ENH tighten up the mouse discussion

tex/references.bib

@@ -2544,6 +2544,45 @@ CONCLUSIONS: We developed a simplified, semi-closed system for the initial selec
   revised         = {2008-07-28},
 }
 
+@Article{Lozza2008,
+  author    = {Laura Lozza and Laura Rivino and Greta Guarda and David Jarrossay and Andrea Rinaldi and Francesco Bertoni and Federica Sallusto and Antonio Lanzavecchia and Jens Geginat},
+  journal   = {European Journal of Immunology},
+  title     = {The strength of T cell stimulation determines {IL}-7 responsiveness, secondary expansion, and lineage commitment of primed human {CD}4+{IL}-7Rhi T cells},
+  year      = {2008},
+  month     = {jan},
+  number    = {1},
+  pages     = {30--39},
+  volume    = {38},
+  doi       = {10.1002/eji.200737852},
+  publisher = {Wiley},
+}
+
+@Article{Lanzavecchia2005,
+  author    = {Antonio Lanzavecchia and Federica Sallusto},
+  journal   = {Current Opinion in Immunology},
+  title     = {Understanding the generation and function of memory T cell subsets},
+  year      = {2005},
+  month     = {jun},
+  number    = {3},
+  pages     = {326--332},
+  volume    = {17},
+  doi       = {10.1016/j.coi.2005.04.010},
+  publisher = {Elsevier {BV}},
+}
+
+@Article{Corse2011,
+  author    = {Emily Corse and Rachel A. Gottschalk and James P. Allison},
+  journal   = {The Journal of Immunology},
+  title     = {Strength of {TCR}{\textendash}Peptide/{MHC} Interactions and In Vivo T Cell Responses},
+  year      = {2011},
+  month     = {apr},
+  number    = {9},
+  pages     = {5039--5045},
+  volume    = {186},
+  doi       = {10.4049/jimmunol.1003650},
+  publisher = {The American Association of Immunologists},
+}
+
 @Comment{jabref-meta: databaseType:bibtex;}
 
 @Comment{jabref-meta: grouping:

tex/thesis.tex

@@ -2465,6 +2465,9 @@ however, to our knowledge this is the first system that specifically drives
 naïve/memory and CD4+ T cell formation in a scalable, potentially
 bioreactor-compatible manufacturing process.
 
+% DISCUSSION assuage krish by showing that in the isotype control fig that IL2
+% doesn't activation T cells: https://www.jimmunol.org/content/jimmunol/191/12/5822.full.pdf
+
 Memory and naïve T cells have been shown to be important clinically. Compared to
 effectors, they have a higher proliferative capacity and are able to engraft for
 months; thus they are able to provide long-term immunity with smaller
@@ -4148,8 +4151,6 @@ other groups in regard to the final tumor burden.
 
 \section{discussion}
 
-% FIGURE add CD45RA to this to rule out one of the alternative possibilities
-% explaining this data
 \begin{figure*}[ht!]
   \begingroup
 
@@ -4163,7 +4164,8 @@ other groups in regard to the final tumor burden.
     \subcap{fig:mouse_summary_1}{the first mouse experiment} and 
     \subcap{fig:mouse_summary_2}{the second mouse experiment}. The y axis
     maximum is set to the maximum number of cells injected between both
-    experiments (\num{1.25e6}).
+    experiments (\num{1.25e6}). Note that the \gls{car} was quantified using a
+    separate panel than the rest of the markers.
   }
   \label{fig:mouse_summary}
 \end{figure*}
@@ -4180,32 +4182,32 @@ tumor burden was higher than DMS groups across all the total T cell doses tested
 here. More interestingly, when only CAR-expressing T cell doses between bead and
 DMS groups were compared, DMS group had significantly higher survival effects
 over similar or higher CAR expression T cell doses from bead group. All these
-results suggest that the higher proportion of memory T cells in DMS groups
-(compared to bead group) resulted in highly effective CAR-T cells that can
-efficiently kill tumor cells as recently reported in
-literature\cite{Fraietta2018, Sommermeyer2015}.
+results suggest that the T cells in DMS groups (compared to bead group) resulted
+in highly effective CAR-T cells that can efficiently kill tumor cells.
 
