From e329f072dbfc010fe006c89b6fddaf7f50fa4a12 Mon Sep 17 00:00:00 2001 From: ndwarshuis Date: Mon, 26 Jul 2021 13:50:51 -0400 Subject: [PATCH] ENH integrate tables and figs into aim 3 --- ...ng_input_cells.svg => mouse_dosing_qc.svg} | 0 ...nput_cells.svg => mouse_timecourse_qc.svg} | 0 tables/mouse_dose_car.tex | 4 +- tex/thesis.tex | 130 ++++++++++++++++-- 4 files changed, 123 insertions(+), 11 deletions(-) rename figures/{mouse_dosing_input_cells.svg => mouse_dosing_qc.svg} (100%) rename figures/{mouse_timecourse_input_cells.svg => mouse_timecourse_qc.svg} (100%) diff --git a/figures/mouse_dosing_input_cells.svg b/figures/mouse_dosing_qc.svg similarity index 100% rename from figures/mouse_dosing_input_cells.svg rename to figures/mouse_dosing_qc.svg diff --git a/figures/mouse_timecourse_input_cells.svg b/figures/mouse_timecourse_qc.svg similarity index 100% rename from figures/mouse_timecourse_input_cells.svg rename to figures/mouse_timecourse_qc.svg diff --git a/tables/mouse_dose_car.tex b/tables/mouse_dose_car.tex index 64c6e6f..63aa6e2 100644 --- a/tables/mouse_dose_car.tex +++ b/tables/mouse_dose_car.tex @@ -1,7 +1,7 @@ -\begin{tabular}{lcc} +\begin{tabular}{lccc} \\[-1.8ex]\hline \hline \\[-1.8ex] -\\[-1.8ex] & Dose & 1e6 T cells/mouse & 1e6 CAR T cells/mouse 1e6 (DMS) & CAR T cells/mouse (Bead) \\ +\\[-1.8ex] Dose & 1e6 T cells/mouse & 1e6 CAR T cells/mouse 1e6 (DMS) & CAR T cells/mouse (Bead) \\ \hline \\[-1.8ex] High & 1.25 & 0.855 & 0.315 \\ Medium & 0.8325 & 0.570 & 0.210 \\ diff --git a/tex/thesis.tex b/tex/thesis.tex index 89d007d..890b9e0 100644 --- a/tex/thesis.tex +++ b/tex/thesis.tex @@ -1603,18 +1603,130 @@ between survival groups. \subsection{DMS-expanded T cells show greater anti-tumor activity \invivo{} compared to beads} -% figure showing the experimental model and dosing strategy -% table for % CAR+ T cells injected into the mice -% figure for the mem and CAR+ percent injected into the mice -% figure showing IVIS images -% figure showing the surival curves +\begin{figure*}[ht!] + \begingroup + + \includegraphics{../figures/mouse_dosing_overview.png} + + \endgroup + \caption[Mouse Dosing Experimental Overview] + {Overview of \invivo{} experiment to test \gls{car} T cells expanded with + either \glspl{dms} at different doses. } + \label{fig:mouse_dosing_overview} +\end{figure*} + + +\begin{table}[!h] \centering + \caption{Results for \gls{car} T cell \invivo{} dose study} + \label{tab:mouse_dosing_results} + \input{../tables/mouse_dose_car.tex} +\end{table} + +% TODO put growth first in this figure +\begin{figure*}[ht!] + \begingroup + + \includegraphics{../figures/mouse_dosing_qc.png} + \phantomsubcaption\label{fig:mouse_dosing_qc_mem} + \phantomsubcaption\label{fig:mouse_dosing_qc_cd4} + \phantomsubcaption\label{fig:mouse_dosing_qc_growth} + + \endgroup + \caption[Mouse Dosing T cell Characteristics] + {Characteristics of T cells harvested at day 14 injected into NSG + mice at varying doses. + Fractions of T cell subtypes in the day 14 product including + \subcap{fig:mouse_dosing_qc_mem}{\ptmemp{}}. + \subcap{fig:mouse_dosing_qc_cd4}{\pthp{}}, and + \subcap{fig:mouse_dosing_qc_growth}{Fold change of T cells.