The histone acetyltransferase protein, Tip60, has many important functions in epigenetic regulation of gene expression and DNA repair. Our objective is to design, synthesize, and evaluate potent inhibitors for Tip60. Full-length Tip60 (fl-Tip60) and catalytic domain of Tip60 (cat-Tip60) were expressed in E. coli and purified with nickel affinity chromatography. Quantitative analysis of enzyme activities demonstrated that both enzyme forms had very high activity with the substrate H4. To create new Tip60 inhibitors, various histone H3 peptides conjugated with CoA were synthesized using the Fmoc solid-phase peptide synthesis and solution phase synthesis protocols. The results from the inhibition radioactive assay showed that the synthetic H3-CoA conjugates inhibited effectively the enzymatic activity of both fl-Tip60 and cat-Tip60; and the addition of methyl groups to the Lys-4 or Lys-9 residue of H3 aided in a 7-9 fold enhancement in potency in comparison to nascent H3-CoA inhibitor.

Histone modifications are crucial in activities such as transcriptional activation, gene silencing, and epigenetic cellular memory. In particular, lysine acetylation via lysine (K) acetyltransferases (KATs) has been implicated in cancer development. Interestingly, KAT5, also known as Tip60 (tat-interactive protein-60kDa), has been reported to possess both tumor promoting and tumor suppressing properties depending on the context of malignancy. Herein we report that KAT5 contributes to tumorigenesis in epidermal growth factor receptor (EGFR) mutated lung cancer, and Kat5-knockout mice models demonstrate significantly reduced lung tumor burden. To probe the aberrant modification of KAT5, we demonstrated that KAT5 binds to and is phosphorylated by oncogenic EGFR in co-immunoprecipitation experiments. Next, to investigate whether KAT5 is involved in cell proliferation and survival, H1975 cells harboring L858R-T790M double-activating mutations were transfected with doxycycline inducible short helical RNA (shRNA) targeting KAT5 (shKAT5). Following treatment, shKAT5 cells were observed to have suppressed proliferation rates. Pharmacological inhibition using TH1834, a known KAT5 inhibitor, also suppressed proliferation rates in shKAT5 cells; in contrast BEAS2B cells, an immortalized normal human bronchial cell line, surprisingly exhibited increased viability compared to transformed human lung H1975 cells. This finding supports KAT5’s context-dependent role in in normal and abnormal cell homeostasis. To further investigate KAT5 in lung tumorigenesis in vivo, we generated EGFR-mutant conditional Kat5 knockout mice using a tetracycline-induced Cre/loxP system. Following doxycycline treatment for 10 weeks, isolated mice lungs for EGFRTL/CCSP-rtTA/Cre/Kat5F/F possessed significantly lower tumor volume compared to EGFRTL/CCSP-rtTA/Cre/Kat5wt/F and EGFRTL/CCSP-rtTA/Cre/Kat5wt/wt mice lungs. Hemotoxylin and eosin staining showed no evident hyperproliferation in lungs isolated from EGFRTL/CCSP-rtTA/Cre/Kat5F/F mice whereas lungs isolated from EGFRTL/CCSP-rtTA/Cre/Kat5wt/wt and EGFRTL/CCSP-rtTA/Cre/Kat5wt/F did, signifying that KAT5 has a potential regulatory role in cellular proliferation. RNA-Seq analysis of shKAT5 H1975 cells identified downstream targets involved in tumorigenic pathways. Subsequent quantitative polymerase chain reaction (PCR) of shKAT5 cells served to validate the reported targets. Taken together, these data offer insight into a KAT5 mediated oncogenic pathway that can provide novel therapeutic approaches in treating lung cancer.

