bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 2712: Establishing the early genetic progression of cancers with unobtainable premalignant disease
Authors: Leshchiner Ignaty , Mroz Edmund A. , Cha Justin , Rosebrock Daniel , Spiro Oliver , Bonilla-Velez Juliana , Faquin William , Lefranc-Torres Armida , Lin Derrick , Michaud William , Getz Gad , Rocco James W. 
Published: June 2022

Abstract
Premalignant tissue samples collected at different timepoints along the path to invasive tumors have been used to establish the typical order of somatic genetic events in several cancer types. For many other cancer types, however, precancer tissue is unobtainable, leaving the genetic progression unknown. Here, we demonstrate an approach that can reconstruct progression histories for such cancers from exome sequencing of primary tumors. We validated our recent computational method, PhylogicNDT, on classic, HPV-negative head and neck squamous cell carcinoma (HNSCC), recapitulating the previous experimentally determined sequence of genetic events that occur during progression. We uncovered progression of HPV-positive HNSCC tumors, which lack premalignant tissue, identifying subtype specific early drivers. We associated the timing of major changes in ploidy with the development of intra-tumor genetic heterogeneity and shorter overall survival. In cancers with unobtainable premalignant tissue, our approach can fill the knowledge gap about early progression, providing the basis for development of experimental models and methods for early detection, interception, and prognostication.
Citation Format: Ignaty Leshchiner, Edmund A. Mroz, Justin Cha, Daniel Rosebrock, Oliver Spiro, Juliana Bonilla-Velez, William Faquin, Armida Lefranc-Torres, Derrick Lin, William Michaud, Gad Getz, James W. Rocco. Establishing the early genetic progression of cancers with unobtainable premalignant disease [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2712.
Abstract 2731: Longitudinally modeling anti-neoantigen immunity under paradigms of immunodominance
Authors: Qi Tim , Vincent Benjamin , Cao Yanguang 
Published: June 2022

Abstract
Neoantigen clonal architecture is known to influence the efficacy of immunotherapy. The immunodominance of clonal neoantigens over a canvas of heterogeneous subclonal neoantigens is particularly challenging to recapitulate in experimental models. We developed a computational model of neoantigen evolution that longitudinally tracks the “presentome” - that is, a cell’s aggregate neoantigen repertoire and HLA status - of simulated non-small cell lung cancer (NSCLC) prior to and during treatment with checkpoint blockade. Using neoantigen immunogenicity parameters from published reports, we first recapitulated the presentome of early-stage NSCLC. Upon simulating checkpoint blockade treatment of advanced NSCLC, we found salient correlates and consequences of response, including a profound clonal collapse among completely responding tumors. Our work could be adapted to longitudinally model the neoantigen architecture of other cancers and modalities of immunotherapy, ultimately informing cognizant strategies for future therapeutic development.
Citation Format: Tim Qi, Benjamin Vincent, Yanguang Cao. Longitudinally modeling anti-neoantigen immunity under paradigms of immunodominance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2731.
Abstract 2755: Transcriptomic changes experienced by activated and expanded NK cells for their use in the treatment of hematological malignancies
Authors: Reina-Ortiz Chantal , Alonso Pilar Mozas , Cebollada Alberto , Ovelleiro David , Bernal Luis Alberto Anel 
Published: June 2022

Abstract
Natural Killer (NK) cells have shown great promise as a viable cell-based cancer immunotherapy. We have developed a protocol that produces expanded and highly activated NK (eNK) cells from healthy human donors that have been shown to be effective alone and in combination with monoclonal antibodies in a variety of hematological malignancies. The eNK cells showed a dramatic increase in cytolytic capacity after their expansion and activation using IL-2, IL-15, and 721.221 feeder cells. In order to elucidate the underlying mechanisms behind the changes, mRNAseq and miRNA arrays were performed on mRNA and miRNA samples, respectively, extracted from several NK expansions, taken at Day 0 (before activation) and Day 20 (after activation and expansion). Bioinformatic analysis was performed to identify differential gene expression changes and their downstream effects. Based on the genes with greatest differential expression, we quantified their corresponding proteins using flow cytometry, western blots, and ELISAs. Results reveal several discrete changes in the transcriptome that are reflected in changes in protein expression levels within the eNK cells. We conclude that the increased cytolytic capacity of eNK cells is due to the synergistic effect of variations in different genes responsible for target recognition, effector function, cell cycle progression and cell survival. These data can be used in the future to produce better eNK cells as treatment for hematological malignancies.
Citation Format: Chantal Reina-Ortiz, Pilar Mozas Alonso, Alberto Cebollada, David Ovelleiro, Luis Alberto Anel Bernal. Transcriptomic changes experienced by activated and expanded NK cells for their use in the treatment of hematological malignancies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2755.
Abstract 2768: Whole-slide multispectral imaging reveals the immune subtypes of melanoma associated with the tumor microenvironment
Authors: Patel Bhavika , Allen Stephanie , Boldt Brittney , Mammadova Najiba , Haggerty Agnes , Mehra Navi 
Published: June 2022

