Abstract Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive cancers, the 5-year survival rate being less than 5%. At the time of diagnosis, 90% of PDACs extend beyond the pancreas and distant metastases are often present. Due to aggressive growth, local expansion and early appearance of metastasis, primary PDAC tumours are local enough for curative surgical resection in only 10–20% of the cases. Adjuvant chemotherapy is indicated in these curative-treated cases, with slight improvement in survival. PDAC is considered to represent a heterogeneous group of biologically and prognostically different malignancies. Characterization of these subgroups is essential and there is an urgent need for more accurate biomarkers and targeted treatments in PDAC. In the current work, we immunohistochemically investigated the expression levels and prognostic values of oxidative stress markers (8-OHdG, Keap1, Prx I, II, III, V and VI), epigenetic histone modifiers (KDM4A, KDM4B, KDM4D and SIRT1–4), and cell-cycle regulators (p16, Rb, CDK4) and DNA-repair enzymes (FEN1 and MGMT) in the cohort of surgically treated PDAC patients. We found that Keap1 expression was associated with better pancreatic cancer-specific survival. Expression of antioxidative peroxiredoxins I, III, V and VI was also connected with a more favourable tumour characteristics and Prx I and VI showed prognostic value. When considering the biology of PDAC, we noticed that pivotal epigenetic regulation also occurred in exocrine pancreatic tissue adjacent to resection margins. Overexpression of the cell-cycle regulator CDK4 and the DNA-repair enzyme FEN1 in the whole population, and elevated expression level of MGMT in the most high-risk patients were connected with worse prognosis. The results of the study can be utilized in the future when individualized therapies are being designed for PDAC patients. Due to occurrence of the epigenetic regulation also in exocrine pancreatic tissue adjacent to resection margins, it could be evaluated in future for routine diagnostics and treatment optimization. The potential role of MGMT in the development of PDAC chemoresistance should be studied in the future. / Tiivistelmä Haiman duktaalinen adenokarsinooma (PDAC) on yksi aggressiivisimmista syöpäsairauksista. Viiden vuoden elossaoloennuste on vain lähellä 5 prosenttia. Diagnoosihetkellä 90% haiman adenokarsinoomista yltää haiman ulkopuolelle ja usein kasvain on jo lähettänyt etäpesäkkeitä. Kasvutaipumuksen sekä metastasoinnin takia kuratiivinen kirurginen hoito on mahdollista vain 10–20% tapauksista. Liitännäissolunsalpaajahoito on aiheellista näissä kuratiivistavoitteisesti hoidetuissa tapauksissa. Kuitenkin vaikutus kokonaiselossaoloaikaan on melko vähäinen. Uusimman tutkimustiedon valossa PDAC:aa pidetäänkin heterogeenisenä ryhmänä biologisesti ja ennusteellisesti erilaisia tautiryhmiä. Näiden tautiryhmien tunteminen ja tunnistaminen riittävän tarkkojen merkkiaineiden avulla olisi ensiarvoisen tärkeää, jotta hoitoja voitaisiin kohdentaa niistä hyötyville potilaille. Väitöskirjatutkimuksessa selvitimme immunohistokemiallisin menetelmin oksidatiivisen stressin merkkiaineiden (8-OHdG, Keap1, Prx I, II, III, V ja VI), epigeneettisten histonimodifikaattorien (KDM4A, KDM4B, KDM4D ja SIRT1–4) sekä solusyklin säätelijöiden (p16, Rb, CDK4) ja DNA-korjausentsyymien (FEN1 ja MGMT) ilmentymistä ja ennusteellista arvoa kirurgisesti hoidetuilla PDAC-potilailla. Tutkimuksessamme totesimme, että kasvainkudoksen Keap1-ilmentymä yhdistyi parempiennusteiseen taudinkuvaan. Antioksidatiivisten peroksiredoksiinien I, III, V ja VI ilmentyminen yhdistyi niin ikään suotuisampaan kasvaimen fenotyyppiin ja Prx I ja VI osoittivat ennusteellista arvoa. Havaitsimme lisäksi, että PDAC:n biologiaan keskeistesti vaikuttavaa epigeneettistä säätelyä tapahtuu myös malignin haimakudoksen viereisessä eksokriinisessä haimakudoksessa. Solusyklin säätelijä CDK4:n ja DNA-korjausentsyymi FEN1:n voimakas ilmentyminen koko tutkimuspopulaatiossa sekä kohonnut MGMT:n ilmentyminen korkeimman riskin potilailla yhdistyivät huonompaan taudin ennusteeseen. Väitöskirjatyön tutkimustuloksia voidaan tulevaisuudessa hyödyntää, kun tutkitaan yksilöllisiä hoitomuotoja PDAC-potilailla. Koska epigeneettistä säätelyä tapahtuu myös syövän viereisessä eksokriinisessa haimakudoksessa, voidaan tulevaisuudessa tämän kudoksen arviointia mahdollisesti käyttää rutiinisti diagnostiikassa sekä hoidon optimoinnissa. MGMT:n mahdollinen rooli PDAC:n kemoresistenssin kehittymisessä tulisi tulevaisuudessa selvittää.

