ADD references to T cell background

tex/references.bib

@@ -1473,14 +1473,14 @@ CONCLUSIONS: We developed a simplified, semi-closed system for the initial selec
   issn            = {0732-0582},
   pages           = {365--400},
   volume          = {8},
-  nasa            = {90262672},
   chemicals       = {Integrins, Receptors, Very Late Antigen},
   citation-subset = {IM, S},
   completed       = {1990-07-02},
   country         = {United States},
   doi             = {10.1146/annurev.iy.08.040190.002053},
   issn-linking    = {0732-0582},
-  keywords        = {Animals; Cell Adhesion; Extracellular Matrix, physiology; Humans; Integrins, biosynthesis, physiology; Leukocytes, physiology; Receptors, Very Late Antigen, biosynthesis, physiology; Structure-Activity Relationship},
+  keywords        = {Animals; Cell Adhesion; Extracellular Matrix, physiology; Humans; Integrins, biosynthesis, physiology; Leukocytes, physiology; Receptors, Very Late Antigen, physiology; Structure-Activity Relationship},
+  nasa            = {90262672},
   nlm-id          = {8309206},
   owner           = {NLM},
   pmid            = {2188667},
@@ -1490,6 +1490,237 @@ CONCLUSIONS: We developed a simplified, semi-closed system for the initial selec
   revised         = {2021-01-02},
 }
 
