Face aux agressions constantes que subit l’ADN, les cellules ont développé des mécanismes de protection, nommés checkpoints pour maintenir l’intégrité de leur génome. Chez Saccharomyces cerevisiae, la kinase Rad53 joue un rôle central dans ces voies et son activation conduit à de nombreux effets cellulaires tels que le ralentissement du cycle cellulaire, le ralentissement de la réplication, l’activation de la transcription de certains gènes, l’activation de la réparation… Lors d’un crible transcriptomique, utilisant une souche exprimant une forme hyperactive de Rad53, nous avons identifié le gène HUG1 comme l’un des gènes les plus transcrits suite à l’activation de la voie RAD53. Cependant les fonctions de Hug1 demeurent énigmatiques.Pour mieux comprendre les fonctions de Hug1 dans la réponse aux dommages de l’ADN, nous avons recherché ses partenaires physiques et avons identifié les protéines Rnr2 et Rnr4, les deux composants de la petite sous-unité de la Ribonucléotide Réductase (RNR). La RNR est un complexe enzymatique qui catalyse l’étape limitante de synthèse des nucléotides. Nous avons alors cherché à caractériser cette interaction par diverses méthodes. Nous avons ainsi montré que Hug1 est une protéine intrinsèquement désordonnée capable d’interagir physiquement avec la petite sous-unité de la RNR et qu’au moins onze acides aminés de Hug1 sont impliqués dans son interaction avec la RNR. Lors de nos investigations, nous avons observé que le fait d’étiqueter Rnr2 en position C-terminale sensibilisait les souches aux stress génotoxiques et que cette sensibilité était supprimée si on abrogeait la fonction de HUG1, faisant de Hug1 un nouvel inhibiteur de la RNR. Ainsi nous sommes parvenus à proposer un modèle de régulation de la RNR par Hug1. / To maintain genome integrity, cells have developed protection mechanisms, called checkpoints, in response to DNA damage insults. In Saccharomyces cerevisiae, Rad53 protein kinase is one of the major actors in these mechanisms, and its activation triggers several cellular responses such as cell cycle delay, replication delay, transcription modifications, activation of DNA repair pathways… Using an hyperactivative allele of RAD53, we identified HUG1, as one of the most induced gene in a transcriptomic analysis upon RAD53 pathway activation. However Hug1’s functions remains elusive.To better understand Hug1’s functions in DNA damage response, we searched for physical partners and identified Rnr2 and Rnr4 proteins, which are the two small subunits of Ribonucleotide Reductase (RNR). The RNR is an enzymatic complex that catalyses nucleotide reduction, a step limiting for dNTPs synthesis. We next experimentally tackled the Hug1-RNR interaction using various methods. We showed so that Hug1 is a small intrinsically disordered protein able to interact physically with the small RNR subunit and that at least eleven amino acids in Hug1 are involved in this interaction. During our investigations, we observed that C-terminal tagging of Rnr2 sensitizes strains to genotoxics stress and that this sensitivity was suppressed when HUG1’s function is abrogated. Hence, we showed that Hug1 is a negative RNR regulator and propose a model for Hug1’s function.

Investigations of DNA damage response (DDR) mechanisms in normal tissues have implications for both cancer prevention and treatments. The accumulating knowledge about protein function and molecular markers makes it possible to directly trace and interpret cellular DDR in a tissue context. Using immunohistochemical techniques and digital image analysis, we have examined several principal DDR events in epidermis from patients undergoing fractionated radiotherapy. Acquiring biopsies from different regions of the skin provides the possibility to determine in vivo dose response at clinically relevant dose levels throughout the treatment. A crucial event in cellular DDR is the repair of DNA double strand breaks (DSBs). These serious lesions can be directly visualised in cells by detecting foci forming markers such as γH2AX and 53BP1. Our results reveal that DSB-signalling foci can be detected and quantified in paraffin-embedded tissues. More importantly, epidermal DSB foci dose response reveals hypersensitivity, detected as elevated foci levels per dose unit, for doses below ~0.3Gy. The low-dose hypersensitive dose response is observed throughout the treatment course and also in between fractions: at 30 minutes, 3 hours and 24 hours following delivered fractions. The dose response at 24 hours further reveals that foci levels do not return to background levels between fractions. Furthermore, a low-dose hypersensitive dose response is also observed for these persistent foci. Investigations of end points further downstream in the DDR pathways confirmed that the low-dose hypersensitivity was preserved for: the checkpoint regulating p21 kinase inhibitor; mitosis suppression; apoptosis induction and basal keratinocyte reduction. Our results reveal preserved low-dose hypersensitivity both early and late in the DDR pathways. A possible link between the dose-response relationships is therefore suggested. The preserved low-dose hypersensitivity is a cause for re-evaluation of the risks associated with low-dose exposure and has implications for cancer treatments, diagnostics and radiation protection.

