L’avènement du séquençage haut débit a mis en lumière l’hétérogénéité des cancers du sein qui peuvent être groupés en fonction d’altérations moléculaires spécifiques qui sont pour certaines à la base de thérapies ciblées dans le cadre de la médecine personnalisée. Néanmoins de nombreuses complications viennent compromettre le succès thérapeutique de ces approches. En effet, l’une des thérapies ciblées les plus efficaces développées récemment, les inhibiteurs de CDK4/6, sont prescrits chez tous les patients HR+/HER aux stades avancés de la maladie alors même qu’aucun biomarqueur n’a pour l’heure été identifié. Ainsi les données pharmacodynamiques et les marqueurs pronostics font cruellement défaut pour ces patients. Afin d’identifier de tels marqueurs, nous avons conduit une étude clinique « fenêtre d’opportunité » incluant 100 patients à un stade précoce de la maladie. L’analyse en IHC et les études de profilage expression génomique des tumeurs a permis de montrer qu’une courte exposition au palbociclib, un inhibiteur de CDK4/6 induisait un arrêt du cycle cellulaire révélé par une diminution de phospho-Rb et Ki67. Cette corrélation entre diminution du phospho-Rb et la diminution de la prolifération suggère d’ailleurs son utilisation comme biomarqueur de la réponse au palbociclib. Une analyse sur puce à cDNA a permis d’identifier un panel de gènes régulateurs de la prolifération (MKI67, TOP2A, BIRC5) et de la machinerie du cycle cellulaire (PLK1, FOXM1) modulé par le palbociclib. Bien que nous n’ayons pu identifier de marqueurs de résistance au palbociclib en condition basale, nous avons observé des niveaux élevés de CCNE chez les patients traités résistants au palbociclib. Cette donnée a été confirmée chez les patients aux stades avancés de la maladie dans le cadre d’une étude menée en collaboration avec un groupe britannique. D’autres données obtenues en collaboration avec une équipe de l’université Vanderbilt, ont par ailleurs permis de suggérer une contribution des inhibiteurs de CDK4/6 à la réversion de la résistances aux hormonothérapie en inhibant l’expression les gènes cibles du facteur de transcription E2F4. Pour finir, les activités biologiques et cliniques des différents inhibiteurs de CDK4/6 disponibles n’étant pas exactement identiques, un second essai clinique « fenêtre d’opportunité » nous a permis de mettre en évidence un profil de toxicité distinct de l’abemaciclib et de montrer que, contrairement au palbociclib, l’abemaciclib montre une efficacité lorsqu’il est utilisé seul. Une des explications possible de ces différentes activités serait un spectre d’action de l’abemaciclib ciblant plus efficacement la CDK9, même si l’impact clinique associé n’a pas été examiné en détail et qu’une comparaison rigoureuse de l’activité de ces deux inhibiteurs de CDK n’a pas encore été réalisée. / New sequencing methods have revealed that breast cancer is heterogeneous and characterized by different subgroups harboring specific molecular alterations for which targeted therapies have been developed with the hope of implementing personalized medicine. However, this approach has been proven far too simplistic. Indeed, one of the latest and more efficient targeted therapies to be developed in breast cancer are the CDK4/6 inhibitors, approved for all HR+/HER2- advanced breast cancers. So far, and despite the significant number of patients treated with these drugs, no biomarkers of efficacy have been identified and no clear information about pharmacodynamics have been presented. In order to determine biomarkers of efficacy and pharmacodynamics of palbociclib, the first approved CDK4/6 inhibitor, we conducted a window of opportunity clinical trial in 100 early breast cancer patients. IHC and GE analyses identified that a short period of palbociclib treatment was able to induce cell cycle arrest as determined by decreased phospho-Rb expression and this was accompanied by a profound decrease in proliferation as determined by lnKi67<1 after treatment, with a correlation between changes in proliferation and changes in phospho-Rb, suggesting that early decrease in phospho-Rb could be linked to sensitivity to this drug. Microarray analyses identified that palbociclib modulates genes involved in proliferation (such as MKI67, TOP2A, BIRC5) and cell cycle (such as PLK1, FOXM1). Despite we were not able to identify baseline biomarkers of resistance to this treatment, we observed that levels of CCNE remained high in palbociclib-resistant patients. This finding was further validated in collaboration with an-UK research group who had conducted biomarker research in the advanced setting. Moreover, our data helped also to determine in a different collaboration with Vanderbilt University, that CDK/6 inhibitors might contribute to reverse endocrine resistance generated by activation of genes linked to the E2F4 transcription factor. Finally, as preclinical and clinical data suggest some diversity between different CDK4/6 inhibitors, we decided to conduct a second window of opportunity trial with a second CDK4/6 inhibitor, abemaciclib, who has shown different toxicity profile and, unlike palbociclib, significant efficacy as single-agent. One suggested explanation could be due to a higher impact on CDK9, although its clinical impact has not been determined and no comparison between these two drugs has been performed.

