Bc.Veronika Hrabcová BRAF mutations in metastatic malignant melanoma. Diploma thesis Charles University in Prague, Faculty of Pharmacy in Hradec Králové Healthcare bioanalytics - Specialist in Laboratory Methods Backround: Melanoma is malignant disease with increasing incidency. Treatment of advanced stage of melanoma is still limited. With a progress of knowledge in genetics and tumorigenesis, the incidence of mutated BRAF protein was observed at 50 % of melanomas. In 80-90 % mutated melanomas contain BRAF V600E mutation. The aim of study was to establish a suitable molecular biological method for the diagnosis of mutations in codon V600 BRAF. Methods: Cobas 4800 BRAF V600 mutation test and BRAF StripAssay test were used to analyze DNA. Cobas 4800 BRAF V600 mutation test is based on PCR using TaqMan probes designed for the wild-type and mutant BRAF V600E sequence. BRAF StripAssay test is based on PCR amplification with biotinylated primers and subsequent hybridization of the stripped with allele-specific oligonucleotide probes. Examined DNA samples were derived from 35 patients with advanced malignant melanoma or from archive of laboratory. Results: BRAF V600 mutation was detected in approximately half of the tumors, consistent with the results of other studies. In comparison methods Cobas test...

Le mélanome métastatique est resté longtemps synonyme de pronostic catastrophique en raison de la faible efficacité des traitements disponibles. Depuis quelques années, de nombreuses innovations thérapeutiques ont révolutionné la prise en charge de ces patients, avec l’autorisation de mise sur le marché de traitements modulateurs de l’immunothérapie d’une part et de thérapies ciblant la voie des MAP kinases destinées aux patients porteurs de la mutation BRAF (présente dans environ 50% des mélanomes) d’autre part.Les inhibiteurs de BRAF et de MEK sont à l’origine de réponses spectaculaires, mais le contrôle de la maladie est généralement limité dans le temps, avec l’apparition de résistances au traitement entraînant une progression de la maladie. Etablir des stratégies thérapeutiques permettant de retarder ou de contourner ces résistances s’avère donc primordial. Pour ce faire, des biomarqueurs ou outils prédictifs de la réponse, in vitro et in vivo, peuvent contribuer à mieux stratifier les patients, et personnaliser leur prise en charge.Dans une première partie, nous avons comparé l’apport respectif d’un traceur de prolifération cellulaire, la 18F-FLT, et du traceur de consommation de glucose le 18F-FDG, dans l’évaluation thérapeutique d’une xénogreffe de mélanome BRAF muté traité par un inhibiteur de BRAF. Nous avons confirmé la place prépondérante du 18F-FDG, et étayé l’intérêt des index volumiques pour le suivi thérapeutique, notamment avec la 18F-FLT.Dans une seconde partie nous avons évalué in vivo la capacité d’un schéma d’administration intermittente à retarder l’apparition de résistance par rapport à un schéma d’administration continue dans des xénogreffes BRAF mutées traitées par une combinaison d’inhibiteurs BRAF/MEK. Dans nos modèles expérimentaux, il ne semblait pas y avoir de supériorité de l’administration intermittente. Toutefois nos expérimentations n’ont pas permis de trancher de façon formelle la question.Dans une troisième partie, nous avons voulu reproduire le schéma d’administration intermittent ex vivo en utilisant la technique d’histocultures. Nous avons par ailleurs évalué la possibilité pour des histocultures issues de tumeurs de patients de prédire la réponse aux thérapies ciblées chez ces mêmes patients. Les histocultures semblent un outil fiable pour guider les choix thérapeutiques. La documentation des modifications génétiques et de l’hétérogénéité moléculaire du mélanome pourrait également inciter à adapter la stratégie en fonction de l’agressivité présumée du mélanome chez un patient donné / Metastatic melanoma has long been synonymous of dismal prognosis, due to the weak efficacy of available treatments. Numerous therapeutic innovations have profoundly