ADD hypotheis

tex/thesis.tex

@@ -55,6 +55,9 @@
 \newacronym{dc}{DC}{dendritic cell}
 \newacronym{il2}{IL2}{interleukin 2}
 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% my commands
+
 \newcommand{\mytitle}{
   \Large{
     \textbf{
@@ -73,6 +76,15 @@
   \end{flushleft}
 }
 
+\newcommand{\invivo}{\textit{in vivo}}
+
+\newcommand{\invitro}{\textit{in vitro}}
+
+\newcommand{\exvivo}{\textit{ex vivo}}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% my environments
+
 \newenvironment{mytitlepage}{
   \begin{singlespace}
     \begin{center}
@@ -82,6 +94,9 @@
   \end{singlespace}
 }
 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% document
+
 \begin{document}
 
 \begin{titlepage}
@@ -191,7 +206,7 @@ Thank you to Lex Fridman and Devin Townsend for being awesome and inspirational.
 manufacturing large numbers of high quality cells remains challenging. Currently
 approved T cell expansion technologies involve anti-CD3 and CD28 \glspl{mab},
 usually mounted on magnetic beads. This method fails to recapitulate many key
-signals found \textit{in vivo} and is also heavily licensed by a few companies,
+signals found \invivo{} and is also heavily licensed by a few companies,
 limiting its long-term usefulness to manufactures and clinicians. Furthermore,
 we understand that highly potent T cells are generally less-differentiated
 subtypes such as central memory and stem memory T cells. Despite this
@@ -208,7 +223,7 @@ CD4+ T cells, and showing compatibility with existing \gls{car} transduction
 methods. In aim 2, we use \gls{doe} methodology to optimize the \gls{dms}
 platform, and develop a computational pipeline to identify and model the effect
 of measurable \glspl{cqa} and \glspl{cpp} on the final product. In aim 3, we
-demonstrate the effectiveness of the \gls{dms} platform \textit{in vivo}. This
+demonstrate the effectiveness of the \gls{dms} platform \invivo{}. This
 thesis lays the groundwork for a novel T cell expansion method which can be used
 in a clinical setting, and also provides a path toward optimizing for product
 quality in an industrial setting.
@@ -240,6 +255,8 @@ quality in an industrial setting.
 
 \chapter{introduction}
 
+\section*{overview}
+
 T cell-based immunotherapies have received great interest from clinicians and
 industry due to their potential to treat, and often cure, cancer and other
 diseases\cite{Fesnak2016,Rosenberg2015}. In 2017, Novartis and Kite Pharma
@@ -253,14 +270,14 @@ superparamagnetic, iron-based microbeads (Invitrogen Dynabead, Miltenyi MACS
 beads), on nanobeads (Miltenyi TransACT), or in soluble tetramers
 (Expamer)\cite{Roddie2019,Dwarshuis2017,Wang2016, Piscopo2017, Bashour2015}.
 These strategies overlook many of the signaling components present in the
-secondary lymphoid organs where T cells expand in vivo. Typically, T cells are
+secondary lymphoid organs where T cells expand \invivo{}. Typically, T cells are
 activated under close cell-cell contact, which allows for efficient
 autocrine/paracrine signaling via growth-stimulating cytokines such as
 \gls{il2}. Additionally, the lymphoid tissues are comprised of \gls{ecm}
 components such as collagen, which provide signals to upregulate proliferation,
 cytokine production, and pro-survival pathways\cite{Gendron2003, Ohtani2008,
   Boisvert2007, Ben-Horin2004}. We hypothesized that culture conditions that
-better mimic these in vivo expansion conditions of T cells, can significantly
+better mimic these \invivo{} expansion conditions of T cells, can significantly
 improve the quality and quantity of manufactured T cells and provide better
 control on the resulting T cell phenotype.
 
@@ -278,7 +295,7 @@ Matrigel\cite{Rio2018} or 3d-printed lattices\cite{Delalat2017}, ellipsoid
 beads\cite{meyer15_immun}, and \gls{mab}-conjugated \gls{pdms}
 beads\cite{Lambert2017} that respectively recapitulate the cellular membrane,
 large interfacial contact area, 3D-structure, or soft surfaces T cells normally
-experience in vivo. While these have been shown to provide superior expansion
+experience \invivo{}. While these have been shown to provide superior expansion
 compared to traditional microbeads, none of these methods has been able to show
 preferential expansion of functional naïve/memory and CD4 T cell populations.
 Generally, T cells with a lower differentiation state such as naïve and memory
@@ -316,18 +333,19 @@ only provide superior expansion, but consistently provide a higher frequency of
 naïve/memory and CD4 T cells (CCR7+CD62L+) across multiple donors. We also
 demonstrate functional cytotoxicity using a CD19 \gls{car} and a superior
 performance, even at a lower \gls{car} T cell dose, of \gls{dms}-expanded
-\gls{car}-T cells in vivo in a mouse xenograft model of human B cell \gls{all}.
+\gls{car}-T cells \invivo{} in a mouse xenograft model of human B cell \gls{all}.
 Our results indicate that \glspl{dms} provide a robust and scalable platform for
 manufacturing therapeutic T cells with higher naïve/memory phenotype and more
 balanced CD4+ T cell content.
 
-\section*{overview}
-
-Insert overview here
-
 \section*{hypothesis}
 
-Insert hypothesis here
+The hypothesis of this dissertation was that using \glspl{dms} created from
+off-the-shelf microcarriers and coated with activating \glspl{mab} would lead to
+higher quantity and quality T cells as compared to state-of-the-art bead-based
+expansion. The objective of this dissertation was to develop this platform, test
+its effectiveness both \invivo{} and \invivo{}, and develop computational
+pipelines that could be used in a manufacturing environment.
 
 \section*{specific aims}
 \subsection*{aim 1}