VictorJuiz/thesis huggingface dataset:
Dissecting the impact of chimeric antigen receptor expression levels on T cell behaviour and response

Chimeric antigen receptor (CAR) T cells have heralded in a new age in cancer treatment. CAR T therapy has demonstrated remarkable responses in cancer patients of blood cancers. The therapy's success lies in the expression of a chimeric antigen receptor (CAR) that reprograms and redirects T cells to specifically target and attack cancer cells. However, CAR T therapy has faced numerous challenges with attempts to translate this success into solid cancers. Issues related to on-target, off-tumour toxicity, tonic signalling, and T cell dysfunction have limited numerous efforts. However, recent evidence demonstrated that CAR expression levels are a critical determinant in T cell activity and therapeutic efficacy – even more so in mediating T cell exhaustion. While insightful, this work assesses only two levels of CAR expression. Thus, there is a notable, outstanding gap in thoroughly understanding how CAR expression levels impact T cell function and response. In this thesis, I report the effects of extensive fine-tuning of CAR expression levels on the T cell transcriptome. First, I adapt microRNA silencing-mediated fine-tuners (miSFITs) technology to tune CAR expression levels in a T cell model. I leverage this model to show that tuning CAR expression correspondingly tunes CAR T cell activation. Next, I translate this technology into primary, human T cells, showing that miSFITs robustly and precisely tune CAR expression. I then demonstrate how tuned CAR expressions controls the expression of CD69 to stepwise levels. Finally, I use single-cell RNA-sequencing to comprehensively dissect the effects of tuning CAR expression in T cell responses, generating a transcriptomic atlas against step-wise levels of CAR expression. I use this atlas to first demonstrate how tuning CAR expression impacts several genes related to T cell activation, dysfunction, and memory. Using gene signatures, I demonstrate how CAR expression can be optimised to mitigate T cell dysfunction yet spare T cell activation and memory. Embarking on an unbiased discovery analysis, I identify genes, regulons, and signaling pathways that are influenced by CAR expression, providing a novel view on T cell dysfunction. My findings underscore the important role CAR expression levels have on T cell response and provide a promising avenue to address pressing, longstanding challenges hindering the success of CAR-T therapies.

Keywords: scRNA-seq
T cells
microRNA
synthetic biology
immunotherapy
CAR T cells
immunogenomics
tumour immunology
Advisor: Fulga, T
Michaels, Y
Sauka-Spengler, T
Neural mechanisms underlying memory in drosophila melanogaster

In a complex and constantly changing environment, animals are required to guide behaviour in a dynamic way to adapt to the current environment as well as the organism’s needs. Although the ability to remember past events allows animals to predict future outcomes and thereby guide behaviour, an input does not always produce stereotypical behaviours. Factors such as conflicting information from parallel memories, cue specificity and context will impact the predictability of an outcome across time. Similarly, the animal’s internal state influences whether the predicted outcome should be pursued at a given moment. Moreover, biological relevance of the memory, such as nutrient-reinforced associations, are thought to affect the lability of the memory and therefore how accessible it will be. Integration of predictability, motivation and memory stability allows a dynamic retrieval of appropriate memories to guide behaviour to properly balance their internal state.
Previous research in Drosophila has yielded detailed mechanisms describing the neural circuitry and molecular correlates involved in memory processing, but we lack a full understanding of how factors affecting memory retrieval become integrated to produce changes in behaviour. The work presented throughout this thesis uses Drosophila melanogaster to investigate the neuronal and behavioural mechanisms and how these factors regulate behavioural outcomes across time. In this work, repeated stimulus presentations were used to address how stimulus exposure prior to learning affects the formation and expression of new memories across time. Our results show that odour pre-exposure leads to an aversive memory which competes with subsequently acquired memories, leading to latent inhibition of memory expression. Changes in context between pre-exposure and testing allow conflict resolution, retrieval of the appropriate trained memory and inhibition of pre-exposure memory.
The second experimental chapter examines nutrient-reinforced long-term memory and the dynamics of its retrieval across time. Interestingly, neuronal stimulation studies have suggested that emergence of long-term nutrient-reinforced memory is independent of short-term memory, suggesting a delayed association between stimuli and nutrient-reward. However, the results presented here suggest that this apparent emergent memory results from an inhibition of short-term memory, potentially due to a motivational switch produced by co-activation of retrieval-inhibiting neurons. Taken together, the work presented throughout this thesis delves into how different mechanisms, from memory integration to motivational suppression and context, lead to a temporal inhibition of memory retrieval to shape a changing behaviour across time.