L’identification de la notion de driver oncogene et le développement de molécules capables de cibler leur activité a entrainé d’importants changements dans le traitement des cancers CBNPC.L’EGFR est un récepteur transmembranaire à activité TK (Tyrosine Kinase) permettant latransmission de signaux extracellulaires jusqu’au sein de la cellule grâce à l’activation de voies de signalisations. Parmis ces voies de signalisation on retrouve les voies de prolifération et de survie cellulaire. Des mutations activatrices dans le domaine TK confèrent à ce dernier un rôle de driver oncogene. Dans ce domaine l’EGFR a joué un rôle avant gardiste. Ainsi de nombreuses molécules ciblant l’activité de l’EGFR muté (EGFR-TKI, gefitinib) ont été développées. L’utilisation de ces molécules en clinique a représenté une vraie révolution dans la prise en charge des patients. Cependant ces derniers développent inéluctablement des mécanismes de résistance. L’analyse transcriptomique de modèles ayant acquis une résistance aux EGFR-TKI a mis en évidence une dérégulation de l’expression des transcrits. Par ailleurs des résultats del’équipe ont montré que l’expression des protéines SR (facteurs d’épissage impliqués dans la régulation de nombreux transcrits) était dérégulée dans les CBNPC. Sur la base de ces résultats nous avons émis l’hypothèse que l’épissage alternatif des transcrits médié par les protéines SR pourrait jouer un rôle dans la résistance acquise par les tumeurs pulmonaires en réponse aux EGFR-TKI.Au sein du laboratoire des clones résistants ont été générés après exposition chroniqueau gefitinib de modèles cellulaires d’adénocarcinomes pulmonaires exprimant une mutation activatrice de l’EGFR.Nous avons tout d’abord mis en évidence une accumulation de l’expression de SRSF2 dans les clones résistants comparativement à la lignée sensible. Dans deux clones résistants au gefitinib, issus de la lignée d’adénocarcinome pulmonaire sensible PC9 exprimant un EGFR mutant Del19, nous montrons que la neutralisation de la protéine SRSF2 sensibilise les clones à l’apoptose induite par le gefitinib. Une analyse RNA-seq nous a permis d’identifier Atg16L1 comme un acteur potentiel de la resensibilisation à l’apoptose médiée par SRSF2. La neutralisation de SRSF2 entraine une modulation de l’épissage de l’exon8 de la protéine Atg16L1 en réponse à un traitement au gefitinib. Et la neutralisation de l’expression des transcrits ARN d’ATG16L1 comportant l’exon8 sensibilise les clones résistant à l’apoptose induite par le gefitinib. Ce switch d’épissage entraine une modulation de l’activité autophagique des cellules en réponse au gefitinib. Nous montrons qu’une expression majoritaire des transcrits comportant l’exon 8 favorise une inhibition de l’autophagie en réponse au gefitinib. De plus les modèlesrésistants pour lesquels on observait une resensibilisation à l’apoptose suite à une neutralisation des transcrits contenant l’exon 8, conservent leur phénotype de résistance lorsque dans ces mêmes conditions l’activité autophagique est inhibée. L’ensemble de ces travaux met en avant l’existence d’un switch d’épissage de la protéine Atg16L1 au niveau de son exon 8 contribuant à une inactivation de l’autophagie corrélée avec un phénotype de résistance à l’apoptose en réponse à un traitement par EGFR-TKI. Enfin SRSF2 participerait à la modulation de cet épissage en réponse à un traitement au gefitinib. / Identifying what is a driver oncogene and developping small molecules that are able to targetits activity led to drastic changes in NSCLC treatments. EGFR is a transmembrane receptorwith Tyrosine Kinase (TK) activity allowing signal transmission from the environment towardsthe inner of the cell by signaling pathways activation. Among those signaling pathways arefound survival and proliferation pathways. Activating mutations make EGFR a driver onco-gene, which was the first protein to be identified as such. Hence numerous chemical compoundtargeting mutated EGFR (EGFR-TKI, gefitinib) have been developped. Their use in clinicsrepresent a huge improvement for patients care. However resistance mechanisms ultimatelyoccur. Transcriptomic analyses of acquired resistant models to EGFR-TKI have shown thattheir RNA transcripts expression is abnormal. Moreover results from the team have demons-trated