Oncocytomas are uncommon tumors of the salivary gland. They have an abundance of mitochondria, which is manifested as granular eosinophilic cytoplasm by light microscopy. On histological sections, presence of cytoplasmic glycogen and/or fixation artifact can impart cytoplasmic clearing, and oncocytomas with a predominance of clear cytoplasm are labeled clear cell oncocytomas. Two forms of oncocytoma, eosinophilic and clear cell, have been described in the surgical pathology literature. The purpose of this manuscript is to conduct a comparative cytological assessment to ascertain parallels and differences between the two variants.

Final article is available at "wileyonlinelibrary.com" Takako Okamoto, Masaki Mandai, Noriomi Matsumura, Ken Yamaguchi, Hiroshi Kondoh, Yasuaki Amano, Tsukasa Baba, Junzo Hamanishi, Kaoru Abiko, Kenzo Kosaka, Susan K. Murphy, Seiichi Mori, Ikuo Konishi "Hepatocyte nuclear factor-1β (HNF-1β) promotes glucose uptake and glycolytic activity in ovarian clear cell carcinoma" Molecular Carcinogenesis 54:35–49 (2013) / 京都大学 / 0048 / 新制・論文博士 / 博士(医学) / 乙第12804号 / 論医博第2076号 / 新制||医||1001(附属図書館) / 80848 / 京都大学大学院医学研究科医学専攻 / (主査)教授 野田 亮, 教授 武藤 学, 教授 稲垣 暢也 / 学位規則第4条第2項該当 / Doctor of Medical Science / Kyoto University / DFAM

Ovarian cancer is a significant concern for women’s health as it is the most lethal of all gynaecological malignancies. One of the reasons for the high mortality of this disease is that traditionally used chemotherapeutic treatments tend to have poor initial or sustained efficacy against ovarian tumours. Resistance to such treatments may in part be mediated by autophagy, a cell survival process in which unnecessary or damaged components of the cytoplasm are engulfed within a double-membraned vesicle known as an autophagosome and ultimately degraded upon fusion of the autophagosome with a lysosome. Autophagy has been shown to be employed by cells to aid in their survival under stresses such as nutrient deprivation, hypoxia, chemotherapy treatment, and growth factor withdrawal. As these stresses are commonly encountered by ovarian cancer cells, it is possible that autophagy promotes ovarian cancer cell survival. This thesis aims to investigate which stimuli induce autophagy in ovarian cancer cells and whether or not this induction can promote cell survival. In addition, there is a particular focus on the comparison of autophagy utilization between subtypes of ovarian cancer, as the subtypes are in fact considered different diseases and may vary in their usage of autophagy. The first chapter of this thesis provides relevant background information on autophagy as well as ovarian cancer and its subtypes. In the second chapter, I describe studies in which tumours from a large cohort of patients with ovarian cancer are assessed for LC3A, a marker of autophagy, in addition to markers of other cellular processes including hypoxia. Here I found that LC3A was significantly associated with poor patient survival in patients with the clear cell subtype of ovarian cancer, but not other subtypes. I also found that LC3A expression was associated with markers of hypoxia in the clear cell patient tumours and that clear cell carcinoma cell lines preferentially induced autophagy in response to hypoxia in vitro as compared to cell lines of the high-grade serous subtype. These results indicate that clear cell ovarian tumours are uniquely dependent upon autophagy in response to hypoxia. In the third chapter, I investigated the autophagic response to treatment with the standard ovarian cancer chemotherapy drugs carboplatin and paclitaxel in a syngeneic mouse model of ovarian cancer. I found that these drugs did indeed induce autophagy and that the cancer cells utilized autophagy to promote resistance to these chemotherapeutics. In addition, when the tumour cells were grown in syngeneic mice, treatment with the autophagy inhibitor hydroxychloroquine resulted in a significant suppression of tumour growth. Together, my findings indicate that further investigation into the use of autophagy inhibitors in ovarian cancer patients is warranted and that different specific rational drug combinations for each subtype will likely yield optimal results. / Graduate