Keywords: mushroom body
dopamine
retrieval
differential associative learning
Advisor: Waddell, S
Okray, Z
Exploring mammalian chromatin architecture and its impact on gene regulation

Mammalian chromatin architecture appears hierarchically organised and is composed of chromosome territories, compartments, topologically associating domains (TADs), loops and nucleosomes. The study of chromatin architecture has recently become prevalent due to the advancement of chromosome conformation capture (3C) and microscopy-based techniques. Many studies have predicted that TADs display important functional characteristics such as forming tissue and species-invariant regulatory domains, promoting co-regulation and insulating genes from aberrant regulation. Even with the increasing availability of data, the relationship between chromatin structures such as TADs, gene expression and function is still not fully understood. In this thesis, I use publicly available Hi-C data to rigorously assess this relationship.
To further investigate the characteristics of TADs I compiled a re-annotated TAD dataset consisting of 13 human and 20 mouse genomes, covering 8 broad tissue/cell type groups. Using this TAD dataset as a foundation, I investigated the functional features of TADs in three main areas: tissue and species specificity, functional annotations, and phenotypic characteristics. Comparative analyses between TADs and randomly placed TADs revealed that there is some evidence that TADs are both tissue- and species-specific, genes which singly occupy a TAD are highly constrained and enriched for developmental functions, and genes sharing a CTCF TAD are not more functionally similar than can be explained by their linear proximity alone. Lastly, using adipose TADs as well as chromatin loops, I investigate the aetiology of genetic variants associated with fat distribution.
The comprehensive analyses outlined suggest that contrary to common claims in the literature, TADs display a significant degree of both tissue and species specificity and play a limited role in promoting gene co-expression. These results contribute to understanding the relationship between 3D mammalian chromatin structure and gene regulation which is crucial for dissecting gene regulatory programs.

Keywords: TADs
Hi-C
Advisor: Lindgren, C
Mallon, A-M
Simon, M
Globular multicategories with homomorphism types

We introduce various notions of globular multicategory with homomorphism types. We develop a higher dimensional modules construction that constructs globular multicategories with strict homomorphism types. We illustrate how this construction is related to iterated enrichment. We show how various collections of “higher category-like”objects give rise to globular multicategories with homomorphism types. We show how these structures suggest a new globular approach to the semantics of (directed) homotopy type theory.

Keywords: higher category theory
homomorphism types
directed identity types
globular operads
iterated enrichment
globular multicategories
homotopy type theory
Advisor: Kremnitzer, Y
Vicary, J
The generation of Paneth-like cells in colorectal cancer to alter T-cell responses

