Dans la leucémie aigue myéloïde (LAM), la cytogénétique et les anomalies moléculaires sont fortement associées au pronostic : au sein des LAM à caryotype normal, les duplications de FLT3 (FLT3-ITD) ont un mauvais pronostic alors que les mutations de NPM1 et de CEBPA sont associées à un pronostic favorable. Récemment, les mutations du gène TET2 ont été identifiées dans les pathologies myéloïdes malignes. De plus, les approches de séquençage à haut débit ont permis de mettre en évidence la présence dans la LAM de mutations récurrentes du gène IDH1 dont les altérations avait été préalablement reportées dans le gliome au même titre qu’IDH2. Nous avons donc évalué la fréquence et la signification pronostique des altérations de TET2, IDH1 et IDH2 dans la LAM de novo. Les altérations génomiques et les variations de séquence du gène TET2 ont été étudiées dans une cohorte de 147 patients atteints de LAM de novo, tous traités par chimiothérapie intensive. Les mutations d’IDH1 et IDH2 (IDH1m et IDH2m) ont été étudiées dans une cohorte plus étendue réunissant 520 patients adultes inclus dans les protocoles thérapeutiques ALFA-9801 et ALFA9802. Dans la LAM de novo, les mutations ponctuelles de TET2 ont été retrouvées chez 17% des patients étudiés, soit une fréquence non significativement différente de celle retrouvée dans les syndromes myélodysplasiques ou dans les néoplasmes myéloprolifératifs. En revanche, les délétions et les pertes d’hétérozygotie sans perte de copie impliquant le gène TET2 sont vraiment rares dans la LAM. La fréquence des mutations de TET2 ne semble pas significativement différente chez les patients ayant atteints la rémission complète comparée à celle des patients en échec thérapeutiques. Les mutations de TET2 sont associées aux mutations de NPM1 (p=.032) mais ne semblent avoir d’impact sur la survie globale (OS) ou la survie sans maladie (DFS), ni dans la cohorte globale, ni dans le sous-groupe des LAM à caryotype normal.. La prévalence des mutations de IDH1 et IDH2 s’élève respectivement à 9.6% et 3% des LAM étudiées. Ces mutations sont principalement retrouvées dans le sous-groupe des LAM à caryotype normal. Dans ce sous groupe, les mutations d’IDH1 sont associées avec celles de NPM1 (p=.008) mais mutuellement exclusives avec celles atteignant CEBPA (p=.03). La fréquence de FLT3-ITD est similaire chez les patients avec et sans mutation d’IDH1. En revanche, aucune mutation de NPM1 ou de CEBPA et aucune duplication de FLT3 n’a été détectée chez les patients portant une mutation d’IDH2. Dans les LAM à caryotype normal, les mutations d’IDH1 ont été détectées chez 19% des patients avec le génotype favorable défini par la présence d’une mutation de NPM1 ou de CEBPA en l’absence de duplication de FLT3. Au sein de ce sous-groupe, la présence de mutations d’IDH1 est associé à un risque plus élevé de rechute (5y-RR: 71% pour IDH1m vs 38%, p=.01). Dans les LAM à caryotype normal, le génotype favorable pourrait ainsi etre redéfini par la présence d’une mutation de NPM1 ou de CEBPA sans duplication de FLT3 ni mutation de IDH1. Dans la cohorte étudiée, les patients caractérisés par ce génotype ont en effet un risque de rechute inférieur (5y-RR: 39% vs 76%, p<.0001) et une survie globale plus longue (5y-OS: 68% vs 29%, p<.0001). Les mutations d’IDH2 ont quant à elles un pronostic fortement péjoratif. Au sein des LAM à caryotype normal, les patients avec mutation de IDH2 ont un risque de rechute plus élevé (5y-RR: 100% pour IDH2m vs 60%, p=.01) et une survie globale plus courte (5y-OS: 0% pour IDH2m vs 46%, p=.005). Ainsi, l’étude des altérations concernant les gènes TET2, IDH1 et IDH2 a apporté des éléments supplémentaires de caractérisation des sous types de LAM. La détection des altérations de TET2 a permis d’évaluer leur fréquence dans la LAM mais n’a pas mis en évidence de sous groupe possédant une signification clinique ou pronostique particulière. / In acute myeloid leukemia (AML), both cytogenetic and molecular abnormalities are strongly associated with prognosis. In particular, in cytogenetically normal AML (CN-AML), FLT3-ITD (internal tandem duplication) carries adverse prognostic factor whereas NPM1 or CEBPA mutations are associated with favorable outcome. Recently, mutations of the ten eleven translocation 2 gene (TET2) have been reported in myeloid neoplasms. Further more, whole-genome sequencing identified recurrent mutations of IDH1 and IDH2 previously reported to be involved in gliomas. We evaluated the frequency and prognostic value of