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Malt lymphoma is a malignant disease that can arise in a variety of extra nodal sites. Previous studies indicate that tumour arise from more mature B-cells. Our purpose was to examine the presence of clonality and somatic hypermutation of immunoglobulin (IgVн) of MALT lymphomas. Paraffin-embedded tumour samples from13 MALT lymphoma were subjected to rearrangement analysis, by using PCR, heteroduplex gels and sequence analysis. Successful amplification was seen in 10/13 cases and sequences of IgVн genes were obtained in 6/13, all of them were mutated. The percentage of mutation compared to germline sequences was 1,1% to 8,6% monoclonal rearrangemang. It was demonstrated that 5 of 7 clones were derived from the Vн3 family, 2 from Vн1 and 1 from the Vн 4 family.

Plasmablastic lymphoma (PBL) was originally described in 1997 as an AIDS associated tumour although cases have been described in individuals not infected with HIV. Due to the high number of people living with HIV in South Africa, a substantial number of cases are diagnosed annually and 45 cases were included in this study. This represented the largest cohort of PBL affecting the oral mucosa published to date. Three main aspects of PBL were investigated: pathological features, viral status and certain genetic characteristics. The results from the genetic studies were the most important and interesting. These included rearrangements of the IGH gene in 63% and MYC- rearrangements in 62% of PBL’s. Seven of 43 cases (16%) showed rearrangement of both the IGH gene alleles, a finding never described before. New genetic findings also included increased CCND1 gene copy numbers in 17/41 (42%) and increased IGH gene copy numbers in 6/41 (15%) of cases. The exact role of MYC-rearrangements in the development of PBL is unclear. Many factors may be responsible for MYC deregulation but in the case of PBL of the oral cavity the possible role of Epstein Barr Virus (EBV) infection was considered. All but one of the patients with known HIV-status (32/45) was HIV positive and I supported the proposal that the diagnosis of PBL should serve as a sign of immunodeficiency, either as diagnostic thereof or as a predictor of a progressive state of immunodeficiency in patients with known HIV/AIDS status. The HIV-negative patient in this study was the only one that presented with an EBV-negative PBL on in situ hybridisation. The clinico-pathological features of the current study therefore strongly suggested an association between EBV, PBL and HIV/AIDS although the exact nature thereof remains uncertain. Routine genetic evaluation of tumours diagnosed as PBL should be introduced, as this may have prognostic and eventually treatment implications in the future. The exact panel of genes to be evaluated with a possible diagnosis of PBL should still be determined but examination of IGH and MYC for rearrangements should be included. This study proved the histomorphological features including the degree of plasmacytic differentiation not to have any diagnostic role although its prognostic value should be determined. The results of the immunohistochemical investigations performed in this study confirmed PBL always to be negative for CD20 but proved PBL not to be a morphological or immunohistochemical diagnosis by any means. In conclusion, it became clear that PBL should never be diagnosed without thorough clinical, systemic, pathological and genetic investigations, especially in the backdrop of HIV/AIDS. No pathologist should make the diagnosis of PBL and no clinician should accept such a diagnosis or decide on the treatment modality for the patient involved unless all other possibilities of systemic plasma cell disease have been excluded. / Thesis (PhD)--University of Pretoria, 2011. / Oral Pathology and Oral Biology / unrestricted

Polycyclic Polyprenylated Acylphloroglucinols (PPAPs) are a vast family of natural products, which includes more than 200 members. They contain a stunningly complex molecular architecture which in most cases includes a bicyclo[3.3.1]nonane core. PPAPs have been of interest to the scientific community for their intricate structure, their powerful aid in treating many ailments and large portfolio of biological activities. More particularly, they have been of synthetic interest since 1999 with the first report of an approach to these complicated cores by Nicolaou. Herein, we present the first total synthesis of papuaforin A, papuaforin B, papuaforin C, hyperforin and the formal synthesis of nemorosone following a report by Simpkins and co-workers. We relied on a gold(I)-catalyzed carbocyclization for the construction of the core of this family of natural products. Ginkgolides are isolated from the ginko tree, Ginkgo biloba, a living fossil with records of its existence dating back 280 million years. For centuries, the plant and its extracts have been used extensively for their beneficial properties, especially in China, Japan and India. For example, extract Egb761, one of the most potent fraction, generates over $500 million a year alone. The ginkgolides possess a truly unique compact diterpene framework of six 5-membered rings with a high content oxygen. Eleven oxygens can be found in ginkgolide C for a core containing only 23 carbons. The ginkgolides also include a very unique feature: a tert-butyl group located on the most convoluted ring system: the B ring. Few groups have found success in limning a synthetic route to ginkgolides. Corey’s group was the first to achieve the total synthesis of ginkgolide B in 1987. He was also able to complete ginkgolide A a year later. Crimmins and co-workers also achieved the total synthesis of ginkgolide B a decade later in 1999. Herein, we present our new approach toward ginkgolides through a newly developed methodology for the α-allylation of ketones and the creation of highly hindered contiguous quaternary centers. The synthesis is still at an early stage but a synthetic pathway giving access to the ring B with all the key moieties has been extensively investigated.