Les cancers sont l’une des causes majeures de mortalité dans le monde. Les mécanismes en jeu dans la croissance tumorale sont qualitativement connus, mais on se sait pas à l’heure actuelle prédire précisément quel sera le développement d’une tumeur donnée, ni estimer de façon certaine le protocole thérapeutique optimal pour chaque patient. Il est entendu que la modélisation mathématique pourrait apporter des éléments de réponse à ces questions. Durant cette thèse on s'est alors intéressé à la construction de formalismes mathématiques pour décrire la croissance tumorale et l’action de traitement anti-cancéreux. En particulier, on s'est intéressé à la prise en compte des mécanismes aussi bien moléculaires que cellulaires et tissulaires, par la construction d’un modèle continu, multi-échelles, de croissance de tumeur solide et d’angiogenèse. A partir de ce modèle, nous a pu envisager de façon qualitative un protocole optimal de combinaison entre un anti-angiogénique et une chimiothérapie.Le modèle multi-échelles inclut une représentation mathématique des voies de signalisation du VEGF dont on détaille la construction.Dans une autre approche, on a considéré un modèle discret, cellule-centré, reproduisant le développement de sphéroïdes de cellules épithéliales mammaires telles qu’observées lorsque ces cellules sont cultivées in vitro. On a pu mettre en évidence les différents mécanismes cellulaires impliqués dans la morphogenèse de structures composées de cellules saines, et celles composées de cellules mutées.Ces contributions montrent l’intérêt du formalisme multi-échelles adopté pour intégrer les connaissances et données sous-jacentes à l’étude du traitement des tumeurs. / Cancer is one of the leading causes of death in Europe. The mechanisms involved in tumour growth are qualitatively known, but we are still unable to precisely predict how a given tumour will evolve, nor estimate with certainty the optimal therapeutic protocol for each patient.It is well understood that mathematical modelling could give part of the answer to these questions. That is why during this thesis we considered the building of mathematical formalisms to describe tumour growth and the action of anti-cancer treatments. In particular, we investigated the molecular to tissular mechanisms of cancer development and angiogenesis through the building of a continuous multi-scale model. We were able to reproduce the effect of anti- angiogenesis treatments on tumour growth, and qualitatively study an optimal therapeutic protocol of anti-angiogenic combined with cytotoxic drugs. This multi-scale model integrates a mathematical representation of the signalling pathways of VEGF (Vascular Endothelial Growth Factor). We detail the development of this model which is based solely on information available in the literature and dedicated databases. In another approach, we considered a discrete, cell-based model to reproduce the development of spheroid structures of mammary epithelial cells. This model considers the behaviour of these cells when observed while grown in vitro in an appropriate medium. We were able to highlight the different mechanisms involved in the morphogenesis of wild and mutated cells structures.This work shows the importance of the multi-scale formalism we used to integrate the knowledge and data related to the study of cancer treatment.

Submitted by Fabio Sobreira Campos da Costa (fabio.sobreira@ufpe.br) on 2017-04-07T12:49:00Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Tese Mayara final [08-09-2016].pdf: 6000027 bytes, checksum: 8aba9ff907d1176a530d19ec2bb6fad1 (MD5) / Made available in DSpace on 2017-04-07T12:49:00Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Tese Mayara final [08-09-2016].pdf: 6000027 bytes, checksum: 8aba9ff907d1176a530d19ec2bb6fad1 (MD5) Previous issue date: 2015-09-02 / CAPES / Doença inflamatória intestinal descreve um grupo heterogêneo de doenças inflamatórias crônicas do trato gastrointestinal. Os dois principais tipos de DII são retocolite ulcerativa idiopática e doença de Crohn. A patogênese dessas doenças é caracterizada pela inflamação persistente no intestino, envolvendo uma interação entre fatores genéticos, ambientais e imunológicos. Foram investigados aspectos clínico-epidemiológicos e analisados os polimorfismos dos genes da reposta imune em pacientes brasileiros com doença inflamatória intestinal em diferentes formas anátomo-clínicas. Um total de 101 pacientes foram analisados (43 - retocolite ulcerativa idiopática e 58 - doença de Crohn) para os polimorfismos dos genes do fator de necrose tumoral alfa (TNF-α -308 G/A; rs1800629), interleucina-10 (IL-10 -1082 G/A; rs1800896), domínio do recrutamento e ativação da caspase 15/receptor tipo NOD2 (CARD15/NOD2; rs2066844 e rs2066845), receptor tipo NOD contendo domínio pirina – NLRP1 (rs12150220), NLRP3 (rs35829419) e interleucina -1beta (IL-1β -511T/C; rs16944). A forma anatómica-clínica de DC predominante foi a fistulizante (29,31%), seguida por inflamatória (27,58%) e estenosante (27,58%). O grupo controle foi composto por 91 indivíduos saudáveis. Os genes