TET2, IDH1 and IDH2 alterations in de novo AML. Genomic alteration and sequence variation of TET2 gene were investigated in a cohort of 147 patients with de novo AML all treated with intensive chemotherapy. IDH1 and IDH2 mutations (IDH1m and IDH2m) were investigated on a wider cohort of 520 adults with AML homogeneously treated in the French ALFA-9801 and -9802 trials In de novo AML, point mutations of TET2 were found in 17% of studied patients which appear to be as frequent as in myelodysplastic syndrome or myeloproliferative neoplasms whereas TET2 deletion or copy neutral loss of heterozygosity are rare. The incidence of TET2 mutations were associated with NPM1 mutations (NPM1m) (p=0.032) and appeared similar in patients who achieved or not CR with intensive chemotherapy, but the presence of TET2 mutations did not affect OS and DFS in the overall population and in CN-AML patients. The prevalence of IDH1m and IDH2m was respectively 9.6% and 3.0% in the studied cohort, mostly associated with normal cytogenetics. In patients with CN-AML, IDH1m were associated with NPM1m (p=.008) but exclusive of CEBPAm (p=.03). The rate of FLT3-ITD was similar in IDH1m and IDH1wt patients. In contrary, no other mutations were detected in IDH2m patients. In CN-AML patients, IDH1m were found in 19% of favorable genotype ((NPM1m or CEBPAm) without FLT3-ITD) and were associated with a higher risk of relapse (5y-RR: 71% for IDH1m vs 38%, p=.01) and a trend to shorter overall survival (5y-OS: 45% for IDH1m vs 64%, p=.10). Favorable genotype in CN-AML could thus be defined by the association of NPM1m or CEBPAm with neither FLT3-ITD nor IDH1m. Patients with this favourable profile (N=62) had a lower RR (5y-RR: 39% vs 76%, p<.0001) and a better OS (5y-OS: 68% vs 29%, p<.0001). In IDH2m CN-AML patients (N=7), we observed a higher risk of induction failure, a higher RR (5y-RR: 100% for IDH2m vs 60%, p=.01) and a shorter OS (5y-OS: 0% for IDH2m vs 46%, p=.005). The investigation of alterations concerning TET2, IDH1 and IDH2 genes brought new elements of characterization of AML subtypes. Detection of TET2 alterations permit to obtain an evaluation of their frequency in AML but did not highlight a subset of cases with clinical or prognostic significance. However, investigation of IDH1m and IDH2m showed that these mutations are associated with a poor prognosis in AML contrarily to what is reported in gliomas. Screening of IDH1m could help to identify high risk patients within the subset of CN-AML with a favorable genotype.

Indiana University-Purdue University Indianapolis (IUPUI) / Hydrodynamic delivery is a powerful tool that allows delivery of macromolecules to the kidney culminating in gene expression. This finding is important in the fight against kidney disease. Current therapy for kidney injury, specifically acute kidney injury, is lacking. Supportive care in the form of IV fluids and medications aimed at restoring Glomerular Filtration Rate (GFR) and urine output are currently used. However, even with these treatments, prognoses of patients diagnosed with this disease remains poor. We believe that hydrodynamic delivery provides a mechanism that can be used to reverse and prevent AKI. Hydrodynamic delivery following ischemic injuries leads to reductions in serum creatinine and infiltrating mononuclear cells, as well as increased renal blood flow and survival. These changes are due to reductions in vascular congestion and inflammation typically seen following injury. To determine the underlying mechanisms of gene delivery preventing AKI, we used candidate genes identified in a proteomic screen on kidneys that recovered from AKI. We selected Isocitrate Dehydrogenase II (IDH2) and Sulfotransferase 1C2 (SULT1C2) for study and found that delivery prior to injury prevents serum creatinine increase and reduces cell death. We found that gene delivery of IDH2 prevents a glycolytic shift typically seen following ischemic injuries. The mechanism underlying the prevention of this shift are seen in increased ATP stores and spare respiratory capacity allowing the cell to remain in an oxidative state. Additionally, we show that SULT1C2 post-translationally modifies the mitochondria membrane, increasing oxidative phosphorylation providing the cell with additional energy needed in times of oxidative stress. These candidate genes allow cells to remain in an oxidative state preventing the activation of cell death pathways typically activated following injury, thereby preserving normal kidney function.

