京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第21161号 / 農博第2287号 / 新制||農||1060(附属図書館) / 学位論文||H30||N5135(農学部図書室) / 京都大学大学院農学研究科応用生命科学専攻 / (主査)教授 栗原 達夫, 教授 小川 順, 教授 阪井 康能 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DGAM

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<p>This project is undergoing the patent application, so it is confidential and should not be disclosed. Further questions can be asked by contacting Dr. Jeroen Goos, whose contact information was shown in the supervisor section.</p>

Immune-orchestrating biomaterials that precisely modulate the immune reac-tion to the host could lead the way for improving the implantation outcomein the transplantation field, in comparison to passive biomaterials. The lab-oratory of Dr. Thomas Crouzier has shown hydrogels derived from mucinsare capable of orchestrating the immune response mediated by foreign bodyresponse (FBR), as a result of evading fibrosis. Further, a recent study fromhis group showed sialic acid on mucin hydrogels is essential for the immuno-logical activity of those materials. Mucin glycans transiently activated thendampened macrophages, important orchestrators for material-mediated FBR,in a sialic acid-dependent manner for the majority of cytokines followed. Thematerial properties such as rheological properties, self-healing capacity, andstability, can be governed by the crosslinking chemistry used and have a drasticimpact on the functionalities of the materials. In this project, various cross-linking strategies are applied to tune the hydrogel properties. We show thatthe robust cross-linking formed mucin hydrogels having a 1.5% (wt/v) bettersupported insulin-secreting cells form islet-like organoids, compared to 2.5%mucin hydrogels. We then investigate the self-healing properties of the newmucin hydrogels and their interactions with various cell systems. / Immunologiska biomaterial som specifikt modulerar en immunologisk reak-tion hos värden kan vara vägen till att förbättra resultatet av en transplantationi jämförelse med att använda passiva biomaterial. Inom laboratoriet lett av Dr.Thomas Crouzier har det kunnat påvisas att hydrogels erhållna från mucinerär kapabla till att förändra en immunlogisk respons, Foreign Body Respon-se (FBR) vilket resulterat i att kringgå fibrosis. Utöver detta har ytterligareen studie utförts av hans grupp vilken kunde påvisa att sialinsyra på mucinhydrogel är essentiellt för den immunologiska aktiviteten för dessa biomateri-al. Mucin glykaner aktiveras tillfälligt för att dämpa bildandet av makrofager,vilket är viktigt vid biomaterial FBR i ett sialinsyra-beroende för bildandet avmajoriteten av cytokiner. Materialegenskaperna såsom reologiska egenskaper,självläkande kapacitet, och stabilitet kan regleras genom en krosslänkad kemisom har en drastisk impakt för funktionen för biomaterialen. I detta projekt, ärflera krosslänkande strategier tillämpade för att förstå egenskaperna för hyd-rogelerna. Vi har kunnat påvisa att robusta krosslänkande system av mucinhydrogel bestående av 1.5% (wt/v) ger bättre support till insulin sekreterandeceller att bilda islet liknande organider, att jämföra med 2.5% mucin hydrogel.Vi undersöker sedan den självläkande egenskaperna av nya mucin hydrogeleroch deras interaktioner med ett flertal olika cellsystem.

