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1. Computational model of CAR T-cell immunotherapy dissects and predicts leukemia patient responses at remission, resistance, and relapse

   https://doi.org/10.1136/jitc-2022-005360  

   Liu, Lunan ; Ma, Chao ; Zhang, Zhuoyu ; Witkowski, Matthew T ; Aifantis, Iannis ; Ghassemi, Saba ; Chen, Weiqiang ( December 2022 , Journal for ImmunoTherapy of Cancer)

   Background Adaptive CD19-targeted chimeric antigen receptor (CAR) T-cell transfer has become a promising treatment for leukemia. Although patient responses vary across different clinical trials, reliable methods to dissect and predict patient responses to novel therapies are currently lacking. Recently, the depiction of patient responses has been achieved using in silico computational models, with prediction application being limited. Methods We established a computational model of CAR T-cell therapy to recapitulate key cellular mechanisms and dynamics during treatment with responses of continuous remission (CR), non-response (NR), and CD19-positive (CD19 + ) and CD19-negative (CD19 − ) relapse. Real-time CAR T-cell and tumor burden data of 209 patients were collected from clinical studies and standardized with unified units in bone marrow. Parameter estimation was conducted using the stochastic approximation expectation maximization algorithm for nonlinear mixed-effect modeling. Results We revealed critical determinants related to patient responses at remission, resistance, and relapse. For CR, NR, and CD19 + relapse, the overall functionality of CAR T-cell led to various outcomes, whereas loss of the CD19 + antigen and the bystander killing effect of CAR T-cells may partly explain the progression of CD19 − relapse. Furthermore, we predicted patient responses by combining the peak and accumulated valuesmore »of CAR T-cells or by inputting early-stage CAR T-cell dynamics. A clinical trial simulation using virtual patient cohorts generated based on real clinical patient datasets was conducted to further validate the prediction. Conclusions Our model dissected the mechanism behind distinct responses of leukemia to CAR T-cell therapy. This patient-based computational immuno-oncology model can predict late responses and may be informative in clinical treatment and management.« less
2. Integrating genome-wide CRISPR immune screen with multi-omic clinical data reveals distinct classes of tumor intrinsic immune regulators

   https://doi.org/10.1136/jitc-2020-001819  

   Hou, Jiakai ; Wang, Yunfei ; Shi, Leilei ; Chen, Yuan ; Xu, Chunyu ; Saeedi, Arash ; Pan, Ke ; Bohat, Ritu ; Egan, Nicholas A. ; McKenzie, Jodi A. ; et al ( February 2021 , Journal for ImmunoTherapy of Cancer)

   Background Despite approval of immunotherapy for a wide range of cancers, the majority of patients fail to respond to immunotherapy or relapse following initial response. These failures may be attributed to immunosuppressive mechanisms co-opted by tumor cells. However, it is challenging to use conventional methods to systematically evaluate the potential of tumor intrinsic factors to act as immune regulators in patients with cancer. Methods To identify immunosuppressive mechanisms in non-responders to cancer immunotherapy in an unbiased manner, we performed genome-wide CRISPR immune screens and integrated our results with multi-omics clinical data to evaluate the role of tumor intrinsic factors in regulating two rate-limiting steps of cancer immunotherapy, namely, T cell tumor infiltration and T cell-mediated tumor killing. Results Our studies revealed two distinct types of immune resistance regulators and demonstrated their potential as therapeutic targets to improve the efficacy of immunotherapy. Among them, PRMT1 and RIPK1 were identified as a dual immune resistance regulator and a cytotoxicity resistance regulator, respectively. Although the magnitude varied between different types of immunotherapy, genetically targeting PRMT1 and RIPK1 sensitized tumors to T-cell killing and anti-PD-1/OX40 treatment. Interestingly, a RIPK1-specific inhibitor enhanced the antitumor activity of T cell-based and anti-OX40 therapy, despite limited impact onmore »T cell tumor infiltration. Conclusions Collectively, the data provide a rich resource of novel targets for rational immuno-oncology combinations.« less
3. Optimizing Cytotoxic T Cell Growth in a Centrifugal Bioreactor through Kinetic Growth Models

   Kitana Kaiphanliam, Brenden Fraser-Hevlin ( November 2021 , Annual meeting American Institute of Chemical Engineers)

