Poliovirus Antigen Specific T cells (DRAFT)

Fig. 1: TSNE projection of cells analyzed using flow cytometry. Each subplot is red-blue colored by fluorescent intensity of different Antigens (rows) and separated columnwise by which treatment the sample was exposed to. From left to right: Positive Control, Negative Controls, Experimental Treatments. From top to bottom: CD137, CD69, OX40.

Introduction

Background

This research is exploratory in nature and aims to identify the presence, or absence, of Antigen (Ag.) Specific T cell response to Poliovirus (PV).

The primary Ags. examined were CD4+/CD137+OX40+ and CD8+/CD137+CD69+. The volunteers (N = 57) come from three different vaccine cohorts:

• IPV primed/IPV boosted (n = 29)

• IPV primed/OPV boosted (n = 12)

• OPV primed/OPV boosted (n = 16)

For flow cytometric analysis, PBMCs isolated from whole blood were collected prior to boosting vaccination (Day 0), and twice afterwards (Days 7 and 10 IPV/IPV, or Days 7 and 28 IPV/OPV + OPV/OPV). Each sample of PBMCs was divided and exposed to the following treatments:

• Unstimulated

• DMSO: Negative Control ($\times$ 3)

• PHA: Positive Control

• Non-Structural Stimulation⁴

• Structural Stimulation⁴

Further explanations of experimental design, methodology, analysis, and results related to this research can be found here[link].

Authors, Contributors, and Roles

• Jessica W. Crothers^1,2: Lead Author

• Julia P. Snyder^1,2,3: Design and Execution of Experiments

• Alba Grifoni⁴: Peptide Synthesis and Cytometric Analysis Methodology

• Marni Slavik¹: Contributing Author

• Patrick L. Harvey^1,2: Data Scientist

University of Vermont, Larner College of Medicine, Vaccine Testing Center, Translational Global Infectious Disease Research¹

University of Vermont, Larner College of Medicine, Department of Microbiology and Molecular Genetics²

Where is Julia?³

La Jolla Institue for Immunology, Center for Vaccine Innovation⁴

Organization

The repository is organized in the manner below:

├── code
│   ├── public_process_OMIQ.R
│   ├── functions
│   │   ├── func_01_pivot_prior.R
│   │   ├── func_02_calc_response.R
│   │   ├── func_03_calc_peak.R
│   │   ├── func_04_kinetics_plot.R
│   │   ├── func_05_pivot_barplot.R
│   │   ├── func_06_pivot_donut.R
│   │   ├── func_07_summary_barplot.R
│   │   ├── func_08_summary_donut.R
│   │   ├── func_09_epitope_barplot.R
│   │   ├── func_10_calc_AUC.R
│   │   ├── func_11_calc_SNA_delta.R
│   │   ├── func_12_SNA_AG_plot.R
│   │   ├── func_13_figure_2.R
│   │   ├── func_14_SNA_max_BS.R
│   │   ├── run_calculations.R
│   │   ├── run_visualizations.R
│   │   ├── stats_and_tables_MAIN.R
├── data
│   ├── input
│   │   ├── DM_dmLT.csv
│   │   ├── DM_nOPV.csv
│   │   ├── HVAD.csv
│   │   ├── nOPV_CBC_1.csv
│   │   ├── nOPV_CBC_2.csv
│   │   ├── nOPV_dmLT_ALL.csv
│   │   ├── nOPV_dmLT_FLOW.csv
│   │   ├── nOPV_SNA_RNA.csv
│   ├── output
├── figures
├── references

Requirements

This code was written using R version 4.4.0 with the following packages:

• DescTools version 0.99.54

• extrafont version 0.19

• hrbrthemes version 0.8.7

• munsell version 0.5.1

• rstudioapi version 0.16.0

• svglite version 2.1.3

• tidyverse version 2.0.0