that SR proteins (splicing factor) expression is deregulated in NSCLC. Based on thoseresults we hypothesized that SRSF2 mediated alternative splicing of mRNA could be involvedin resistance mechanims acquired by lung carcinoma in response to EGFR-TKIThe lab developped resistant clones by chronic exposure to gefitinib of EGFR mutated lungadenocarcinoma cellular models.We first observed the accumulation of the expression of SRSF2 protein in resistant clonescompared to the sensitive cell line. Secondly, sensitivity to gefitinib induced apoptosis of twoclones was resored when neutralising SRSF2. A RNA-seq analysis led us to identify Atg16L1 aspotentially being involved in the SRSF2-mediated sensitization to gefitinib-induced apoptosis.SRSF2 neutralisation modulates Atg16L1 splicing in response to gefitinib. Neutralisation ofExon 8 containing transcripts of Atg16L1 sensitizes resistant clones to gefitinib induced apop-tosis. This alternative splicing switch modulates autophagic activity of the cells in reponseto gefitinib. We have shown that exon8 containing transcripts favor autophagy inhibition inreponse to gefitinib. This work emphasize the role of Atg16L1 alternative splicing switch ofexon8 in autophagy inhibition and its correlation with a resistant phenotype in response toEGFR-TKI. SRSF2 may participate in the modulation of this alternative splicing switch inreponse to gefitinib.

リポジトリの登録にあたっては、Peer reviewされた最終版のみ可能であり、その際には下記の出版社のウェブサイトのアドレスを記載することが求められる。当該論文は2014年6月の出版であり、12ヶ月を経過していることから、公開には差し支えはない。http://clincancerres.aacrjournals.org/content/20/12/3087.full / 京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第19617号 / 医博第4124号 / 新制||医||1015(附属図書館) / 32653 / 京都大学大学院医学研究科医学専攻 / (主査)教授 小川 誠司, 教授 野田 亮, 教授 伊達 洋至 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

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Breast cancer is a multifaceted disease that affects 1 in every 8 women. Triple negative breast cancer (TNBC) accounts for ~15-20% of all diagnosed breast cancers and is characterized by the absence of ER, PR, and HER2 on the tumor cell surface. As most cancer therapies to date target these cell surface receptors, TNBC is the only subtype of breast cancer without a targeted therapy and thus prognosis for it remains poor. The heterogeneity of TNBC also makes finding a targeted therapy particularly difficult. This work focuses on different methods of targeting distinct subpopulations of TNBC in order to identify potential novel therapeutic nodes to exploit as targeted therapies. The first chapter describes the use of a directed siRNA synthetic lethality screen to target vulnerabilities associated with basal TNBC, the most common TNBC subtype. The screen identified multiple dependency genes associated with RNA splicing, particularly those in the U4/U6.U5 tri-snRNP complex (PRPF8, PRPF38A). Depletion of these genes or the upstream splicing inhibitor E7107 in basal TNBC cell lines resulted in intronic retention and altered splicing of transcripts in pathways necessary for TNBC survival, including mitosis and apoptosis. In vivo, E7107 hindered the growth of both basal cell line and patient derived xenographs, a phenotype that was enhanced with the addition of the proteasome inhibitor bortezomib. This suggests that splicing and proteasome inhibition could be an effective basal TNBC treatment. The second chapter investigates the role of G-Protein Pathway Suppressor 2 (GPS2) as a tumor suppressor in the PI3K/AKT pathway in TNBC. Previous work has shown that GPS2 acts as a negative regulator of this pathway through inhibition of Ubc13-mediated activation of AKT in the insulin signaling pathway. In this study, MDA-MB231-GPS2KO cells were found to have increased proliferative, migratory, and invasive properties, which were rescued upon treatment with the allosteric AKT inhibitor MK2206. In vivo, GPS2 depleted cells conferred greater tumor burden in an orthotopic mouse model that was also responsive to AKT inhibition. Transcriptomic analysis showed significant overlap between MB231-GPS2KO and MB231 cells modified to have constitutively active AKT, indicating that the phenotypes observed in MB231-GPS2KO were at least in part due to loss of GPS2-mediated regulation of AKT activation. These studies point to GPS2 as a potential biomarker for a subclass of breast cancers that would be responsive to PI3K-class inhibitor drugs. In sum, these studies elucidate interactions and processes that seem to specifically adversely affect TNBC cells, which broaden our knowledge of TNBC biology and its potential weaknesses. / 2022-03-03T00:00:00Z

