a key role in the control of cell-matrix interactions and in the tumor micro-environment. Their biosynthesis is performed by a complex enzymatic machinery involving glycosyltransferases and sulfotransferases, the latter adding a sulfate group at different residue positions of the polysaccharide chain. These modifications provide to the HSPG the ability to interact with many ligands such as growth factors and their receptors, and to regulate multiple pathophysiological processes such as cell proliferation and survival, angiogenesis and tumor development. I focused on a sulfotransferase family, the heparan sulfate 3-O-sulfotransferases (HS3STs) responsible for a rare, terminal modification of HS chains. Specifically, we investigated the HS3ST3A isoform whose role in tumor development has been previously demonstrated by our team. Here I explored the role of HS3ST3A in breast cancer. My studies demonstrate that HS3ST3A gene is epigenetically regulated in a panel of breast cancer cell lines. Cell proliferation and apoptosis assays in cellulo showed that HS3ST3A exerts an oncogenic or tumor suppressor effect in a cell-dependent context. A clinical study performed in a cohort of breast cancer patients showed that a high expression level of HS3ST3A in tumors is associated with reduced relapse-free survival in HER2+ patients. For the first time, we report a functional role of HS3ST3A as a tumor regulator of breast cancer cells behavior and this study allows considering it as a prognostic marker of the HER2 breast cancer evolution. The last part of my work attempted to understand the mechanisms that explain the deleterious consequences of the high expression level of HS3ST3A on the aggressiveness of HER2+ breast cancer. In this regard, my results suggested that the HS3ST3A may induce HER2 receptor activation following the formation of the ternary complex HS 3-O-sulphated/FGF-7/FGFR2IIIb in SKBR3 (HER2+) cells

In the demyelinating autoimmune disease multiple sclerosis (MS) there is a great need for validated prognostic biomarkers that can give information about both prognosis and disease course. So far only clinical parameters have been shown to predict future outcome. CXCL13 is a potent B cell chemoattractant that has been suggested to be a potential biomarker candidate. The aim of this study was to investigate the usefulness of CXCL13 as a prognostic biomarker for MS. Clinical, paraclinical, laboratory and MRI data about a large group of MS patients and controls were collected. CXCL13 levels in cerebrospinal fluid (CSF) samples from these patients were determined by standard enzymelinked immunosorbent assay (ELISA). In general CXCL13 were increased in CSF in MS, especially in relapsing-remitting MS during relapses, i.e. with ongoing inflammations in the central nervous system. CXCL13 is a good candidate prognostic marker for MS, since newly diagnosed MS with high CXCL13 levels showed worsened disease course within five years. Most importantly, MS conversion occurred in higher rate in possible MS patients with high concentrations of CXCL13 in CSF, and in a shorter time point. This observation may support an early treatment decision in these patients. In conclusion, this study provides support for an association between CXCL13 levels in the CSF and later development of disease severity in MS.