Abstract
Immunotherapy and precision medicine are rapidly developing approaches to cancer therapy. Biomarkers that detect the tumor and tumor microenvironment allow for the development of strategies that accelerate the advancement of treatments to enhance a patient’s immune system. Akoya’s MOTiF™ PD-1/PD-L1 Auto Melanoma Kit is a validated, multiplex immunoassay enabling detection of the 6 most clinically relevant immuno-oncology and spatial biomarkers: FoxP3, PD-L1, Sox10/S100, PD-1, CD8 and CD68. In this study, the MOTiF™ PD-1/PD-L1 panel was used to analyze the tumor microenvironment and specifically assess immune phenotypes within melanoma samples from 3 patients. This study demonstrates a fully optimized and end-to-end workflow solution for biomarker discovery in melanoma. We demonstrate the utility of Akoya’s MOTiF™ PD-1/PD-L1 Melanoma panel kit in studying the cellular diversity while retaining spatial context. Stained slides were analyzed using the InForm® and PhenoptrReports image analysis platforms to identify phenotypes and better understand spatial relationships between cell phenotypes. The MOTiF™ PD-1/PD-L1 panel kit provides reproducibility across different patient samples. This data provides insight into the innate and adaptive immune landscape for targeted design of new immunotherapies as well as improved efficacy and reduced toxicity in the treatment of melanoma.
Citation Format: Bhavika Patel, Stephanie Allen, Brittney Boldt, Najiba Mammadova, Agnes Haggerty, Navi Mehra. Whole-slide multispectral imaging reveals the immune subtypes of melanoma associated with the tumor microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2768.
Abstract 2798: A multi-biomarker panel of nuclear transport proteins with potential as novel secreted cancer biomarkers
Authors: van der Watt Pauline , Okpara Michael , Wishart Andrew , Parker Iqbal , Soares Nelson , Blackburn Jonathan , Leaner Virna D. 
Published: June 2022

Abstract
Members of the nuclear transport protein family have been identified to have increased expression in many cancer types, with some being investigated as anticancer therapeutic targets. Recently, individual nuclear transport proteins have been reported to be secreted by cancer cells and found in the serum of cancer patients. In this study we investigated a multi-marker panel of nuclear transport proteins for their potential as diagnostic markers for cancer using cervical and oesophageal cancer as disease models. Mass spectrometry identified ten nuclear transport proteins in the secretome and exosomes of cultured cancer cells which was confirmed by western blot analysis showing increased secreted levels in cancer cells compared to normal. The presence of multiple nuclear transport proteins was confirmed in patient serum using ELISA assays which revealed significantly increased levels of KPNβ1, CRM1, CAS, IPO5 and TNPO1 in cervical and oesophageal cancer patient serum compared to non-cancer controls. Significantly elevated KPNα2 and RAN levels were also identified in oesophageal cancer serum samples. Logistics regression analyses revealed IPO5 and TNPO1 to be the best performing individual candidate biomarkers in discriminating between cancer cases and controls. The combination of KPNβ1, CRM1, KPNα2, CAS, RAN, IPO5 and TNPO1 as a multi-marker panel of biomarkers had the highest diagnostic capacity with an area under the curve (AUC) of 0.944 and 0.963, for cervical cancer and oesophageal cancer, and sensitivity of 92.5% at 86.8% specificity and 95.3% sensitivity at 87.5% specificity, respectively. These results suggest that nuclear transport proteins have potential as diagnostic biomarkers for cervical and oesophageal cancers, with a multi-panel protein combination being the best predictor.
Citation Format: Pauline van der Watt, Michael Okpara, Andrew Wishart, Iqbal Parker, Nelson Soares, Jonathan Blackburn, Virna D. Leaner. A multi-biomarker panel of nuclear transport proteins with potential as novel secreted cancer biomarkers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2798.
Abstract 2817: GD2 CAR-T cells engineered using retroviral transduction or CRISPR editing exhibit strong cytolytic potency against glioma stem cells
Authors: Chvatal Stacie A. , Logun Meghan T. , Sullivan Denise D. , Hayes Heather B. , Millard Daniel , Katie Mueller P. , Piscopo Nicole J. , Das Amritava , Saha Kris , Brat Daniel J. , Karumbaiah Lohitash 
Published: June 2022