Abstract Breast cancer is the most common cancer among women, and inherited predisposition is one of the major recognized causes of increased breast cancer risk. Only about half of the hereditary cases are explained by mutations in the known susceptibility genes, including the DNA damage response genes BRCA1, BRCA2 and PALB2, leaving the majority still uncovered. Identification of the missing genetic predisposing factors is important for more effective diagnostics and counseling of the risk families, and also for better understanding of the etiology and cellular characteristics of breast cancer. The first aim of this study was to investigate the cancer associations of six rare germline copy number variant (CNV) deletions, which were previously identified in breast cancer patients by a genome-wide microarray approach. The second aim was to identify novel susceptibility alleles, both protein-truncating variants and missense mutations, by next-generation sequencing (NGS) of nearly 800 DNA damage response genes in 189 hereditary breast cancer patients. The cancer-associations of all selected candidate alleles (6 CNVs, 39 protein-truncating variants and 35 missense mutations) were studied by case-control approach using DNA samples from several hundred breast cancer patients and healthy controls. The prevalence of the studied CNVs did not significantly differ between the cases and controls, but when studying the associations with specific clinical parameters, deletion in the CYP2C19 gene showed enrichment in the breast cancer patients with hormonally triple-negative tumors (p=0.021). As CYP2C19 functions in estrogen metabolism, the results indicate that disturbance of hormonal balance due to enzyme defects may predispose specifically to the estrogen receptor-negative subtype of breast cancer. Two protein truncating-variants, TEX15 c.7253dupT and FANCD2 c.2715+1G>A showed significant breast cancer association in the Northern Finnish cohort (p=0.018 and p=0.036, respectively). Similarly, two of the studied missense variants, RECQL p.Ile156Met (p=0.043) and POLG p.Leu392Val (p=0.010), were enriched in the breast cancer cases. Thus, this study provided novel connections between increased breast cancer risk and inherited mutations in TEX15, FANCD2 and POLG genes, and further supported the recently established role of RECQL as a breast cancer susceptibility gene. / Tiivistelmä Rintasyöpä on naisten yleisin syöpä, ja perinnöllinen alttius on yksi merkittävimmistä sairastumisriskiin vaikuttavista tekijöistä. Tunnetuimpia alttiustekijöitä ovat mutaatiot BRCA1-, BRCA2- ja PALB2-DNA-vauriovastegeeneissä, mutta ne yhdessä muiden altistavien geenimutaatioiden kanssa selittävät kuitenkin vain noin puolet perinnöllisistä rintasyöpätapauksista. Uusien alttiusgeenien löytäminen mahdollistaa tehokkaamman diagnostiikan ja korkeassa syöpäriskissä olevien sukujen perinnöllisyysneuvonnan, sekä auttaa ymmärtämään syvemmin rintasyövän etiologiaa ja syntymekanismeja solutasolla. Tämän väitöskirjan ensimmäisenä päämääränä oli tutkia tarkemmin aiemmin genominlaajuisella mikrosirumenetelmällä rintasyöpäpotilailta tunnistettujen harvinaisten perinnöllisten DNA-kopiolukuvariaatioiden (CNV) yhteyttä rintasyöpäriskiin. Toisena tavoitteena oli tunnistaa uusia rintasyöpäalttiusalleeleja, sekä proteiinitrunkaatioita että missense-mutaatioita, hyödyntämällä uuden sukupolven sekvensointitekniikkaa, jonka avulla tutkittiin mutaatioita lähes 800 DNA-vauriovastegeenistä 189 pohjoissuomalaiselta rintasyöpäpotilaalta. Valittujen kandidaattialleelien (6 deleetion aiheuttavaa CNV:tä, 39 proteiinitrunkaatiota ja 35 missense-mutaatiota) yhteyttä rintasyöpään tutkittiin tapaus-verrokkimenetelmällä käyttäen DNA-näytteitä usealta sadalta rintasyöpäpotilaalta ja terveeltä kontrollihenkilöltä. Tutkittujen CNV:iden esiintyvyydessä ei ollut merkitseviä eroja potilaiden ja kontrollien välillä, mutta tarkasteltaessa yhteyttä potilaiden kasvaimista saatuihin kliinisiin parametreihin, deleetio CYP2C19-geenissä oli yleisempi hormonaalisesti kolmoisnegatiivisissa rintatuumoreissa kuin muissa tuumorityypeissä (p=0.021). Koska CYP2C19 on estrogeenimetaboliaan osallistuva entsyymi, sen viallinen toiminta voi mahdollisesti altistaa erityisesti estrogeenireseptorinegatiiviselle rintasyövälle. Kaksi tutkituista proteiinitrunkaatioista, TEX15 c.7253dupT ja FANCD2 c.2715+1G>A, olivat rikastuneet perinnöllisessä rintasyöpäpotilasaineistossa verrattuna kontrolleihin (p=0.018 ja p=0.036). Myös kaksi missense-alleelia, RECQL p.Ile156Met (p=0.043) ja POLG p.Leu392Val (p=0.010), olivat yleisempiä rintasyöpäpotilailla. Tulokset osoittivat uuden yhteyden kohonneen rintasyöpäriskin ja perinnöllisten muutosten TEX15-, FANCD2- ja POLG-geenien välillä, sekä tukivat aiempia tutkimustuloksia, joiden mukaan RECQL on kohtalaisen riskin rintasyöpäalttiusgeeni.