-% DISCUSSION cite a bunch of data saying memory and CD4 T cells are better in
-% mice
 When comparing the total number of T cells of different phenotypes, we observed
 that when comparing low-dose \gls{dms} group to the mid- bead groups (which had
-similar numbers of \gls{car} T cells), the number of \ptmem{} T cells injected
-was much lower in the \gls{dms} group (\cref{fig:mouse_summary_1}). This could
-mean several things. First, the \ptmem{} phenotype may have nothing to do with
-the results seen here, at least in this model. Second, the distribution of
-\gls{car} T cells across different subtypes of T cells was different between the
-\gls{dms} and bead groups (with possibly higher correlation of \gls{car}
-expression and the \ptmem{} phenotype). Third, the \ptmem{} phenotype may not be
-precise enough, and the functional `memory' phenotype is a subset of \ptmem{}
-which may be higher in the \gls{dms} group and explains the discrepancy between
-the two methods.
+similar numbers of \gls{car} T cells), the number of \ptmem{} (both with and
+without CD45RA) T cells injected was much lower in the \gls{dms} group
+(\cref{fig:mouse_summary_1}). This could mean several things. First, the
+\ptmem{} phenotype may have nothing to do with the results seen here, at least
+in this model. While this may have been the case in our hands, this would
+contradict previous evidence suggesting that \gls{tn} and \gls{tcm} cells work
+better in almost the same model (the only difference being Raji cells in place
+of Nalm-6 cells, both of which express CD19)\cite{Sommermeyer2015}. Second, the
+distribution of \gls{car} T cells across different subtypes of T cells was
+different between the \gls{dms} and bead groups (with possibly higher
+correlation of \gls{car} expression and the \ptmem{} phenotype). It is hard to
+assess this without strong assumptions as the \gls{car} was quantified using a
+separate flow panel relative to the other markers.
 
-% DISCUSSION cite why CD4 or CD8 matters in this model
 We can also make a similar observation for the number of \pth{} T cells injected
 (\cref{fig:mouse_summary_1}). In this case, either the \pth{} phenotype doesn't
 matter in this model (or the \ptk{} population matters much more), or the
 distribution of \gls{car} is different between CD4 and CD8 T cells in a manner
-that favors the \gls{dms} group.
+that favors the \gls{dms} group. While in a glioblastoma model and not a B-cell
+\gls{all} model, previous groups have shown that \pthp{} T cells are important
+for response\cite{Wang2018}.
 
 When testing \gls{car} T cells at earlier timepoints relative to day 14 as used
 in the first \invivo{} experiment, we noted that none of the \gls{car}
@@ -4221,10 +4223,11 @@ to perform better at day 6 as it held off the tumor longer, and also slowed the
 tumor progression relative to the bead group at day 14
 (\cref{fig:mouse_timecourse_ivis_plots}).
 
-Taken together, these data suggest that on average, the \gls{dms} platform
-produces T cells that have an advantage \invivo{} over beads. While we may not
-know the exact mechanism, our data suggests that the responses are
-unsurprisingly influenced by the \ptcarp{} of the final product.
+Taken together, these data suggest that the \gls{dms} platform produces T cells
+that have an advantage \invivo{} over beads. While we may not know the exact
+mechanism, our data suggests that the responses are unsurprisingly influenced by
+the \ptcarp{} of the final product. Followup experiments would need to be
+performed to determine the precise phenotype responsible for these responses.
 
 \chapter{conclusions and future work}\label{conclusions}
 
@@ -4287,13 +4290,13 @@ to control and optimize the \gls{dms} system. We determined that altering the
 \gls{dms} concentration temporally has profound effects on the phenotype and
 expansion rate. This agrees with other data we obtained in \cref{aim2a} and with
 what others have generally reported about signal strength and T cell
-differentiation\cite{Gattinoni2012}. We did not find any mechanistic
-relationship between either integrin signaling or \gls{il15} signaling. In the
-case of the former, it may be more likely that the \glspl{dms} surfaces are
-saturated to the point of sterically hindering any integrin interactions with
-the collagen surface. In the case of \gls{il15} more experiments likely need to
-be done in order to plausibly rule out this mechanism and/or determine if it is
-involved at all.
+differentiation\cite{Gattinoni2012, Lozza2008, Lanzavecchia2005, Corse2011}. We
+did not find any mechanistic relationship between either integrin signaling or
+\gls{il15} signaling. In the case of the former, it may be more likely that the
+\glspl{dms} surfaces are saturated to the point of sterically hindering any
+integrin interactions with the collagen surface. In the case of \gls{il15} more
+experiments likely need to be done in order to plausibly rule out this mechanism
+and/or determine if it is involved at all.
 
 % TODO make this tighter and cite paper showing that this makes at least some
 % sense