} + } + \label{fig:mouse_dosing_qc} +\end{figure*} + +% TODO explain what statistical test was used here +\begin{figure*}[ht!] + \begingroup + + \includegraphics{../figures/mouse_dosing_ivis.png} + \phantomsubcaption\label{fig:mouse_dosing_ivis_images} + \phantomsubcaption\label{fig:mouse_dosing_ivis_plots} + \phantomsubcaption\label{fig:mouse_dosing_ivis_survival} + \phantomsubcaption\label{fig:mouse_dosing_ivis_survival_comp} + + \endgroup + \caption[Mouse Dosing IVIS and Survival Results] + {T cells expanded with \glspl{dms} confer greater anti-tumor potency \invivo{} + even at lower doses. + \subcap{fig:mouse_dosing_ivis_images}{IVIS images of Nalm-6 tumor-bearing + \gls{nsg} mice injected with varying doses of T cells} + \subcap{fig:mouse_dosing_ivis_plots}{Plots showing quantified photon counts + of the results from (\subref{fig:mouse_dosing_ivis_plots}).} + \subcap{fig:mouse_dosing_ivis_survival}{Survival plots of mice} + \subcap{fig:mouse_dosing_ivis_survival_comp}{Survival plots of mice showing + only those that received a comparable number of \gls{car} T cells.} + } + \label{fig:mouse_dosing_ivis} +\end{figure*} \subsection{Beads and DMSs perform similarly at earlier timepoints} -% figure showing the experimental model and dosing strategy -% figure for the mem and CAR+ percent injected into the mice -% figure showing IVIS images -% figure showing the photon plots per time +\begin{figure*}[ht!] + \begingroup + + \includegraphics{../figures/mouse_timecourse_overview.png} + + \endgroup + \caption[Mouse Timecourse Experimental Overview] + {Overview of \invivo{} experiment to test \gls{car} T cells using either + \glspl{dms} or bead harvested at varying timepoints. + } + \label{fig:mouse_timecourse_overview} +\end{figure*} + +\begin{figure*}[ht!] + \begingroup + + \includegraphics{../figures/mouse_timecourse_qc.png} + \phantomsubcaption\label{fig:mouse_timecourse_qc_growth} + \phantomsubcaption\label{fig:mouse_timecourse_qc_car} + \phantomsubcaption\label{fig:mouse_timecourse_qc_cd4} + \phantomsubcaption\label{fig:mouse_timecourse_qc_mem} + + \endgroup + \caption[Mouse Timecourse T cell Characteristics] + {Characteristics of T cells harvested at varying timepoints injected into NSG + mice. + \subcap{fig:mouse_timecourse_qc_growth}{Fold change of T cells (each + timepoint only includes the runs that were harvested at day 14).} + Fractions of T cell subtypes in the day 14 product including + % TODO refactor CAR+ percent into nice macro + \subcap{fig:mouse_timecourse_qc_car}{\gls{car}+~\si{\percent}}, + \subcap{fig:mouse_timecourse_qc_cd4}{\pthp{}}, and + \subcap{fig:mouse_timecourse_qc_mem}{\ptmemp{}}. + } + \label{fig:mouse_timecourse_qc} +\end{figure*} + +\begin{figure*}[ht!] + \begingroup + + \includegraphics{../figures/mouse_timecourse_ivis.png} + \phantomsubcaption\label{fig:mouse_timecourse_ivis_images} + \phantomsubcaption\label{fig:mouse_timecourse_ivis_plots} + + \endgroup + \caption[Mouse Timecourse IVIS Results] + {\glspl{dms} exhibit superior anti-tumor activity \invivo{} at day 14 compared + to beads but are similar to beads at lower timepoints. + \subcap{fig:mouse_timecourse_ivis_images}{IVIS images for day 6 to day 42 of + mice treated with varying doses of \gls{car} T cells grown with beads or + \glspl{dms}.} + \subcap{fig:mouse_timecourse_ivis_plots}{Quantified dotplots of the images + in (\subref{fig:mouse_timecourse_ivis_images}). Numbers beneath each dot + represent the number of mice at that timepoint.}, + } + \label{fig:mouse_timecourse_ivis} +\end{figure*} \section{discussion}