Abstract The prognosis of patients with head and neck squamous cell carcinoma has improved only little during the last decades. Clinical markers for the biological aggressiveness of the cancer are few. The most reliable prognostic indicator is the stage of the disease. Research of the significance of the TP53 tumor suppressor gene as a predictive marker for prognosis and response to treatment in head and neck cancer has given discrepant results. One reason is probably the attempt to use p53 immunohistochemistry as a surrogate for TP53 mutations. However, in immunohistochemistry the protein is analyzed and thus the result does not usually correlate with TP53 mutations. The marker for prognosis of the response to treatment has to be reliable, and the analytical method needs to be both sensitive and specific. In addition to a sensitive method for TP53 mutation analysis the localization and quality of the mutations have to be analyzed to reveal the significance of the mutation on the function of the p53 protein. In this study, TP53 mutations were analyzed, using a sensitive PCR-SSCP method, in the tumors of patients with head and neck squamous cell carcinoma. The quality and localization of mutations were analyzed by sequencing. The frequency of the TP53 mutations and the effect on the function of the p53 protein were studied using IARC TP53 mutation database and literature. Correlation of TP53 mutations with chemical exposure and their significance on prognosis and response to radiation treatment was studied. In addition, the significance of cell cycle regulators cyclin D1, p16, p21 as potential markers of biological aggressiveness of tumors was studied. The results of this study showed that the patients carrying in their tumor TP53 mutations in the DNA binding region of the gene had been exposed to chemicals more than patients with no mutation or other types of mutations. These mutations also correlated with biological aggressiveness and prognosis and the response to radiation treatment. It was also shown that a combination of cyclin D1 and p16 analyzed by immunohistochemistry correlated with worse prognosis in head and neck cancer. / Tiivistelmä Pään ja kaulan alueen levyepiteelisyöpää sairastavien potilaiden ennuste ei ole juurikaan parantunut viime vuosikymmeninä. Syövän biologista aggressiivisuutta kuvaavia ennustetekijöitä on vähän, luotettavimpana niistä taudin levinneisyys. Tutkimustulokset TP53-kasvunrajoitegeenin merkityksestä prognostisena ja hoitovastetta kuvaavana, prediktiivisenä merkkiaineena pään ja kaulan alueen syövissä ovat ristiriitaisia. Tämä johtuu muun muassa siitä, että p53-immunohistokemiaa on yritetty käyttää TP53-mutaatioiden analysoimiseen. Immunohistokemiassa analysoidaan proteiinia, eikä tulos siksi yleensä korreloi TP53-mutaatioiden esiintymiseen. Prognostisen tai hoitovastetta ennustavan merkkiaineen tulee mitata haluttua asiaa luotettavasti, ja sen analysoimiseen tulee käyttää herkkää ja spesifistä menetelmää. Herkän mutaatioanalyysimenetelmän lisäksi mutaatioiden paikan ja laadun tarkempi analysoiminen on välttämätöntä, jotta saadaan selville mutaation merkitys p53 proteiinin toiminnalle. Tässä työssä tutkittiin pään ja kaulan alueen levyepiteelisyöpää sairastavien potilaiden kasvaimista TP53- mutaatioiden esiintymistä validoidulla, herkällä PCR-SSCP-menetelmällä. Mutaatioiden laatu ja sijainti geenissä analysoitiin sekvensoimalla. IARC:n TP53-mutaatiotietopankin ja kirjallisuuden tietojen avulla selvitettiin mutaatioiden yleisyys ja niiden vaikutus p53-proteiinin toimintaan. Tutkimuksessa selvitettiin TP53-mutaatioiden korrelaatiota kemialliseen altistumiseen ja niiden merkitystä potilaan ennusteeseen ja sädehoitovasteeseen. Lisäksi tutkittiin solusyklin säätelijöiden sykliini D1-, p16- ja p21-proteiinien merkitystä taudin biologiseen aggressiivisuuteen. Väitöskirjatutkimuksen tulokset osoittivat, että potilaat, joiden kasvaimessa oli TP53-mutaatio DNA-sitoutumisalueella, olivat altistuneet kemikaaleille enemmän kuin potilaat, joiden kasvaimissa oli toisenlaisia mutaatioita tai ei mutaatiota ollenkaan. Tutkimuksessa havaitut mutaatiot liittyivät taudin biologiseen aggressiivisuuteen ja huonoon ennusteeseen sekä heikompaan sädehoitovasteeseen. Lisäksi havaittiin, että sykliini D1- ja p16-proteiinin yhdistelmä immunohistokemiallisesti analysoituna korreloi huonoon ennusteeseen pään ja kaulan syövissä.