A proteína Cdc42 (Cell Division Cycle 42) é um membro da família das Rho GTPases, sinalizadores intracelulares conhecidos pelo seu papel na regulação do citoesqueleto. Essa proteína e capaz de ciclar entre um estado ativo (ligado à GTP) e um estado inativo (ligado à GDP) e essa ativação é modulada por diversas proteínas, conhecidas como GEFs (guanine nucleotide-exchange factors), GAPs (GTPase-activating proteins) e GDIs (guanine nucleotide-dissociation inhibitors). Trabalhos recentes têm demonstrado um papel de Cdc42 na apoptose e na senescência, respostas relacionadas e comumente desencadeadas por estresse genotóxico. Neste contexto este trabalho procurou identificar interações de Cdc42 com outras proteínas, que podem ou não estar envolvidas nos mecanismos de resposta ao dano do DNA. Para isso foram utilizadas as linhagens celulares HeLa e MRC-5 submetidas a tratamento com radiação ultravioleta tipo C, a fim de provocar danos no DNA. Foram realizados dois diferentes tratamentos em cada uma das linhagens com diferentes tempos de incubação pós radiação UV, visando a busca de proteínas envolvidas em uma resposta rápida ou tardia ao dano causado. Os lisados celulares desses tratamentos foram submetidos ao pull-down com proteínas recombinantes GST, GST-Cdc42WT (Selvagem) e GST-Cdc42V12 (Mutação constitutivamente ativa). As proteínas purificadas foram digeridas e submetidas à análise por espectrometria de massa e os dados obtidos foram utilizados para a construção de redes de interação proteica. Dentre as proteínas identificadas as que despertaram maior atenção foram: Proibitina-2 (PHB2) encontrada nas amostras incubadas por 48 horas pós irradiação e Cullina-4A (CUL4A) e P53, encontradas em amostra incubada por 5 minutos pós radiação. Essas proteínas possuem papéis em apoptose e reparo de DNA e foram observadas em posições muito próximas de Cdc42 nas redes de interação, fazendo delas interessantes alvos para futuras validações de interação proteica por análises experimentais distintas / The Cdc42 protein (Cell Division Cycle 42) is a member of the Rho family of GTPases, intracellular signalling molecules well known for their role in the cytoskeleton regulation. This protein cycles between an active state (GTP-bound) and an inactive state (GDP-bound) and this regulation is modulated by proteins known as GEFs, GAPs and GDIs. Recent studies demonstrated roles for Cdc42 in apoptosis and senescence, cellular responses commonly triggered by genotoxic stress. This work sought to identify Cdc42 interactions with other proteins that possibly involved in response to DNA damage mechanisms. To reach this aims we used HeLa and MRC-5 cell lines submitted to treatments with ultraviolet C radiation to induce DNA damage. Two experimental conditions were used in each cell line with different times and doses post UV irradiation in order to search for proteins involved in either rapid or delayed response to the installed DNA damage. Cell lysates obtained from these treatments were subjected to pull-down experiments using recombinant proteins GST, GST-Cdc42-WT (Wild type) and GST-Cdc42-V12 (constitutively active mutant). Purified proteins were digested by trypsin, analyzed by mass spectrometry and th obtained data were used for the construction of protein-protein interaction (PPI) networks. Among the identified proteins those that seem more relevant to the aims of this project were: Prohibitin-2 (PHB2), found in samples incubated 48 hours post irradiation; Cullin-4A (CUL4A) and P53, found in samples incubated 5 minutes after radiation. These proteins have roles in apoptosis and DNA repair and were observed in close proximity to Cdc42 in PPI networks, making them interesting targets for future validation by different experimental approaches