modified the management of these patients, with marketing authorizations of therapies targeting the MAP Kinases pathway for patient with BRAF mutated melanoma (about 50% of patients) on the one hand and immune checkpoint inhibitors on the other hand.BRAF and MEK inhibitors result in dramatic responses, but disease control is generally short-lived, with onset of drug resistance leading to disease progression. Designing therapeutic strategies allowing delaying or bypassing this resistance phenomenon is of primary importance. Thus, in vitro and vivo biomarkers or tools predictive of response could help stratifying patients, and personalize each patient’s management.In the first part, we compared the respective value of a proliferation tracer, 18F-FLT, and of the glucose consumption tracer, 18F-FDG for therapeutic evaluation of a BRAF mutated melanoma xenograft, treated by a BRAF inhibitor. We confirmed the predominant role of 18F-FDG, and backed up the potential interest of volumetric parameters for therapeutic follow-up, especially with 18F-FLT.In a second part we assessed in vivo the ability of an intermittent schedule to delay resistance onset, compared with a continuous schedule in BRAF mutated xenografts treated by a BRAF/MEK inhibitors combination. In our experimental models, there did not seem to be any superiority for the intermittent schedule. However our experiments did not allow us to draw any final conclusions on the subject.In a third part, we tried to reproduce ex vivo the intermittent schedule with histocultures device. We also assessed the possibility for histocultures with patient derived tumours to predict response to targeted therapies in the same patients. Histocultures appear as a relevant tool to guide therapeutic choice. Determination of genetic modifications and molecular heterogeneity may also prompt tailoring therapeutic strategy depending on the supposed aggressiveness of a melanoma in a given patient

The most frequent mutation identified in both benign nevi and malignant melanoma is the constitutively activating V600E substitution of BRAF. However, how additional mutations co-operate with BRAFV600E to promote subtypes of melanoma in animals is only beginning to be understood. In this thesis, I generate and analyze zebrafish BRAFV600E melanoma models and also develop the first animal model for BRAFV600E nevus recurrence. In my first data chapter, I develop a unique animal model of nevus recurrence. In people it is not uncommon for a nevus to recur following removal, even when no pigmented nevus cells remain. The biology of how and why this happens is unknown. By partial amputation of the nevus in the zebrafish tail fin, we described both nevus regrowth, as well as nevi that do not regrow. Utilising melanin as a lineage tracer, I was able to show that recurrent nevi are repopulated from an unpigmented precursor population. This suggested that BRAFV600E nevi are supported by an undifferentiated stem cell population that is recruited to regenerate and pigment the nevus after removal. In my second data chapter, I use genetics to develop BRAFV600E zebrafish models of melanoma. In collaboration with Dr. James Lister and Professor Jeroen den Hertog, I describe three differing models of zebrafish melanoma. All three models show progression to melanoma, and in collaboration with Dr. Marie Mathers I establish that while BRAFV600E is present in all three models, co-operating mutations affect melanoma pathology. In my third data chapter, I develop tools to study the molecular differences in the BRAFV600E melanoma models. I described the optimisation of a broad range of antibodies, raised against human peptides due to the lack of reliable antibodies in the zebrafish field. I use punch core biopsies of both zebrafish and human tumours, and whole sagittal sections of juvenile zebrafish, to show specific staining throughout many organs of the developing fish. I then use some of these antibodies to analyse molecular pathways in the melanoma models.

No description available.