+@Article{Wang2014,
+  author    = {Mingjun Wang and Bingnan Yin and Helen Y Wang and Rong-Fu Wang},
+  journal   = {Immunotherapy},
+  title     = {Current advances in T-cell-based cancer immunotherapy},
+  year      = {2014},
+  month     = {dec},
+  number    = {12},
+  pages     = {1265--1278},
+  volume    = {6},
+  doi       = {10.2217/imt.14.86},
+  publisher = {Future Medicine Ltd},
+}
+
+@Article{Foppen2015,
+  author    = {M.H. Geukes Foppen and M. Donia and I.M. Svane and J.B.A.G. Haanen},
+  journal   = {Molecular Oncology},
+  title     = {Tumor-infiltrating lymphocytes for the treatment of metastatic cancer},
+  year      = {2015},
+  month     = {oct},
+  number    = {10},
+  pages     = {1918--1935},
+  volume    = {9},
+  doi       = {10.1016/j.molonc.2015.10.018},
+  publisher = {Wiley},
+}
+
+@Article{Solinas2017,
+  author    = {Cinzia Solinas and Grazia Pusole and Laura Demurtas and Marco Puzzoni and Roberta Mascia and Gilberto Morgan and Riccardo Giampieri and Mario Scartozzi},
+  journal   = {Critical Reviews in Oncology/Hematology},
+  title     = {Tumor infiltrating lymphocytes in gastrointestinal tumors: Controversies and future clinical implications},
+  year      = {2017},
+  month     = {feb},
+  pages     = {106--116},
+  volume    = {110},
+  doi       = {10.1016/j.critrevonc.2016.11.016},
+  publisher = {Elsevier {BV}},
+}
+
+@Article{June2007,
+  author    = {Carl H. June},
+  journal   = {Journal of Clinical Investigation},
+  title     = {Adoptive T cell therapy for cancer in the clinic},
+  year      = {2007},
+  month     = {jun},
+  number    = {6},
+  pages     = {1466--1476},
+  volume    = {117},
+  doi       = {10.1172/jci32446},
+  publisher = {American Society for Clinical Investigation},
+}
+
+@Article{Santoiemma2015,
+  author    = {Phillip P Santoiemma and Daniel J Powell},
+  journal   = {Cancer Biology {\&} Therapy},
+  title     = {Tumor infiltrating lymphocytes in ovarian cancer},
+  year      = {2015},
+  month     = {apr},
+  number    = {6},
+  pages     = {807--820},
+  volume    = {16},
+  doi       = {10.1080/15384047.2015.1040960},
+  publisher = {Informa {UK} Limited},
+}
+
+@Article{Clark1989,
+  author    = {W. H. Clark and D. E. Elder and D. Guerry and L. E. Braitman and B. J. Trock and D. Schultz and M. Synnestvedt and A. C. Halpern},
+  journal   = {{JNCI} Journal of the National Cancer Institute},
+  title     = {Model Predicting Survival in Stage I Melanoma Based on Tumor Progression},
+  year      = {1989},
+  month     = {dec},
+  number    = {24},
+  pages     = {1893--1904},
+  volume    = {81},
+  doi       = {10.1093/jnci/81.24.1893},
+  publisher = {Oxford University Press ({OUP})},
+}
+
+@Article{Nishimura1999,
+  author          = {Nishimura, M. I. and Avichezer, D. and Custer, M. C. and Lee, C. S. and Chen, C. and Parkhurst, M. R. and Diamond, R. A. and Robbins, P. F. and Schwartzentruber, D. J. and Rosenberg, S. A.},
+  journal         = {Cancer research},
+  title           = {MHC class I-restricted recognition of a melanoma antigen by a human CD4+ tumor infiltrating lymphocyte.},
+  year            = {1999},
+  issn            = {0008-5472},
+  month           = dec,
+  pages           = {6230--6238},
+  volume          = {59},
+  abstract        = {It is generally considered that MHC class I-restricted antigens are recognized by CD8+ T cells, whereas MHC class II-restricted antigens are recognized by CD4+ T cells. In the present study, we report an MHC class I-restricted CD4+ T cell isolated from the tumor infiltrating lymphocytes (TILs) of a patient with metastatic melanoma. TIL 1383 I recognized HLA-A2+ melanoma cell lines but not autologous transformed B cells or fibroblasts. The antigen recognized by TIL 1383 I was tyrosinase, and the epitope was the 368-376 peptide. Antibody blocking assays confirmed that TIL 1383 I was MHC class I restricted, and the CD4 and CD8 coreceptors did not contribute significantly to antigen recognition. TIL 1383 I was weakly cytolytic and secreted cytokines in a pattern consistent with it being a Th1 cell. The avidity of TIL 1383 I for peptide pulsed targets is 10-100-fold lower than most melanoma-reactive CD8+ T cell clones. These CD4+ T cells may represent a relatively rare population of T cells that express a T-cell receptor capable of cross-reacting with an MHC class I/peptide complex with sufficient affinity to allow triggering in the absence of the CD4 coreceptor.},
+  chemicals       = {Antigens, Neoplasm, Cytokines, HLA-A2 Antigen, Histocompatibility Antigens Class I},
+  citation-subset = {IM},
+  completed       = {2000-01-24},
+  country         = {United States},
+  issn-linking    = {0008-5472},
+  issue           = {24},
+  keywords        = {Antigens, Neoplasm, immunology; CD4-Positive T-Lymphocytes, immunology; Cytokines, immunology; HLA-A2 Antigen, immunology; Histocompatibility Antigens Class I, immunology; Humans; Lymphocytes, Tumor-Infiltrating, immunology; Melanoma, blood, immunology; Tumor Cells, Cultured},
+  nlm-id          = {2984705R},
+  owner           = {NLM},
+  pmid            = {10626817},
+  pubmodel        = {Print},
+  pubstate        = {ppublish},
+  revised         = {2004-11-17},
+}
+
+@Article{Cordova2012,
+  author    = {Adriana Cordova and Francesca Toia and Carmela La Mendola and Valentina Orlando and Serena Meraviglia and Gaetana Rinaldi and Matilde Todaro and Giuseppe Cicero and Leonardo Zichichi and Paolo Li Donni and Nadia Caccamo and Giorgio Stassi and Francesco Dieli and Francesco Moschella},
+  journal   = {{PLoS} {ONE}},
+  title     = {Characterization of Human $\upgamma$$\updelta$ T Lymphocytes Infiltrating Primary Malignant Melanomas},
+  year      = {2012},
+  month     = {nov},
+  number    = {11},
+  pages     = {e49878},
+  volume    = {7},
+  doi       = {10.1371/journal.pone.0049878},
+  editor    = {Andrzej T. Slominski},
+  publisher = {Public Library of Science ({PLoS})},
+}
+
+@Article{Morgan2006,