Immunotherapy in colorectal cancer (CRC), the third most diagnosed cancer worldwide, results in limited and unpredictable responses. There are two main molecular subtypes of CRC: microsatellite unstable and the more common microsatellite stable type. Microsatellite unstable CRC develops as a result of somatic or germline, genetic or epigenetic perturbations to DNA mismatch repair genes. Importantly, microsatellite stable cancers mostly respond poorly to immunotherapies due to their apparent lack of neoantigen presentation and immune infiltration. The main curative treatment of these cancers thus remains surgical resection of the tumour and adjacent lymph nodes with some patients then offered conventional chemotherapy. Traditional views propose the benefit of lymphadenectomy is to either prevent further spread of the disease from involved lymph nodes or to improve staging. However, a recent transcriptomic analysis from the Buczacki Group demonstrated a strong enrichment in adaptive immune response related gene sets associated with high lymph node (LN) yields. Given more immunogenic tumours are associated with better outcomes, these data suggest a tumour-intrinsic reason for the enhanced survival seen. Interestingly, our analysis also found signatures for Paneth cells were enriched in this high LN yield group. Paneth cells are a cell type found in the small intestine and only rarely in the large intestine, where colon cancer develops. In the small intestine they secrete antimicrobial peptides and regulate the inflammatory response. I hypothesise that the presence of Paneth-like cells in colon cancer enhances the host immune response against the tumour. In this study, in-silico analysis revealed heterogeneity within Paneth cell populations in CRC, separating LYZ- and DEFA5-specific clusters. ATOH1 plasmid overexpression and SATB2 CRISPR-cas9-knockout induced Paneth cell-specific DEFA5 gene and protein expression in CRC cell lines and spheroids. Paneth cell differentiated models were co-cultured with Jurkat cells to test for immune effects. Co-culturing with ATOH1-overexpressing and SATB2- knockout cells caused an increase in spheroid infiltration and IL2 secretion of Jurkat cells. Therefore, I propose that differentiation therapy could potentially augment current immuno-oncology approaches by enhancing the host immune response against CRC.

Keywords: immune response
colorectal cancer
paneth cells
Advisor: Buczacki, S
Parkes, E
Inelastic neutron and resonant elastic x-ray scattering studies of honeycomb quantum magnets

This thesis presents results from inelastic neutron scattering experiments on the magnetically ordered phases of the stacked honeycomb quantum magnets CoTiO3 and FeTiO3. The two materials are isostructural with ferromagnetic alignment within the honeycomb layers, and antiferromagnetic alignment between neighbouring honeycomb layers. In CoTiO3, the magnetic moments have an easy-plane anisotropy and high resolution inelastic neutron scattering measurements reveal the presence of a finite energy gap. Such a gap implies the existence of bond-dependent anisotropic couplings and a quantum order-by-disorder mechanism. Furthermore, the inelastic scattering measurements reveal a winding of the scattering intensity at linear crossing points in the vicinity of the corners of the two-dimensional Brillouin zone. On the other hand, the magnetic moments of FeTiO3 possess an easy-axis anisotropy with doubly degenerate magnetic modes. This degeneracy is lifted under the application of an external magnetic field, and if this magnetic field exceeds a critical value of 8 T the magnetic structure transitions from an antiferromagnetic phase to a spin-polarised phase. The magnon dispersions in FeTiO3 have a small avoided crossing at the corners of the two-dimensional Brillouin zone, and such a gap arises due to the presence of an antisymmetric Dzyaloshinskii-Moriya exchange interaction. Nonetheless, the azimuthal dependence of the inelastic neutron scattering intensity around these avoided crossing points was found to have a similar profile to that observed in CoTiO3. This periodicity appears to be a universal feature of magnetic excitations supported by the honeycomb lattice and was found in both low energy magnons and higher energy spin-orbit excitons in CoTiO3, and in the magnon excitations of FeTiO3 in both the antiferromagnetic and spin-polarised magnetic phases. Finally, results of elastic x-ray scattering experiments measuring the structural and magnetic properties of crystalline samples of lithium substituted Na2IrO3 are presented. Such systems have previously been found to exhibit anisotropic Kitaev exchange between the Ir4+ moments, which may stabilise exotic magnetic phases. Studies of the structural order of these samples reveal stacking faults and rotational twins. Resonant elastic x-ray scattering studies allow the magnetic structure of a 5% Li-substituted sample of Na2IrO3 to be determined as a zigzag ordered magnetic state, which implies the presence of both isotropic Heisenberg and anisotropic Kitaev exchange interactions.