Les mutations de TET2, IDH2 et DNMT3A, 3 gènes impliqués dans la régulation de la méthylation de l'ADN, sont fréquentes dans les lymphomes T périphériques (PTCL), mais leurs conséquences sont mal connues. Nous avons montré que les mutations d'IDH2 dans les lymphomes angioimmunoblastiques (AITL) sont restreintes aux cellules T tumorales et que l'enzyme mutée, exprimée dans des lymphocytes T, produit bien l'oncometabolite D-2 hydroxyglutarate (D-2HG). Utilisant des modèles de souris transgéniques, nous avons montré que, dans un lymphocyte T, seule la mutation IDH2R172K produit suffisamment de D-2HG pour inhiber les protéines TET et altérer la différentiation lymphoïde. Ceci peut expliquer qu'IDH2R172 soit la seule mutation d'IDH retrouvée dans les AITL. Les mutations d'IDH2 inhibant les protéines TET, ce qui conduit à une baisse de la 5 hydroxyméthylcytosine (5hmC), nous avons évalué le niveau de 5hmC dans des PTCL mutés ou non pour TET2, IDH2 et/ou DNMT3A. Par rapport aux lymphocytes T normaux, nous avons vu une perte de 5hmC dans les cellules tumorales des PTCL, qui de façon intéressante était présente dans toutes les entités étudiées, quel que soit le statut mutationnel, à l'exception des lymphomes T hépatospléniques. Dans une démarche plus transversale, nous avons montré que la fréquence élevée de mutations de TET2, IDH2 et DNMT3A dans des PTCL présentant des caractéristiques TFH permet d'apporter un argument moléculaire, qui s'ajoute aux similitudes histologiques et phénotypiques pour regrouper ces lymphomes avec les AITL. Enfin, la description de l'efficacité d'un traitement par 5 azacytidine chez une patiente atteinte de AITL mutée pour TET2, suggère que les traitements ciblant l'épigénétique pourraient être efficaces dans ces maladies. / TET2, IDH2 and DNMT3A, 3 genes involved in the regulation of DNA methylation, are frequently mutated in Peripheral T Cell Lymphomas (PTCL). However, the consequences of these mutations are poorly understood. Focusing on IDH2 mutation, we demonstrated that this mutation is restricted to tumor T cells within angioimmunoblastic lymphoma (AITL) tumor tissue. We also demonstrated that, in AITL, IDH2 mutated T cells had the ability to produce D-2 hydroxyglutarate (D-2HG), a metabolite that has oncogenic effect. Using transgenic mouse models, we showed that IDH2R172K was the only IDH mutation that, when expressed in T cells, produced enough D-2HG to inhibit TET proteins and impairing lymphoid differentiation. This likely explains why IDH2R172 is the only IDH mutation found in AITL. As IDH2 mutation results in TET2 inhibition, which impairs 5hmC formation, we assessed the level of 5hmC in AITL, and described 5hmC loss, compared to normal TFH, in all AITL, regardless of the TET2, IDH2 and DNMT3A mutational status. We extended these finding to main nodal and extranodal PTCL entities, showing that 5hmC loss was a general mechanism present in all PTCL, with the exception of hepatosplenic T cell lymphoma. In a translational approach, we saw that the high frequency of TET2, DNMT3A and RHOA mutations in TFH like PTCL suggest a common molecular basis shared with AITL that could argue, in addition to phenotypic and histological similarities, to group these 2 entities into a single category. Finally, we described the first complete remission of a patient with a TET2 mutated AITL with 5 azacytidine, suggesting that hypomethylating agents could be active in PTCL.