Cancer is the second leading cause of death in the United States, and it results from genetic alterations that promote the survival and proliferation of neoplastic cells. One of the most commonly disrupted cancer gene networks is the ARF-Mdm2-Tip60-p53 pathway. Inactivation of the ARF, Tip60 and p53 tumor suppressors and/or overexpression of the Mdm2 oncogene occurs in most, if not all, human cancers. An improved molecular understanding of that pathway, especially how it becomes activated, is expected to advance the development of innovative therapeutics aimed at restoring its function in tumors. Our group originally discovered NIAM (Nuclear Interactor of ARF and Mdm2) as a novel binding partner of ARF that has several functional ties to Mdm2 and p53. Early studies showed that NIAM is negatively regulated by Mdm2, can collaborate with ARF to block cell proliferation, and is a new activator of p53-mediated transcription. NIAM could also act independent of those factors to suppress cell proliferation and promote chromosomal stability, and microarray studies suggested its expression is significantly reduced in many human cancers. Those findings led us to speculate that NIAM is a tumor suppressor that functions in both the ARF-Mdm2-p53 pathway as well as other undefined anti-cancer pathways. My thesis research explored two different aspects of that hypothesis: 1) how does NIAM activate p53, and 2) is NIAM a tumor suppressor? Initial work showed that NIAM could stimulate p53 independently of ARF, the major activator of p53, indicating that other factors must be required. My studies revealed that NIAM indirectly promotes p53 activation through functional interactions with two other p53 regulators, Tip60 and Mdm2. Tip60 is an acetyltransferase that activates p53 through direct association on p53 target promoters as well as acetylation of p53 at lysine 120 (K120). I found that NIAM can induce K120 acetylation of p53; however, NIAM's association with Tip60 (not the acetylation of p53) was essential for maximal p53 transcriptional activation. Mdm2, the major antagonist of p53, is an E3 ubiquitin ligase that promotes p53 ubiquitylation and degradation. I found that NIAM disrupts Mdm2-p53 complexes and blocks p53 ubiquitylation, thereby interfering with p53 inhibition by Mdm2. Thus, NIAM regulates two critical pathways that control p53 function and are altered in human cancers, implying an important role for NIAM in tumorigenesis. To test that idea directly, we generated NIAM gene-trap knockout mice (hypomorphs) that expressed greatly reduced yet detectable levels of NIAM in all tissues. Fifty percent of the NIAM knockout mice developed benign and early stage cancers, including B-cell lymphoma, whereas all age-matched control animals were tumor-free. These results showed that NIAM loss causes increased susceptibility to tumorigenesis. In sum, my work suggests a significant role for NIAM in p53 control and tumor biology. Additional studies will be needed to determine which physiological or pathological signals normally engage NIAM to promote p53 function and suppress tumor development. It is anticipated that the NIAM knockout mice will provide an outstanding platform to interrogate NIAM's biological role in cancer, particularly in ARF-Mdm2-Tip60-p53 signaling as well as other pathways affecting genome maintenance. Ultimately, insights gained from such studies may justify novel therapies that seek to restore NIAM activity in tumors.

Η πρωτεΐνη Tip60 (Tat-interactive protein, 60 kDa) είναι μέλος της οικογένειας πρωτεϊνών MYST και αρχικά προσδιορίστηκε ως αλληλεπιδρώσα πρωτεΐνη με την HIV-1 ΤΑΤ πρωτεΐνη. Πολλά από τα μέλη της οικογένειας MYST μεταξύ αυτών και η Tip60, δρουν ως ακετυλοτρανσφεράσες ιστονών, γεγονός που υποδηλώνει πιθανούς ρόλους στην αναδιαμόρφωση της χρωματίνης και στην γονιδιακή ρύθμιση. Στη παρούσα διπλωματική, στόχος ήταν η μελέτη του προφίλ έκφρασης της ακετυλοτρανσφεράσης Τip60 σε πληθυσμούς Τ βοηθητικών παρθενικών (CD3+CD4+CD45RA+) και Τ βοηθητικών μνημονικών (CD3+CD4+CD45RO+) λεμφοκυττάρων καθώς και η δράση της στην μεταγραφή του HIV-1 και της IL-2. Οι λόγοι που μας οδήγησαν στην μελέτη της Τip60 προκύπτουν από πρόσφατα