ENH spruce up the T cell activation section

tex/references.bib

@@ -2339,6 +2339,40 @@ CONCLUSIONS: We developed a simplified, semi-closed system for the initial selec
   publisher = {Springer Science and Business Media {LLC}},
 }
 
+@InCollection{Azuma2019,
+  author    = {Miyuki Azuma},
+  booktitle = {Co-signal Molecules in T Cell Activation},
+  publisher = {Springer Singapore},
+  title     = {Co-signal Molecules in T-Cell Activation},
+  year      = {2019},
+  pages     = {3--23},
+  doi       = {10.1007/978-981-32-9717-3_1},
+}
+
+@Article{Luckheeram2012,
+  author    = {Rishi Vishal Luckheeram and Rui Zhou and Asha Devi Verma and Bing Xia},
+  journal   = {Clinical and Developmental Immunology},
+  title     = {{CD}4+ T Cells: Differentiation and Functions},
+  year      = {2012},
+  pages     = {1--12},
+  volume    = {2012},
+  doi       = {10.1155/2012/925135},
+  publisher = {Hindawi Limited},
+}
+
+@Article{OConnor2012,
+  author    = {Roddy S. O'Connor and Xueli Hao and Keyue Shen and Keenan Bashour and Tatiana Akimova and Wayne W. Hancock and Lance C. Kam and Michael C. Milone},
+  journal   = {The Journal of Immunology},
+  title     = {Substrate Rigidity Regulates Human T Cell Activation and Proliferation},
+  year      = {2012},
+  month     = {jun},
+  number    = {3},
+  pages     = {1330--1339},
+  volume    = {189},
+  doi       = {10.4049/jimmunol.1102757},
+  publisher = {The American Association of Immunologists},
+}
+
 @Comment{jabref-meta: databaseType:bibtex;}
 
 @Comment{jabref-meta: grouping:

tex/thesis.tex

@@ -783,7 +783,7 @@ operator to load, feed, and harvest the cell product. Grex bioreactors have been
 using to grow \glspl{til}\cite{Jin2012} and virus-specific T
 cells\cite{Gerdemann2011}.
 
-\subsection{overview of T cell quality}
+\subsection{overview of T cell quality}\label{sec:background_quality}
 
 T cells are highly heterogeneous and can exist in a variety of states and
 subtypes, many of which can be measured (at least indirectly) though biomarkers
@@ -840,49 +840,74 @@ using retro- or lentiviral vectors as their means of gene-editing must be tested
 for replication competent vectors\cite{Wang2013} and for contamination via
 bacteria or other pathogens.
 
-\subsection*{current T cell manufacturing technologies}
+\subsection*{T cell activation}
 
-Despite these success of T cell therapies (especially \gls{car} T cell
-therapies) they are constrained by an expensive and difficult-to-scale
-manufacturing process\cite{Roddie2019, Dwarshuis2017}.
+% Despite these success of T cell therapies (especially \gls{car} T cell
+% therapies) they are constrained by an expensive and difficult-to-scale
+% manufacturing process\cite{Roddie2019, Dwarshuis2017}.
 
-Of critical concern, state-of-the-art manufacturing techniques focus only on
-Signal 1 and Signal 2-based activation via \acd{3} and \acd{28} \glspl{mab},
-typically presented on a microbead (Invitrogen Dynabead, Miltenyi MACS beads) or
-nanobead (Miltenyi TransACT), but also in soluble forms in the case of antibody
-tetramers (Expamer)\cite{Wang2016, Piscopo2017, Roddie2019, Bashour2015}. These
-strategies overlook many of the signaling components present in the secondary
-lymphoid organs where T cells normally expand. Typically, T cells are activated
-under close cell-cell contact via \glspl{apc} such as \glspl{dc}, which present
-peptide-\glspl{mhc} to T cells as well as a variety of other costimulatory
-signals. These close quarters allow for efficient autocrine/paracrine signaling
-among the expanding T cells, which secrete gls{il2} and other cytokines to
-assist their own growth.
+In order for T cells to be expanded \exvivo{} they must be activated with a
+stimulatory signal (Signal 1) and a costimulatory signal (Signal 2). \invivo{}
+Signal 1 is administered via the \gls{tcr} and the CD3 receptor when \glspl{apc}
+present a peptide via \gls{mhc} that the T cell in question is able to
+recognize. Signal 2 is administered via CD80 and CD86 which are also present on
+\glspl{apc} and is necessary to prevent the T cell from becoming anergic. While
+these two signal are the bare minimum to trigger a T cell to expand, there are
+many other potential signals present. T cells have many other costimulatory
+receptors such as OX40, 4-1BB and ICOS which are costimulatory along with CD28,
+and \glspl{apc} have corresponding ligands for these depending on the nature of
+the pathogen they have detected\cite{Azuma2019}. Furthermore, T cells exist in
+high cell density within the secondary lymphoid organs, which allows efficient
+cytokine cross-talk in an autocrine and paracrine manner. These cytokines are
+responsible for expansion (in the case of \il{2}) and subset differentiation (in
+the case of many others)\cite{Luckheeram2012}. By tuning the signal strength and
+duration of Signal 1, Signal 2, the various costimulatory signals, and the
+cytokine milieu, a variety of T cell phenotypes can be actualized.
 
