Date of Award

4-2023

Document Type

Thesis (Ph.D.)

Department or Program

Quantitative Biomedical Sciences

First Advisor

H. Robert Frost

Abstract

Single-cell RNA-sequencing (scRNA-seq) has provided a new frontier for the investigation of complex tissues. One ideal candidate for the utilization of this method is the tumor microenvironment (TME). The TME is often host to a complex set of cell populations and behaviors that can be highly influential for cancer inhibition or progression. This is especially true of the immune compartment of the TME: the presence of certain types of immune cells in the TME and their expression profiles can significantly affect cancer prognosis in some cases. By providing individual cell-level gene expression data, scRNA-seq can be highly informative for characterizing the cells present in the TME and investigating what mechanisms those cells are undergoing to either hurt or help tumor development. The use of this method is not without its limitations, however. The data from scRNA-seq can often suffer from high sparsity and noise and the protocol necessary to collect the data requires that vital information regarding cell formation and tissue architecture is largely lost. In response to this, we developed the three methods outlined in this thesis, collectively referred to as the C Menagerie. These methods serve to assist in the identification and characterization of immune cells in the TME with single-cell RNA-sequencing and other high resolution ‘omics technologies. The first method, Cell-typing using variance Adjusted Mahalanobis distances with Multi-Labeling (CAMML), performs cell-typing on scRNA-seq data by leveraging weighted sets of cell type-specific genes. The second method, CAMML with the Integration of Marker Proteins (ChIMP), builds upon this method but allows for the integration of cell surface marker information via cellular indexing of transcriptomes and epitopes (CITE-seq), allowing for higher specificity. Lastly, the third method, Cell type-specific Interaction Analysis using Doublets in scRNA-seq (CIcADA), utilizes CAMML and ChIMP, along with validation from Visium spatial transcriptomics (ST), to identify and analyze doublets potentially undergoing juxtacrine interactions. In total, the C Menagerie provides tools for identifying and assessing the immune compartment of the TME using scRNA-seq and, where available, additional, complementary ‘omics modalities.

Original Citation

Courtney Schiebout, H. Robert Frost. (2022). CAMML with the integration of marker proteins (ChIMP). Bioinformatics.

Courtney Schiebout, H. Robert Frost. (2022). CAMML: Multi-Label Immune Cell-Typing and Stemness Analysis for Single-Cell RNA-sequencing. Pacific Symposium on Biocomputing.

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