Part A: Synthesis of 5- and 6-Membered Camphor-Based Hydrazides as Organocatalysts for Cycloaddition Reactions The favorable environmental and reactivity qualities of organocatalysts are contributing to the popularization of this method for the acceleration of enantioselective reactions. Research in our group has been focused on the synthesis of camphor-derived hydrazide based organocatalysts for enantioselective cycloaddition processes. Recent results suggest that the presence of an exocyclic electron withdrawing group on the hydrazide moiety, as well as the incorporation of the hydrazide moiety into a 6-membered ring, may have a beneficial effect on the kinetics of the catalysts. A variety of camphor-based cyclic hydrazides have been synthesized and tested in Diels-Alder reactions, varying both the ring size and placement of the electron withdrawing group. Part B: Synthesis of Isocampholenic Acids by the Rearrangement of Camphor Derivatives A variety of substituted isocampholenic acid derivatives have been prepared by rearrangement of the camphor skeleton of a variety of tertiary alcohols derived from ketopinic acid. The reaction is highly reliable and retains the stereochemical information from the camphor scaffold. This rearrangement represents an efficient way to prepare synthetically useful isocampholenic acids. Mechanistic experiments show that the rearrangement does not involve exogenous water and that a short-lived carbocation is implicated in the reaction. Part C: Diastereoselective Formation of Quaternary Centers from Stereodefined Trisubstituted Alkenes Previous work in our laboratory has focused on the preparation of single-isomer tri- and tetra-substituted olefins. This methodology has been used in the construction of a variety of alkenyl esters in good to excellent yields. These alkenyl esters could then be transformed into the corresponding 3,3-disubstituted allyl boronates in a stereocontrolled fashion. There are a limited number of methods available to prepare single isomer 3,3-disubstituted allyl boronates, which can be important precursors in the stereoselective preparation of all-carbon quaternary centers. Our methodology has therefore been applied to the construction of single isomer 3,3-disubstituted allyl boronates and subsequently used in the stereoselective generation of all-carbon quaternary centers by the reaction of these allyl boronates with aldehydes.

Nitrones are alternatives to azides in rapid strain-promoted 1,3-dipolar cycloadditions with cyclooctynes. To evaluate the differences between nitrones and azides we have performed kinetic studies of strain-promoted alkyne-nitrone cycloaddition (SPANC) reactions of biarylazacyclooctynone (BARAC) with various acyclic and cyclic nitrones. The reactions were conducted under pseudo first-order reaction conditions using UV-visible spectroscopy. The reactivity of the acyclic nitrones was evaluated by varying the stereoelectronic and steric character of substituents at both the α-aryl and nitrogen positions. Cyclic nitrone reactivity was assessed according to the size of the ring and additional steric and strain effects. The obtained second-order rate constants for reactions of BARAC with cyclic nitrones were found to be greater than those for acyclic nitrones. However, all nitrones employed in the kinetic studies herein displayed significantly greater reactivity than azides in the analogous cycloadditions with BARAC. It is of particular note that the five-membered cyclic nitrones showed exceptional reactivity and, if used as rapid alternatives to azides in reactions with BARAC, can increase the reaction rates by up to 50 fold. An attempt to synthesize an allylated BARAC analogue is also described; the rearrangement reaction leading to the unexpected products is reported. The reaction rate for the novel rearrangement under both neutral and acidic conditions was obtained and plausible mechanisms for formation of products are proposed. Based on the results reported herein we anticipate that development of a labelling probe based on BARAC and a five-membered cyclic nitrone would allow for significant decrease of the concentrations of labelling reagents, thereby minimizing reaction time and reagent usage in life sciences applications. Nevertheless, a possible labelling decrease due to side reactions should be given consideration for prolonged labelling.