αποτελέσματα του εργαστηρίου μας, που δείχνουν ότι υπάρχει μια πιθανή αλληλεπίδραση της Tip60 με τον παράγοντα Εts-2, ο οποίος συμμετέχει στη ρύθμιση της μεταγραφής τόσο του γονιδίου της IL-2 όσο και του HIV-1. Επιπλέον η IL-2 και ο HIV-1 παρουσιάζουν κοινή μεταγραφική ρύθμιση που ελέγχεται από την πρόσδεση μεταγραφικών παραγόντων σε κοινά cis στοιχεία. Επίσης, η Tip60 είναι μια Τat-αλληλεπιδρώσα πρωτεΐνη που κωδικοποιείται από το γονίδιο Tat του HIV-1. Τέλος το γεγονός ότι ο HIV-1 παραμένει σε λανθάνουσα κατάσταση στα εν ηρεμία Τ βοηθητικά λεμφοκύτταρα καθώς και ότι ο παράγοντας Εts-2, που πιθανόν αλληλεπιδρά με την Tip60, συμμετέχει στη καταστολή της έκφρασης του ιού, υποδηλώνει μια πιθανή συμμετοχή της Tip60 σε αυτή τη διαδικασία. Αρχικά ελέγξαμε την έκφραση της Tip60 σε υποπληθυσμούς μονοπύρηνων κυττάρων περιφερικού αίματος (PBMCs). Η υψηλότερη έκφραση παρατηρήθηκε στα Τ βοηθητικά λεμφοκύτταρα (CD4+). Για να εξακριβώσουμε το αν και πώς εκφράζεται στους υποπληθυσμούς των Τ λεμφοκυττάρων, απομονώσαμε Τ βοηθητικά μνημονικά λεμφοκύτταρα (CD3+CD4+CD45RO+) από ολικό αίμα ενηλίκων και Τ βοηθητικά παρθενικά λεμφοκύτταρα (CD3+CD4+CD45RA+) από αίμα νεογνών (ομφαλίου λώρου). Τα αποτελέσματά μας έδειξαν ότι σε συνθήκες μη ενεργοποίησης η Τip60 εκφράζεται περισσότερο στα μνημονικά Τh λεμφοκύτταρα σε σχέση με τα παρθενικά Τh λεμφοκύτταρα (στα οποία η έκφραση του παράγοντα παραμένει ουσιαστικά αμετάβλητη). Μετά από την ενεργοποίηση των κυττάρων με PMA/IONO (P/I) η έκφραση της Tip60 αυξάνεται σημαντικά στα μνημονικά Th λεμφοκύτταρα ενώ στα παρθενικά Th παραμένει ουσιαστικά αμετάβλητη. Για να εντοπίσουμε μια λευχαιμική κυτταρική σειρά κατάλληλη για να χρησιμοποιηθεί για πειράματα διαμολύνσεων και ανοσοφθορισμού, ελέγξαμε την έκφραση της Tip60 σε εννέα λευχαιμικές κυτταρικές σειρές και είδαμε ότι η Τ λεμφοκυτταρική λευχαιμική σειρά Jurkat παρουσίαζε την υψηλότερη έκφραση της Τip60. Η κυτταρική σειρά Jurkat παρουσιάζει επίσης παρόμοιο μοτίβο έκφρασης σε επίπεδο mRNA με τα Τ βοηθητικά παρθενικά λεμφοκύτταρα. Την έκφραση της Tip60 την ελέγξαμε και σε πρωτεϊνικό επίπεδο με τη μέθοδο Western blot σε ολικά πρωτεϊνικά εκχυλίσματα που απομονώσαμε από κύτταρα Jurkat. Για να ελέγξουμε τον εντοπισμό της Τip60 στα Jurkat, προχωρήσαμε σε πειράματα ανοσοφθορισμού. Τα αποτελέσματα έδειξαν, ότι σε συνθήκες μη ενεργοποίησης (CM) και ύστερα από ενεργοποίηση των κυττάρων (P/I) η Τip60 εντοπίζεται στον πυρήνα των κυττάρων Jurkat. Επίσης η ποσότητα της πρωτεΐνης Τip60 δεν αλλάζει ύστερα από την ενεργοποίηση των κυττάρων με μιτογόνα, αποτέλεσμα που συμφωνεί με τα πειράματα Western blot. Προκειμένου να ελέγξουμε τη δράση της Τip60 στη μεταγραφική δραστηριότητα του HIV-1 και της IL-2 προχωρήσαμε σε πειράματα διαμόλυνσης Jurkat κυττάρων. Αρχικά διαμολύναμε τα κύτταρα με αυξανόμενες ποσότητες πλασμιδίου υπερέκφρασης της Τip60 (pCMX-tip60) και ελέγξαμε την έκφραση της IL-2 σε μεταγραφικό επίπεδο. Παρατηρήθηκε ότι αυξανομένης της ποσότητας του pCMX-tip60, αυξανόταν και η έκφραση του IL-2 mRNA. Μέσω πειραμάτων CAT-assays σε κύτταρα Jurkat, τα οποία συνδιαμολύναμε με αυξανόμενες ποσότητες πλασμιδίου pCMX-tip60 και πλασμιδίου αναφοράς CAT, που βρίσκεται κάτω από τον έλεγχο του HIV-1-LTR, διαπιστώσαμε ότι η υπερέκφραση της Τip60 αυξάνει και τη μεταγραφική ενεργότητα του υποκινητή του HIV-1. Προκειμένου να διαπιστώσουμε εάν η Tip60 δρα απευθείας στον υποκινητή του HIV-1 και της IL-2 μέσω της πρόσδεσής της σε αυτόν είτε άμεσα, είτε έμμεσα μέσω συμπλόκου με άλλες πρωτεΐνες, προχωρήσαμε σε πειράματα ανοσοκρατακρήμνισης χρωματίνης (ChIP assays) του υποκινητή της IL-2. Παράλληλα επειδή δεν υπάρχει γνωστή θέση πρόσδεσης της Tip60 απευθείας στην LTR αλληλουχία του HIV-1 και στον υποκινητή της IL-2 αναζητήσαμε την πρωτεΐνη με την οποία θα μπορούσε να αλληλεπιδρά προκειμένου να προσδεθεί στα παραπάνω. Με πειράματα συνανοσοκατακρήμνισης διαπιστώσαμε ότι υπάρχει αλληλεπίδραση ανάμεσα στην Tip60 και στον παράγοντα Ets-2, ο οποίος προσδένεται άμεσα στην LTR αλληλουχία του HIV-1 και στον υποκινητή της IL-2 και έτσι επαληθεύσαμε τις αρχικές υποθέσεις για την αλληλεπίδραση τους. Τα πειράματα που πραγματοποιήσαμε μας οδήγησαν στα παρακάτω συμπεράσματα: Υπάρχει διαφορική έκφραση της Tip60 