do receptor tipo NOD contendo domínio pirina 1 e 3 e do domínio do recrutamento e ativação da caspase 15/receptor tipo NOD2 variantes R702W e G908R não foram associados à susceptibilidade a doença inflamatória intestinal. Em relação ao polimorfismo da interleucina 10, nenhuma diferença estatística foi encontrada entre os genótipos e alelos para a doença inflamatória intestinal comparado aos controles. Fator de necrose tumoral alfa mostrou uma associação estatisticamente significativa entre pacientes e controles de retocolite ulcerativa idiopática que sugere que a presença do alelo A predispõe o aparecimento de retocolite ulcerativa idiopática, mas não doença de Crohn. Verificou-se ainda que o genótipo AG da interleucina 1 foi associado com o desenvolvimento de retocolite ulcerativa idiopática. Os resultados sugerem que os polimorfismos de única base do fator de necrose tumoral alfa e da interleucina 1 estão envolvidos com a retocolite ulcerativa idiopática e podem contribuir para a patogênese na população brasileira estudada. / Inflammatory bowel disease describes a heterogeneous group of chronic inflammatory diseases of the gastrointestinal tract. The two main types of inflammatory bowel disease are ulcerative colitis and Crohn disease. The pathogenesis of the disease is characterized by unpredictable attacks of inflammation of the intestine, besides involving an interaction between genetic, environmental and immunological factors. Clinical and epidemiological aspects were investigated and the polymorphisms of genes of the immune response in Brazilian patients with inflammatory bowel disease in different anatomic-clinical forms were analyzed. A total of 101 patients were analyzed (43 - ulcerative colitis and 58 - Crohn disease) for the tumour necrosis factor alpha (TNF-α -308 G/A; rs1800629), interleukin-10 (IL-10 -1082 G/A; rs1800896), caspase activation and recruitment domains 15/ NOD like receptor 2 (CARD15/NOD2; rs2066844 and rs2066845), NOD like receptor pyrin domain containing – NLRP1 (rs12150220), NLRP3 (rs35829419) and interleukin-1beta (IL-1β 511T/C; rs16944) genes polymorphisms. The anatomic-clinical form of Crohn disease predominant was the fistulizing (29.31%), followed by inflammatory (27.58%) and stricturing (27.58%). A control group was composed by 91 healthy subjects group. NOD like receptor pyrin domain containing 1 and 3 and caspase activation and recruitment domains 15/ NOD like receptor 2 genes R702W and G908R variants were not associated to inflammatory bowel disease susceptibility. With respect to the polymorphism of interleukin-10, no statistical difference was found between the genotypes and alleles for inflammatory bowel disease compared to controls. Tumour necrosis factor alpha showed a statistically significant association between ulcerative colitis patients and controls which suggests that the presence of A allele predisposes the onset of ulcerative colitis but not Crohn disease. It was found yet that AG genotype of interleukin-1beta was associated with the development of ulcerative colitis. The results suggest that the tumour necrosis factor alpha and interleukin-1beta single nucleotide polymorphisms are involved with ulcerative colitis and may be contributing to pathogenesis in Brazilian population.

My research was focused on understanding the importance of mammalian RAD51 paralogs in genome maintenance and suppression of tumorigenesis. The investigation carried out during this study has been addressed toward gaining more insights into the involvement of RAD51 paralogs in DNA damage signalling, repair of various types of lesions including double stranded breaks (DSBs), daughter strand gaps (DSGs), interstrand crosslinks (ICLs), and in the protection of stalled replication forks. My study highlights the molecular functions of RAD51 paralogs in Fanconi anemia (FA) pathway of ICL repair, in the ATM and ATR mediated DNA damage responses, in homologous recombination (HR), and in the recovery from replication associated lesions. My research also focused on the development of a novel photoinducible ICL agent for targeted cancer therapy. The thesis has been divided into following sections as follows: Chapter I: General introduction that describes about DNA damage responses and the known functions of RAD51 paralogs across species in DNA repair and checkpoint The genome of every living organism is susceptible to various types of DNA damage and mammalian cells are evolved with various DNA damage surveillance mechanisms in response to DNA damages. In response to DNA damage, activated checkpoints arrest the cell cycle progression transiently and allow the repair of damaged DNA. Upon completion of DNA repair, checkpoints are deactivated to resume the normal cell cycle progression. Defective DNA damage responses may lead to chromosome instability and tumorigenesis. Indeed, genome instability is associated with several genetic disorders, premature ageing and various types of cancer in humans. The major cause of chromosome instability is the formation of DSBs and DSGs. Both DSBs and DSGs are the most dangerous type