Abstract Breast cancer is the most common malignancy in women and it is strongly influenced by hereditary risk factors. So far, most of the breast cancer-associated genes, including BRCA1/2, have been identified among those that encode proteins involved in DNA damage response (DDR) pathways. However, known genetic risk factors explain less than half of the familial risk of breast cancer. Identification of novel genes and mutations that predispose to breast cancer is important for the understanding of the mechanisms that contribute to the disease development and also for the identification of those individuals who are at high risk. The first aim of this study was to resolve the complementation groups of Finnish patients with Fanconi anemia (FA), which is a rare genetic disease caused by defects in a specific DDR pathway, and to study the role of the causative gene mutations in breast cancer predisposition. The second aim of this study was to identify novel breast cancer susceptibility genes and alleles by targeted next-generation sequencing (NGS) of multiple (~800) DDR related genes. In both approaches, the identified gene mutations were subjected to case-control association analysis utilizing DNA samples of over 1,000 breast cancer cases and 1,000 healthy controls. Investigation of the Finnish FA patients revealed six different disease-causing mutations in three different genes (FANCA, FANCG and FANCI). All of the studied mutations were recurrent in the Finnish population but did not associate with breast cancer. Targeted NGS identified three novel potential breast cancer susceptibility genes. A significant enrichment of TEX15 c.7253dupT and FANCD2 c.2715+1G>A mutations was observed among the hereditary breast cancer cases (P = 0.018 and P = 0.036, respectively). The strongest evidence was found for a Finnish founder mutation in MCPH1 (c.904_916del), which associated with breast cancer susceptibility both in familial (P = 0.003, OR 8.3) and unselected (P = 0.016, OR 3.3) patient cohorts. The tumor suppressive function of MCPH1 was indicated by the loss of the wild-type allele of MCPH1 in 40% of the studied carrier tumors. Furthermore, carriers exhibited a significant increase in genomic instability measured by spontaneous chromosomal rearrangements in peripheral blood lymphocytes. / Tiivistelmä Rintasyöpä on naisten yleisin syöpä. Sairastumisriskiin vaikuttavat voimakkaasti perinnölliset alttiustekijät, ja suurin osa tähän asti tunnistetuista rintasyöpäalttiusgeeneistä, kuten BRCA1/2, koodaa DNA-vauriovasteessa (DDR) toimivia proteiineja. Tunnistetut tekijät selittävät yhä kuitenkin vain alle puolet rintasyövän perinnöllisestä alttiudesta. Uusien alttiusgeenien tunnistaminen on tärkeää rintasyövän patomekanismien ymmärtämiseksi sekä korkean rintasyöpäriskin omaavien henkilöiden tunnistamiseksi. Tämän tutkimuksen tarkoituksena oli määrittää viallisesta DDR-signaalinsiirtoreitistä johtuvan Fanconin anemian (FA) komplementaatioryhmät suomalaisilta FA-potilailta sekä tutkia sairauden taustalla olevien geenimutaatioden yhteyttä rintasyöpäriskiin. Uusia alttiusgeenejä etsittiin myös kohdennetulla uuden sukupolven sekvensointimenetelmällä, jonka avulla tutkittiin yhtäaikaisesti n. 800 DDR-geeniä. Molemmilla lähestymistavoilla tunnistettujen geenimuutosten yhteyttä rintasyöpään selvitettiin tapaus-verrokkitutkimuksen avulla, jossa tutkittiin DNA-näytteitä yli tuhannelta rintasyöpäpotilaalta sekä yli tuhannelta terveeltä henkilöltä. Suomalaisten FA-potilaiden geenimuutoksia selvittävässä tutkimuksessa tunnistettiin yhteensä kuusi mutaatiota kolmessa eri geenissä (FANCA, FANCG ja FANCI). Kaikki tutkimuksessa tunnistetut mutaatiot olivat toistuvia suomalaisessa väestössä, mutta merkitsevää assosiaatiota näiden mutaatioiden ja rintasyöpäalttiuden välillä ei havaittu. DDR-geenien sekvensoinnin avulla tunnistettiin kolme uutta mahdollista rintasyöpäalttiusgeeniä. Tutkimuksessa havaittiin TEX15 c.7253dupT ja FANCD2 c.2715+1G>A mutaatioiden rikastuminen perinnöllisessä rintasyöpäaineistossa (P = 0.018 ja P = 0.036). Merkittävin yhteys rintasyöpäalttiuden kanssa todettiin MCPH1-geenin perustajamutaatiolle (c.904_916del). Tämä mutaatio assosioitui rintasyöpäalttiuden kanssa sekä perinnöllisessä (P = 0.003, OR 8.3) että valikoimattomassa potilasaineistossa (P = 0.016, OR 3.3). Useissa mutaatiokantajien tuumoreissa (40 %) normaali MCPH1 vastinalleeli oli hävinnyt, mikä viittaisi siihen, että MCPH1 toimii tuumorisuppressorina. Mutaatiokantajilla todettiin myös kohonnut määrä kromosomaalisia muutoksia veren periferaalisissa lymfosyyteissä, mahdollisesti kohonneeseen genomiseen epävakauteen liittyen.