Despite progress in our understanding of the molecular drivers that propagate the overall process of metastasis, the adaptation of specific organs upon these molecular interactions for metastatic entry remains poorly understood. This is particularly true for liver metastases, the liver being a common site for metastatic disease, and metastatic hepatic tumors are more prominent than primary hepatocellular or biliary tumors. Liver metastases most commonly arise from colorectal cancer than any other cancer and constitute one of the most detrimental outcomes of cancer, characterized by poor prognosis, high mortality, and no effective therapies available other than surgical interventions. Since interactions between tumour cells and the tumour microenvironment play an important part in the engraftment, survival, and progression of the metastases, the discovery of new drivers of liver metastasis with the potential to become therapeutic and preventive targets is required to advance the care of liver metastasis patients as well as cancer patients at risk of metastatic spread to the liver. The alteration of the physical structure of the tissue is extremely important in the progression of malignant diseases, such as cancer metastasis, as it directly affects the extravasation and colonization of tumour cells. The major hurdles in liver metastasis research, stem not only from our insufficient understanding of the molecular mechanisms directing and mediating metastasis particularly to the liver but also from the limited number of pre-clinical models available that mimic human disease and enable the study of the complex interactions between tumor cells and the liver microenvironment. The liver metastatic process underlies the acquisition of key adaptations by tumor-derived factors and is determined by both tumour-intrinsic properties and the crosstalk between tumour cells and stromal cells in the liver. A normal functioning and structurally intact extracellular matrix (ECM) constitute a hostile “soil” for seeding tumor cells to colonize. Eventually, it is the ability of tumor cells to remodel the liver microenvironment and create a supportive niche for metastatic tumor cell survival and outgrowth that determines successful metastatic colonization. Among tumour-secreted factors, which are recognized as major contributors to the formation of pre-metastatic and metastatic niches, tumor-derived extracellular vesicles (EVs) have recently arisen as crucial players in cell-to-cell communication and in the remodeling of distant microenvironments that favor organ-specific metastasis. Therefore, we sought to determine the role of tumor-derived EVs in the modulation of the liver microenvironment and their specific contribution to supporting metastatic colonization of the liver. The preliminary step to this process was to establish a model system to identify EV-associated targets and their effect on the ECM remodelling. Immunohistochemical analyses of primary colon tumour (CRC) and secondary liver metastases (CRC liver MET) tissue samples from patients with CRC revealed higher stromal TIMP1 levels in CRC liver MET than in CRC. The elevated stromal TIMP1 signature in the invasive front was associated with poor progression-free survival in patients with CRC liver MET. Our characterisation of the CRC tumour-derived EVs showed TIMP1 enrichment in the EVs (TIMP1EV) compared to its parental cell. Using cultures of primary liver fibroblasts, we could demonstrate that TIMP1 enrichment in the CRC-EVs was associated with regulation of TIMP1 levels in the EV-conditioned liver fibroblasts. Using our optimized ex vivo 3D ECM remodelling assay, we observed that pre-conditioning the liver fibroblasts with EVs from CRC cells promotes ECM remodelling. In accordance with our cell line model, we showed that serum-derived TIMP1EV from CRC patients promotes ECM remodelling. Moreover, high serum TIMP1EV expression in CRC liver MET patients was significantly associated with poor