of DNA lesions that arise endogenously as well as through exogenous sources such as radiations and chemicals. Spontaneous DNA damage is due to generation of reactive oxygen species (ROS) through normal cellular metabolism. Replication across ROS induced modified bases and single strand breaks (SSBs) leads to DSGs and DSBs, respectively. Such DNA lesions need to be accurately repaired to maintain the integrity of the genome. To understand the various cellular responses that are triggered after different types of DNA damage and the possible roles of RAD51 paralogs in these processes, chapter I of the thesis has been distributed in to multiple sections as follows: Briefly, the initial portion of the chapter provides a glimpse of various types of DNA damage responses and repair pathways to deal with the lesions arising from both endogenous as well as exogenous sources. Owing to the vast range of cellular responses and pathways, the following section provides the detailed description and mechanisms of various pathways involved in taking care of wide range of DNA lesions from SSBs to DSBs. Subsequent section of chapter I provides a comprehensive description of maintenance of genome stability at the replication fork and telomeres. Germline mutations in the genes that regulate genome integrity cause various genetic disorders and cancer. Mutations in ATM, ATR, MRE11, NBS1, BLM and FANC (1-16), BRCA1 and BRCA2 that are known to regulate DNA damage signaling, DNA repair and genome integrity lead to chromosome instability disorders such as ataxia-telangiectasia, ATR-Seckel syndrome, AT-like disorder, Nijmegen breakage syndrome, Bloom syndrome, FA, and breast and ovarian cancers respectively. Interestingly, RAD51 paralog mutations are reported in patients with FA-like disorder and various types of cancers including breast and ovarian cancers. Mono-allelic germline mutations in all RAD51 paralogs are reported to cause cancer in addition to the reported cases of FA-like disorder with bi-allelic germline mutations in RAD51C and XRCC2. In accordance, the last section of the chapter has been dedicated to describe the genetics of breast and ovarian cancers and the known functions of tumor suppressors such as BRCA1, BRCA2 and RAD51 paralogs in the protection of genome. Despite the identification of five RAD51 paralogs nearly two decades ago, the molecular mechanism(s) by which RAD51 paralogs regulate HR and genome maintenance remain obscure. To gain insights into the molecular mechanisms of RAD51 paralogs in DNA damage responses and their link with genetic diseases and cancer, the following objectives were laid for my PhD thesis: 1) To understand the functional role of RAD51 paralog RAD51C in FA pathway of ICL repair and DNA damage signalling. 2) To dissect the ATM/ATR mediated targeting of RAD51 paralog XRCC3 in the repair of DSBs and intra S-phase checkpoint. 3) To uncover the replication restart pathway after transient replication pause and the involvement of distinct complexes of RAD51 paralogs in the protection of replication forks. 4) To design photoinducible ICL agent that can be activated by visible light for targeted cancer therapy. Chapter II: Distinct roles of FANCO/RAD51C protein in DNA damage signaling and repair: Implications for Fanconi anemia and breast cancer susceptibility RAD51C, a RAD51 paralog has been implicated in HR. However, the underlying mechanism by which RAD51C regulates HR mediated DNA repair is elusive. In 2010, a study identified biallelic mutation in RAD51C leading to FA-like disorder, whereas a second study reported monoallelic mutations in RAD51C associated with increased risk of breast and ovarian cancers. However, the role of RAD51C in the FA pathway of DNA cross-link repair and as a tumor suppressor remained obscure. To understand the role of RAD51C in FA pathway of ICL repair and DNA damage response, we employed genetic, biochemical and cell biological approaches to dissect out the functions of RAD51C in genome maintenance. In our study, we observed that RAD51C deficiency leads to ICL sensitivity, chromatid-type errors, and G2/M accumulation, which are hallmarks of the FA phenotype. We found that RAD51C is dispensable for ICL unhooking and FANCD2 monoubiquitination but is essential for HR, confirming the downstream role of RAD51C in ICL repair. Furthermore, we demonstrated that RAD51C plays a vital role in the HR-mediated repair of DSBs associated with replication. Finally, we showed that RAD51C participates in ICL and DSB induced DNA damage signaling and controls intra-S-phase checkpoint through CHK2 activation. Our analyses with pathological mutants of RAD51C displayed that RAD51C regulates HR and DNA damage signaling distinctly. Together, these results unravel the critical role of RAD51C in the FA pathway of ICL repair and as a tumor suppressor. Chapter III: ATM-and ATR-mediated phosphorylation of XRCC3 regulates DNA double-strand break-induced checkpoint activation and repair The RAD51 paralogs XRCC3 and RAD51C have been implicated in HR and DNA damage responses, but the molecular mechanism of their participation