Les inhibiteurs de BRAFV600-, dont le vemurafenib, sont efficaces contre les tumeurs présentant cette mutation activatrice de la voie des MAPK, ce qui est le cas d’un mélanome sur deux. Mais la plupart des malades traités rechutent dans l’année, et développent des tumeurs paradoxales secondaires.Divers mécanismes de résistance aux inhibiteurs de BRAF ont été décrits, cette résistance passant soit par réactivation de la voie des MAPK, soit par activation de la voie parallèle Akt/mTor, soit par anomalie de régulation de l’apoptose. Dans le cadre de cette thèse, nous avons mis en évidence une nouvelle cible thérapeutique: l’initiation de la traduction cap-dépendante. L’augmentation de la traduction de certains ARNm en protéines est une étape capitale de l’expression des gènes dans les processus oncogènes. Une étape limitante de cette traduction est son initiation. La protéine eIF4E (eukaryotic Initiation Factor 4E) se lie à la coiffe m7GTP des ARNm et régule la synthèse protéique en fonction de ses partenaires 4EBP1 et eIF4G. Quand eIF4E est assemblé à eIF4G et eIF4A, on parle du complexe « eIF4F », situé au point de convergence de la voie des MAPK et de la voie Akt/mTor via 4EBP1. Ce complexe est nécessaire à la traduction des protéines de survie et de prolifération cellulaire ayant une structure secondaire complexe en 5’UTR. Pour déterminer le statut d’activation du complexe eIF4F dans des lignées cellulaires, nous avons réalisé une immunoprécipitation des protéines liées au cap (« cap-binding assay »). Nous avons observé que le vemurafenib entraînait une diminution d’eIF4G fixé à eIF4E dans les cellules sensibles mais aucune modification dans les lignées résistantes. Parallèlement, la fixation de 4EBP1 à eIF4E augmente sous vemurafenib pour les lignées sensibles. Pour confirmer ces résultats, nous avons utilisé la technique de « Proximity Ligation Assay » (PLA), qui nous a permis de visualiser les complexes eIF4E-eIF4G et eIF4E-4EBP1 sous forme de points fluorescents observables en microscopie. Le nombre de complexes eIF4E-eF4G était bien diminué dans les cellules sensibles sous vemurafenib ce qui n’était pas le cas dans les cellules résistantes. Parallèlement, le nombre d’interactions eIF4E-4EBP1 augmentait dans les cellules sensibles et restait stable dans les cellules résistantes. De même, dans les tumeurs de patients, le rapport des complexes eIF4E-eIF4G sur eIF4E-4EBP1 diminuait dans les métastases en réponse au vemurafenib puis réaugmentait lors des récidives tumorales. De plus, nous avons testé des composés ciblant la traduction cap-dépendante et plus particulièrement eIF4A : les flavaglines. Nous avons montré que leur capacité à cibler l’initiation de la traduction était corrélée à l’inhibition de la prolifération des lignées cellulaires résistantes. Enfin, nous avons testé l’une d’elles in vivo. Les résultats montrent un effet synergique de cette drogue combinée au vemurafenib et une inhibition de la croissance tumorale.Concernant l’autre inconvénient majeur des anti-BRAF, l’induction fréquente de tumeurs secondaires, nous avons visualisé, aussi par PLA, les dimères BRAF-CRAF pour la première fois dans une série de tumeurs paradoxales de patients, cutanées et extra-cutanées. Ces dimères sont significativement plus nombreux dans les tumeurs cutanées apparaissant sous anti-BRAF que dans une série tumeurs contrôles de même type.En conclusion, nous avons identifié un nouveau biomarqueur de résistance aux anti-BRAF, visualisable par PLA. Pour optimiser la réponse tumorale à ces thérapies ciblées, qui constituent le traitement de choix des mélanomes métastatiques mutés, nous proposons d’y associer un inhibiteur de l’initiation de la traduction. Nous avons en parallèle mis au point le PLA BRAF-CRAF dans les tumeurs paradoxales induites par les anti-BRAF, et nous avons identifié des sous-populations plus à risque de développer ce type de tumeurs. / BRAFV600- inhibitors, including vemurafenib, are efficient against tumors harboring this MAPK pathway activating mutation, which is the case of ~50% of melanomas. But most of the patients under treatment progress within a year, and develop paradoxical secondary tumors. Most resistance mechanisms to drugs that target the BRAF and/or MEK kinases in cancer rely on reactivation of the RAS-RAF-MEK-ERK signal transduction pathway (ERK-dependent), on activation of the alternative PI3K-AKT-mTOR pathway (ERK-independent) or on modulation of the caspase-dependent apoptotic cascade. All three pathways converge to regulate the formation of the eIF4F translation initiation complex that binds to the 7-methyl-guanine cap at the 5’ end of mRNAs, thereby modulating mRNA translation of specific mRNAs. We show here that persistent formation of the eIF4F complex, comprising the eIF4E cap binding protein, the eIF4G scaffolding protein and the eIF4A RNA helicase, is associated with resistance to anti-BRAF, anti-MEK and to anti-BRAF + anti-MEK combinations in BRAFV600- mutant melanoma, colon and thyroid cell lines. Unresponsiveness to treatment and maintenance of eIF4F complex formation is associated with either reactivation of MAPK signaling or absence of ERK-independent decreased phosphorylation of the inhibitory eiF4E binding protein 4EBP1 or increased pro-apoptotic Bcl-2 modifying factor (BMF)-dependent degradation of eIF4G. Development of an in situ method shows by proximity ligation assay (PLA) that the formation of the eIF4F complex is decreased in tumors responding to anti-BRAF therapy and increased in resistant metastases. Strikingly, inhibiting the eIF4F complex, either by blocking the eIF4E-eIF4G interaction or by targeting eIF4A with small compounds is synergistic with BRAFV600- inhibition. The other main problem arising during anti-BRAF treatment is the frequent induction of secondary cutaneous and extra-cutaneous tumors, through the formation of BRAF-CRAF dimers that we visualized in vivo for the first time. In conclusion, we have identified by PLA a novel biomarker of resistance against BRAF inhibitors, which is also a promising therapeutic target. Combinations of drugs targeting BRAF (and/or MEK) and eIF4F may overcome most of the resistance mechanisms arising in BRAFV600- cancers. In parallel, we established a BRAF-CRAF PLA method in paradoxical secondary tumors induced by BRAF inhibitors, leading to the identification of several subpopulations more at risk of developing this type of tumors.