overall survival. In addition, our data also indicated that the determination of EV-associated TIMP1 is superior for non-invasive diagnosis than the analysis of soluble TIMP1 from total serum. Finally, we showed that HSP90AA is constitutively bound to TIMP1EV and that targeting HSP90AA leads to TIMP1 downregulation and inhibits ECM-mediated remodelling. This study defining the contribution of extravesicular TIMP1 to liver metastasis brings a novel insight into the molecular mechanisms through which tumor-secreted factors packaged via EVs promote remodelling of the liver microenvironment. The clinical significance of overexpression of extravesicular TIMP1 in patients with colorectal liver metastases highlights its potential as a prognostic biomarker and therapeutic target. With further clinical studies, Heparin and HSP90 inhibitors targeting the EV mediated TIMP1 regulation could be a putative treatment strategy to treat colorectal liver metastases.:Table of Contents Abbreviations v 1. Introduction 1 1.1 Colorectal cancer 1 1.1.1. Incidence and mortality 1 1.1.1. Tumor staging 2 1.1.1. Pattern of distant metastases in colorectal cancer 5 1.2 Colorectal liver metastases 6 1.2.1 Current evaluation and treatment strategies for colorectal liver metastases 7 1.2.2 The liver metastasis cascade - a multi-step process 10 1.3 Tumor microenvironment 12 1.3.1 Tumour-stroma interactions 15 1.3.2 ECM remodelling and its role in CRC tumor progression 17 1.4 Extracellular vesicles 21 1.4.1 EV types 21 1.4.2 Biogenesis and secretion of EVs 22 1.4.3 Molecular composition of EVs 24 1.4.4 Biological functions of EVs 26 1.4.5 EVs in Tumor microenvironment 28 1.4.6 EVs in Tumor-fibroblast communication 29 1.4.7 Role of EVs in colorectal cancer 31 1.5 Tissue inhibitor of metalloproteinases (TIMP1) 35 1.5.1 TIMP1 in cancer 37 2. Background and Research Aims 39 3. Material and Methods 40 3.1 Material 40 3.1.1 Devices 40 3.1.2 Additional material and equipment 42 3.1.3 Fine chemicals 43 3.1.4 Biochemicals 45 3.1.5 Primary antibodies 46 3.1.6 Secondary antibodies 47 3.1.7 Nucleic acids 47 3.1.8 Consumables 50 3.1.9 Softwares 51 3.2 Methods 52 3.2.1 Patients 52 3.2.2 Immunohistochemistry 52 3.2.3 Hematoxylin eosin staining 54 3.2.4 Cell lines 54 3.2.5 Primary liver fibroblast cell lines 54 3.2.6 Passaging and freezing of cells 55 3.2.7 Revival of frozen cells 55 3.2.8 Cell counting 56 3.2.9 EV Isolation from CRC cell lines 56 3.2.10 Isolation of serum-derived EVs from liquid biopsies 56 3.2.11 Characterisation of EVs 57 3.2.12 Treatment of Fibroblasts with EVs 58 3.2.13 Stimulation of PFs with recombinant TIMP1 59 3.2.14 RNA isolation 59 3.2.15 cDNA synthesis 59 3.2.16 Quantitative Real-Time PCR (qRT-PCR) 60 3.2.17 Protein quantification 61 3.2.18 Immunoblotting and co-immunoprecipitation 61 3.2.19 ELISA 62 3.2.20 TIMP1 Knock-Out (KO) and Over-Expression (OE) 62 3.2.21 17 AAG and HSP90AA antibody treatment 63 3.2.22 3D ECM-remodelling assay 63 3.2.23 PKH staining 65 3.2.24 In vivo experiments 65 3.2.25 DAPI staining 66 3.2.26 Tissue explant model 66 3.2.27 Statistical analysis and reproducibility 67 4. Results 68 4.1 Identification of TIMP1 as target molecule 68 4.1.1 Identification of TIMP1 as a target through data mining 68 4.1.2 Localization pattern of TIMP1 in CRC and CRC liver MET 70 4.1.3 Invasion front-specific overexpression of TIMP1 in the stroma of patients with CRC liver MET is associated with poor progression-free survival (PFS) 72 4.2 Model system to study CRC-EV mediated ECM remodelling 73 4.2.1 Investigating the role of CRC- derived EVs in the evolution of colorectal liver metastases 73 4.2.2 Characterizsation of isolated EVs from the CRC cell lines 74 4.2.3 TIMP1 enrichment in EVs derived from CRC cell lines 75 4.2.4 CRC-derived TIMP1EV regulates TIMP1 levels in recipient fibroblasts 76 4.2.5 TIMP1EV mediated TIMP1 upregulation in the recipient fibroblast is an EV-mediated effect 79 4.2.6 Recombinant TIMP-1 induces TIMP1 levels in recipient pFs in a time- and concentration-dependent manner 81 4.2.7 Alteration of TIMP1 levels in HCT 116 cells translates into EVs but does not affect EV packaging. 