   Cancer is the second leading cause of death globally and remains a significant issue in medicine. Immunotherapy treatments such as Chimeric Antigen Receptor T cell (CAR-T) therapies are becoming a more promising option because of their effectiveness in killing cancer cells without harming healthy tissue in the body. CAR-T therapies, however, are inaccessible to many due to the high cost—a result of inefficient cell expansion and manufacturing methods. To address this issue, we have developed the Centrifugal Fluidized Expansion (CentriFLEX) bioreactor that balances centrifugal and fluid forces, allowing the system to operate in perfusion and maintain a high cell density. Shown in past applications for similar cell types, the CentriFLEX can expand cultures up to 2.1 billion cells in an 11.4 mL chamber over the course of one week. Recently, we have used this system to expand bovine T cells as part of a collaboration with the College of Veterinary Medicine at Washington State University. Through the project, we conducted kinetic studies to model substrate consumption and metabolite production of bovine T cells and have enhanced the bioreactor design by making it more compact to fit entirely within a biosafety cabinet— mitigating contamination concerns. Current efforts have been spent determiningmore »the remaining parameters for the kinetic models and using such models to understand how the cells grow over time and in the space of a high-population density chamber. In this presentation, we will share how we use growth models that are based on a series of kinetic studies to predict substrate and metabolite levels over time in the bioreactor, allowing us to alter feed and dosing rates of medium and nutrients to maintain cell growth at the maximum specific growth rate.« less
4. Quantifying the efficacy of checkpoint inhibitors on CD8+ cytotoxic T cells for immunotherapeutic applications via single-cell interaction

   https://doi.org/10.1038/s41419-020-03173-7  

   Sullivan, Matthew Ryan ; Ugolini, Giovanni Stefano ; Sarkar, Saheli ; Kang, Wenjing ; Smith, Evan Carlton ; Mckenney, Seamus ; Konry, Tania ( November 2020 , Cell Death & Disease)

   The inhibition of the PD1/PDL1 pathway has led to remarkable clinical success for cancer treatment in some patients. Many, however, exhibit little to no response to this treatment. To increase the efficacy of PD1 inhibition, additional checkpoint inhibitors are being explored as combination therapy options. TSR-042 and TSR-033 are novel antibodies for the inhibition of the PD1 and LAG3 pathways, respectively, and are intended for combination therapy. Here, we explore the effect on cellular interactions of TSR-042 and TSR-033 alone and in combination at the single-cell level. Utilizing our droplet microfluidic platform, we use time-lapse microscopy to observe the effects of these antibodies on calcium flux in CD8⁺T cells upon antigen presentation, as well as their effect on the cytotoxic potential of CD8⁺T cells on human breast cancer cells. This platform allowed us to investigate the interactions between these treatments and their impacts on T-cell activity in greater detail than previously applied in vitro tests. The novel parameters we were able to observe included effects on the exact time to target cell killing, contact times, and potential for serial-killing by CD8⁺T cells. We found that inhibition of LAG3 with TSR-033 resulted in a significant increase in calcium fluctuations ofmore »CD8⁺T cells in contact with dendritic cells. We also found that the combination of TSR-042 and TSR-033 appears to synergistically increase tumor cell killing and the single-cell level. This study provides a novel single-cell-based assessment of the impact these checkpoint inhibitors have on cellular interactions with CD8⁺T cells.

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5. CAR T-cells that target acute B-lineage leukemia irrespective of CD19 expression

   https://doi.org/10.1038/s41375-020-0792-2  

   Fousek, Kristen ; Watanabe, Junji ; Joseph, Sujith K. ; George, Ann ; An, Xingyue ; Byrd, Tiara T. ; Morris, Jessica S. ; Luong, Annie ; Martínez-Paniagua, Melisa A. ; Sanber, Khaled ; et al ( March 2020 , Leukemia)

   Chimeric antigen receptor (CAR) T-cells targeting CD19 demonstrate remarkable efficacy in treating B-lineage acute lymphoblastic leukemia (BL-ALL), yet up to 39% of treated patients relapse with CD19(−) disease. We report that CD19(−) escape is associated with downregulation, but preservation, of targetable expression of CD20 and CD22. Accordingly, we reasoned that broadening the spectrum of CD19CAR T-cells to include both CD20 and CD22 would enable them to target CD19(−) escape BL-ALL while preserving their upfront efficacy. We created a CD19/20/22-targeting CAR T-cell by coexpressing individual CAR molecules on a single T-cell using one tricistronic transgene. CD19/20/22CAR T-cells killed CD19(−) blasts from patients who relapsed after CD19CAR T-cell therapy and CRISPR/Cas9 CD19 knockout primary BL-ALL both in vitro and in an animal model, while CD19CAR T-cells were ineffective. At the subcellular level, CD19/20/22CAR T-cells formed dense immune synapses with target cells that mediated effective cytolytic complex formation, were efficient serial killers in single-cell tracking studies, and were as efficacious as CD19CAR T-cells against primary CD19(+) disease. In conclusion, independent of CD19 expression, CD19/20/22CAR T-cells could be used as salvage or front-line CAR therapy for patients with recalcitrant disease.