Chimeric antigen receptors (CARs) are able to specifically direct T cells to tumor antigens and therapy with anti-CD19 CARs has already cured cancer patients with B-cell lymphomas who have undergone long-term therapy non-successful. Despite this impressive result, the therapy is currently only approved as a last treatment option for blood cancers due to its life-threatening deficiencies. For patient safety and to enable additional application such as the treatment of solid tumors, CAR-T cells must be controllable, e. g. by chemically programmable CARs (cpCARs) regulated by hapten-like compounds. This thesis reports the synthesis and characterization of such hapten-like compounds. In the first step, seven different warheads with two different spacers were bound to biotin in order to find a suitable warhead for programming the cpCAR. In a second step, synthetic routes for the three pharmacophores folate, c(RGD), and an RGD peptidomimetic were developed. The routes allow the modification of the pharmacophores with one of the warheads from the first step. CuAAC was chosen as a bioorthogonal approach to link pharmacophores and warheads. In total, three different pharmacophores were modified with the 1,3-diketone motif of compound 21 leading to 112, 113 and 128. Activation of the T-cell signaling cascade was tested after binding of these hapten-like compounds to the cpCAR in the presence of suitable target structures. For 112, only a slight, non-significant, activation of the T-cell signaling cascade was observed, whereas for 113 and 128, a significant activation of the T-cell signaling cascade was observed. The poor solubility of the folate compounds led to alternative strategies. Folic acid was exchanged by pteroic acid and the bifunctional, linear compounds were enlarged to trifunctional dendrimers. Besides the reported regioisomer in 112, a second one, which was not reported to date, occurred by the cyclization of the linear RGD pentapeptide leading to 113. After the reported synthesis of an RGD peptidomimetic analogous to 128 could not be reproduced, a new synthetic route was developed. It also consists of 17 steps, but reduces the number of linear steps from 13 to 10. Moreover, the developed route contains an asymmetric hydrogenation step and is, compared to the published one, more flexible by the use of the copper-catalyzed azide-alkyne cycloaddition (CuAAC). In addition, an unknown reaction was observed. Instead of the formation of a Schiff base in the reductive amination of 129, an insertion of propargylamine occurred forming 131. The reaction is almost quantitative and in high purity. After requiring no purification, it could be predestined for industrial purposes, such as the synthesis of N-functionalized 1,2-dihydroquinolines or as a building block with various orthogonal functional groups. Besides the sulfonamide 16, the diketone (21, 27, 31) and lactam compounds (39 – 41), experiments on adapter molecules with further warheads were performed. In the synthesis of a proadapter approach, in which the warhead is formed only after the retro-aldol reaction catalyzed by the mAb, 6 of 10 steps were successfully performed. A newly developed synthesis to keto-sulfonyl and keto-sulfoxide compounds could not be completed but was performed on a small scale to the point of keto-sulfonyl and keto-sulfoxide. Furthermore, a universal synthesis route was designed to allow the introduction of the warhead at the end of the synthesis by acylation. Thus, after 5 shared steps, 3 of them in quantitative yield, different warheads may be introduced. Moreover, this also facilitates the purification and the analysis of the compounds by the absence of tautomerism or labile groups. However, the acylation experiments were not successful with either the acid cyanide or the Weinreb amide. In summary, this thesis has proven that the 1,3-diketone motif is a suitable warhead for programming the cpCAR, which was developed by Hudecek et al. (unpublished data). The hapten-like compounds 112, 113 and 128 simultaneously bind to integrin ${\alpha}_v{\beta}_3$ and the cpCAR activating the T-cell signaling cascade. The modular synthesis strategy and the use of the bioorthogonal CuAAC allow straightforward access to these valuable immunotherapeutics but revealed the need for an additional purification step to remove copper ions. / Chimäre Antigen-Rezeptoren (CARs) ermöglichen es T-Zellen spezifisch auf Tumorantigene auszurichten. Die Therapie mit anti-CD19 CARs konnte bereits eindrucksvolle Ergebnisse liefern und austherapierte Krebspatienten mit B-Zell-Lymphomen heilen. Durch zum Teil lebensbedrohliche Nebenwirkungen ist sie aktuell jedoch nur als letzte Therapiemöglichkeit zugelassen. Um Patienten zu schützen und ihr Einsatzgebiet zu erweitern, beispielsweise zur Behandlung von soliden Tumoren, müssen CAR-T-Zellen kontrollierbar sein, z. B. durch chemisch programmierbare CARs (cpCARs), die durch hapten-artigen Verbindungen reguliert werden. Die vorliegende Arbeit beschreibt die Synthese und Charakterisierung von solchen Verbindungen. Dafür wurden im ersten Schritt sieben verschiedene reaktive Gruppen mit zwei unterschiedlichen Spacern an Biotin gebunden, um eine geeignete reaktive Gruppe für die Programmierung des cpCARs zu finden. Im zweiten Schritt wurden Syntheserouten für die drei Pharmakophore Folat, c(RGD) und ein RGD-Peptidomimetikum entwickelt. Die Routen ermöglichen es das jeweilige Pharmakophor mit einer der reaktiven Gruppe aus dem ersten Schritt zu modifizieren. Zur Verbindung von Pharmakophor und reaktiver Gruppe, wurde die CuAAC als bioorthogonaler Ansatz gewählt. Insgesamt wurden im Rahmen dieser Arbeit drei verschiedene Pharmakophore mit dem 1,3-Diketon-Motiv von Verbindung 21 modifiziert. Mit den resultierenden Verbindungen 112, 113 und 128 wurde die Aktivierung der T-Zell-Signalkaskade bei Anwesenheit geeigneter Zielstrukturen untersucht. Bei 112 konnte nur eine leichte, nicht signifikante Aktivierung der T-Zell-Signalkaskade beobachtet werden, während bei 113 und 128 eine deutliche Aktivierung der T-Zell-Signalkaskade beobachtet wurde. Die schlechte Löslichkeit der Folatverbindungen führte zu Versuchen Folsäure gegen Pteroinsäure zu tauschen und die linearen Verbindungen zu trifunktionalen, dendrimeren Verbindungen mit weiteren Triethylenglycol-Ketten zu vergrößern. Neben dem publizierten Regioisomer in 112 trat bei der Zyklisierung des linearen RGD-Pentapeptides ein zweites Regioisomer auf, das zu 113 führte. Nachdem die veröffentlichte Syntheseroute eines RGD-Peptidomimetikums, das analog zu 128 ist, nicht reproduziert werden konnte, wurde eine neue Syntheseroute entwickelt. Sie besteht ebenfalls aus 17 Schritten, die Anzahl der linearen Schritte konnte jedoch von 13 auf 10 reduziert werden. Zusätzlich enthält die entwickelte Route einen asymmetrischen Hydrierungsschritt und ist durch den Einsatz der Kupfer-katalysierten Azid-Alkin-Cycloaddition (CuAAC) flexibler als die bereits publizierte Synthese. Während der Entwicklung der Syntheseroute wurde eine Reaktion beobachtet, die in der Literatur bisher nicht bekannt ist. Anstatt der Bildung eines Imins bei der reduktiven Aminierung von 129 kam es zu einer Insertion von Propargylamin, was zu 131 führte. Die Reaktion verläuft dabei nahezu quantitativ und in hoher Reinheit, so dass keine Aufreinigung notwendig ist. Sie könnte somit prädestiniert für industrielle Zwecke sein, wie zum Beispiel die Synthese von N-funktionalisieren 1,2-Dihydrochinolinen oder als Baustein mit mehreren funktionellen Gruppen, die orthogonal zu einander sind. Zusätzlich zum Sulfonamid 16, den Diketon- (21, 27, 31) und Lactamverbindungen (39 – 41), wurden Versuche zu Adaptermolekülen mit weiteren reaktiven Gruppen durchgeführt. Bei der Synthese eines Proadapter-Ansatzes, bei dem die reaktive Gruppe erst nach der vom mAb katalysierten Retroaldolreaktion entsteht, konnten 6 von 10 Schritten erfolgreich durchgeführt werden. Eine neu entwickelte Synthese von Keto-Sulfonyl- und Keto-Sulfoxid-Verbindungen konnte nicht abgeschlossen, aber im kleinen Maßstab bis zum Keto-Sulfonyl bzw. Keto-Sulfoxid durchgeführt werden. Des Weiteren wurde eine universelle Syntheseroute entworfen, um die Einführung der reaktiven Gruppe am Ende der Synthese durch Acylierung zu ermöglichen. So können nach den ersten 5 gemeinsamen Schritten, 3 davon in quantitativer Ausbeute, verschiedene reaktive Gruppen eingeführt werden. Darüber hinaus wird durch die Abwesenheit von Tautomerie oder labilen Gruppen sowohl die Aufreinigung als auch die Analytik der Verbindungen erleichtert. Die Acylierungsversuche waren jedoch weder mit dem Säurecyanid noch mit dem Weinreb-Amid erfolgreich. Zusammenfassend konnte in dieser Arbeit bewiesen werden, dass das 1,3-Diketon-Motiv eine geeignete reaktive Gruppe zur Programmierung des cpCARs ist, der von Hudecek et al. (bisher unveröffentlicht) entwickelt wurde. Es konnte außerdem gezeigt werden, dass die hapten-artigen Verbindungen gleichzeitig an Integrin ${\alpha}_v{\beta}_3$ und den cpCAR binden und die T-Zell-Signalkaskade aktivieren. Die modulare Synthesestrategie und der Einsatz der bioorthogonalen CuAAC für die Herstellung der Verbindungen ermöglichen einen unkomplizierten Zugang zu diesen wertvollen Immuntherapeutika, offenbarten jedoch die Notwendigkeit für einen zusätzlichen Reinigungsschritt zur Entfernung der Kupferionen.