ανάμεσα στα Τ βοηθητικά παρθενικά και μνημονικά λεμφοκύτταρα, αφού σε συνθήκες μη ενεργοποίησης (CM) η έκφραση της Tip60 είναι μεγαλύτερη στα μνημονικά σε σχέση με τα παρθενικά Τh λεμφοκύτταρα. Η ενεργοποίηση των κυττάρων με μιτογόνα προκαλεί επαγωγή της έκφρασης της Tip60 στα μνημονικά Τh λεμφοκύτταρα, ενώ στα παρθενικά δεν προκαλεί καμία ουσιαστική αλλαγή. Η πρωτεΐνη Tip60 δρα σαν συνενεργοποιητής της μεταγραφής του ιού HIV-1 και της IL-2 μιας και προκαλεί επαγωγή στην μεταγραφική τους δραστηριότητα. Η πρωτεΐνη Tip60 αλληλεπιδρά in vivo με τον παράγοντα Εts-2 και παρουσιάζει το ίδιο πρότυπο πρόσδεσης με αυτόν, στον υποκινητή της IL-2 στην κυτταρική σειρά Jurkat. / Tip60 (Tat-interactive protein, 60 kDa) is a member of the MYST protein family and was initially identified as an interacting protein with the HIV-1 TAT protein. Several members of MYST family, Tip60 among them, act as histone acetyltransferases, suggesting their possible roles in chromatin remodeling and gene regulation. We chose to study Tip60 because it is a Tat-interactive protein and Tat is encoded by the Tat gene of HIV-1. Recent results from our laboratory suggest that there is a possible interaction between Tip60 and Εts-2 proteins, which is involved in the regulation of the transcription of both IL-2 and HIV-1. In addition, the transcription of IL-2 and HIV-1 is regulated by common transcription factors that act through binding to common cis-trans elements. We also know that the HIV-1 virus is transcriptionally active in activated CD4 T cells, and inactive in naïve CD4 T cells and that HIV-1 expression is blocked in naive Th cells by the transcriptional factor Ets-2. So the possible interaction between Tip60 and Εts-2 protein led us to study the Tip60 protein. The main purpose of this study was to determine the expression profile of Tip60 acetyltransferase in naive T helper (CD3+CD4+CD45RA+) and memory T helper (CD3+CD4+CD45RO+) lymphocytes and its effect on the transcription of HIV-1 and IL-2 (due to their common transcriptional regulation in T helper cells). The expression of Tip60 mRNA was measured in subpopulations of peripheral blood mononuclear cells (PBMCs) and the highest levels were observed in Th lymphocytes. We therefore isolated from human peripheral blood and cord blood, CD3+CD4+CD45RO+ and CD3+CD4+CD45RA+ Th lymphocytes and we examined the expression of Tip60 at the transcriptional level by RT-PCR. The results showed that Tip60 mRNA expression levels were higher in CD3+CD4+CD45RO+ compared to CD3+CD4+CD45RA+ Th cells. Following cell activation with PMA/IONO (P/I), the transcriptional expression of Tip60 was increased in memory Th cells, whereas it remained unchanged in naive Th cells. To identify a suitable cell line for transfection and immunofluorescence experiments, we measured Tip60 expression in nine cell lines and we observed that the T lymphocytic leukemia Jurkat presented the highest expression of Tip60 mRNA. Jurkat cells also presented a similar pattern of Tip60 mRNA expression levels with naïve Th lymphocytes. In addition to determine the localization of Tip60 into the cells, we proceeded in immunofluorescence experiments. As a result, we observed that when cells were cultured in CM media +/- P/I, Tip60 was identified in the nucleus of Jurkat cells. The amount of Tip60 protein remained unchanged after cell activation (which was also determined by Western blot experiments). To study the effect of Tip60 in transcription of HIV-1 and IL-2 we transfected Jurkat cells with increasing amounts of a Tip60 overexpressing vector (pCMX-tip60) and measured the expression of IL-2 and HIV-1 at the transcriptional level. Overexpression of Tip60, induced the transcription of IL-2 and also increased the transcriptional activity of HIV-1. Co-transfection experiments in Jurkat cells with increasing amounts of PCMX-tip60, led to a gradual increase of HIV1-LTR-CAT Finally, we studied if Tip60 acts directly on the promoter of HIV-1 and IL-2 exercising its effect directly or through complexing with other proteins. According to the literature there is no Tip60 binding site in the promoter of HIV-1 and IL-2, so we searched for a protein that could interact with Tip60. We performed co-immunoprecipitation experiments that showed that there was an interaction between Tip60 and Ets-2, a factor that binds directly both on the LTR of HIV-1 and the IL-2 promoter. In this work we suggest that Tip60 is expressed differentially in naïve and memory helper T cells and participates in the transcriptional activation of both HIV-1 LTR and IL-2. Also Tip60 protein interacts in vivo with Ets-2 protein and Tip60 binding activity is similar with Ets-2 binding activity to the ARRE-2 element of the IL-2 promoter in Jurkat cell line.