in these pathways remained obscured. In our study, we showed that an SQ motif serine 225 in XRCC3 is phosphorylated by ATR kinase in an ATM signaling pathway. We found that RAD51C in CX3 complex but not in BCDX2 complex is essential for XRCC3 phosphorylation, and this modification follows end resection and is specific to S and G2 phases. XRCC3 phosphorylation was found to be required for chromatin loading and stabilization of RAD51 and HR-mediated repair of DSBs. Notably, in response to DSBs, XRCC3 participates in the intra-S-phase checkpoint following its phosphorylation and in the G2/M checkpoint independently of its phosphorylation. Strikingly, we found that XRCC3 distinctly regulates recovery of stalled and collapsed replication forks such that phosphorylation was required for the HR-mediated recovery of collapsed replication forks but is dispensable for the recovery of stalled replication forks. Together, our findings suggest that XRCC3 is a new player in the ATM/ATR-induced DNA damage responses to control checkpoint and HR-mediated repair. Chapter IV: RAD51 paralogs protect stalled forks and mediate replication restart in an FA-BRCA independent manner Mammalian RAD51 paralogs RAD51 B, C, D, XRCC2 and XRCC3 are critical for genome maintenance. To understand the crucial roles of RAD51 paralogs during spontaneously arising DNA damage, we have studied the RAD51 paralogs assembly during replication and examined the replication fork stability and its restart. We found that RAD51 paralogs are enriched onto the S-phase chromatin spontaneously. Interestingly, the number of 53BP1 nuclear bodies in G1-phase and micro-nucleation which serve as markers for under replicated lesions increases after genetic ablation of RAD51C, XRCC2 and XRCC3. Furthermore, we showed that RAD51 paralogs are specifically enriched at two major fragile sites FRA3B and FRA16D after replication fork stalling. We found that all five RAD51 paralogs bind to nascent DNA strands after replication fork stalling and protect the fork. Nascent replication tracts created before fork stalling with hydroxyurea degrade in the absence of RAD51 paralogs but remain stable in wild-type cells. This function was dependent on ATP binding at the walker A motif of RAD51 paralogs. Our results also suggested that RAD51 paralogs assemble into BCDX2 complex to prevent generation of DSBs at stalled replication forks, thereby safeguarding the pre-assembled replisome from the action of nucleases. Strikingly, we showed that RAD51C and XRCC3 in complex with FANCM promote the restart of stalled replication forks in an ATP hydrolysis dependent manner. Moreover, RAD51C R258H mutation that was identified in FA-like disorder abrogates the interaction of RAD51C with FANCM and XRCC3, and prevents fork restart. Thus, assembly of RAD51 paralogs in different complexes prevents nucleolytic degradation of stalled replication forks and promotes restart to maintain genomic integrity. Chapter V: Trans-dichlorooxovandium(IV) complex as a potent photoinducible DNA interstrand crosslinker for targeted cancer therapy Although DNA ICL agents such as MMC, cisplatin and psoralen are known to serve as anticancer drugs, these agents affect normal cells as well. Moreover, tumor resistance to these agents has been reported. We have designed and synthesized a novel photoinducible DNA crosslinking agent (ICL-2) which is a derivative of oxovanadiumterpyridine complex with two chlorides in trans position. We found that ICL-2 can be activated by UV-A and visible light to enable DNA ICLs. ICL-2 efficiently activated FA pathway of ICL repair. Strikingly, photoinduction of ICL-2 induces prolonged activation of cell cycle checkpoint and high degree of cell death in FA pathway defective cells. Moreover, we showed that ICL-2 specifically targets cells that express pathological RAD51C mutants. Our findings suggest that ICL-2 can be potentially used for targeted cancer therapy in patients with gene mutations in FA and HR pathway.

Breast cancer is a global public health problem since it is the most frequently diagnosed cancer in women in Western countries. Clinical guidelines for breast cancer prognosis/diagnosis are currently based on tumour size, histological type and grade, lymph node status as well as the expression of various cellular receptors. Yet, current predictions remain unsatisfactory to identify the best treatment for the individual patient. The search for identifying new predictive and prognostic factors is ongoing. Furthermore, compelling evidences have solidified the notion that the evolving epithelial cells, founders of the breast disease, are helped in their malignant course by the tumour microenvironment. Better characterizing the dual effect of the immune regulation but also the epithelial-stromal cross-talk on both tumour-promotion and -suppression is essential for understanding patient uniqueness and their implication in disease outcome. Because of its potential to probe tissues and cells at the molecular level without requirement for extrinsic contrast agents, infrared spectroscopy was seen as an attractive