Advisor: Coldea, R
Reliable and spectrally efficient encoding and modulation techniques

Due to remarkable growth in mobile data traffic, intelligent devices, and connectivity, the need for spectrally/energy efficient and reliable communication systems increases day by day. Moreover, to meet the fast-growing demand for data communication and massive connectivity, next-generation networks will require to deploy more advanced modulation techniques than the existing ones. In this respect, index modulation (IM) and its combinatorial encoding structure have gained considerable popularity thanks to their attractive advantages, including low-complexity implementation, better error performance, and improved energy/spectral efficiency over conventional modulation and multiplexing schemes. Although IM is a potential candidate for the next-generation networks due to its beneficial properties, one needs to design more reliable and spectrally efficient modulation techniques to satisfy the requirements of the next-generation networks. Therefore, this thesis investigates reliable and spectrally efficient encoding and modulation techniques, proposing novel designs based on combinatorial and well-known encoding mechanisms. Our designs uncover novel applications of combinatorial tools such as set partitioning and composition in encoding. The resulting concepts are general modulation methods, which comprehend the classical and IM techniques as particular cases. They also exhibit a better error performance and higher achievable rate than the IM and classical modulation techniques, making them a better candidate for future wireless networks. Apart from the combinatorial framework, we exploit a simple maximum distance separable code to show the actual potential of the IM and related schemes as well as design a modulation concept that achieves better error and achievable rate performance than the classical and combinatorial methods while exhibiting a low-complexity structure.

Keywords: spectral efficiency
reliability
encoding
maximum distance separable codes
orthogonal frequency division multiplexing (OFDM)
index modulation
modulation
Advisor: Coon, J
Theory and application of PBPK modelling in drug development: the double-edged sword of complexity

Physiologically-based pharmacokinetic modelling has become an integral part of model-informed drug development. However, the extensive structure and parameterisation of such models may give rise to issues with model identifiability, parameter estimation and model analysis techniques. In this thesis, we examine the strengths and limitations of whole-body physiologically-based pharmacokinetic models in regard to their complexity by investigating methods of extracting information from such models in clinically relevant applications with limited or no data, as well as how the complexity may be managed in practice. We first address the gaps in the quantitative understanding of the immunological role of the spleen. We do this by assessing how in silico splenectomy affects T cell distribution and bioavailability of T cells in the secondary lymphoid tissue in human. Based on the predicted lack of significant difference in the T cell concentration in secondary lymphoid tissue, we conclude that the remaining tissue is predicted to have insufficient cellular and trafficking capacity to compensate for immune functions normally mediated by the spleen. We then discuss the potential limitations of single versus multiple lymph node compartment models in the development of immunotherapeutic modalities. Illustrating the concept by comparing two models with different lymph node compartmentalisation, we show how the choice of the number of lymph node compartments affects the model predictions and, thus, how its application dictates the necessary level of detail in the model. Finally, we propose a model describing the deposition, pharmacokinetics and pharmacodynamics of anti-CD20 monoclonal antibodies administered intravenously and subcutaneously, and analyse the model’s identifiability in the context of clinical data format. We fit the model to antibody blood data and show that the model predictions are consistent with the current knowledge on the mechanism of action of anti-CD20 antibodies. We further discuss the data needed for the framework to facilitate consideration of efficacy- and safety-related problems. The thesis concludes with a discussion of the results in the context of model-based drug development, regulatory perspective and the extent to which physiologically-based mathematical models can contribute toward insight and decision support for therapeutic development.

Keywords: compartment lumping
secondary lymphoid tissue
model reduction
cell-based therapy
PBPK modelling
monoclonal antibody
model simplification
physiology
Advisor: Gaffney, E
Quantitative histology for assessing organ health