Au sein du noyau des cellules eucaryotes, la molécule d'ADN s'enroule autour de protéines histones, formant la chromatine. Ce mécanisme de compaction est dynamique selon les régions et les processus en cours, régulant l'accès à l'ADN. Pour exemple, la transcription d'un gène nécessite localement la décompaction de la chromatine, ce qui permet l'accès à la machinerie de transcription. Au contraire, La répression de ce gène sera corrélée à une forme compactée de cette portion de chromatine. Le phénomène d'acétylation des histones est associé à une décompaction. Les régions d'hétérochromatine (forme compactée considérée comme peu dynamique et peu transcrite) sont donc pauvres en acétylations d'histones. Pourtant des études chez la levure, suggèrent la présence de ces acétylations de manière fine dans l'hétérochromatine afin d'en permettre la plasticité. De récentes données chez la souris impliquent ces acétylations dans la compaction via le recrutement de protéines à doubles bromodomaine (BET). Notre vision de la fonction des acétylations d'histones est donc en train de changer. Les péricentromères sont des zones d'hétérochromatine dont la compaction correcte est nécessaire pour le bon déroulement de la ségrégation des chromosomes lors de la division cellulaire. Ici nous travaillons sur des cellules de souris SUV39H 1/2 -/-, où la voie classique de compaction des péricentromères est défectueuse. Nos données nous permettent de poser un modèle où l'acétyltransférase TIP60 est recrutée à l'hétérochromatine péricentromérique dans les cellules SUV39H 1/2 -/-, où elle maintient la compaction en acétylant H4K12, permettant le recrutement d'une protéine à double bromodomaine. Ceci constitue un nouveau cas de compaction via une acétylation d'histone et une protéine BET chez les mammifères. Cette voie alternative de compaction pourrait être utilisée par les cellules lors de déstructurations de ces régions au cours de divers processus physiologiques, ou pathologiques, comme dans le cadre des cancers. En effet, c'est la première fois qu'un rôle de TIP60 est décrit aux péricentromères, région importante pour la stabilité génétique de la cellule, ce qui est cohérent avec la fonction connue de suppresseur de tumeur de TIP60. / In eukaryote cells, DNA is wrapped around histones proteins, organizing a nucleo-proteic structure called chromatin. Chromatin can compact or decompact itself in a very dynamic manner, depending on specific regions and processes. One example is that, to be transcribed, a gene needs chromatin to be in a decompacted state, whereas transcriptional repression will correlate with compacted chromatin. Among mechanisms implicated in this dynamics, histones acetylation is largely associated with chromatin decompaction. Thus, compacted chromatin, called heterochromatin, is generally considered as hardly dynamic with hypo-acetylated histones. However, studies in yeast suggest the involvement of histone acetylation in heterochromatin in order to allow its plasticity. Moreover, recent data in mouse directly involve histone acetylation in compaction processes via double bromodomain proteins (BET) recruitment, shedding a new light on the biological function of histones acetylation. Pericentromeres are heterochromatin regions whose correct compaction is critical to allow normal chromosome segregation during cell division. Here, we used SUV39H 1/2 -/- mouse cells, in which the classical pericentromeric heterochromatin pathway is affected. Our results support a model in which the histone acetyl transferase TIP60 is recruited to pericentromeres in SUV39H 1/2 -/- cells, allowing compaction by H4K12 acetylation and BET proteins recruitment, which constitute a new example of acetylation-mediated compaction via a BET protein in mammals. This back-up compaction pathway may be used by the cell in physiological or pathological contexts with defective pericentric heterochromatin, such as some types of cancers. Indeed, this is the first time that TIP60 is implicated in pericentromeres, an important structure for genetic stability, which makes sense with the known function of TIP60 as a tumor suppressor.