tool for clinical and diagnostic analysis in order to complement the existing methods. <p>In a first step, recording and processing methodology had to be defined in order to optimally compare IR spectra. The methodology developed and the analysis tools tested on carcinoma cell lines, demonstrated that spectra could be distinguished based on the cell line phenotypic nature. <p>The potential of IR imaging for breast tissular structure differentiation was highlighted in this thesis, demonstrating that spectral signature can be correlated with the major histological cell types observed in breast disease tissues. In order to develop a robust algorithm translating spectral data into helpful histopathological information, a spectral database of histologically well-defined breast tissues was built and used for the development of a cell type classifier. This latter one was extensively validated on independent clinical cases. Firstly, the IR-based histopathological classifier correctly assigned spectra acquired on eleven breast disease samples based on their histological nature. Secondly, lymphocyte and Collagen & Fibroblasts spectral signatures were demonstrated to be independent from tissue type and organ since, although trained on reference spectra recorded into breast disease samples, the cell type classifier correctly assigned spectra acquired on lymph nodes/tonsils and scar tissues respectively. Thirdly, we concluded that spectroscopically, breast carcinoma cell lines in culture are well-suited tumour models since spectra acquired on these carcinoma cell lines were correctly recognized as epithelium by the IR-based histological classifier. <p>By spectral characterizing lymphocytes from lymph nodes and tonsils, we demonstrated that the spectra acquired contained enough information to statistically discriminate them according to their lymphocyte activation states. Although considered as activated, the breast disease lymphoid infiltrates were found to present distinct spectral signature from lymphocytes acquired on activated lymph nodes and tonsils. Furthermore, tumour microenvironment, characterized by IR-imaging was demonstrated to exhibit a distinct spectral signature from wound healing tissues. These studies proved the uniqueness of the signature of both lymphoid infiltrate and tumour microenvironment in breast disease context. Correlating these specific spectral signatures to patient outcome and therapeutics response could help better consider the uniqueness of the patient. In a last step, considering the epithelial signature of carcinomas of both low and high grades, we demonstrated that the biochemical information reflected in the IR micro-spectra was clinically relevant for grading purpose.<p><p> <p><p>Le cancer du sein est le cancer le plus fréquemment diagnostiqué chez les femmes dans les pays occidentaux. Jusqu’à peu, les cellules épithéliales tumorales étaient vues comme les seuls acteurs de la carcinogenèse ;processus se déroulant dans un milieu extracellulaire considéré au pire comme passif ou permissif à l’évolution tumorale des cellules épithéliales adjacentes. Cependant, de nombreuses études ont montré que ce microenvironnement tumoral pouvait soit promouvoir le processus de carcinogenèse soit le combattre empêchant par la même, l’occurrence de la maladie. <p>Ce projet de thèse s’inscrit dans une problématique actuelle, à savoir une meilleure compréhension de la maladie mais également une prise en charge plus individualisée des patientes. Nous abordons ici une voie de recherche novatrice basée sur la signature globale des molécules cellulaires via leur spectre infrarouge. La technologie utilisée, à savoir la spectroscopie infrarouge, nous fournit une observation quantitative et qualitative de milliers de vibrations moléculaires. L’adaptation de réseaux de plusieurs milliers de détecteurs indépendants aux microscopes infrarouges permet, grâce aux méthodes statistiques multivariées, d’investiguer l’architecture macromoléculaire des cellules au sein d’une coupe tissulaire et de corréler les informations spectrales ainsi obtenues à l’histopathologie des tissus. Par cette technologie, nous visons à mettre au point un outil diagnostique et pronostique pour le cancer du sein basé sur l’imagerie IR. <p>Durant ce projet, nous avons montré que les différents types cellulaires observés dans les carcinomes mammaires pouvaient être distingués par le biais de leur spectre IR, qu’un modèle de reconnaissance histologique pouvait être construit, validé et surtout automatisé et que ce modèle pouvait être transposé à l’étude d’autres tissus (ganglions, amygdales et cicatrices) et d’autres types d’échantillons (cellules épithéliales en culture). Nous avons également montré que les spectres de cellules épithéliales pouvaient être corrélés au grade histopathologique de la tumeur. Les spectres acquis de ganglions/amygdales ont montré que les profils spectraux pouvaient être corrélés à l’état d’activation lymphocytaire. De plus, l’étude de l’état d’activation lymphocytaire et fibroblastique a permis de mettre en avant un profil spectral propre et bien distinct des infiltrats lymphocytaires d’une part et de la matrice extracellulaire aux abords des tumeurs invasives d’autre part. <p> / Doctorat en Sciences agronomiques et ingénierie biologique / info:eu-repo/semantics/nonPublished