83 4.2.8 TIMP1EV levels in CRC EVs determine TIMP1 levels in recipient fibroblasts 85 4.2.9 EV-mediated TIMP1 upregulation in pFs induces ECM remodelling 86 4.2.10 TIMP1 levels in the PFs influence the extent of ECM remodelling 88 4.3 Clinical significance of TIMP1EV 89 4.3.1 TIMP1 enriched in serum-derived EVs of CRC patients compared to healthy controls 89 4.3.2 Serum derived TIMP1EV from CRC patients regulate TIMP1 levels in primary liver fibroblasts 91 4.3.3 Serum derived TIMP1EV from CRC patients promote ECM remodelling 93 4.3.4 TIMP1EV exhibits superior stratification power compared to soluble TIMP1 in liquid biopsies 93 4.3.5 TIMP1EV is a non-invasive independent prognostic marker in colorectal liver metastases 94 4.4 Targeting TIMP1EV mediated ECM remodelling 97 4.4.1 TIMP1EV binds to HSP90AA 97 4.4.2 HSP90 inhibition interferes with TIMP1 protein stabilisation 99 4.4.3 17AAG attenuates TIMP1EV-mediated ECM remodelling 101 4.5 EVs derived from murine CRC cell lines regulate TIMP1 levels in recipient fibroblasts 104 4.6 Increased homing of CRC EVs to the liver compared to other organs 106 4.7 TIMPEV regulates TIMP1 levels in liver tissues 108 5. Discussion 112 5.1 TIMP1 Localization and its significance in liver metastases 112 5.2 Model system to study the role of CRC-EVs in liver metastasis 113 5.3 In-vitro model to study the pro-metastatic effects of TIMP1EV 114 5.4 Serum-derived extravesicular TIMP1 and its pro-metastatic functions underlying remodeling of the extracellular matrix 116 5.5 Clinical significance of TIMP1EV in colorectal liver metastases 117 5.6 Scope of HSP90 inhibitors in the prevention and treatment of CRC liver metastases...……………………………………………………………………………………..118 6. Future perspectives and concluding remarks 120 7. Graphical summary of the findings 122 Zusammenfassung 123 Summary 125 List of figures 127 List of Tables 129 References 130 Acknowledgements 163 Appendix 165

Cirka 300 000 individer drabbas årligen i världen av oral cancer och mer än nittio procent av alla orala cancerformer utgörs av skivepitelcancer. Den femåriga prognosen är generellt 50 % och den 5-åriga relativa överlevnaden har under en tioårsperiod förblivit densamma. Detta motiverar utvecklingen av bättre prognostiska markörer och diagnostiska metoder för att tidigt identifiera de patienter som har risk att utveckla oral skivepitelcancer för att förbättra prognosen och minska lidandet genom tidig insatt behandling. β-catenin är en adhesionsmolekyl som är viktig för bibehållandet av cellulär integration och avvikelser i celladhesionsmolekyler tros spela en central roll när tumörceller invaderar närliggande vävnad det vill säga metastaserar till andra organ.Syftet med studien är att med hjälp av immunohistokemi undersöka om β-catenin kan fungera som en prognostisk markör för utvecklingen av oral skivepitelcancer. Detta görs genom att jämföra förekomsten av β-catenin med hjälp av monoklonala antikroppar i normalt skivepitel, dysplasi och cancer från 18 patienter som har diagnostiserats med oral skivepitelcancer. Infärgningen av Beta catenin jämfördes i normalt oralt skivepitel med cancer och dysplasi för alla biopsier för att undersöka om det förekommer någon skillnad av infärgningen. Förutom detta skedde även en jämförelse av normalt skivepitel med dysplasi och cancer inom varje enskild biopsi.Resultaten visade att det finns en skillnad i uttrycket av β-catenin i normalt skivepitel jämfört med dysplasi och cancer i denna patientgrupp. I denna studie visade mer än 70 % av biopsierna en stark eller måttlig och stark infärgning av β-catenin i normalt skivepitel, mer än 60 % av biopsierna visade en måttlig eller måttlig och svag infärgning av dysplasi och 58,8 % av alla biopsier visade svag infärgning eller ingen och svag infärgning av skivepitelcancer. Då studien visar att mängden av β-catenin