Hepatocellular carcinoma (HCC) is an aggressive subtype of liver cancer with a poor prognosis. Currently, prognosis for HCC patients remains poor as few therapies are available. The clinical need for more effective HCC treatments remains unmet partially because HCC is genetically heterogeneous and HCC driver genes amenable to targeted therapy are largely unknown. Mutations in the TP53 gene are found in ~30% of HCC patients and confer poor prognosis to patients. Identifying genes whose depletion can inhibit HCC growth, and determining the mechanisms involved, will aid the development of targeted therapies for HCC patients. Therefore, the first half of this thesis focuses on identifying genes that are required for cell growth in HCC independent of p53 status. We performed a kinome-wide CRISPR screen to identify genes required for cell growth in three HCC cell lines: HepG2 (p53 wild-type), Huh7 (p53-mutant) and Hep3B (p53-null) cells. The kinome screen identified 31 genes that were required for cell growth in 3 HCC cell lines independent of TP53 status. Among the 31 genes, 8 genes were highly expressed in HCC compared to normal tissue and increased expression was associated with poor survival in HCC patients. We focused on TRRAP, a co-factor for histone acetyltransferases. TRRAP function has not been previously characterized in HCC. CRISPR/Cas9 mediated depletion of TRRAP reduced cell growth and colony formation in all three cell lines. Moreover, depletion of TRRAP reduced its histone acetyltransferase co-factors KAT2A and KAT5 at the protein level with no change at the mRNA level. I found that depletion of KAT5, but not KAT2A, reduced cell growth. Notably, inhibition of proteasome- and lysosome-mediated degradation failed to rescue protein levels of KAT2A and KAT5 in the absence of TRRAP. Moreover, tumor initiation in an HCC mouse model failed after CRISPR/Cas9 depletion of TRRAP due to clearance via macrophages and HCC cells depleted of TRRAP and KAT5 failed to grow as subcutaneous xenografts in vivo. RNA-seq and bioinformatic analysis of HCC patient samples revealed that TRRAP positively regulates expression of genes that are involved in mitotic progression. In HCC, this subset of genes is clinically relevant as they are overexpressed compared to normal tissue and high expression confers poor survival to patients. I identified TOP2A as one of the mitotic gene targets of the TRRAP/KAT5 complex whose inhibition greatly reduces proliferation of HCC cells. Given that this was the first time the TRRAP/KAT5 complex has been identified as a therapeutic target in HCC, the second half of this thesis focuses on identifying the mechanism via which depletion of this complex inhibits proliferation of HCC cells. I discovered that depletion of TRRAP, KAT5 and TOP2A reduced proliferation of HCC cells by inducing senescence. Typically, senescence is an irreversible state of cell cycle arrest at G1 that is due to activation of p53/p21 expression, phosphorylation of RB, and DNA damage. Surprisingly, induction of senescence after loss of TRRAP, KAT5 and TOP2A arrested cells during G2/M and senescence was independent of p53, p21, RB and DNA damage. In summary, this thesis identifies TRRAP as a potential oncogene in HCC. I identified a network of genes regulated by TRRAP and its-cofactor KAT5 that promote mitotic progression. Moreover, I demonstrated that disruption of TRRAP/KAT5 and its downstream target gene TOP2A result in senescence of HCC cells independent of p53 status. Taken together, this work suggests that targeting the TRRAP/KAT5 complex and its network of target genes is a potential therapeutic strategy for HCC patients.