IntroductionAcute myeloid leukemia (AML) is caused by a wide range of genetic aberrations, includingmutations within the genes that encode the enzymes isocitrate dehydrogenase 1 and 2(IDH1/2). Drugs that target mutant IDH1/2 are now available, which makes assessment of themutational status of IDH1/2 important in clinical diagnostics of AML. A promising method todetect these mutations is the droplet digital polymerase chain reaction (ddPCR), which showsadvantages of a high sensitivity and a simple workflow.AimTo evaluate ddPCR as method of choice to detect hotspot mutations in IDH1 (codon R132)and IDH2 (codon R140 and R172) in patients with AML.MethodsFifteen AML patients known to be positive for IDH1/2 diagnosed by a previously performednext generation sequencing (NGS) were selected for evaluation of ddPCR. Diagnosticsamples were tested for 14 patients, whereas follow-up samples were tested for one patient.ddPCR was performed using QX200™ Droplet Digital PCR system and data were presentedas fractional abundance of mutant allele.ResultsThe amount of mutant IDH1/2 in samples reported by ddPCR correlated well with the resultsfrom NGS when using probes that target their specific mutation. The detection limit formutant allele in the background of wild type IDH1/2 was 0,5% for IDH2 p.R140Q and 0.1%for IDH1 p.R132C/H.ConclusionddPCR that target specific mutations shows a great potential in measuring minimal residualdisease during follow-up. However, its use in screening for mutant IDH1/2 at the time ofdiagnosis is limited and alternative approaches should be considered.

<p>Gliomas are tumors of the central nervous system for which improvements in treatment are critically needed. Mutations in IDH1 and IDH2, which encode the cytosolic and mitochondrial NADP+-dependent isocitrate dehydrogenases, respectively, are frequent in gliomas. Here, we summarize recent literature concerning gliomas, the normal cellular functions of IDH1/2, the epidemiology of IDH1/2 mutations, and the understanding of the function of IDH1/2 mutations in cancer. We then show in vitro using liquid chromatography-mass spectrometry that a function of many IDH1/2 mutations is to produce 2-hydroxyglutarate. Next, we use a mass spectrometry based platform to characterize metabolic changes in a glioma cell line expressing IDH1/2 mutants and show that the IDH mutants are associated with lowered N-acetylated amino acids both in this cell line model and in primary tumor tissue. Finally, we develop and characterize a Drosophila melanogaster (fruit fly) model of IDH1/2-mutated cancer by expressing the mutated Drosophila homolog of IDH1 in fly tissues using the UAS-Gal4 binary expression system. These results delineate downstream molecular players that likely play a role in IDH1/2-mutated cancer and provide a model organism for interrogation of genetic networks that interact with IDH1/2 mutation. These findings refine our understanding of glioma pathogenesis and may inform the design of new glioma therapies.</p> / Dissertation

Les neuroblastomes olfactifs (NBOs) sont des tumeurs rares de la base du crâne. Les outils de classification de ces tumeurs sont insuffisants, il n’existe notamment aucune classification moléculaire des NBO. La biologie de ses tumeurs est mal connue. Nos travaux se sont appuyés sur l’analyse des exomes, du transcriptome, du méthylome et des caractéristiques histopathologiques et immunitaires d’une série de 59 NBOs bien annotés cliniquement. Nous avons mis en évidence l’existence de 2 sous-types de NBO présentant un profil d’expression et un profil anatomo-clinique différent. Le type neural, correspond à une tumeur bien différenciée, peu agressive, présentant des caractéristiques plutôt neuronales et partageant des caractéristiques phénotypiques avec les progéniteurs directs de neurones olfactifs. Le type basal correspond à une tumeur moins différenciée, plus agressive, ayant des caractéristiques plutôt embryonnaires, partageant des caractéristiques phénotypiques avec les cellules basales de renouvellement de l’épithélium olfactif. Nous avons mis en évidence que la charge mutationnelle était plus élevée dans le type basal, avec notamment des mutations IDH2 R172 récurrentes, associées à un phénotype CpG Island Methylator (CIMP). Nous avons également montré que les NBOs de type basal étaient infiltrés par un nombre plus important de lymphocytes T