Abstract
Glioblastoma (GBM) is an aggressive brain cancer without effective treatments. CAR-T cells targeted to tumor-associated antigens offer promise for treating GBM. Here, we used cellular impedance assays to compare the cytolytic potency and kinetics of conventional viral vs non-viral CRISPR engineered GD2 CAR-T cells against glioma stem cells (GSC), a subpopulation of glioblastoma cells.
Patient-derived N08 GSCs were plated at 50k cells/well on 96-well plates, and impedance was continuously monitored on the Maestro Z impedance platform (Axion BioSystems). GD2 CAR-T cells were engineered using either retroviral transduction (RV) or non-viral CRISPR editing (NV). At 48 hours, GD2 CAR-T cells were added at Effector:Target ratios of 0.1:1, 1:1, and 10:1. Comparisons were made to mCherry T cells (mCh) as a control. Impedance and cytolysis were monitored up to 7 days.
RV and NV GD2 CAR-T cells caused decreases in impedance consistent with T cell-mediated lysis of GSCs, whereas mCh T cells induced little change. NV CAR-T cells exhibited faster killing kinetics compared to RV CAR-T cells. The time to 50% cytolysis (KT50) was significantly shorter for NV vs RV CAR-T cells at 1:1 and 10:1 E:T ratios.
Cytotoxic function was validated with flow cytometry and cytokine analysis at 7 days. All T cells exhibited chronic activation measured by CD69 and CD137 upregulation. Importantly, NV CAR-T cells exhibited less exhaustion, as measured by PD1 and LAG3 expression.
Both RV and NV GD2 CAR-T cells effectively cytolyzed GSCs, with NV CAR-T cells exhibiting more potent and efficient killing. The high potency, fast kinetics, and reduced exhaustion of NV CRISPR GD2 CAR-T cells offer great clinical promise for treating GBM.
Citation Format: Stacie A. Chvatal, Meghan T. Logun, Denise D. Sullivan, Heather B. Hayes, Daniel Millard, Mueller P. Katie, Nicole J. Piscopo, Amritava Das, Kris Saha, Daniel J. Brat, Lohitash Karumbaiah. GD2 CAR-T cells engineered using retroviral transduction or CRISPR editing exhibit strong cytolytic potency against glioma stem cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2817.
Abstract 2819: Suppression of NKG2A mediated inhibition in ex vivo expanded natural killer cells increases their cytotoxicity
Authors: Croom-Perez Tayler J. , Robles-Carrillo Liza D. , Dieffenthaller Thomas A. , Copik Alicja J. 
Published: June 2022

Abstract
In this study we propose to circumvent HLA-E/NKG2A mediated Natural Killer (NK) cell inhibition by suppression of NKG2A, to enhance cytotoxicity of ex vivo expanded NK cells. One mechanism employed by tumor cells to evade immunosurveillance is through induction of the surface expression of unconventional HLA ligands that agonize inhibitory receptors on immune cells. Specifically on some tumors, HLA-E is either expressed or its expression is known to be induced by IFNγ and is indicative of resistance to immunotherapy. HLA-E agonizes the CD94/NKG2A inhibitory complex on NK cells and some T cells to lessen their cytotoxicity, potentially decreasing the efficacy of cellular therapy with these immune cells. The CD94/NKG2A inhibitory complex is in balance with CD94/NKG2C stimulatory complex. HLA-E binds both of these complexes and the cytolytic activity of NK cells is influenced by the relative ratios of CD94 complexed to NKG2A or NKG2C. Thus, altering the ratio to increase NKG2C will increase NK cell cytotoxicity. In this study we show that NK cells ex vivo expanded with PM21-particle technology are highly cytotoxic and have elevated expression of NKG2A. These expanded NK cells also secrete high levels of IFNγ, inducing expression of HLA-E in tumor cells. To increase the cytotoxic potential of these ex vivo expanded NK cells, the potential to form CD94/NKG2A inhibitory complex was suppressed by either antibody blockade of NKG2A or deletion of the NKG2A gene by CRISPR/Cas9 editing. Cytotoxicity of NK cells against a lung cancer cell line stably expressing HLA-E were determined by kinetic live-cell imaging. Multiple NK cell:target (NK:T) ratios were used to show an increase in cytotoxicity over control NK cell conditions (alone or with isotype control) in the presence of NKG2A blocking antibodies with 39% increase observed at 1:10 NK:T ratio at 96h with anti-NKG2A and 56% increase with NKG2A knockout NK cells. These data suggest that blockade of CD94/NKG2A complex can improve cytotoxic activity of ex vivo expanded NK cells and could provide a promising effector population with the potential for enhanced therapeutic efficacy.
Citation Format: Tayler J. Croom-Perez, Liza D. Robles-Carrillo, Thomas A. Dieffenthaller, Alicja J. Copik. Suppression of NKG2A mediated inhibition in ex vivo expanded natural killer cells increases their cytotoxicity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2819.
Abstract 282: Breast cancer microphysiological systems based on human breast tissue
Authors: Lau Frank H. , Byrne C. Ethan , Brown Loren , Fontenot Jake , Tiongco Rafael P. , Gurrala Rakesh R. , Cuccia Jonathan , DiNardo Andrew , Burow Matthew , Martin Elizabeth C. 
Published: June 2022