Submitted by ANDRÉ LUIS GIACOMETTI CONCEIÇÃO null (andre4487@gmail.com) on 2016-03-08T12:40:30Z No. of bitstreams: 1 Arquivo_Completo_-_Tese_Doutorado_-_André_Luis_Giacometti_Conceição.pdf: 1296182 bytes, checksum: 29c1b4fbebefc1b96e79210f433f4d2f (MD5) / Approved for entry into archive by Ana Paula Grisoto (grisotoana@reitoria.unesp.br) on 2016-03-09T16:44:10Z (GMT) No. of bitstreams: 1 conceicao_alg_dr_sjrp.pdf: 1296182 bytes, checksum: 29c1b4fbebefc1b96e79210f433f4d2f (MD5) / Made available in DSpace on 2016-03-09T16:44:10Z (GMT). No. of bitstreams: 1 conceicao_alg_dr_sjrp.pdf: 1296182 bytes, checksum: 29c1b4fbebefc1b96e79210f433f4d2f (MD5) Previous issue date: 2016-02-16 / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / O carcinoma renal de células claras (ccRCC) é o mais comum dos subtipos histológicos de carcinoma renal. Este carcinoma é histologicamente caracterizado pela presença de células com citoplasma claro e abundante. O processo inicial de metástase pode ser atribuída à transição epitélio mesênquima (EMT). Neste estudo, buscou-se identificar genes diferencialmente expressos em ccRCC, construindo assim um perfil molecular para este tumor. Nós selecionamos genes descritos na literatura que apresentam relação com EMT, diferenciação e proliferação celular. Analisou-se por PCR quantitativo e imuno-histoquímica a expressão dos genes e suas proteínas, respectivamente, e os possíveis mecanismos epigenético que regulam a sua expressão em amostras de ccRCC e linhagem celular. Os genes OCLN e GAS1 foram encontrados com baixa expressão em ccRCC, e nós sugerimos que o miR-122 e miR- 34a podem regular sua expressão, respectivamente, neste tipo de câncer. Além disso, mostramos, por qPCR e imuno-histoquímica, a alta expressão de SLC2A1 foi significantemente alta em ccRCC. O conjunto de genes identificados neste estudo possibilita a compreensão das bases moleculares e de desenvolvimento do ccRCC. / Clear cell renal cell carcinoma (ccRCC) is the most common histological subtype of kidney cancer. This carcinoma is histologically characterized by the presence of clear and abundant cytoplasm. The initial process of ccRCC metastatic tumor formation can be attributed to epithelial- mesenchymal transition (EMT). In this study, we sought to identify genes differentially expressed in ccRCC and build a molecular profile of this cancer. We selected genes described in the literature to be related to EMT, cellular differentiation and proliferation. We analyzed the gene and protein expression by quantitative PCR and immunohistochemistry, respectively, and examined possible epigenetic mechanisms that regulate their expression in ccRCC samples and cell lines. OCLN and GAS1 genes were under-expressed in ccRCC, and we report that miR-122 and miR- 34a, respectively, may regulate their expression in this cancer. Furthermore, we showed by quantitative PCR (qPCR) and immunohistochemistry that SLC2A1 was significantly over-expressed in ccRCC. The set of genes identified in this study furthers our understanding of the molecular basis and development of ccRCC. / FAPESP: 2012/08853-0