Charles University Faculty of Pharmacy in Hradec Králové Department of Pharmacology & Toxicology Student: Zuzana Miškovčíková Supervisor: RNDr. Jana Maixnerová, PhD. Title of diploma thesis: Determination of organ toxicity of BRAF inhibitors in vitro. Malignant melanoma is one of the most serious skin diseases today. Therapy of advanced melanoma is difficult and often ineffective. BRAF inhibitors (dabrafenib and vemurafenib) have dramatically changed the results of melanoma treatment in the last few years. BRAF inhibitors are one of the most effective drugs against melanoma, but their clinical application is largely limited by drug resistance. Available clinical studies have shown an adverse nephrotoxic effect of BRAF inhibitors, but information on its mechanism is limited. Published studies further suggest that the toxic effect of BRAF inhibitors is primarily directed to podocytes located in the glomerular membrane. Thus, the aim of our study was to assess the cytotoxic effect of BRAF inhibitors on selected model renal cells in vitro in order to confirm the renal target toxicity. The main objective of the study was to analyse whether the nephrotoxic effect of BRAF inhibitors is specifically limited to podocytes or whether it can damage other renal cells. The experiments were performed on human cell lines...

Made available in DSpace on 2016-08-10T10:38:32Z (GMT). No. of bitstreams: 1 ROSANA CORREA DA SILVA.pdf: 1155135 bytes, checksum: a1c142c1de3c5263b64fc25cab61f452 (MD5) Previous issue date: 2012-03-28 / Papillary carcinomas are the most common tumors of the thyroid, corresponding to 80% of all tumors that affect the gland. In such tumors, a common mutation at the BRAF gene has been detected, comprising a nucleotide transversion, T1799A, at the exon 15 of gene. This mutation has been identified in about 50 % of the thyroid papillary carcinomas (TPC). Clinical and experimental studies have demonstrated important associations between BRAF mutations and different TPC clinical factors related to tumor progression, invasion and recurrence. The objective of this study was to analise BRAF protein expression, by using immunohistochemistry, and V600E BRAF mutations in a group of patients with thyroid papillary carcinoma. BRAF protein expression and V600E BRAF mutations were compared to TPC clinical and pathological aspects. The study group comprised 116 TPC patients that were selected at the Pathology Department of Hospital Araujo Jorge, in Goiânia. BRAF immunohistochemical analysis employed a labeled polymer peroxidase method and primary BRAF monoclonal antibody (clone F-7), Santa Cruz Biotechnology Inc. BRAF V600E molecular analysis was carried by PCR (Polimerase Chain Reaction) associated to RFLP (Restriction Fragment Length Polymorphism). Statistical analysis was performed by using univariate analysis (Chi-square test with Yates correction, and Fischer). Our results indicated that BRAF overexpression was detected in 54 TPC cases (46.0%), while BRAF V600E mutation was detected in 74 TPC cases (63.8%). Significant associations were detected between BRAF overexpression with distant metastasis (p=0.001) and tumor extrathyroidal extensions (p=0.0183). BRAF V600E mutations were significantly associated with lymph nodes methastasis (p=0.0385) and BRAF protein overexpression (p=0.0063). / Os carcinomas papilíferos são os tumores mais comuns da tireóide, sendo responsáveis por 80% de todos os cânceres da glândula. Nesses tumores, uma mutação comum no gene BRAF tem sido observada, compreendendo a transversão do nucleotídeo T1799A, localizado no exon 15, verificada em 50% dos carcinomas papilíferos de tireóide (CPT). Essa mutação acarreta a substituição do aminoácido valina na posição 600 da proteína, por ácido glutâmico, sendo assim designada V600E. Estudos experimentais e clínicos têm mostrado uma associação entre a mutação do gene BRAF e diferentes parâmetros clínicos de progressão, invasão e recorrência no CPT. O objetivo deste estudo foi detectar os níveis da proteína BRAF utilizando o método de imuno-histoquímica, e avaliar a mutação V600E do gene BRAF em um grupo de pacientes com carcinoma papilífero de tireóide. A detecção imuno-histoquímica da proteína BRAF e a mutação V600E do gene BRAF, foram comparadas em relação aos aspectos clínico-patológicos dos tumores. O grupo de estudo incluiu 116 pacientes com carcinoma papilífero de