Avec 59 000 nouveaux cas en 2017, le cancer du sein est le cancer le plus fréquemment diagnostiqué chez les femmes françaises, et pose un réel problème de santé publique en France, mais aussi au niveau mondial. Il est bien établi que la complexité de la carcinogenèse implique des modifications épigénétiques profondes qui contribuent au processus du développement tumoral. La dérégulation des marques d'histones acétylées H3 et H4 font partie de ces modifications. L'acétylation et la désacétylation des protéines sont des modifications posttraductionnelles majeures qui régulent l'expression des gènes liés au cancer et à l'activité d'une myriade d'oncoprotéines. Ainsi, une activité désacétylase aberrante peut alors favoriser ou supprimer la tumorigenèse dans différents types de cancers humains, y compris le cancer du sein. La désacétylase SIRT1 et l’acétyltransférase TIP60 sont 2 enzymes épigénétiques antagonistes qui sont impliquées dans l'apoptose, la régulation des gènes, la stabilité génomique, la réparation de l'ADN, et le développement du cancer. Dans le cadre de cette thèse, nous avons étudié la dérégulation des profils d’acétylation des histones H3 et H4 dans les différents sous-types moléculaires du cancer du sein, et investigué l’implication de SIRT1 et de TIP60 dans la progression tumorale de cancer du sein. Tout d’abord, nous avons signalé les rôles de SIRT1 et de TIP60 comme des biomarqueurs pronostiques potentiels en révélant leurs expressions différentielles en fonction de l’agressivité du cancer. Ensuite, nous avons montré leur régulation épigénétique différentielle des cibles histones en fonction du sous-type moléculaire, ainsi que leur modulation de la marque activatrice H3K4ac. En outre, l’inhibition de ces 2 enzymes par des Épidrogues s’est avérée comme une stratégie efficace dans le traitement du cancer. Ces travaux mettent en relief alors, SIRT1 et TIP60 comme des cibles thérapeutiques potentielles du cancer sporadique du sein. / With 59,000 new cases in 2017, breast cancer is the most frequently diagnosed cancer among French women, and poses a real public health problem in France, but also worldwide. It is well established that the complexity of carcinogenesis involves profound epigenetic deregulations that contribute to the tumorigenesis process. Deregulated H3 and H4 acetylated histone marks are amongst those alterations. Acetylation and deacetylation are major post-translational protein modifications that regulate gene expression and the activity of a myriad of oncoproteins. Aberrant deacetylase activity can promote or suppress tumorigenesis in different types of human cancers, including breast cancer. The deacetylase SIRT1 and the acetyltransferase TIP60 are 2 antagonistic epigenetic enzymes that are well implicated in apoptosis, gene regulation, genomic stability, DNA repair, and cancer development. In this manuscript, we identified the dysregulation of the histones H3 and H4 acetylation profiles in different molecular subtypes of sporadic breast cancer, and investigated the involvement of SIRT1 and TIP60 in breast tumorigenesis. First, we highlighted the roles of SIRT1 and TIP60 as potential prognostic biomarkers by revealing their differential expression patterns depending on breast cancer aggressiveness. Then, we demonstrated their differential epigenetic regulation of histone targets according to molecular subtype, and revealed their modulation of the H3K4ac epigenetic marker. Moreover, Epi-drugs mediated inhibition of these 2 enzymes has proven to be an effective strategy in the treatment of cancer. Thus, this work highlights the potential use of SIRT1 and TIP60 as epigenetic therapeutic targets for sporadic breast cancer.