Background and Objectives: Economic evaluation and decision analysis provide a framework to evaluate incremental costs and effects associated with alternative health interventions. These methods can also be used as a tool to evaluate alternative clinical behaviours or practice patterns. The objective of this thesis was to investigate the impact of current Canadian practices in human epidermal growth factor receptor-2 (HER2) testing to target trastuzumab in early-stage breast cancer (BC). Methods: Project 1: A systematic review of previous trastuzumab and HER2 testing economic analyses was conducted to identify methodological gaps and key lessons. Project 2: A population-level, retrospective cohort was studied to determine HER2 testing and trastuzumab treatment patterns in Ontario early-stage BC patients. Project 3: A cost-utility analysis of alternative test-treat strategies was conducted using a Markov model of BC calibrated to the Canadian setting, and incorporating Project 2 findings. Results: Project 1: Previous economic evaluations demonstrated that HER2 test accuracy and sequencing were key considerations when modelling the cost-effectiveness of trastuzumab treatment. Consideration of local testing and treatment practices was lacking. Project 2: HER2 testing and treatment practice differed from guidelines, where documentation was available. Only 88% of equivocal results were confirmed, while 57% of HER2 positive patients received trastuzumab. Project 3: Calibration of the BC model minimised gaps between trial-based survival and expected Canadian survival patterns. Deviations from guidelines in practice suggest that primary testing with fluorescence in situ hybridization (FISH) would produce greater health gains at a reduced cost vs. primary immunohistochemistry with FISH confirmation. This finding was more apparent as the prevalence of HER2 positive disease increased. Introduction of newer in situ hybridisation tests may be cost-effective as well. Conclusions: Practice deviations from guidelines are an important consideration when modelling the cost-effectiveness of trastuzumab therapy. Underlying local disease progression and prevalence can also significantly impact outcomes. / Dissertation / Doctor of Philosophy (PhD)

BACKGROUND: Aberrant MET receptor tyrosine kinase (RTK) activation leads to invasive tumor growth in different types of cancer. Overexpression of MET and its ligand hepatocyte growth factor (HGF) occurs more frequently in glioblastoma (GBM) than in low-grade gliomas. Although we have shown previously that HGF-autocrine activation predicts sensitivity to MET tyrosine kinase inhibitors (TKIs) in GBM, whether it initiates tumorigenesis remains elusive. METHODS: Using a well-established Sleeping Beauty (SB) transposon strategy, we injected human and cDNA together with a short hairpin siRNA against (SB-hHgf.Met.ShP53) into the lateral ventricle of neonatal mice to induce spontaneous glioma initiation and characterized the tumors with H&E and immunohistochemistry analysis. Glioma sphere cells also were isolated for measuring the sensitivity to specific MET TKIs. RESULTS: Mixed injection of SB-hHgf.Met.ShP53 plasmids induced de novo glioma formation with invasive tumor growth accompanied by HGF and MET overexpression. While glioma stem cells (GSCs) are considered as the tumor-initiating cells in GBM, both SB-hHgf.Met.ShP53 tumor sections and glioma spheres harvested from these tumors expressed GSC markers nestin, GFAP, and Sox 2. Moreover, specific MET TKIs significantly inhibited tumor spheres' proliferation and MET/MAPK/AKT signaling. CONCLUSIONS: Overexpression of the HGF/MET axis along with p53 attenuation may transform neural stem cells into GSCs, resulting in GBM formation in mice. These tumors are primarily driven by the MET RTK pathway activation and are sensitive to MET TKIs. The SB-hHgf.Met.ShP53 spontaneous mouse glioma model provides a useful tool for studying GBM tumor biology and MET-targeting therapeutics.