O tratamento padrão para pacientes com câncer de reto localmente avançado consiste no uso de quimioradioterapia neoadjuvante (QRTn), seguida por cirurgia. Uma fração significativa dos pacientes responde completamente ao tratamento e no momento da reavaliação não apresenta evidência clínica nem radiológica de doença. Uma abordagem alternativa, Watch and Wait, propõe não operar imediatamente esses pacientes e submetê-los a um protocolo de observação frequente, a fim de evitar as morbidades associadas à cirurgia. No entanto, a avaliação da resposta ao tratamento ainda é um desafio, devido à subjetividade da avaliação clínica e a ausência de exames radiológicos suficientemente sensíveis e específicos para garantir a ausência de células tumorais residuais ou capazes de detectar a recorrência precoce da doença. DNA circulante contendo alterações genéticas específicas do tumor (ctDNA) pode ser encontrado na fração livre de células do sangue e tem sido utilizado para monitorar a dinâmica tumoral em tumores sólidos. Avanços recentes das tecnologias de sequenciamento permitem a identificação eficiente e rápida e a um custo relativamente baixo de alterações genéticas em tumores individuais, superando o problema imposto pela ausência de alterações genéticas recorrentes nesses tumores. Essas alterações podem ser utilizadas como biomarcadores personalizados para monitorar a resposta ao tratamento, detectar doença residual e a recidiva precoce do tumor. O objetivo deste trabalho foi identificar e estudar biomarcadores personalizados em pacientes com câncer de reto localmente avançado tratados com QRTn e avaliar a capacidade desses biomarcadores para monitorar a dinâmica tumoral, e auxiliar na definição da conduta cirúrgica e na detecção da recidiva precoce da doença. Biópsias de seis pacientes com adenocarcinoma de reto distal (cT2- 3N0-1M0), foram coletadas prospectivamente pré-tratamento. O DNA genômico extraído a partir das biópsias foi usado para construir bibliotecas tipo mate-pair para o sequenciamento do genoma completo, utilizando a plataforma SOLiD. Rearranjos inter e intracromossômicos foram identificados utilizando programas computacionais desenvolvidos pelo nosso grupo de pesquisa e em seguida foram validados utilizando PCR e sequenciamento Sanger. Foram validadas, pelo menos, três variações estruturais para cada paciente. Amostras de plasma foram coletadas no momento do diagnóstico, depois da QRTn e durante o seguimento. DNA circulante total foi extraído a partir das amostras de plasma e ensaios personalizados foram desenvolvidos para monitorar a presença de variações estruturais através de PCR Digital. ctDNA foi detectado em todas amostras de plasma pré-tratamento de pacientes com tumores T3. A detecção desses biomarcadores apresentou boa correlação com a resposta ao tratamento, no entanto, esta abordagem não foi sensível o suficiente para detectar doença residual. Para dois pacientes que desenvolveram doença metastática foi verificado um aumento nos níveis de ctDNA com pelo menos 36 semanas antes do diagnóstico clínico de doença metastática, sendo possível correlacionar os níveis de ctDNA detectados em coletas subsequentes com a resposta ao tratamento sistêmico de segunda linha. Este estudo, embora de caráter exploratório, gerou dados relevantes e suficientes para justificar a realização de estudos adicionais para avaliar a aplicação dos biomarcadores personalizados na definição da conduta cirúrgica e no acompanhamento de pacientes com câncer de reto tratados com QRTn. / The standard treatment for patients with locally advanced rectal cancer comprises in neoadjuvant chemo radiotherapy (nCRT), followed by surgery. A significant fraction of these patients show complete response to the treatment and at the time of reassessment, there are no clinical and nor radiological evidence of residual tumor. An alternative approach, Watch and Wait, proposes not to immediately operate these patients, but to submit them to a protocol of frequent observation in order to avoid the morbidities associated with radical surgery. However, assessment of treatment response remains a significant challenge due to the subjectivity of the clinical examination and to the lack of sufficiently sensitive tools to ensure the absence of tumor cells or to detect early disease recurrence. Circulating DNA carrying tumor-specific genetic alterations (circulating tumor DNA - ctDNA) can be found in the cell-free fraction of the blood and has been successfully used to monitor the tumor dynamics in solid tumors. Recent advances in sequencing technologies have enabled the rapid and cost effective identification of genetic alterations in individual tumors, overcoming the problem imposed by the absence of recurrent genetic alterations in these tumors. These alterations can be used as personalized biomarkers to monitor treatment response, detect residual disease and early tumor recurrence. The purpose of this work was to identify and validate the use of personalized biomarkers for patients with locally advanced rectal cancer treated with nCRT and to evaluate the ability of these biomarkers to monitor the tumor dynamics, to define surgical approach and to detect early recurrence of the disease. Pre-treatment biopsies from 6 patients with cT2-3N0-1M0 distal rectal adenocarcinoma were prospectively collected. Genomic DNA extracted from the biopsies was used to construct mate-pair libraries for whole genome sequencing using SOLiD platform. Inter and intrachromosomal rearrangements were identified using an in-house bioinformatics pipeline and validated using PCR amplification and Sanger sequencing. At least three structural variations were validated for each patient. Plasma samples were collect at diagnosis, after nCRT and follow-up. Circulating DNA was obtained from the plasma samples and personalized assays were designed to monitor the presence of structural variations using Droplet Digital PCR. ctDNA was detected in all pre-treatment plasma samples for patients with T3 tumors. The detection of these biomarkers showed a good correlation with the treatment response, nonetheless, the approach was not sensitive enough to detect residual disease. In two patients who developed metastatic disease, an increase in ctDNA levels was observed at least 36 weeks before clinical detection of metastatic disease, and it was possible to correlate the level of ctDNA in subsequent plasma samples with response to the second-line treatment. This study, although exploratory, generated relevant and sufficient data to support additional studies to evaluate the use of personalized biomarkers in the surgical management and follow-up of rectal cancer patients treated with nCRT.