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Abstract Background and aims: Stage and grade are the most widely used prognostic parameters for renal cell carcinoma (RCC). The clinical course of this disease is not, however, always predictable by traditional prognostic factors. In the era of new molecular targeted therapies a more accurate prognostication of RCC patient survival is important for the individualization of treatment and follow-up of patients. Despite exhaustive research there are still no prognostic biomarkers for RCC in clinical practice. In order to find novel prognostic tissue markers for RCC, we examined the expression of 14 biomarkers involved in carcinogenesis and clarified their prognostic significance in RCC. Material and methods: Out of 189 consecutive patients who underwent surgery for kidney cancer at Oulu University Hospital in the 1990s, 152 patients with histologically verified RCC were included in this study. The stage distribution was 70 (46%), 12 (8%), 51 (34%) and 19 (12%) patients with stages I-IV, respectively. The majority of the tumours (83 tumours, 55%) were nuclear grade II and 5 (3%), 40 (27%) and 22 (15%) of the tumours were grades I, III and IV, respectively. Clinical and follow-up data were obtained from patient records, the Finnish Cancer Registry and on demand from the Population Register Centre of Finland. The biomarkers studied included markers of the oxidative and neuroendocrine systems as well as proteins related to cell adhesion and migration, invasion, metastasis, inflammation and immune responses. The expression of various biomarkers was characterized via immunohistochemical tests of archival tumour material. The staining intensity was compared to clinicopathological parameters and patient RCC-specific survival. Results: The 5-year RCC-specific survival was 77%. The expression of Toll-like receptor 9 (TLR9) was an independent marker of favourable RCC-specific survival whereas cytoplasmic myosin VI expression was found to be an independent prognostic factor of poor RCC-specific survival. Cell culture experiments showed how cyclooxygenase-2 (COX-2) expression is regulated by HuR in RCC. HuR and COX-2 immunoexpression were also related to decreased RCC-specific survival. Immunostaining of Keap1 was associated with advanced RCC and a marker of a poorer RCC-specific prognosis. The expression of different neuroendocrine markers was evaluated but we could not establish any prognostic value for them. Conclusions: In particular, TLR9, HuR and myosin VI can be regarded as promising novel prognostic biomarkers in RCC. Stage, however, is the most important single prognostic factor for RCC. / Tiivistelmä Munuaissyöpä on vuosikymmenten ajan jatkuvasti yleistynyt. Vaikka se diagnosoidaan nykyisin useimmiten sattumalöydöksenä vatsan alueen kuvantamistutkimuksissa ja hoitomenetelmät ovat viime vuosikymmenten aikana kehittyneet, munuaissyöpäkuolleisuus ei ole laskenut. Munuaissyövän ennusteen määrittäminen voi olla haasteellista. Perinteiset ennustetekijät, levinneisyys ja erilaistumisaste, eivät riitä selittämään kaikkien potilaiden taudinkulkua, eikä munuaissyövälle vielä ole kliinisessä käytössä ennusteellista merkkiainetta. Munuaissyöpähoitojen kehittyessä taudinkulun ennustaminen on yhä tärkeämpää, jotta potilaiden hoito ja seuranta voidaan yksilöidä. Tämän väitöskirjatyön tarkoituksena oli etsiä uusia ennusteellisia kudosmerkkiaineita munuaissyöpäkasvaimille. Väitöskirjatutkimus perustuu 1990-luvulla Oulun yliopistollisessa sairaalassa leikatun 152 munuaissyöpäpotilaan aineistoon. Lähes puolet aineiston kasvaimista edusti levinneisyysluokkaa I, ja yli puolet munuaissyöpäkasvaimista oli hyvin erilaistuneita (tumagradus I ja II). Tutkimuspotilaista kerättiin kattavat seurantatiedot. Leikkauksessa poistettujen munuaissyöpäkasvainten arkistomateriaalista tutkittiin eri merkkiaineiden ilmenemistä. Tutkitut merkkiaineet käsittivät oksidatiivisen ja neuroendokriinisen järjestelmän merkkiaineita sekä valkuaisaineita, jotka liittyvät keskeisiin syövän ominaisuuksiin, kuten solujen välisiin liitoksiin ja solujen liikkumiseen sekä etäpesäkkeiden syntymiseen. Lisäksi tutkittiin merkkiaineita, jotka liittyvät tulehdusreaktioihin ja immuunipuolustukseen. Väitöskirjatutkimus paljasti useita uusia kudosmerkkiaineita, joiden ilmeneminen munuaissyöpäkasvaimessa on yhteydessä potilaan ennusteeseen. Näistä merkittävimpiä ovat myosiini VI, joka liittyy syöpäkasvainten metastasointiin, sekä immuunipuolustuksessa vaikuttava Tollin kaltainen reseptori 9 (Toll-like receptor 9, TLR9). Molemmat merkkiaineet osoittautuivat itsenäisiksi ennustetekijöiksi munuaissyövässä. Muita ennusteeseen vaikuttavia merkkiaineita ovat tutkimuksen mukaan oksidatiivista stressiä aistiva Keap1 sekä immunologisiin reaktioihin liittyvä syklo-oksigenaasi 2 (COX-2) ja sen ilmenemistä säätelevä HuR.