+  author    = {R. A. Morgan and M. E. Dudley and J. R. Wunderlich and M. S. Hughes and J. C. Yang and R. M. Sherry and R. E. Royal and S. L. Topalian and U. S. Kammula and N. P. Restifo and Z. Zheng and A. Nahvi and C. R. de Vries and L. J. Rogers-Freezer and S. A. Mavroukakis and S. A. Rosenberg},
+  journal   = {Science},
+  title     = {Cancer Regression in Patients After Transfer of Genetically Engineered Lymphocytes},
+  year      = {2006},
+  month     = {oct},
+  number    = {5796},
+  pages     = {126--129},
+  volume    = {314},
+  doi       = {10.1126/science.1129003},
+  publisher = {American Association for the Advancement of Science ({AAAS})},
+}
+
+@Article{Ikeda2016,
+  author    = {Hiroaki Ikeda},
+  journal   = {International Immunology},
+  title     = {T-cell adoptive immunotherapy using tumor-infiltrating T cells and genetically engineered {TCR}-T cells: Table 1.},
+  year      = {2016},
+  month     = {apr},
+  number    = {7},
+  pages     = {349--353},
+  volume    = {28},
+  doi       = {10.1093/intimm/dxw022},
+  publisher = {Oxford University Press ({OUP})},
+}
+
+@Article{Gross1989,
+  author    = {G. Gross and T. Waks and Z. Eshhar},
+  journal   = {Proceedings of the National Academy of Sciences},
+  title     = {Expression of immunoglobulin-T-cell receptor chimeric molecules as functional receptors with antibody-type specificity.},
+  year      = {1989},
+  month     = {dec},
+  number    = {24},
+  pages     = {10024--10028},
+  volume    = {86},
+  doi       = {10.1073/pnas.86.24.10024},
+  publisher = {Proceedings of the National Academy of Sciences},
+}
+
+@Article{Brentjens2011,
+  author    = {Renier J. Brentjens and Isabelle Rivi{\`{e}}re and Jae H. Park and Marco L. Davila and Xiuyan Wang and Jolanta Stefanski and Clare Taylor and Raymond Yeh and Shirley Bartido and Oriana Borquez-Ojeda and Malgorzata Olszewska and Yvette Bernal and Hollie Pegram and Mark Przybylowski and Daniel Hollyman and Yelena Usachenko and Domenick Pirraglia and James Hosey and Elmer Santos and Elizabeth Halton and Peter Maslak and David Scheinberg and Joseph Jurcic and Mark Heaney and Glenn Heller and Mark Frattini and Michel Sadelain},
+  journal   = {Blood},
+  title     = {Safety and persistence of adoptively transferred autologous {CD}19-targeted T cells in patients with relapsed or chemotherapy refractory B-cell leukemias},
+  year      = {2011},
+  month     = {nov},
+  number    = {18},
+  pages     = {4817--4828},
+  volume    = {118},
+  doi       = {10.1182/blood-2011-04-348540},
+  publisher = {American Society of Hematology},
+}
+
+@Article{Kochenderfer2010,
+  author    = {James N. Kochenderfer and Wyndham H. Wilson and John E. Janik and Mark E. Dudley and Maryalice Stetler-Stevenson and Steven A. Feldman and Irina Maric and Mark Raffeld and Debbie-Ann N. Nathan and Brock J. Lanier and Richard A. Morgan and Steven A. Rosenberg},
+  journal   = {Blood},
+  title     = {Eradication of B-lineage cells and regression of lymphoma in a patient treated with autologous T cells genetically engineered to recognize {CD}19},
+  year      = {2010},
+  month     = {nov},
+  number    = {20},
+  pages     = {4099--4102},
+  volume    = {116},
+  doi       = {10.1182/blood-2010-04-281931},
+  publisher = {American Society of Hematology},
+}
+
+@Article{Maude2014,
+  author    = {Shannon L. Maude and Noelle Frey and Pamela A. Shaw and Richard Aplenc and David M. Barrett and Nancy J. Bunin and Anne Chew and Vanessa E. Gonzalez and Zhaohui Zheng and Simon F. Lacey and Yolanda D. Mahnke and Jan J. Melenhorst and Susan R. Rheingold and Angela Shen and David T. Teachey and Bruce L. Levine and Carl H. June and David L. Porter and Stephan A. Grupp},
+  journal   = {New England Journal of Medicine},
+  title     = {Chimeric Antigen Receptor T Cells for Sustained Remissions in Leukemia},
+  year      = {2014},
+  month     = {oct},
+  number    = {16},
+  pages     = {1507--1517},
+  volume    = {371},
+  doi       = {10.1056/nejmoa1407222},
+  publisher = {Massachusetts Medical Society},
+}
+
+@Article{Till2012,
+  author    = {Brian G. Till and Michael C. Jensen and Jinjuan Wang and Xiaojun Qian and Ajay K. Gopal and David G. Maloney and Catherine G. Lindgren and Yukang Lin and John M. Pagel and Lihua E. Budde and Andrew Raubitschek and Stephen J. Forman and Philip D. Greenberg and Stanley R. Riddell and Oliver W. Press},
+  journal   = {Blood},
+  title     = {{CD}20-specific adoptive immunotherapy for lymphoma using a chimeric antigen receptor with both {CD}28 and 4-1BB domains: pilot clinical trial results},
+  year      = {2012},
+  month     = {apr},
+  number    = {17},
+  pages     = {3940--3950},
+  volume    = {119},
+  doi       = {10.1182/blood-2011-10-387969},
+  publisher = {American Society of Hematology},
+}
+
+@Article{Till2008,
+  author    = {Brian G. Till and Michael C. Jensen and Jinjuan Wang and Eric Y. Chen and Brent L. Wood and Harvey A. Greisman and Xiaojun Qian and Scott E. James and Andrew Raubitschek and Stephen J. Forman and Ajay K. Gopal and John M. Pagel and Catherine G. Lindgren and Philip D. Greenberg and Stanley R. Riddell and Oliver W. Press},
+  journal   = {Blood},
+  title     = {Adoptive immunotherapy for indolent non-Hodgkin lymphoma and mantle cell lymphoma using genetically modified autologous {CD}20-specific T cells},
+  year      = {2008},
+  month     = {sep},
+  number    = {6},
+  pages     = {2261--2271},
+  volume    = {112},
+  doi       = {10.1182/blood-2007-12-128843},
+  publisher = {American Society of Hematology},
+}
+
+@Article{Guo2016,
+  author    = {Yelei Guo and Yao Wang and Weidong Han},
+  journal   = {Journal of Immunology Research},
+  title     = {Chimeric Antigen Receptor-Modified T Cells for Solid Tumors: Challenges and Prospects},
+  year      = {2016},
+  pages     = {1--11},
+  volume    = {2016},
+  doi       = {10.1155/2016/3850839},
+  publisher = {Hindawi Limited},
+}
+
 @Comment{jabref-meta: databaseType:bibtex;}
 