This thesis aims to take the first step in developing a quantitative analysis workflow for characterising histological changes in pre-implantation renal biopsies. Solving this is highly beneficial as there is a significant disparity between organ supply and demand worldwide. It can also help to alleviate the workload caused by a shortage of pathologists. This work would allow quantitative measurement of histological features related to chronic and acute injuries in pre-implantation biopsies. These features can then be linked to scores given by pathologists, post-transplant clinical endpoints, and proteomic biomarkers to help researchers better understand the mechanisms of organ injury and repair.
First, we build the main feature extraction workflow based on convolutional neural networks (CNN) to automatically segment different tissue compartments in renal biopsies. We design handcrafted features and qualitatively show that some of these features can capture visual changes related to chronic and acute injuries.
Then, we find that many tissue compartments in the primary dataset have artefacts not present in the training data. We discuss Bayesian Neural Networks (BNNs) to quantify uncertainties in segmentation and propose a way to improve histological estimates.
Next, we propose using tissue compartment-based features to improve classification and interpretability in a multi-instance learning setting. In addition to learned attention, tissue compartments are weighted by segmentation quality to reduce the impact of instances that bear little resemblance to the training data.
Finally, we combine techniques developed in this project to detect acute injuries from biopsies. We propose an algorithmic score consisting of models trained on pathologists’ assessments and donors’ clinical states. The score is significantly associated with Delayed Graft Function (DGF) in the test data.
These findings suggest that our workflow can facilitate research in kidney transplant where pathologist time is limited. It also shows histology has great potential in predicting post-transplant complications.

Keywords: histopathology
transplant
computer vision
histology
machine learning
image analysis
deep learning
Advisor: Ploeg, R
Sirinukunwattana, K
Kaisar, M
Rittscher, J
Animals in Vedic prose

This thesis examines a well-known axiom of ancient Indian thought: the human being is classified as one of the five domestic animals, paśu. Although this notion is well-known, often mentioned in secondary literature, it has not yet received a comprehensive, scholarly treatment. Drawing on the detailed philological and textual-historical study of the Vedic poetry and prose, this thesis explores the classification of the human as a domestic animal, as well as the categories of “animality” and “humanity” more broadly.
The thesis is composed of three core chapters. The first discusses the semantic history of the three most common Vedic animal terms: paśu, mṛga, and the antonymic dyad, grāmya and āraṇya paśu. As well as introducing the terms in a broad context, it argues that their evolution documents the transition of Vedic lifestyle from semi-nomadic pastoralism to agricultural sedentism.
Building on this, the second and third chapters explore the position of the human being within the paśu group. The second chapter discusses similarities and differences between the human and the rest of the group, in terms of both body and behaviour. The Vedic corpus suggests, however, that in the mythical past, people and domestic animals used to look and behave alike: just like people, domestic animals walked on two-feet, exercised agency, and sacrificed. I argue that this common history indicates that the species of paśus are mutually “related”. There is a sense of what I call “ontological proximity”: an entangled existence driven by a shared history and mutual care. The third chapter further investigates the notion of “ontological proximity” by way of detailed reading of two mythical narratives from the Vedic Brāhmaṇas, arguing that this idea is clearly present and used creatively in Vedic animal imagery.

Keywords: Vedic prose
animals
mr̥ga
paśu
Vedic
human-animal relationship
Veda
Advisor: Minkowski, C
Singularity formation, existence and regularity for degenerate Cahn-Hilliard equations

Cahn-Hilliard models are central for describing the evolution of interfaces in phase separation processes and free boundary problems. In general, they have non-constant and often degenerate mobilities. However, in the latter case, the spontaneous appearance of regions of vanishing mobility and their impact on the solution are not well understood. In this work, we study the axially symmetric 2-dimensional setting, and develop a singular perturbation theory to identify a range of degenerate mobilities for which the solution forms a singularity in infinite time. Moreover, we obtain two different approximate self-similar profiles which divide this range of degeneracies into two. We complement this approach by adapting the known theory for degenerate parabolic partial differential equations and Sobolev spaces of radial functions to obtain the existence and regularity of a weak radially symmetric solution. This is an improvement from the weak existence for the degenerate Cahn-Hilliard equation obtained previously, which does not ensure symmetry. Finally, we raise conjectures on the strict boundedness of the solution, which would restrict the formation of singularities.

Keywords: singularity
partial differential equations
asymptotic expansions
nonlinear equation
touchdown
pinch-off
Advisor: Münch, A
Novick-Cohen, A