L’acétylation des histones est associée à une activation transcriptionnelle. Cette acétylation est mise en place par des histone acétyltransférases (HATs) qui sont le plus souvent les sous-unités catalytiques de complexes multiprotéiques. Mon travail concerne plus particulièrement deux complexes contenant l’acétyltransférase Mof, MSL et NSL, ainsi que le complexe HAT Tip60-p400 dans les cellules souches embryonnaires de souris (mESCs). Nos analyses de localistaion sur l’ensemble du génome par ChIP-seq indiquent que MSL, NSL et Tip60-p400 se lient aux gènes activement transcrits et agissent comme des co-activateurs transcriptionnels majeurs dans les mESCs. MSL, NSL et Tip60-p400 ont des rôles à la fois chevauchants mais aussi distincts dans la régulation transcriptionnelle dans les mESCs. Chaque complexe présent un profil distinct de liaison à la chromatine. NSL lie principalement des gènes de ménage. MSL et Tip60-p400 sont également présent les gènes impliqués dans le développement. MSL est directement impliqué dans l’augmentation de l’expression de ces gènes au cours de la différenciation des mESCs. / Histone acetylation is involved in transcriptional activation of genes and is carried out by histone acetyltransferases (HATs), which are part of molecular protein complexes. This study focuses on the genome-wide role of Mof-containing MSL and NSL complexes and the Tip60-p400 complex in mouse embryonic stem cells (mESCs). I have analysed these complexes by ChIP-seq, shRNA knockdown and biochemical approaches. The genome-wide binding studies show that NSL, MSL and Tip60-p400 have a global overlap at promoters, but also bind to specific gene sets. There distinct binding profiles propose distinct roles in transcriptional regulation. MSL is the main H4K16 acetylase in mESCs.NSL binds mainly to housekeeping genes, whereas MSL and Tip60 are also present at developmental genes. Importantly, these developmental genes are directly regulated by MSL during cellular differentiation.

UHRF1 est une protéine nucléaire responsable du maintien et de la régulation de l'épigénome des cellules. Elle favorise la prolifération cellulaire et est surexprimée dans la plupart des cancers. TIP60, l'un des partenaires le plus important d’UHRF1, est impliqué dans le remodelage de la chromatine et la régulation transcriptionnelle grâce à son activité acétyltransférase. Ensemble, les deux protéines régulent la stabilité et l'activité d'autres protéines telles que la DNMT1 et la p53. Le but de cette étude était d'explorer le mécanisme d'interaction entre UHRF1 et TIP60 en visualisant cette interaction dans les cellules. La microscopie par imagerie à temps de vie de fluorescence et d'autres techniques de biologie moléculaire ont été utilisées. Les résultats ont montré que UHRF1 interagit directement avec le domaine MYST de TIP60 et cette interaction se produit dans la phase S du cycle cellulaire. Les deux protéines ont également montré une réponse similaire aux dommages à l'ADN, ce qui prédit une cohérence dans leur fonction dans le mécanisme de réparation de l'ADN. La surexpression de TIP60 a également induit la baisse du niveau d’UHRF1 et de DNMT1 ainsi qu’une induction d'apoptose dans les cellules ce qui suggère un rôle de TIP60 dans la régulation des fonctions oncogéniques d’UHRF1. / UHRF1 is a nuclear protein maintaining and regulating the epigenome of cells. Its promotes proliferation and is found upregulated in most of cancers. TIP60 is one of the important interacting partner of UHRF1 and is involved in chromatin remodeling and transcriptional regulation through its acetyltransferase activity. Together they regulate the stability and activity of other proteins such as DNMT1 and p53. The aim of this thesis was to explore the mechanism of interaction between UHRF1 and TIP60 by visualizing this interaction in cells. Fluorescent lifetime imaging microscopy and other molecular biology techniques were employed for this purpose. Results of this study showed that UHRF1 interacts directly to the MYST domain of TIP60 and this interaction prevails in the S-phase of cell cycle. Both proteins also showed a similar response to DNA damage predicting a coherence in their function in DNA repair mechanism. Overexpression of TIP60 also downregulated UHRF1 and DNMT1 and induced apoptosis in cells suggesting a role of TIP60 in regulation of oncogenic functions of UHRF1.

Tip60 is a 60 kDa nuclear protein which exists in three isoforms, belongs to the MYST/HAT family of proteins and was discovered after its interaction with the Human HIV-1 Tat. As a nuclear protein, Tip60 can act as a coactivator or repressor. To understand the HAT action of Tip60, two possible catalytic models exist; the ping-pong and the ternary complex formation models. In correlation with the exploration of HAT catalytic action, mutations of a Cys to Ala and a Glu to Gln on Esa1 (yeast homolog of Tip60 and MYST/HAT prototype), was reported to show wild type-like and decreased acetylating properties, respectively. In this work, Tip60 HAT action was explored. In Tip60, the Cys in the active site is important for acetylation of the H4(1-20) substrate and the Glu showed semi loss in acetylating the H4(1-20) peptide substrate. These data highlight a unique mechanism of Tip60 catalysis.