avec, dans certaines tumeurs, une expression plus marquée de checkpoints immunitaires et de facteurs immunosuppresseurs. Ce travail ouvre la perspective d’une classification moléculaire permettant de mieux stratifier les patients et ouvre également le champ de nouvelles stratégies thérapeutiques dans ces tumeurs rares. / Olfactory neuroblastomas (ONBs) are rare tumors arising in the skull base. Classification tools are poor, notably; no molecular classification of ONB has been reported. Literature data about their cell of origin, the existence of molecular therapeutic targets or their immune environment being scarce, the biology of these tumors is still poorly understood. Our work was based on exome, transcriptome and methylome analysis, but also on histopathological and immune characteristics of a series of 59 clinically well annotated ONBs. We highlighted 2 sub-types of ONB showing different expression and clinicopathologic patterns. The neural type is a well differentiated, poorly aggressive tumor which shows neurons characteristics and shares phenotypic similarities with olfactory neuron progenitors. The basal type is a less differentiated tumor, displaying an aggressive phenotype, with embryonic phenotypical characteristics, which shares similarities with basal renewing cells of the olfactory epithelium. We showed that the mutational load was higher in basal tumors, with notably recurrent IDH2 R172 mutations associated with a CpG Island Methylator Phenotype (CIMP). We also showed that basal type ONBs were infiltrated by a greater number of T cells with, in some cases, a higher expression of immune checkpoints and immunosuppressive factors. This work paves the way towards a new molecular classification which will allow a better stratification of patients and will open the field of new therapeutic strategies for this rare tumor.

The isocitrate dehydrogenase (IDH) family of enzymes is central to cellular metabolism, catalyzing the oxidative decarboxylation of isocitrate to α-ketoglutarate (α-KG) and production of NADPH. Recently, cancer-associated heterozygous somatic mutations in family members IDH1 and IDH2 were discovered and present predominantly in glioblastoma multiforme and acute myeloid leukemia. The major consequence of these point mutations is the biochemical production of the ‘oncometabolite’ (R)-2-hydroxyglutarate [(R)-2-HG] from α-KG. Recent studies indicate that unalike mutations of IDH2 produce different intracellular levels of (R)-2-HG, suggesting that IDH2 mutations may differentially influence tumorigenesis. Contrasting clinical studies find IDH mutations to be associated either with increased metastatic potential, or higher survival and enhanced chemosensitivity probabilities. Nevertheless, these studies failed to indicate specifically which of the various IDH mutations were found in each of the patients’ tumors. This raises important questions as to whether specific IDH mutations contribute differently to tumorigenesis. In this study, specific IDH2 mutations were evaluated and compared for their chemosensitivity, tumorigenic activity, and production of (R)-2-HG- all notable determinants for their potential use as tumor biomarkers. Three individual clinically relevant IDH2 mutations (IDH2-R172K, -R172M, and -R140Q) or IDH2-WT were expressed in human U87MG glioblastoma cells. We observed distinct changes in cell morphology, proliferation, migration, invasion, anchorage-independent growth and response to chemotherapeutic agents. Differences in base-line activation of various stress pathways were also observed, lending a plausible explanation to the differing phenotypic outcomes. Interestingly, the variable levels of endogenous (R)-2-HG produced by the cell panel inversely correlated with their respective growth rates, implicating (R)-2-HG as a negative regulator of tumor growth. Indeed, treatment of tumor cell lines, expressing IDH2-WT, with exogenous (R)-2-HG induced a decrease in cell proliferation in a dose-dependent manner. When tested in vivo, treatment of tumor-bearing mice with (R)-2-HG significantly reduced tumor volume. These in vivo results complement the results of soft-agar colony forming assays, demonstrating again that (R)-2-HG inhibits tumor growth. In contrast, immortalized cells subjected to long-term (R)-2-HG treatment showed enhanced cell proliferation. Their response to (R)-2-HG, however, could be switched from growth promotion to that of growth inhibition through expression of oncogenic Ras. Thus, these findings demonstrate conclusively that IDH2 mutations are not alike and that oncometabolite (R)-2-HG plays dual roles in tumorigenesis. / Molecular Biology and Genetics