Microfluidic paper based analytical devices (microPADs) are a novel platform for point of care (POC) diagnostics. Limitations of reagent shelf life have been overcome with the introduction of reagent pencils as a method for solid-based reagent deposition. While useful, little work has been reported on the characterization and optimization of reagent pencils. Herein, an investigation on reagent pencil composition and efficiency is conducted via colorimetric release profile tests utilizing an erioglaucine disodium salt that yields a quantifiable blue colored product in the presence of water. Within this work, an investigation on the molecular weight dependence, polymer chain end functionality, and polymer-graphite ratio was conducted to determine the most desirable parameters in reagent pencil composition. Further, the effects of enzyme stability in the presence of poly(ethylene glycol) (PEG) is investigated. To show the versatility of reagent pencils, a novel reagent pencil incorporating a stimuli responsive polymer, poly(N-isporopylacrylamide) (PNIPAM) was developed. In this work, PNIPAM’s lower critical solution temperature (LCST) was manipulated with various salt solutions to control fluid flow both laterally and vertically through various microPAD designs. It was found that, while PNIPAM successfully blocked or retarded fluid flow in microPADs, the effect was limited when DI H2O wash solutions were run prior to salt solutions. To counteract this, PNIPAM was successfully covalently bound to alkene modified chromatography paper via thiolene click chemistry to reinforce solution wash tolerance.