-A variety of solutions have been proposed to make the T cell expansion process
-more physiological. One strategy is to use modified feeder cell cultures to
-provide activation signals similar to those of \glspl{dc}\cite{Forget2014}.
-While this has the theoretical capacity to mimic several key components of the
-lymph node, it is hard to reproduce on a large scale due to the complexity and
-inherent variability of using cell lines in a fully \gls{gmp}-compliant manner.
-Others have proposed biomaterials-based solutions to circumvent this problem,
-including lipid-coated microrods\cite{Cheung2018}, 3D-scaffolds via either
-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 \textit{in vivo}. While these have been shown to provide superior
-expansion compared to traditional microbeads, no method has been able to show
-preferential expansion of functional memory and CD4 T cell populations.
-Generally, T cells with a lower differentiation state such as memory cells have
-been shown to provide superior anti-tumor potency, presumably due to their
-higher potential to replicate, migrate, and engraft, leading to a long-term,
-durable response\cite{Xu2014, Gattinoni2012, Fraietta2018, Gattinoni2011}.
-Likewise, CD4 T cells are similarly important to anti-tumor potency due to their
-cytokine release properties and ability to resist exhaustion\cite{Wang2018,
-  Yang2017}, and no method exists to preferentially expand the CD4 population
-compared to state-of-the-art systems.
+\invitro{}, T cells can be activated in a number of ways but the simplest and
+most common is to use \glspl{mab} that cross-link the CD3 and CD28 receptors,
+which supply Signal 1 and Signal 2 without the need for antigen (which also
+means all T cells are activated and not just a few specific clones). Additional
+signals may be supplied in the form of cytokines (eg \il{2}, \il{7}, or \il{15})
+or feeder cells\cite{Forget2014}.
 
+As this is a critical unit operation in the manufacturing of T cell therapies, a
+number of commercial technologies exist to activate T cells\cite{Wang2016,
+  Piscopo2017, Roddie2019, Bashour2015}. The simplest is to use \acd{3} and
+\acd{28} \gls{mab} bound to a 2D surface such as a plate, and this can be
+ackomplished in a \gls{gmp} manner as soluble \gls{gmp}-grade \glspl{mab} are
+commericially available. A similar but distinct method along these lines is to
+use multivalent activators such as ImmunoCult (StemCell Technologies) or Expamer
+(Juno Therapeutics) which may have increased cross-linking capacity compared to
+traditional \glspl{mab}. Beyond soluble protein, \glspl{mab} against CD3 and
+CD28 can be mounted on magnetic microbeads (\SIrange{3}{5}{\um} in diameter)
+such as DynaBeads (Invitrogen) and MACSbeads (\miltenyi{}), which are easier to
+separate using magnetic washing plates. Magnetic nanobeads such as TransAct
+(\miltenyi{}) work by a similar principle except they can be removed via
+centrifugation rather than a magnetic washing plate. Cloudz (RnD Systems) are
+another bead-based T cell expansion which mounts \acd{3} and \acd{28}
+\glspl{mab} on alginate microspheres, which are not only easily degradable but
+are also softer, which can have a positive impact on T cell activation and
+phenotype\cite{Lambert2017, OConnor2012}.
+
+A problem with all of these commercial solutions is that they only focus on
+Signal 1 and Signal 2 and ignore the many other physiological cues present in
+the secondary lymphoid organs. A variety of novel T cell activation and
+expansion solutions have been proposed to overcome this. One strategy is to use
+modified feeder cell cultures to provide activation signals similar to those of
+\glspl{dc}\cite{Forget2014}. While this has the theoretical capacity to mimic
+several key components of the lymph node, it is hard to reproduce on a large
+scale due to the complexity and inherent variability of using cell lines in a
+fully \gls{gmp}-compliant manner. Others have proposed biomaterials-based
+solutions to circumvent this problem, including lipid-coated
+microrods\cite{Cheung2018}, 3D-scaffolds via either 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 \textit{in vivo}.
+While these are in theory much easier to produce and \gls{qc} compared to feeder
+cells, none have been demonstrated to demonstrably expand high quality T cells
+as outlined in \cref{sec:background_quality}.
 
 \subsection*{integrins and T cell signaling}
 
@@ -922,8 +947,6 @@ stimulated in the presence of collagen I\cite{Boisvert2007}.
 
 \subsection*{the role of IL15 in memory T cell proliferation}
 
-% get lots of sources from here: https://www.sciencedirect.com/science/article/pii/S0165247809002387
-
 \il{15} is a cytokine that is involved with the proliferation and homeostasis of
 memory T cells. Its role in the work of this dissertation is the subject of
 further exploration in \cref{aim2b}.
@@ -1000,7 +1023,7 @@ possible. While there are many types of \glspl{doe} depending on the nature
 of the parameters and the goal of the experimenter, they all share common
 principles:
 
-% BACKGROUND cite montgomery, because I feel like it
+% BACKGROUND cite wu hamada... because I feel like it
 \begin{description}
 \item [randomization --] The order in which the runs are performed should
   ideally be as random as possible. This is to mitigate against any confounding