[ES] La leucemia mieloide aguda (LMA) se trata de un grupo heterogéneo de desórdenes hematológicos producidos por alteraciones genéticas en las células precursoras mieloides. Las mutaciones en la enzima Isocitrato deshidrogenasa 2 (IDH2) son unas de estas alteraciones. Las mutaciones más frecuentes en esta proteína afectan a las posiciones R140 y R172, provocando una ganancia de función con la producción del oncometabolito D-2-hidroxiglutarato (2-HG). A pesar de que ambas inducen la producción de 2-HG, la mutación R172 produce mayor cantidad de oncometabolito, presenta menos concurrencias con otras alteraciones genéticas y se asocia a una peor respuesta a la quimioterapia y un mayor riesgo de recaída. Los modelos de investigación han permitido conocer el papel de las mutaciones genéticas en el desarrollo de la enfermedad. A pesar de ello, es necesario desarrollar nuevos modelos que expresen de forma endógena estas mutaciones para estudiar en profundidad las vías moleculares afectadas. Por todo ello, en esta Tesis se han desarrollado nuevas estrategias de edición génica mediante el sistema CRISPR/Cas9 con el objetivo de desarrollar nuevos modelos in vitro e in vivo de mutaciones implicadas en LMA. Debido a la baja eficiencia de transfección de los plásmidos CRISPR en las líneas celulares leucémicas, el método más empleado para introducir los elementos CRISPR han sido principalmente vectores lentivirales. Para evitar los inconvenientes de este tipo de vectores, en esta Tesis se ha desarrollado una estrategia alternativa para la introducción de la nucleasa Cas9 y los guías CRISPR. El gen codificante de la Cas9 se introdujo en el genoma de células NB4 mediante transducción con lentivirus, generando una línea celular con expresión constitutiva de la nucleasa. Por otro lado, se desarrolló un sistema sencillo de producción de los guías CRISPR mediante PCR con los elementos esenciales para su expresión y la expresión del reportero GFP de forma opcional. Con el objetivo de optimizar la técnica y probar su eficiencia en distintas dianas se modificaron dos genes implicados en LMA. Estos fueron el gen IDH2, en el cuál se buscó introducir la mutación R172, y el gen MYBL2. Finalmente, las eficiencias de edición obtenidas se compararon con el uso de complejos de ribonucleoproteínas CRISPR, muy utilizados por su alta eficiencia. Mientras que los complejos de ribonucleoproteínas presentaron una mayor eficiencia de corte, la eficiencia de edición de la mutación R172 fue similar en ambas estrategias. Mediante secuenciación masiva se confirmó y caracterizó esta edición y se comprobó que la maquinaria de edición no había producido cortes inespecíficos en regiones similares del genoma. Por tanto, la nueva metodología desarrollada permitió editar de forma precisa líneas celulares leucémicas con eficiencias similares a otras técnicas CRISPR más extendidas y sin producir efectos inespecíficos no deseados. Por otro lado, gracias a la gran conservación evolutiva del gen IDH2, los residuos R140 y R172 se encuentran conservados en la proteína idh-2 de Caenorhabditis elegans. Se empleó la estrategia co-CRISPR para desarrollar y seleccionar cepas mutantes con las mutaciones ortólogas a R140 y R172, y una cepa con ambas mutaciones. A pesar de la conservación, no se observó el aumento del oncometabolito 2-HG esperado en las cepas mutantes en comparación con la cepa salvaje control N2. Un estudio exhaustivo de las vías implicadas nos serviría para desarrollar modelos de investigación con las alteraciones moleculares observadas en los pacientes. Para concluir, la estrategia desarrollada de introducción de elementos CRISPR en líneas celulares, junto a los modelos producidos en C. elegans, permitirán en futuros estudios investigar en detalle los efectos moleculares de mutaciones detectadas en pacientes de LMA, su implicación en el desarrollo y pronóstico de la LMA y comprender su papel en la estratificación de los pacientes. / [CA] La leucèmia mieloide aguda (LMA) es tracta d'un grup heterogeni de desordres hematològics produïts per alteracions genètiques en les cèl·lules