är starkast i normalt oralt skivepitel, måttligt i dysplasi och svagast i cancer tyder detta på att β-catenin skulle kunna vara en viktig faktor i utvecklingen av skivepitelcancer i munhålan vilket stämmer väl överens med resultat från andra studier. / Approximately 300,000 individuals are affected every year in the world of oral cancer and more than ninety percent of all oral cancers consists of squamous cell carcinoma. The five-year prognosis is generally 50 % and the 5-year relative survival has over ten years remained the same. This motivates the development of better prognostic markers and diagnostic methods for the early identification of patients at risk of developing oral squamous cell carcinoma to improve prognosis and reduce the suffering of these patients with early treatment.β-catenin is an adhesion molecule that is important for the maintenance of cellular integration and abnormalities of cell adhesion molecules is thought to play a central role in tumorigenesis. The abnormalites is though to enhance tumour cells to break loose from neighbouring cells and invade nearby tissues and organs, however the exact mechanisms are unknown. The purpose of the study is that using immunohistochemistry to examine whether β-catenin may serve as a prognostic marker for the development of oral squamous cell carcinoma. This is done by examining the presence of β-catenin with monoclonal antibodies in 18 biopsies with normal squamous epithelia, dysplasia and cancer from 18 patients diagnosed with oral squamous cell carcinoma from the department of Oral Pathology at Malmö Högskola, Malmö. The staining of beta catenin was compared in normal oral squamous cancer and dysplasia for all biopsies to see whether there is any difference of dyeing. Besides this, there was also a comparison of normal squamous epithelium with dysplasia and cancer in each biopsy.The results showed that there is a difference in the expression of β-catenin in normal squamous epithelium, dysplasia and cancer in this population. In this study, more than 70 % of the biopsies expressed a strong or moderate and strong staining of β -catenin in normal oral squamous epithelium, more than 60 % of the biopsies showed a moderate or moderate and weak staining of dysplasia and 58.8 % of all biopsies showed weak or no staining and weak staining of squamous cell carcinoma.As the study shows that the amount of β -catenin is strongest in normal oral squamous epithelium, moderate in dysplasia and weakest in cancer, this suggests that β -catenin could be an important factor in the development of squamous cell carcinoma of the oral cavity which is in line with results from other studies.

Burkholderia cenocepcia is one of the serious infectious agents of respiratory tract among cystic fibrosis patients. There are problems mainly with strains which are capable of epidemic spread. The known epidemic in the Czech Republic was caused by ST32 strain in the past. In this work, there was completed whole genome sequence of referential isolate 1232 of B. cenocepacia ST32 in cooperation with bioinformatics by new generation sequencing techniques and by determining the problematic areas by a combination of Sanger sequencing bioinformatics approaches and manual assembling of sequence reads localized in these areas. The final version of the genome sequence was annotated by PGAAP and at the present time it is finalized. Second part of this work is dedicated to looking for a prognostic marker of infection caused by ST32 strain in patients with cystic fibrosis. We analysed the results of ST32 trancriptomic experiment and chose genes possibly connected with the cepacia syndrome - serious, mostly fatal state of infection. By quantitative PCR we compared their expression in isolates from 4 patients from time of cepacia syndrome and month before that. We checked the possibility of direct detection of the expression of these genes in clinical material. We identified genes for type III secretion system as...