Breast cancer (BC) is one of the deadliest forms of cancers with high incidence and mortality rates, especially in women. Encouragingly, targeted therapies have improved the overall<br>survival and quality of life in patients with various subtypes of BC. Unfortunately, these first-line therapies often fail due to inherent as well as acquired resistance of cancer cells. Treatment evading cancer cells can exhibit systemic dormancy in patients over a long period of time without manifesting any symptoms. In a suitable environment, these undetected disseminated tumor cells can relapse in the form of metastasis. Therefore, it is essential to understand the mechanisms of<br><div>BC recurrence and to develop durable therapeutic interventions to improve patient’s survival. In this dissertation work, we studied fibroblast growth factor receptors (FGFR), as therapeutic targets to treat the recurrence of drug-resistant and immune-dormant BC metastasis. <br></div><div><br></div><div>The HER2 subtype of BC is characterized by the overexpression of human epidermal growth factor receptor 2 (HER2), which drives elevated downstream signaling promoting tumorigenesis. Trastuzumab emtansine (T-DM1) is an antibody-drug conjugate in which an anti-HER2 antibody targets HER2 overexpressing tumor cells and delivers a highly potent microtubule inhibitor. Using novel models of minimal residual disease (MRD) following T-DM1 treatments, we found that epithelial to mesenchymal transition is a critical process for cells to persist the TDM1 treatments. The upregulation of FGFR1 may facilitate insensitivity to T-DM1. Our data also showed that FGFR1 overexpression in HER2+ tumors leads to a higher incidence of recurrence, and these recurrent tumors show sensitivity towards covalent inhibition of FGFR. <br></div><div><br></div><div>In addition to drug-induced MRD in the primary tumor sites, disseminated tumor cells (DTCs) can demonstrate dormant phenotype via maintaining an equilibrium with immunemediated tumor clearance. Factors affecting such equilibrium may contribute to the recurrence of breast cancers metastasis. We show that such immune-mediated dormancy can be modeled with the 4T07 tumors. These tumors display immune-exclusion phenotypes in metastatic pulmonary organs. The inhibition of FGFR modulates the immune cell compositions of pulmonary organs favoring anti-tumor immunity. However, inhibition of FGFR may also affect T cell receptor downstream signaling, resulting in the inhibition of cytolytic T cell’s function. Finally, we report that combination therapy using the FGFR kinase inhibitor and an immune checkpoint blockade showed effective targeting of metastatic 4T07 tumors. <br></div><div><br></div><div>FGFR signaling as a therapeutic target in various tumors has been an active focus of cancer research. In this dissertation work, we have expanded our understanding of the role of FGFR in the recurrence of drug-resistant breast cancers as well as in the maintenance of an immune evasive microenvironment promoting pulmonary growth of tumors. Moreover, we presented evidence that it is possible to repurpose FGFR targeted therapy alone or in combination with checkpoint blockades to target recurrent metastatic BCs. In the future, our novel models of minimal residual diseases and systemic immune dormancy may act as valuable biological tools to expand our understanding of the minimal residual disease and dormant tumor cells.</div>

Background: Hibernomas are rare benign soft-tissue tumours arising from brown fat tissue. Although imaging characteristics are not specific certain imaging features, common locations and patient demographics may suggest hibernoma as a differential diagnosis. Case presentation: We report on two 48-year-old male patients with hibernoma. The tumour presented with local swelling of the inguinal region in the first patient and was an incidental imaging finding in the second patient. Imaging included magnetic resonance imaging in both patients and computed tomography as well as 18 F-fluorodeoxyglucose positron emission tomography-computed tomography in the second patient. In both cases histological diagnosis was initially based on excisional and needle core biopsy, respectively. Complete surgical resection confirmed the diagnosis of hibernoma thereafter. Conclusion: In soft tissue tumours with fatty components hibernoma may be included into the differential diagnosis. Because of the risk of sampling errors in hibernoma-like tissue components of myxoid and well-differentiated liposarcoma, complete resection is mandatory. This article also reviews the current imaging literature of hibernomas.

Background To investigate vascular-related pathophysiological characteristics of two human lung cancers with modifiable vascularisation using MRI and CT. Methods Tumour xenografts with modifiable vascularisation were established in 71 rats (approval by the Animal Care Committee was obtained) by subcutaneous transplantation of two human non-small-cell lung cancer (NSCLC) cells (A549, H1299) either alone or co-transplanted with vascular growth promoters. The vascularity of the tumours was assessed noninvasively by MRI diffusion-weighted-imaging (DWI), T2-weighted, and time-of-flight (TOF) sequences) as well as contrast-enhanced CT (CE-CT), using clinical scanners. As a reference standard, histological examinations (CD-31, fluorescent beads) were done after explantation. Results Microvessel density (MVD) was higher in co-transplanted tumours (171 ± 19 number/mm2) than in non-co-transplanted tumours (111 ± 11 number/mm2; p = 0.002). Co-transplanted tumours showed higher growth rates and larger tumour vessels at TOF-MRI as well as larger necrotic areas at CE-CT. In co-transplanted tumours, DWI revealed higher cellularity (lower minimal ADCdiff 166 ± 15 versus 346 ± 27 mm2/s × 10−6; p < 0.001), highly necrotic areas (higher maximal ADCdiff 1695 ± 65 versus 1320 ± 59 mm2/s × 10−6; p < 0.001), and better-perfused tumour stroma (higher ADCperf 723 ± 36 versus 636 ± 51 mm2/s × 10−6; p = 0.005). Significant correlations were found using qualitative and quantitative parameters: maximal ADCperf and MVD (r = 0.326); maximal ADCdiff and relative necrotic volume on CE-CT (r = 0.551); minimal ADCdiff and MVD (r = −0.395). Conclusions Pathophysiological differences related to vascular supply in two human lung cancer cell lines with modifiable vascularity are quantifiable with clinical imaging techniques. Imaging parameters of vascularisation correlated with the results of histology. DWI was able to characterise both the extent of necrosis and the level of perfusion.