Abstract
Breast cancer is a heterogeneous disease that accumulates signaling cues from cell intrinsic and extrinsic factors. Many of these cues are derived from the tumor microenvironment (TME). The TME modulates cellular proliferation, survival, and resistance to therapy in breast cancer. The TME is a bio-mechanical and biochemical reservoir for extracellular matrix and signaling factors (cytokines, growth factors, lipids, and hormones). In addition, the TME houses a diverse array of cell populations including adipocytes, vasculature, stem cells, immune cells, and cancer cells. Currently models do not reprpoduce the TME in vitro. The goal of this study was to develop a complex and dynamic micro-physiological 3D tumor model for pre-clinical studies using the native human breast environment. We developed a technique to maintain healthy human breast tissue (HBT) alive ex vivo for up to 8 weeks in the presence of breast cancer (BC) cells creating a breast cancer micro-physiological system (BC-MPS). In this study, we demonstrate alterations to lipid accumulation, matrix fiber remodeling, and cytokine profile in our BC-MPS system. We used RNA sequencing to detect breast cancer cell line signatures retained in the BC-MPS system. Results demonstrate retention of the breast cancer cell line transcriptome for a minimum of 14 days in vitro. In addition we identify alterations to genes associated with the TME, specifically the extracellular matrix and metabolism. Our novel model will allow for 1) real-time examination of BC-HBT interactions and 2) the isolation of BC-specific factors vs. patient-specific factors on the development and progression of BC.
Citation Format: Frank H. Lau, C. Ethan Byrne, Loren Brown, Jake Fontenot, Rafael P. Tiongco, Rakesh R. Gurrala, Jonathan Cuccia, Andrew DiNardo, Matthew Burow, Elizabeth C. Martin. Breast cancer microphysiological systems based on human breast tissue [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 282.
Abstract 2830: Multiplexed shRNAs targeting FAS and PTPN2 enhance CAR T persistence and anti-tumor efficacy
Authors: Gagnon John , Litterman Adam J. , Hall Jason A. , Polyak Dina , Zhou Stanley , Joshi Sahil , Takacsi-Nagy Oliver , Pope Hans , silva luisa , Singh brenal K. , Granja jeffrey M. , DeTomaso david , Aristil-Lepe Edgar , Tan Michelle , Galvin Brendan , Zheng Grace X. , Santoro Stephen , Cooper Aaron , Bezman Natalie , Haining W Nicholas 
Published: June 2022

