Deciphering immune complexity on the axes of time & space : high-dimensional profiling for tissue microenvironments
Abstract/Contents
- Abstract
- High-dimensional immunoprofiling on the axes of time, tissue, and treatment is necessary to unravel the heterogeneity within systems-wide responses to disease. We are witnessing a renaissance in the development of these methods, which have enabled greater parameterization, accuracy and throughput than previously achieved for studying systems immunology. The impact of T-cell targeted lipid nano particles (LNPs), a promising therapeutic strategy, was first assayed as a function of time and tissue using spectral cytometry. Reporter gene mRNA was packaged into CD3-targeted LNPs to transfect T cells in situ, and immune cells were assayed in the spleen, blood and tumors in the presence of immunotherapy. While promising transfection was achieved, an intense immune activation was associated with the anti-CD3 coating on the LNPs and created questions that required further dissection of immune cell subsets. These questions motivated an expansion of spectral cytometry techniques by engineering a 40-color deep immunophenotyping panel for murine lymphoid tissues and tumors. This tool was then applied to unlock mechanistic insights into combinatorial cancer immunotherapy, tissue leukocyte composition, and developmental trajectories in primary lymphoid tissues. While briefly highlighted herein, I use the majority of this thesis to discuss the engineering design principles behind a panel of this complexity, as such approaches have lacked comprehensive description in the existing literature. After achieving this high-resolution cellular phenotyping, the need to assay the spatial organization of immune and epithelial cells in cancers was apparent. With this focus in mind, a 51-plex CODEX assay was harmonized with Visium spatial transcriptomics to deconvolve the spatial architecture of pancreatic ductal adenocarcinoma (PDAC) and intraductal papillary mucinous neoplasm (IPMN) microenvironments, as well as tertiary immune structure frequency and composition. This thesis concludes by leveraging the spatial transcriptomic assays to model microdosimetry patterns for several beta-emitting radionuclides, in order to inform future theragnostic development.
Description
| Alternative title | Deciphering immune complexity on the axes of time and space |
|---|---|
| Type of resource | text |
| Form | electronic resource; remote; computer; online resource |
| Extent | 1 online resource. |
| Place | California |
| Place | [Stanford, California] |
| Publisher | [Stanford University] |
| Copyright date | 2024; ©2024 |
| Publication date | 2024; 2024 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Author | Kare, Aris John |
|---|---|
| Degree supervisor | Ferrara, Katherine W |
| Thesis advisor | Ferrara, Katherine W |
| Thesis advisor | Cochran, Jennifer R |
| Thesis advisor | Moseley, Michael E. (Michael Eugene), 1951 |
| Degree committee member | Cochran, Jennifer R |
| Degree committee member | Moseley, Michael E. (Michael Eugene), 1951 |
| Associated with | Stanford University, School of Engineering |
| Associated with | Stanford University, Department of Bioengineering |
Subjects
| Genre | Theses |
|---|---|
| Genre | Text |
Bibliographic information
| Statement of responsibility | Aris John Kare. |
|---|---|
| Note | Submitted to the Department of Bioengineering. |
| Thesis | Thesis Ph.D. Stanford University 2024. |
| Location | https://purl.stanford.edu/nd007yq0204 |
Access conditions
- Copyright
- © 2024 by Aris John Kare
- License
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
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