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Technology for Single Cell Protein Analysis in Immunology and Cancer Prognostics

Citation

Sutherland, Alexander Muir (2016) Technology for Single Cell Protein Analysis in Immunology and Cancer Prognostics. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/Z9PK0D3K. http://resolver.caltech.edu/CaltechTHESIS:10012015-132559997

Abstract

The first chapter of this thesis deals with automating data gathering for single cell microfluidic tests. The programs developed saved significant amounts of time with no loss in accuracy. The technology from this chapter was applied to experiments in both Chapters 4 and 5.

The second chapter describes the use of statistical learning to prognose if an anti-angiogenic drug (Bevacizumab) would successfully treat a glioblastoma multiforme tumor. This was conducted by first measuring protein levels from 92 blood samples using the DNA-encoded antibody library platform. This allowed the measure of 35 different proteins per sample, with comparable sensitivity to ELISA. Two statistical learning models were developed in order to predict whether the treatment would succeed. The first, logistic regression, predicted with 85% accuracy and an AUC of 0.901 using a five protein panel. These five proteins were statistically significant predictors and gave insight into the mechanism behind anti-angiogenic success/failure. The second model, an ensemble model of logistic regression, kNN, and random forest, predicted with a slightly higher accuracy of 87%.

The third chapter details the development of a photocleavable conjugate that multiplexed cell surface detection in microfluidic devices. The method successfully detected streptavidin on coated beads with 92% positive predictive rate. Furthermore, chambers with 0, 1, 2, and 3+ beads were statistically distinguishable. The method was then used to detect CD3 on Jurkat T cells, yielding a positive predictive rate of 49% and false positive rate of 0%.

The fourth chapter talks about the use of measuring T cell polyfunctionality in order to predict whether a patient will succeed an adoptive T cells transfer therapy. In 15 patients, we measured 10 proteins from individual T cells (~300 cells per patient). The polyfunctional strength index was calculated, which was then correlated with the patient's progress free survival (PFS) time. 52 other parameters measured in the single cell test were correlated with the PFS. No statistical correlator has been determined, however, and more data is necessary to reach a conclusion.

Finally, the fifth chapter talks about the interactions between T cells and how that affects their protein secretion. It was observed that T cells in direct contact selectively enhance their protein secretion, in some cases by over 5 fold. This occurred for Granzyme B, Perforin, CCL4, TNFa, and IFNg. IL- 10 was shown to decrease slightly upon contact. This phenomenon held true for T cells from all patients tested (n=8). Using single cell data, the theoretical protein secretion frequency was calculated for two cells and then compared to the observed rate of secretion for both two cells not in contact, and two cells in contact. In over 90% of cases, the theoretical protein secretion rate matched that of two cells not in contact.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:Diagnostics, Prognostics, Single Cell, Proteomics, Machine Learning, Microfluidics, DNA Encoded Antibody Library
Degree Grantor:California Institute of Technology
Division:Chemistry and Chemical Engineering
Major Option:Chemistry
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Heath, James R.
Thesis Committee:
  • Tirrell, David A. (chair)
  • Davis, Mark E.
  • Mazmanian, Sarkis K.
  • Heath, James R.
Defense Date:11 June 2015
Funders:
Funding AgencyGrant Number
National Institute of HealthJRH.PQ20-1-CAA.NIH170689
Katherine Ivy FoundationJRH.IVYA2014-1-UCLA.IVY002A
Record Number:CaltechTHESIS:10012015-132559997
Persistent URL:http://resolver.caltech.edu/CaltechTHESIS:10012015-132559997
DOI:10.7907/Z9PK0D3K
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:9185
Collection:CaltechTHESIS
Deposited By: Alexander Sutherland
Deposited On:04 Dec 2015 23:16
Last Modified:03 Feb 2016 22:41

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