>Magister Scientiae - MSc / Kidney cancers, of which clear cell renal cell carcinoma comprises an estimated 70%, have been placed amongst the top ten most common cancers in both males and females. With a mortality rate that exceeds 40%, kidney cancer is considered the most lethal cancer of the genitourinary system. Despite advances in its treatment, the mortality- and incidence rates across all stages of the disease have continued to climb. Since the release of the Human Genome Project in the early 2000’s, most genetics studies have focused on the protein coding region of the human genome, which accounts for a mere 2% of the entire genome. It has been suggested that diverting our focus to the other 98% of the genome, which was previously dismissed as non-functional “junk DNA”, could possibly contribute significantly to our understanding of the underlying mechanisms of complex diseases.In this study a whole genome sequencing somatic mutation data set from the International Cancer Genome Consortium was used. The non-coding somatic mutations within the promoter, intronic, 5-prime untranslated and 3-prime untranslated regions of clear cell renal cell carcinoma-implicated genes were extracted and submitted to RegulomDB for their functional annotation.As expected, most of the variants were located within the intronic regions and only a small subset of identified variants was predicted to be deleterious. Although the variants all belonged to a selected subset of kidney cancer-associated genes, the genes frequently mutated in the non-coding regions were not the same genes that were frequently mutated in the whole exome studies (where the focus is on the coding sequences). This indicates that with whole genome sequencing studies a new set of genes/variants previously unassociated with the clear cell renal cell carcinoma could be identified. In addition, most of the non-coding somatic variants fell within multiple transcriptions factor binding sites. Since many of these variants were also deleterious (as predicted by RegulomDB), this suggests that mutations in the non-coding regions could contribute to disease due to their role in transcription factor binding site disruptions and their subsequent impact on transcriptional regulation. The substantial overlap between the genes with the most aberrantly methylated variants and the genes with the most transcription factor binding site disruptions signifies a potential link between differential methylation and transcription factor binding site affinities. In contrast to the upregulated DNA methylation generally seen in promoter methylation studies, all of the significant hits in this study were hypomethylated, with the subsequent up-regulation of the genes of interest, suggesting that in the clear cell renal cell carcinoma, aberrant methylation may play a role in activating proto-oncogenes, rather than the silencing of genes. When a cross-analysis was carried out between the gene expression patterns and the transcription factor binding site disruptions, the non-coding somatic variants and differential methylation profiles, the genes affected again showed a clear overlap. Interestingly, most of the variants were not present in the 1000genomes data and thus represent novel mutations, which possibly occurred as a result of genomic instability. However, identifying novel variants are always promising, since they epitomise the possibility of developing pioneering ways to target diseases. The numerous detrimental effects a single non-coding mutation can have on other genomic processes have been demonstrated in this study and therefore validate the inclusion of non-coding regions of the genome in genetic studies in order to study complex multifactorial diseases. / National Research Foundation (NRF) and DAAD

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第19591号 / 医博第4098号 / 新制||医||1014(附属図書館) / 32627 / 京都大学大学院医学研究科医学専攻 / (主査)教授 野田 亮, 教授 武田 俊一, 教授 小川 修 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第21011号 / 医博第4357号 / 新制||医||1028(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 万代 昌紀, 教授 戸井 雅和, 教授 鈴木 実 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第21300号 / 医博第4389号 / 新制||医||1030(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 戸井 雅和, 教授 小川 修, 教授 武田 俊一 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

京都大学 / 新制・課程博士 / 博士(医学) / 甲第23763号 / 医博第4809号 / 新制||医||1056(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 中島 貴子, 教授 戸井 雅和, 教授 伊藤 貴浩 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