Les ectéinascidines (la trabectédine, la lurbinectédine) sont de nouveaux dérivés de produits naturels marins qui se lient de façon covalente à l'ADN, actifs contre les cancers chimio-résistants. L'objectif de ma thèse est 1) d'identifier les principales voies de transduction activées en réponse à l'apparition des lésions de l'ADN induites par les ETs 2) d'établir si l'abrogation pharmacologique de la réponse cellulaire induite par l'endommagement de l'ADN (ATM, ATR, Chk1, Chk2) peut moduler l'activité thérapeutique des ETs. Dans un premier temps, nous avons montré que la voie ATR/Chk1 activée principalement en réponse à l'apparition d'un stress réplicatif et la voie ATM/Chk2 qui initie la réponse cellulaire suite à la formation de lésions double-brins, sont activées en réponse aux adduits créés par les ETs. Dans un second temps, nous avons montré que les combinaisons des ETs avec les inhibiteurs Chk1/Chk2 ou les inhibiteurs ATR ou ATM seuls s'accompagnent d'une modeste potentialisation. Inversement, la combinaison simultanée des ETs avec les inhibiteurs ATR et ATM entraine une forte synergie dans les modèles du cancer de l'utérus et de l'ovaire sensibles ou résistants au cisplatine. Enfin, nous avons montré que cette potentialisation passe par l'inhibition du recrutement des protéines impliquées dans l'initiation et la réalisation des mécanismes de réparation par recombinaison homologue. Ces résultats suggèrent qu'en inhibant simultanément les vois initiés par ATR et ATM, l'activité thérapeutique des ETs pourrait être potentialisée en clinique. / Ecteinascidins (Trabectedin, Lurbinectedin) are novel marine derived natural products, DNA minor groove binders and active against chemo-resistant cancers. The purpose of my thesis was to 1) characterize the DNA damage response (DDR) to both trabectedin and lurbinectedin 2) to establish whether the pharmacological abrogation of cell response induced by DNA damage (ATM, ATR, Chk1, Chk2) can modulate the therapeutic activity of ETs. Our results show that both compounds activate the ATM/Chk2 (ataxia-telangiectasia mutated/checkpoint kinase 2) and ATR/Chk1 (ATM and RAD3-related/checkpoint kinase 1) pathways. Interestingly, the pharmacological inhibition of either Chk1/2, ATR or ATM kinases is not accompanied by a significant improvement of either trabectedin or lurbinectedin cytotoxic activity. However, the simultaneous inhibition of both ATM and ATR strongly potentiates the activity of both ETs. Importantly, these results are not restricted to HeLa cells but can also be extended to cisplatin-sensitive or -resistant ovarian carcinoma cell lines. Finally, we showed that the concomitant inhibition of both ATR and ATM is an absolute requirement to efficiently block the initiation and realization of homologous recombination repair mechanisms. Together, our data identify ATR and ATM as central coordinators of the DDR to trabectedin and lurbinectedin and provide a mechanistic rational for combinations of these compounds with both ATR and ATM inhibitors.

Cellular senescence has been proposed to be equivalent to organismal aging and is one of the outcomes of the cell fate decision process in response to DNA damage that occurs in cells. When a cell encounters DNA damage, the cell cycle is immediately halted to evaluate which decision to take in response to genomic insult. The choices are between repairing the damage and continue division, or enter a non-replicative but viable state called senescence or to die if damage is severe (Figure 1). The signaling cascade, which detects this damage and regulates the cell fate decision, is collectively called as DNA damage response (DDR). However, the exact mechanism of how delineation for each decision happens is still not clear. Since DNA damage works as a mediator for cell fate