From ce1beeb54a083bd5f4f97904c571ad8744d04fd8 Mon Sep 17 00:00:00 2001 From: ndwarshuis Date: Mon, 2 Aug 2021 17:25:12 -0400 Subject: [PATCH] ENH spruce up the T cell activation section --- tex/references.bib | 34 ++++++++++++++ tex/thesis.tex | 109 +++++++++++++++++++++++++++------------------ 2 files changed, 100 insertions(+), 43 deletions(-) diff --git a/tex/references.bib b/tex/references.bib index 96d17dc..d1721b7 100644 --- a/tex/references.bib +++ b/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: diff --git a/tex/thesis.tex b/tex/thesis.tex index f28b3ea..51d185c 100644 --- a/tex/thesis.tex +++ b/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