Glioblastoma (GBM) is the most malignant primary brain tumor without effective therapies. Since bevacizumab was FDA approved for targeting vascular endothelial growth factor receptor 2 (VEGFR2) in adult patients with recurrent GBM, targeted therapy against receptor tyrosine kinases (RTKs) has become a new avenue for GBM therapeutics. In addition to VEGFR, the epidermal growth factor receptor (EGFR), platelet-derived growth factor receptor (PDGFR), hepatocyte growth factor receptor (HGFR/MET), and fibroblast growth factor receptor (FGFR) are major RTK targets. However, results from clinical Phase II/III trials indicate that most RTK-targeting therapeutics including tyrosine kinase inhibitors (TKIs) and neutralizing antibodies lack clinical efficacy, either alone or in combination. The major challenge is to uncover the genetic RTK alterations driving GBM initiation and progression, as well as to elucidate the mechanisms toward therapeutic resistance. In this review, we will discuss the genetic alterations in these 5 commonly targeted RTKs, the clinical trial outcomes of the associated RTK-targeting therapeutics, and the potential mechanisms toward the resistance. We anticipate that future design of new clinical trials with combination strategies, based on the genetic alterations within an individual patient's tumor and mechanisms contributing to therapeutic resistance after treatment, will achieve durable remissions and improve outcomes in GBM patients.

Background: We aim to validate a seven-marker immunohistochemical signature, consisting of Bax, Bcl-X, PTEN, COX-2, (loss of) ß-Catenin, (loss of) MTAP and (presence of) CD20, in an independent patient cohort and test clinical feasibility. Methods: We performed staining of the mentioned antibodies in tissue of 88 primary melanomas and calculated a risk score for each patient. Data were correlated with clinical parameters and outcome (recurrence-free, distant metastasis-free and melanoma-specific survival). Results: The seven-marker signature was able to identify high-risk patients within stages IB-III melanoma patients that have a significantly higher risk of disease recurrence, metastasis, and death. In particular, the high sensitivity of relapse prediction (>94%) in sentinel negative patients (stages IB–IIC) was striking (negative predictive value of 100% for melanoma-specific survival and distant metastasis-free survival, and 97.5% for relapse-free survival). For stage III patients (positive nodal status), the negative predictive value was 100% with the seven-marker signature. Conclusions: The seven-marker signature can help to further select high-risk patients in stages IIB-C but also in earlier stages IB–IIA and be a useful tool for therapy decisions in the adjuvant and future neo-adjuvant settings. Stage III patients with measurable lymph node disease classified as high-risk with the seven-marker signature are potential candidates for neoadjuvant immunotherapy.

Affinity proteins constitute an important category of cancer therapeutics. Owing to properties such as high target affinity and selectivity, therapeutic proteins offer more targeted therapy than small molecule drugs. The target molecules are typically proteins that are overexpressed on the surface of tumour cells, such as membrane-bound receptors. However, these surface proteins are usually expressed in normal tissues as well, resulting in on-target off-tumour toxicity. Proteins with a higher tissue selectivity are thus needed. Here, this has been addressed by developing prodrug proteins dependent on cancer-specific proteases for activation. The prodrugs were composed of a target-binding affibody (active domain) connected to a masking affibody (masking domain) by a peptide linker including a protease substrate. The target of the prodrugs developed in this project was the HER2 receptor, which is overexpressed in several cancer types. Three prodrug candidates were developed, produced and characterised based on their ability to be activated by their respective protease. The hypothesis that the prodrugs could be activated and thus bind to HER2 in cancer cells was tested using biosensor assays, as well as preliminary cancer cell assays. One of the three candidates showed strong potential to be used as a targeted therapy for cancer treatment in the future. / Affinitetsproteiner utgör en viktig kategori av cancerläkemedel. Jämfört med småmolekylära läkemedel är affinitetsproteiner mer riktade, då de har högre affinitet och selektivitet än små molekyler. Oftast utgörs det molekylära målet av ett protein som överuttrycks på ytan av cancerceller, så som membranbundna receptorer. Dessvärre uttrycks de flesta cancerspecifika proteiner i mindre mängd även i normal vävnad. Detta leder till oönskade effekter som kan ge upphov till biverkningar. I syfte att utveckla mer vävnadsspecifika läkemedel har här affibody-baserade “prodrugs”, beroende av cancerspecifika proteaser för aktivering, tagits fram. Prodrug-proteinerna i detta projekt är riktade mot HER2-receptorn, som är överuttryckt i flera typer av cancer. Tre kandidater togs fram och utvärderades med avseende på deras förmåga att aktiveras av sina respektive proteaser. För att testa hypotesen att kandidaterna kunde binda till HER2 på cancerceller efter proteasaktivering användes biosensoranalys samt experiment med cancerceller. En av kandidaterna visade stark potential att kunna användas som ett riktat läkemedel mot cancer i framtiden.