decision, my work aimed to study senescence as a DNA damage response. In addition, the role of free radicals like ROS in cellular senescence is not very clear because though an increase in their concentrations is recorded in aged cells, it is not evident if the increase seen the cause or the effect of aging, primarily because they themselves capable of causing DNA damage. This conundrum have always led to confounding observations wrt role of free radicals in the cellular senescence process and if the senescence is caused through agents which rely on ROS to cause DNA damage, ROS becomes absolutely integral to the aging process. To understand this aspect formed the first line of investigation in my work along with identification of the sensor of DNA damage, which drives various cell fates. During organismal ageing there is an accumulation of senescent cells, which could be the major reason for functional decline of tissues and organs with age. However, to study changes associated with signaling molecules with respect to ageing, a cellular model system for senescence driven through DNA damage was needed, using which interplay between senescent / aged cells and cellular niche can be established. Studying the spatial and temporal alterations in signaling dynamics, within the cell as well as with the neighbouring niche during the senescence process in anticipated to provide us better understanding about the complex process of ageing. For this, the objectives were defined to establish and characterize the DNA damage induced senescence model using various parameters, and especially study the signaling dynamics of GPCR mediated signaling in senescence. The role of chemokine receptor, CXCR4 and its ligand, CXCL12 mediated signaling was chosen for the study. The following sections describe the findings that were obtained from the various objectives studied during the course of this study. Section 1. Development and characterization a model system to study cellular senescence as a DNA damage response. In this part of the study, I characterized genotoxic stress induced cellular senescence model using 5-Bromodeoxyrudine as the DNA damaging agent. BrdU, owing to its property of being a thymidine analogue, is incorporated in dividing cells, and this incorporation is recognized as DNA damage. This triggers ‘persistent’ DNA damage response signaling, including activation of ATM kinase, one of the primary DNA damage sensor. As anticipated, the DDR response detected was directly proportional to the dose of BrdU treatment and so was Reactive Oxygen Species (ROS) levels, a known senescence mediator. Using this model system of direct DNA damage mediated DDR activation and induction of cellular senescence, the growth-arrested cells were extensively characterized for presence and quantum of most of the senescence associated markers known in literature. BrdU treated cells, which became senescent showed presence of DNA damage, morphological changes like flat, enlarged, granule rich appearance, expression of senescence associated molecular markers like p21, IL8, showed senescence associated beta galactosidase activity, refractiveness to growth factor for division, increased ROS levels, Golgi dispersion, etc. The secretome of the treated cells also showed increased secretion of inflammatory cytokines which are attributed to a senescence phenotype, called as Senescence Associated Secretory Phenotype (SASP), which triggered proliferative and migratory effect on cancer cells. Overall, in this part of the study, it was established that BrdU can cause DNA damage and induce senescence as one of the cell fate in response to the intermediate dose of damage. The senescent cells generated in the model system was established to be akin to senescence observed by replicative exhaustion of normal cells, thereby making our model applicable to the physiological studies as well. Section 2. Insights into the role of ATM-ROS axis during senescence initiation and maintenance using DDR mediated cellular senescence model. While the BrdU model system for generating senescent cells was being developed and characterized, it was observed that there is an increase in ATM activation as well as ROS production concomitant to the a dose of BrdU. At the same time it was