precursores mieloides. Les mutacions en l'enzim Isocitrato deshidrogenasa 2 (IDH2) son d'aquestes alteracions. Les mutacions més freqüents en aquesta proteïna afecten a les posicions R1240 i R172, produint un guany de funció amb la producció de l'oncometabolit D-2-hidroxiglutarat (2-HG). A pesar que ambdues indueixen la producció de 2-HG, la mutació R172 produeix mes quantitat de oncometabolit, presenta menys co ocurrències con altres alteracions genètiques i s'associa a una pitjor resposta a la quimioteràpia i un major risc de recaiguda. Els models d'investigació han permés conéixer el paper de les mutacions genètiques en el desenvolupament de la malaltia. Malgrat això, és necessari desenvolupar nous models que expressen de manera endògena aquestes mutacions per a estudiar en profunditat les vies moleculars afectades. Per tot això, en aquesta Tesis s'han desenvolupat noves estratègies d'edició gènica mitjançant el sistema CRISPR/Cas9 amb l'objectiu de desenvolupar nous models in vitro i in vivo de les mutacions implicades en la LMA. Degut a la baixa eficiència de transfecció dels plasmids CRISPR en les línies cel·lulars leucèmiques, el mètode més emprat per a introduir els elements CRISPR han sigut principalment vectors lentivirals. Per a evitar els inconvenients d'aquesta mena de vectors, en aquesta Tesis s'ha desenvolupat una estratègia alternativa per a la introducció de la nucleasa Cas9 i els guies CRISPR. El gen codificant de la Cas9 es va introduir al genoma de cèl·lules NB4 mitjançant transducció amb lentivirus, generant una línia cel·lular amb expressió constitutiva de la nucleasa. D'altra banda, es va desenvolupar un sistema fàcil de producció dels guies CRISPR mitjançant PCR amb els elements essencials d'expressió i amb l'expressió del reporter GFP de manera opcional. Amb l'objectiu d'optimitzar la tècnica i provar la seua eficiència en diferents dianes es van modificar dos gens implicats en LMA. Aquests van ser el gen IDH2, en el qual es va buscar introduir la mutació R172, i el gen MYBL2. Finalment, les eficiències d'edició obtingudes amb la nova estratègia es van comparar amb l'ús de complexos ribonucleotproteïnes CRISPR, molt utilitzats per la seua alta eficiència. Mentre que els complexos de ribonucleoproteïnes van presentar una major eficiència de tall, l'eficiència d'edició de la mutació R172 va ser similar en les dues estratègies. Mitjançant seqüenciació massiva es va confirmar i caracteritzar aquesta edició i es va comprovar que la maquinària d'edició no havia produït talls inespecífics en regions similars del genoma. D'aquesta manera, la nova metodologia desenvolupada permet editar de manera precisa línies cel·lulars leucèmiques amb eficiències similars a altres tècniques CRISPR més esteses i sense produir efectes inespecífics no desitjats. D'altra banda, gràcies a la gran conservació evolutiva del gen IDH2, els residus R140 i R172 es troben conservats en la proteïna idh-2 de Caenorhabditis elegans. Es va utilitzar l'estratègia co-CRISPR per a desenvolupar i seleccionar ceps mutants amb les mutacions ortòlogues a R140 i R172, i un cep amb dues mutacions. Malgrat l'alta conservació, no es va observar l'augment del oncometabolit 2-HG esperat en els ceps mutants en comparació amb el cep salvatge control N2. Un estudi exhaustiu de les vies implicades ens serviria per a desenvolupar models d'investigació amb les alteracions moleculars observades en els pacients. Per a concloure, l'estratègia desenvolupada d'introducció d'elements CRISPR en línies cel·lulars, al costat dels models produïts en C. elegans permetran en estudis futurs investigar detalladament els efectes moleculars de mutacions detectades en pacients, la seua implicació en el desenvolupament i prognosi de la LMA i comprendre el seu paper en l'estratificació dels pacients. / [EN] Acute Myeloid Leukaemia (AML) is a heterogeneous group of haematological disorders caused by genetic alterations in myeloid precursors. Mutations in the Isocitrate dehydrogenase enzyme are among these alterations. The most frequent mutations in this protein affect R140 and R172 positions, leading to a gain of function with the production of the oncometabolite D-2-hydroxyglutarate (2-HG). Although both induce the 2-HG production, the R172 mutation generates greater amount of oncometabolite, has fewer co-occurrences with other genetic alterations and is associated with worse