The demand for economical, efficient protein production, reuse, and recovery has never been greater due to their versatility in a large variety of applications ranging from industrial chemical manufacturing to pharmaceutical drug production. The applications for naturally and artificially produced proteins include protein drugs and other pharmaceutical products, as biocatalysts in environmentally friendly chemical manufacturing, as enzymes for food processing purposes, and as an essential component in many biomedical devices. However, protein production suffers from many challenges, which include the cost of production, protein stability especially under harsh conditions, and recoverability and reusability of the proteins. The combination of two developing technologies, cell-free protein synthesis systems (CFPS) and unnatural amino acid incorporation, provides solutions to these protein production challenges.This dissertation reports on the use of cell-free protein synthesis systems and unnatural amino acid incorporation to develop new proteins and enzyme immobilization techniques that significantly increase activity and stability while simplifying recoverability and reuse.

User click modeling in web search is most commonly done through probabilistic graphical models. Due to the successful use of machine learning techniques in other fields of research, it is interesting to evaluate how machine learning can be applied to click modeling. In this thesis, modeling is done using recurrent neural networks trained on a distributed representation of the state of the art user browsing model (UBM). It is further evaluated how extending this representation with a set of latent variables that are easily derivable from click logs, can affect the model's prediction performance. Results show that a model using the original representation does not perform very well. However, the inclusion of simple variables can drastically increase the performance regarding the click prediction task. For which it manages to outperform the two chosen baseline models, which themselves are well performing already. It also leads to increased performance for the relevance prediction task, although the results are not as significant. It can be argued that the relevance prediction task is not a fair comparison to the baseline functions, due to them needing more significant amounts of data to learn the respective probabilities. However, it is favorable that the neural models manage to perform quite well using smaller amounts of data. It would be interesting to see how well such models would perform when trained on far greater data quantities than what was used in this project. Also tailoring the model for the use of LSTM, which supposedly could increase performance even more. Evaluating other representations than the one used would also be of interest, as this representation did not perform remarkably on its own. / Klickmodellering av användare i söksystem görs vanligtvis med hjälp av probabilistiska modeller. På grund av maskininlärningens framgångar inom andra områden är det intressant att undersöka hur dessa tekniker kan appliceras för klickmodellering. Detta examensarbete undersöker klickmodellering med hjälp av recurrent neural networks tränade på en distribuerad representation av en populär och välpresterande klickmodell benämnd user browsing model (UBM). Det undersöks vidare hur utökandet av denna representation med statistiska variabler som enkelt kan utvinnas från klickloggar, kan påverka denna modells prestanda. Resultaten visar att grundrepresentationen inte presterar särskilt bra. Däremot har användningen av simpla variabler visats medföra drastiska prestandaökningar när det kommer till att förutspå en användares klick. I detta syfte lyckas modellerna prestera bättre än de två baselinemodeller som valts, vilka redan är välpresterande för syftet. De har även lyckats förbättra modellernas förmåga att förutspå relevans, fastän skillnaderna inte är lika drastiska. Relevans utgör inte en lika jämn jämförelse gentemot baselinemodellerna, då dessa kräver mycket större datamängder för att nå verklig prestanda. Det är däremot fördelaktigt att de neurala modellerna når relativt god prestanda för datamängden som använts. Det vore intressant att undersöka hur dessa modeller skulle prestera när de tränas på mycket större datamängder än vad som använts i detta projekt. Även att skräddarsy modellerna för LSTM, vilket borde kunna öka prestandan ytterligare. Att evaluera andra representationer än den som användes i detta projekt är också av intresse, då den använda representationen inte presterade märkvärdigt i sin grundform.

One less commonly used “click” reaction is thiazolidine chemistry. Thiazolidine chemistry is a commonly used reaction used in biological systems because the reaction requires the presence of both cysteine (a common amino acid) and an aldehyde or ketone. If cysteine residues could be incorporated into a polymer then a variety of applications could be developed. Polymers containing free thiols (aka thiomers) have developed in the last decade to become great mucoadhesives. If there was a facile route to control the amount of free thiols along the polymer then more fine-tuned and potentially stronger adhesives could be made. For these reasons the attachment of cysteine residues in a facile way via reversible addition fragmentation chain transfer (RAFT) polymerization or small molecule synthesis was researched. The incorporation of latent cysteine residues into the polymer via post polymerization modification proved to be less successful. However protected cysteine molecules have been successfully ligated onto polymerizable monomers and have been show to be easily deprotected in the presence of an acid source.