Le carcinome rénal à cellules claires (cRCC) est le principal type histologique de carcinome rénal et l'une des tumeurs les plus résistantes à la chimio et à la radiothérapie. L'absence de biomarqueurs pour la détection précoce et pour le suivi des patients est responsable d'un mauvais pronostic. Il est nécessaire d'identifier de nouveaux biomarqueurs et des cibles thérapeutiques pour améliorer la prise en charge des patients. Les microARNs, des petits ARN non codants de 22 nucléotides, qui ont été précédemment montrés comme favorisant l'initiation et la progression tumoral, semblent être de bons candidats. Nous avons focalisé notre étude sur (i) miR-21 qui est le principal oncomiR surexprimé dans le cRCC et (ii) le récepteur nucléaire PPARα (Peroxisome Proliferator Activated Receptor), l'une des cibles de miR-21.D'une part, sur une cohorte de 99 échantillons de cRCC primaires, nous avons montré que l'expression de miR-21 était plus élevée dans les tissus cancéreux que dans les tissus non tumoraux adjacents. In vitro, miR-21 est également surexprimé dans les lignées cellulaires de carcinomes rénaux comparées à la lignée cellulaire épithéliale HK-2 provenant de tubes proximaux humains. De plus, nous avons également montré que la surexpression de miR-21 augmente les propriétés de migration et d'invasion des cellules cancéreuses rénales ainsi que les voies de signalisation prolifératives et anti-apoptotiques, alors que des résultats opposés ont été observés en utilisant une stratégie d'inhibition anti-miR-21. Enfin, nous avons évalué le rôle du miR-21 dans la chimiorésistance du cRCC et montré, en outre, que l'inhibition de miR-21 augmentait significativement la chimiosensibilité au paclitaxel, au 5-fluorouracile, à l'oxaliplatine et au dovitinib, diminuait l'expression des transporteurs à efflux MRP1-6/ABCC1-6 et augmentait l'expression des transporteurs à influx SLC22A1/OCT1, SLC22A2/OCT2 et SLC31A1/CTR1. Ces résultats ont permis la publication d'un article dans Tumor Biology se trouvant en annexe.D'autre part, dans les tissus de patients atteints de cRCC, nous avons montré pour la première fois que la surexpression de miR-21 est en corrélation avec une perte d'expression de PPARα. In vitro, nous avons montré que miR-21 cible le 3'-UTR de PPARα et diminue son expression protéique et que la surexpression de miR-21 diminue l'activité transcriptionnelle de PPARα. En outre, la surexpression et l'activation de PPARα diminuent l'expression de miR-21. En effet, PPARα interagit avec les facteurs de transcription AP-1 et NF-κB et empêche ainsi leur liaison au promoteur de miR-21 diminuant ainsi sa transcription.En conclusion, nous avons montré que (i) miR-21 est un acteur clé de la progression du cancer du rein et joue un rôle important dans la résistance aux chimiothérapies et (ii) qu'il existe une boucle de régulation négative entre miR-21 et PPARα dans le cRCC. / Renal clear cell carcinoma (cRCC) is the major histological type of renal carcinoma and one of the most chemo- and radio-resistant tumors. The absence of biomarkers for early detection and for monitoring patients is responsible of a poor prognosis. It is necessary to identify new biomarkers and therapeutic targets to improve patient care. MicroRNAs, small noncoding RNAs of 22 nucleotides, which have been previously shown to promote malignant initiation and progression, appear to be good candidates.We focused our study on (i) miR-21 which is the main overexpressed oncomirs in cRCC and (ii) the nuclear receptor PPARα (Peroxisome Proliferator Activated Receptor), one of miR-21 targets.In one hand, by using a cohort of 99 primary cRCC samples, we showed that miR-21 expression in cancer tissues was higher than in adjacent non-tumor tissues. In vitro, miR-21 was also overexpressed in renal carcinoma cell lines compared to HK-2 human proximal tubule epithelial cell line. Moreover, we also showed that miR-21 overexpression increased migratory, invasive, proliferative, and anti-apoptotic signaling pathways whereas opposite results were observed using an anti-miR-21-based silencing strategy. Finally, we assessed the role of miR-21 in mediating cRCC chemoresistance and further showed that miR-21 silencing significantly increased chemosensitivity of paclitaxel, 5-fluorouracil, oxaliplatin and dovitinib, decreased expression of multi-drug resistance genes and increased SLC22A1/OCT1, SLC22A2/OCT2 and SLC31A1/CTR1 platinum influx transporter expression. These results led to the publication of an article in Tumor Biology in annex.In other hand, in cRCC tissue patients, we showed for the first time that miR-21 overexpression correlates with a loss of expression of PPARα. In vitro, we showed that miR-21 targets PPARα 3'-UTR and decreases its protein expression and miR-21 overexpression decreases the transcriptional activity of PPARα. Furthermore, PPARα overexpression and activation decrease miR-21 expression. In fact, PPARα interacts with AP-1 and NF-kappaB transcription factors and thus prevents their binding to the miR-21 promoter thus decreasing its transcription.In conclusion, we have shown that (i) miR-21 is a key actor of renal cancer progression and plays an important role in the resistance to chemotherapeutic drugs and (ii) there is a negative regulatory loop between miR-21 and PPARα in cRCC.