also observed that senescent cells showed persistent DDR signaling and high levels of ROS. Using this premise, in the second objective of my study I aimed to identify if ATM and ROS are critical during initiation of senescence, when the cells are insulted with the DNA damaging agent or during the maintenance of senescent state of the cells. By quenching ROS during the initiation state, I recorded that ROS is not critical for inducing senescence and perhaps the increase in ROS levels in senescent cells is due to their higher metabolic activity. By inhibiting ATM activation during DNA damage, it was observed that BrdU induces senescence through direct DNA damage, and active ATM and DDR signaling is absolutely critical for the senescence initiation. It was also established that ATM is not just a DNA damage sensor but also a redox regulator in the senescence model system. Prevention of ATM activation in presence of DNA damage blocked senescence initiation and also triggered increased ROS levels in the cells affecting their long term viability, suggesting ATM regulates ROS levels as well in addition to sensing DNA damage. In order to study the role of ATM-ROS axis in the maintenance of senescence state, already senescent cells were subjected to ROS quenching and/ or ATM inhibition and it was identified that both these signaling molecules are essential for maintaining the viability of senescent cells. The findings from these study thereby show that senescence can be divided into two temporally distinct stages, initiation or early senescence stage and second, maintenance stage of senescence. Overall, I was able to characterize the presence of temporally linked ROS – dependent and ROS – independent events in cellular senescence, which are independently mediated by ATM kinase (Figure 1). Dose of Genotoxic Stress damage DDR Senescence initiation Repair Cell cycle ATM arrest kinase Death Growth arrest Senescence maintenance Senescence Cell ROS viability Elevated metabolism Figure 1. Signaling cascades regulating senescence onset and maintenance mediated through DDR. Cells enter senescence state in response to DNA damage, depending on the dose of insult, through an ATM dependent and ROS independent pathway. Unlike this ATM-ROS axis is critical for the maintenance of senescent state of damaged but viable cells. Section 3. Understanding the role of CXCR4 – CXCL12 mediated signaling in senescence. Age dependent changes in cellular signaling are less explored and I was specifically interested in understanding how presence of senescent cells affects its microenvironment or vice versa i.e. how microenvironment affects senescent cells. In this premise the third objective of this study was defined towards identifying role of a GPCR, CXCR4 mediated signaling in cellular senescence and associated inflammation. CXCR4 is a ubiquitously expressed GPCR and it’s only known ligand is CXCL12/ SDF1 (stromal derived factor ), which is a homeostatic chemokine (i.e. its levels does not change under most physiological conditions). During characterization of DNA damage induced senescence model system, it was observed that this receptor expression is induced during DNA damage ells, which was also found to be so from data available from other gene expression studies as well. During the course of my work, I identified that senescent cells show CXCR4 up regulation in response to DNA damage, mediated through activation of ATM kinase - HIF1 axis and plays a critical role in enhancing the senescence associated inflammatory response in presence of its ligand, CXCL12. This CXCL12 dependent enhanced inflammatory response in damaged cells was determined to be sensitive to the pertussis toxin treatment and hence dependent on G protein activation. Further downstream analysis revealed the pro-inflammatory effect of the CXCR4 receptor activation was due to cAMP level suppression post activation by the Gi subunit. Given that cAMP levels are antagonistic to inflammatory phenotype, using a library of pharmacological compound library, I also discovered that cAMP specific PDE, phophodiesterase 4A, is also involved in regulating inflammatory response during the initiation stage of cellular senescence. The screen also confirmed the involvement of previously identified