tireóide, selecionados no Setor de Anatomia Patológica do Hospital Araújo Jorge, em Goiânia-GO. A análise imuno-histoquímica utilizou o método da imunoperoxidase associada a polímeros e o anticorpo BRAF (clone F-7) Santa Cruz Biotechnology Inc. A análise molecular da mutação V600E do gene BRAF foi realizada por meio de PCR (reação em cadeia da polimerase) e RFLP (polimorfismo de comprimento de fragmentos de restrição). As análises estatísticas incluiram o teste do Chi-quadrado com correção de Yates e o teste exato de Fisher. Nossos resultados mostraram que a hiperexpressão de BRAF foi detectada em 54 casos (46%) e a mutação V600E do gene BRAF em 74 casos (63,8%). Dentre as associações investigadas, resultados significativos foram observados entre a hiperexpressão da proteína BRAF e extensão extra-tireoideana do tumor (p=0,0183). A presença da mutação V600E do gene BRAF foi associada as metástases linfonodais (p=0,0385) e à hiperexpressão da proteína BRAF (p=0,0063).

Made available in DSpace on 2016-08-10T10:38:34Z (GMT). No. of bitstreams: 1 JULIANA SAYURI SUGITA INUMARU.pdf: 977119 bytes, checksum: dd9451c21f0c8b8df529c718c8cf5860 (MD5) Previous issue date: 2012-08-24 / Melanoma comprises about 4% of skin cancers, however, more than 95% of stage IV melanoma patients will die within five years and most patients will succumb in a year. The most commonly mutated gene in melanoma is BRAF V600E mutation, described in 40-70% of cutaneous melanomas. This mutation results in the substitution of valine for glutamic acid in codon 600, resulting in the active form of the protein. The objective of this study was to investigate the frequency of BRAF V600E mutation in patients diagnosed with melanoma in Goiânia, as well as the possible associations between this mutation and clinical-pathological aspects of the cases analyzed. Seventy seven cases of melanoma from the Pathology Departament of Araújo Jorge Hospital, in Goiânia, Goiás were analized. Molecular analysis was performed by PCR and RFLP. Descriptive and comparative statistical analysis with Chi-square test were used in this study. The results demonstrated the presence of V600E mutation in 54 (70,1%) patients with cutaneous melanoma and no statistically significant association was found between the presence of mutation with other prognostics parameters such as age, gender, sun exposure, anatomic location, presence of metastasis, histological subtypes and histological parameters (Breslow thickness, presence of ulceration, signs of regression, lymphocytic infiltration and presence of satellites). Our results suggest that BRAF V600E mutation is a common event in melanomas and represents an important molecular target for therapeutic approaches in the treatment of this neoplasia. / O melanoma representa 4% das neoplasias malignas da pele, no entanto, mais de 95% dos pacientes com melanoma estágio IV irão morrer em cinco anos e a grande parte dos pacientes irá sucumbir em um ano. O gene mutado mais comumente no melanoma é o BRAF e a mutação V600E é descrita em 40 a 70% dos melanomas cutâneos. Tal mutação resulta na substituição da valina por ácido glutâmico no códon 600, resultando na forma ativa desta proteína. O objetivo desse estudo consistiu em investigar a frequência da mutação V600E do gene BRAF, em pacientes diagnosticados com melanoma em Goiânia, bem como as possíveis associações, entre tal mutação e os aspectos clinico-patológicos dos casos analisados. Para isso foram analisados 77 casos de melanoma do Setor de Anatomia Patológica do Hospital Araújo Jorge, em Goiânia, Goiás. A análise molecular foi realizada por PCR e RFLP. Análise estatística descritiva e comparativa com o teste Chi-quadrado foi usado neste estudo. A mutação V600E do gene BRAF foi encontrada em 54 (70,1%) pacientes portadores de melanoma cutâneo e nenhuma associação estatisticamente significativa foi detectada entre a presença de mutação com outros parâmetros prognósticos como idade, gênero, exposição solar, localização anatômica, presença de metástases, subtipo histológico e parâmetros histológicos (índice de Breslow, presença de ulceração, sinais de regressão, infiltração linfocitária e presença de satélites). Nossos resultados permitem concluir que a mutação V600E de BRAF é um evento comum nos melanomas e que representa um alvo molecular importante para as abordagens alvo dirigidas no tratamento desta neoplasia.