 @Comment{jabref-meta: grouping:

tex/thesis.tex

@@ -638,16 +638,17 @@ microcarrier for T cells, which are naturally non-adherent.
 % all numbers reflect the citation index in my review paper
 
 One of the first successful T cell-based immunotherapies against cancer is
-\glspl{til} [78]. This method works by taking tumor specimens from a patient,
+\glspl{til}\cite{Rosenberg2015}. This method works by taking tumor specimens
-allowing the tumor-reactive lymphocytes to expand \exvivo{}, and then
+from a patient, allowing the tumor-reactive lymphocytes to expand \exvivo{}, and
-administered back to the patient along with a high dose of \il{2} [44]. In
+then administered back to the patient along with a high dose of \il{2} [44]. In
 particular, \gls{til} therapy has shown robust results in treating melanoma [1],
 although \gls{til} have been found in other solid tumors such as
-gastointestinal, cervical, lung, and ovarian [78-83], and their presence is
+gastointestinal, cervical, lung, and ovarian\cite{Rosenberg2015, Wang2014,
-generally associate with favorable outcomes [84]. \glspl{til} are heterogenous
+  Foppen2015, Solinas2017, June2007, Santoiemma2015}, and their presence is
-cell mixtures and generally are comprised of CD3 T cells and $\upgamma\updelta$
+generally associate with favorable outcomes\cite{Clark1989}. \glspl{til} are
-T cells [85, 86]. To date, there are over 250 open clinical trials using
+heterogenous cell mixtures and generally are comprised of CD3 T cells and
-\glspl{til}.
+$\upgamma\updelta$ T cells\cite{Nishimura1999, Cordova2012}. To date, there are
+over 250 open clinical trials using \glspl{til}.
 