chemotherapy response and higher relapse risk. Research models have made possible to study the role of genetic mutations in disease development. Despite this progress, new models with endogenous expression of these mutations are needed to study in depth the molecular pathways involved. Therefore, in this Thesis we have developed new gene editing strategies using the CRISPR/Cas9 system with the aim of developing new in vitro and in vivo models of mutations involved in AML. Regarding in vitro model, due to the low transfection efficiency of CRISPR plasmids in leukemic cell lines, the most commonly method used for introducing CRISPR elements have been mainly lentiviral vectors. To avoid the disadvantages of this type of vectors, in this Thesis we have developed an alternative strategy for introducing Cas9 nuclease and CRISPR guides. The gene encoding the Cas9 was introduced into NB4 genome by lentiviral transduction producing a stable cell line that constitutively express the nuclease. On the other hand, a simple system for the production of CRISPR guides by PCR with essential elements of expression was developed and with GFP reporter expression optionally. In order to optimise the technique and test its efficiency in different targets, two genes involved in AML were modified. These were IDH2 gene, in which R172 mutation was introduced, and MYBL2 gene. Finally, editing efficiencies obtained with the new strategy were compared with CRISPR ribonucleoproteins methodology, widely used for its high efficiency. Whereas ribonucleoprotein complexes showed higher cut efficiencies, the efficiency of edition of R172 mutation efficiency was similar in both strategies. These results were validated and characterized by means of next generation sequencing, and no off-target effects were found. Therefore, the new developed methodology allows precise gene editing in leukemic cell lines with similar efficiencies with other popular CRISPR techniques and without off-target effects. On the other hand, thanks to the high evolutive conservation of IDH2 gene R140 and R172 residues are conserved in Caenorhabditis elegans idh-2 protein. The co-CRISPR strategy was used to produce and select mutant strains with ortholog mutations to R140, R172 and one strain with both mutations. Despite the high conservation, the expected increase in oncometabolite 2-HG concentration was not detected in mutant strains compared to the N2 wild type strain. A comprehensive study of the pathways involved would help us to develop a research model with molecular alterations noticed in patients. In conclusion, the new developed strategy for CRISPR elements introduction in cell lines, together with C. elegans models, will allow an in-depth research of molecular effect of mutations detected in patients, its implication in AML progression and prognosis and understand their role in patient stratification. / González Romero, E. (2022). Investigación de la Leucemia Mieloide Aguda mediante el desarrollo de modelos in vitro e in vivo [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/181891

Mitochondrial isocitrate dehydrogenase 2 (IDH2) catalyzes reductive carboxylation (RC, reverse Krebs cycle pathway) and 2HG synthesis (2HG) - metabolite of which many scientists are interested. 2HG may be concurrently synthetized in cytosol by IDH1. RC is involved in anabolic reactions necessary for cell proliferation - produces citrate, fatty acid precursor - especially in hypoxia. IDH2 and IDH1 are not the only enzymes that are involved in 2HG synthesis. Recently, several enzymes, which participate in 2HG production, have been discovered. 2HG is useful in cancer diagnostics due to its overproduction by transformed cells. Moreover, 2HG may cause epigenetic changes via inhibition of 2-oxoglutarate dependent dioxygenase. In this work, the importance of RC and 2HG synthesis in cancer and healthy cells was investigated by gas chromatography with mass spectrometry detection as well as IDH2 influence. We found that IDH2 significantly participates in reverse RC and 2HG synthesis in breast cancer cell lines and uses glutaminolysis as a supplementary anaplerotic pathway. RC is increased by hypoxia, inhibition of respiration, and decreased by activation of respiration or hypocapnia. We confirmed 2HG synthesis and RC in healthy cells (fibroblasts, breast epithelial cells etc.) as well as in cancer cells....