Aberrant methylation of CpG island promoters is a frequent observation in cancer and is known to affect many genes, including tumour suppressor genes. Genes with methylated promoters are usually repressed and inactive, and there is good evidence that most genes that become methylated in cancer are already repressed in the normal tissues from which tumours arise. However, the methylation of some genes appears to arise at previously active loci, suggesting either a stochastic epigenetic event or that these genes are somehow predisposed to becoming methylated. The DNA mismatch repair gene MLH1 is expressed in normal colonic epithelial cells but methylated and down-regulated in some sporadic mismatch repair-deficient colon tumours. These tumours are almost invariably associated with the simultaneous methylation of multiple cancer-specific loci, termed the CpG island methylator phenotype (CIMP) and an activating mutation of BRAF (V600E), raising the possibility that a hypermethylator phenotype may arise in cancer in direct association with a specific genetic alteration. The possibility that MLH1-deficiency caused BRAF mutation was discounted as genetic deficiency of MLH1 is not associated with BRAFV600E. I explored the possibility that BRAFV600E might induce MLH1 methylation but found no evidence in support of this. I then focused on factors that might mediate CIMP gene methylation, of which MLH1 methylation is known to be a part. Bioinformatic analysis of the genes methylated in BRAFV600E colon tumours indicated a significant enrichment in binding sites for the transcription factor MAZ (MYC-associated zinc finger protein). I hypothesised that loss of MAZ might lead to MLH1 down-regulation and its subsequent methylation. In this thesis I provide evidence that both MAZ and MLH1 expression are deregulated during normal colonic epithelial differentiation. The down-regulation of MAZ by RNA interference led to a reduction in MLH1 expression and methylation of its promoter. I speculate that MLH1 methylation may be associated with BRAF mutation because transformation by BRAFV600E allows progenitor cells to undergo a degree of differentiation whilst maintaining their malignant proliferation. I speculate that it is during this process of differentiation that MLH1 becomes susceptible to methylation.

Yes / Metastatic melanoma, a deadly form of skin cancer, often develops resistance to the BRAF inhibitor drug vemurafenib, highlighting the need for understanding the underlying mechanisms of resistance and exploring potential therapeutic strategies targeting integrins and TGF-β signalling. In this study, the role of integrins and TGF-β signalling in vemurafenib resistance in melanoma was investigated, and the potential of combining vemurafenib with cilengitide as a therapeutic strategy was investigated. In this study, it was found that the transcription of PAI1 and p21 was induced by acquired vemurafenib resistance, and ITGA5 levels were increased as a result of this resistance. The transcription of ITGA5 was mediated by the TGF-β pathway in the development of vemurafenib resistance. A synergistic effect on the proliferation of vemurafenib-resistant melanoma cells was observed with the combination therapy of vemurafenib and cilengitide. Additionally, this combination therapy significantly decreased invasion and colony formation in these resistant cells. In conclusion, it is suggested that targeting integrins and TGF-β signalling, specifically ITGA5, ITGB3, PAI1, and p21, may offer promising approaches to overcoming vemurafenib resistance, thereby improving outcomes for metastatic melanoma patients.