Abstract
Cell therapies have shown limited efficacy in solid tumors, in part due to limitations in CAR T cell survival, expansion, and resistance to immunosuppressive pathways operating in the tumor microenvironment (TME). To overcome these hurdles, we screened a library of 171 pair-wise gene knockouts using CRISPR-Cas9 to identify gene pairs that confer greater proliferation and persistence with repetitive stimulation. Combined KO of FAS and PTPN2 led to a significant improvement in T cell effector function and proliferative capacity. FAS, the receptor for FASLG, is highly expressed on patient-derived T cells and has been shown to induce T cell apoptosis and limit T cell persistence in the TME. PTPN2 is a phosphatase, in which deletion increases T cell proliferation and cytotoxicity. To develop this clinically, we generated CAR T cells with a shRNA module capable of multiplexed knockdown of both FAS and PTPN2. The FAS/PTPN2 shRNA module protected T cells from FAS-mediated apoptosis and resulted in a marked increase in T cell expansion over the course of a repetitive stimulation assay. Consistent with these observations, RNAseq analysis revealed enhanced transcriptome-wide signatures of cell cycle and T cell effector function. Finally, in a tumor xenograft model, CAR T cells containing FAS/PTPN2 shRNA module demonstrated significantly improved tumor control in addition to increased cell numbers in circulation compared with CAR T cells expressing an irrelevant shRNA module.
The use of a multiplexed shRNA module is a powerful approach to improve T cell intrinsic functionality in cellular therapies, enabling: 1) tailored levels of inhibition of multiple key regulators of T cell biology with constitutive or antigen-gated expression, and 2) a method for genetic perturbations in T cells with reduced risk of toxicity or transformation compared with multiple DNA edits. The FAS/PTPN2 shRNA module described here will be tested as a component of AB-1015, an integrated circuit T cell therapy for solid tumors expressing ALPG and mesothelin.
Citation Format: John Gagnon, Adam J. Litterman, Jason A. Hall, Dina Polyak, Stanley Zhou, Sahil Joshi, Oliver Takacsi-Nagy, Hans Pope, luisa silva, brenal K. Singh, jeffrey M. Granja, david DeTomaso, Edgar Aristil-Lepe, Michelle Tan, Brendan Galvin, Grace X. Zheng, Stephen Santoro, Aaron Cooper, Natalie Bezman, W Nicholas Haining. Multiplexed shRNAs targeting FAS and PTPN2 enhance CAR T persistence and anti-tumor efficacy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2830.
Abstract 2843: Development of a translatable CD19 CAR-T platform for drug discovery
Authors: Kelsey Lauren , Self-Fordham Jezrom , Oswald Eva , Aylott Ilona , Rocca Daniel , Nunan Robert , Harris David , Schueler Julia , Jenkinson Rhiannon 
Published: June 2022

Abstract
Chimeric Antigen Receptor (CAR)-T cell therapy has achieved great success with specificity, efficacy, safety and ingenuity. CAR cell technology is advancing rapidly, with ever increasing capabilities for cancer treatment both with regard to tumor types and the CAR cell used (NK, Macrophage, T). To date, the most successful application remains the treatment of B cell lymphoma using CD19-specific CAR-T cells. Here we describe how to efficiently generate and expand a CD19 CAR-T cell and validate their efficacy in in-vitro and in-vivo studies. HLA-A*02:01+ CD3+ T-cells were transduced to express a clinically tested CD19-specific CAR to &gt;80% efficiency and reproducibly expanded to &gt;68 fold over a 19-day period. After sufficient expansion, cells were validated in in-vitro studies to assess their efficacy, utilizing a HLA-A*02:01+ patient derived xenograft (PDX) CD19+ cell line, alongside human cancer cell lines RAJI (CD19+) and K562 (CD19-). Flow cytometry analysis revealed the potent ability of CD19-CAR-T cells to kill CD19+ targets in a dose-dependent fashion. Highly specific killing at all E:T ratios was observed, with negligible off target killing identified. Supportive supernatant analysis showed highly elevated pro-inflammatory cytokine concentrations, identifying enhanced activation of CAR-T cells in the presence of CD19+ target cells only. After successful in-vitro batch testing for on-target killing CAR-T cells were released for in-vivo survival studies. Mice were inoculated with the same strains of CD19+ cells used during in-vitro validation to produce a tumor burdened model. CAR-T cells or non-transduced cells from the same donor were transfused and survival rates, tumor progression and tolerability assessments were observed over several weeks. Ex-vivo tissue and sera analysis further characterized these highly efficacious human CAR-T cells. These assays represent the capability to produce, expand and study CAR-effector cells both in-vitro and in-vivo. Careful consideration of human target cells enables the efficient translation of in-vitro efficacy data to whole organism mouse models.
Citation Format: Lauren Kelsey, Jezrom Self-Fordham, Eva Oswald, Ilona Aylott, Daniel Rocca, Robert Nunan, David Harris, Julia Schueler, Rhiannon Jenkinson. Development of a translatable CD19 CAR-T platform for drug discovery [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2843.