molecular components such as p38 MAPK and leukotrienes in the senescence associated inflammatory phenotype. The examination of the role of the CXCR4- CXCL12 axis in the deeply senescent cells surprisingly revealed that deeply senescent cells are refractory to CXCL12 stimulation in terms of inflammatory response, which was experimentally determined to be associated with impaired calcium release. Overall, the findings from this part of the study revealed a novel signaling cascade where CXCR4 up regulation is a part of the DDR response in cells, which utilizes the Local Excitation Global Inhibition (LEGI) mechanism to enhance the sensitivity of the damaged cells to its ligand CXCL12. This enhanced sensitivity mediates the CXCL12 dependent inflammatory response, which aids in attracting immune cells for clearance of these damaged cells. Once the cells have entered the senescent state, the axis is physiologically down modulated and the senescent cells showed refractiveness to CXCL12 stimulation, probably to prevent persistent acute inflammation, if the senescent cells are not cleared (Figure 2). Figure 2. CXCL12-CXCR4 axis in cellular senescence. During senescence initiation stage, when cells encounter DNA damage (Step 1), there is induction of CXCR4 receptor (Step 2), which enhances of CXCL12 mediated signaling for increased inflammatory response (Step 3). In the maintenance stage, where the cells are not cleared (Step 4), the axis is suppressed (Step 4), thereby bringing the levels of inflammatory secretome down, and thereby preventing damage to the cells (Step 5).

Therapy resistance of malignant cells represents the main reason responsible for the failure of cancer therapy. The growth of malignant cells at primary tumour sites but most importantly the dissemination of tumour cells and their growth at secondary sites, are the main reasons why patients eventually succumb to the disease. Even novel immune-based therapies find their limitation in most tumour types. The therapy resistance is mediated by the tumour cells but also by other cellular components of the tumour microenvironment. Understanding the tumour cells mechanisms and the tumour microenvironment features responsible for therapy resistance enables the development of novel therapeutic strategies. Here, we show that ionizing irradiation, 5-azacytidine, and IFNγ treatments induced expression of suprabasin (SBSN) and therapy-resistant low-adherent phenotype in cancer cells. Knockdown of SBSN resulted in suppression of the phenotype. Next, we identified aberrantly elevated SBSN in the bone marrow of a subgroup of myelodysplastic syndromes (MDS) patients. SBSN was expressed by myeloid-derived suppressor cells (MDSCs) and showed significant anti-correlation with T cell abundance and CCL2 levels, hence promises a prognostic value in clinical use. We compiled the most of the relevant knowledge of SBSN...

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Ovarian cancer is serious and one of the most common gynecologic cancers. Carboplatin is the therapeutic agent of the first choice in the ovarian cancer therapy. However, after the primary therapeutic response to carboplatin, the relapse of the disease may occur with developed resistance to carboplatin. Chemoresistance and insufficient therapy response are considered to be the reason of the high mortality rate of ovarian cancer. The DNA damage response pathways play an important role in the therapeutic response and chemoresistance development. Restoration of homologous recombination function in cancers is the key mechanism of resistance development to platinum agents. Based on this knowledge, we formed our hypothesis, that the inhibition of homologous recombination could increase the sensibility to carboplatin. The main goal of this thesis was to define the role of double-strand breaks repair in response to chemotherapy of ovarian cancer. Protein MRE11 is part of the MRN complex, that participates in double-strand breaks repair. Using mirin as a pharmaceutic inhibitor of MRE11 we were aiming to determine the impact of homologous recombination on the effect of carboplatin and its role in resistant development to carboplatin. In the practical part of the thesis, we described the association between...