 Besides \gls{til}, the other broad class of T cell immunotherapies that has
 achieved great success in treating cancer in recent decades are gene-modified T
@@ -655,15 +656,15 @@ cells. Rather than expand T cells that are present natively (as is the case with
 \gls{til} therapy), gene-modified T cell therapies entail extracting T cells
 from either the cancer patient (autologous) or a healthy donor (allogeneic) and
 reprogramming them genetically to target a tumor antigen. In theory this offers
-much more flexibility.
+much more flexibility\cite{Rosenberg2015}.
 
 T cells with transduced \glspl{tcr} were first designed to overcome the
-limitations of \gls{til} [78,79]. In this case, T cells are transduced \exvivo{}
+limitations of \gls{til}\cite{Rosenberg2015, Wang2014}. In this case, T cells
-with a lentiviral vector to express a \gls{tcr} targeting a tumor antigen. T
+are transduced \exvivo{} with a lentiviral vector to express a \gls{tcr}
-cells transduced with \glspl{tcr} against MART-1 have shown robust results in
+targeting a tumor antigen. T cells transduced with \glspl{tcr} have shown robust
-melanoma patients [9], and analogous therapies targeted toward MY-ESO-1 have
+results in melanoma patients\cite{Robbins2011}, synovial
-shown robust results against synovial sarcoma [10]. To date, there are over 200
+sarcoma\cite{Morgan2006}, and others\cite{Ikeda2016}. To date, there are over
-clinical trials using T cells with transduced \glspl{tcr}.
+200 clinical trials using T cells with transduced \glspl{tcr}.
 
 While transduced \glspl{tcr} offer some flexibility in retargeting T cells
 toward relevant tumor antigens, they are still limited in that they can only
@@ -672,14 +673,15 @@ overcome this limitation by using a the heavy and light chains (scFv) from a
 \gls{mab} which can target any antigen recognizable by antibodies. \gls{car} T
 cells were first demonstrated in 1989, where the author swapped the
 antigen-recognition domains of a native \gls{tcr} with a that of a foreign
-\gls{tcr} [91]. Since then, this method has progressed to using an scFv with a
+\gls{tcr}\cite{Gross1989}. Since then, this method has progressed to using an
-CD3$\upzeta$ stimulatory domain along with the CD28, OX-40, or 4-1BB domains for
+scFv with a CD3$\upzeta$ stimulatory domain along with the CD28, OX-40, or 4-1BB
-costimulation. Since these can all be expressed with one protein sequence,
+domains for costimulation. Since these can all be expressed with one protein
-\gls{car} T cells are relatively simple to produce and require only a single
+sequence, \gls{car} T cells are relatively simple to produce and require only a
-genetic transduction step (usually a lentiviral vector) to reprogram a batch T
+single genetic transduction step (usually a lentiviral vector) to reprogram a
-cells \exvivo{} toward the desired antigen. \gls{car} T cells have primarily
+batch T cells \exvivo{} toward the desired antigen. \gls{car} T cells have
-found success in against CD19- and CD20-expressing tumors such as \gls{all} and
+primarily found success in against CD19- and CD20-expressing tumors such as
-\gls{cll} (eg B-cell malignancies).
+\gls{all} and \gls{cll} (eg B-cell malignancies)\cite{Kalos2011, Brentjens2011,
+  Kochenderfer2010, Maude2014, Till2012, Till2008}.
 
 % BACKGROUND where else have they been approved?
 Out of all the T cell therapies discussed thus far, \gls{car} T cells have
@@ -691,8 +693,8 @@ malignancies.
 \gls{car} T cells are under further exploration for use in many other tumors,
 including multiple myeloma, mesothelioma, pancreatic cancer, glioblastoma,
 neuroblastoma, and prostate cancer, breast cancer, non-small-cell lung cancer,
-and others [78,79,94,95]. To date, there are almost 1000 clinical trials using
+and others\cite{Rosenberg2015, Wang2014, Fesnak2016, Guo2016}. To date, there
-\gls{car} T cells.
+are almost 1000 clinical trials using \gls{car} T cells.
 
 % TODO there are other T cells like virus-specific T cells and gd T cells, not
 % that they matter...
@@ -1582,7 +1584,7 @@ the T cells receive downstream.
     All statistical tests where p-values are noted are given by two-tailed t
     tests.
   }
-  \label{fig:dms_flowchart}
+  \label{fig:dms_qc}
 \end{figure*}
 
 To answer this question, we first performed a \gls{doe} to understand the effect