Ciliates are model organisms for studying programmed genome rearrangement because each cell houses two distinct genomes. During postzygotic development, the somatic genome rearranges from a copy of the germline genome via extensive genome remodeling, including DNA elimination, religation and sometimes translocation or inversion of genomic regions. Previous studies of this process were restricted to a few model ciliates including Tetrahymena thermophila, Paramecium tetraurelia and Oxytricha trifallax. Oxytricha diverged from Tetrahymena and Paramecium over one billion years ago, and it possesses a massively fragmented and scrambled germline genome. My thesis compares Oxytricha to more closely related ciliates to address the evolutionary origin of genome complexity. Chapter 1 provides a general introduction to genome architecture, comparison of well-studied ciliate genomes and challenges of studying genome rearrangement in non-model ciliates. Chapter 2 describes a computational pipeline, SIGAR (Split-read Inference of Genome Architecture and Rearrangements), which infers genome rearrangement features without a germline genome assembly. We validated the pipeline using a published Oxytricha dataset, and also applied it to six diverse ciliate species including Ichthyophthirius multifiliis, a fish pathogen. This pipeline enables pilot surveys or exploration of chromosomal rearrangement in ciliates with limited germline DNA access, thereby providing new insights into the evolution of DNA rearrangement. Chapter 3 presents a comparative genomic study of three ciliate species including Oxytricha trifallax, Tetmemena sp. and Euplotes woodruffi. Collaborating with my colleagues, I assembled and annotated germline genomes in Tetmemena and E. woodruffi, as well as E. woodruffi’s somatic genome. We identified scrambled genes in all three species, especially the earlier-diverged E. woodruffi, though at a lower level (7.3% of gene loci) compared to Oxytricha (15.6%) and Tetmemena (13.6%). E. woodruffi may therefore represent an intermediate between the nonscrambled ancestral genome and more massively scrambled genomes as can be seen in Oxytricha and Tetmemena. We also found that scrambled genes tend to have more paralogs or have partial MDS duplications, suggesting that local duplications might play a role in the evolutionary origin of scrambled genes. Chapter 4 reports a new genetic code identified in a basal spirotrich ciliate, Licnophora macfarlandi. Ciliates have been a hot spot for the evolution of alternative genetic codes. All variant genetic codes in ciliates reassign canonical stop codons to amino acids, and in most cases the UAA and UAG are reassigned to the same amino acid, or are both used as stop codons. The codon usage analysis in Licnophora revealed an unprecedented genetic code that translates the UAA to glutamic acid and the UAG to glutamine. We also detected candidate tRNAs from the somatic genome which can recognize the UAA and UAG. Chapter 5 describes possible future directions to understand the genome complexity of ciliates.

An efficient approach to the hydrobenzofuro[3,2-b]chromenone core of sanggenon-type natural products has been developed. The key transformation involves a protecting group-free double rearrangement of a bis-allyloxyflavone ether substrate. A sequence involving asymmetric 3-allyl rearrangement followed by aromatic Claisen rearrangement has been established for the asymmetric synthesis of the hydrobenzofuro[3,2-b]chromenone core structure. This methodology has been successfully applied to asymmetric syntheses of both sanggenol F and sanggenon A. Efficient chiral, racemic syntheses for sanggenons C and O have been achieved. The key transformation entails a biomimetic Diels-Alder cycloaddition between a flavonoid diene and a 2'-hydroxychalcone. The flavonoid diene was produced from a protected flavonoid chromene via isomerization. Metal-catalyzed alkynyl Claisen (Saucy-Marbet) rearrangements of 3-alkynyl flavone ethers have been evaluated, and a 1,2-acyl migration cascade which afforded novel furanyl benzofuranone scaffolds was discovered. Mechanistic studies have revealed that the rearrangement is likely initiated by 5-endo enyne cyclization to a platinum-containing spiro-oxocarbenium intermediate, which may be intercepted by methanol to produce a spirodihydrofuran or further rearranged to afford allenyl chromanediones and benzofuranones at higher reaction temperature. Lewis acid-catalyzed [1,3]-rearrangements of 3-aryl substituted flavone ethers have also been developed.

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