bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 1905: Accelerating clinically-translatable discoveries using a network- and RNA-based precision-oncology framework
Authors: Vasciaveo Alessandro , Zou Min , Arriaga Juan M. , de Almeida Francisca Nunes , Douglass Eugene F. , Shen Michael , Califano Andrea , Abate-Shen Cory
Published: June 2022

Despite recent advances, prioritizing therapy at the individual patient level remains challenging. In fact, inter-patient tumor heterogeneity remains one of the major challenges in cancer therapy, making it difficult to optimize available treatments on an individual patient basis. Likewise, the systematic prediction of drug sensitivity in vivo is still a major challenge in translational research, where targeted therapeutics are currently selected based on the presence of either actionable oncogene dependencies or aberrant cellular mechanisms. A further challenge is the limited availability of models that faithfully recapitulate the biology, complexity, and heterogeneity of human tumors, including their interaction with a conserved microenvironment and a competent immune system.

To address these challenges, we introduce OncoLoop, a highly-generalizable, network-based precision medicine framework to triangulate between available mouse models, human tumors, and large-scale drug perturbational assays with in vivo validation to predict personalized treatment. OncoLoop requires only transcriptomic data (i.e., RNA-seq profiles) and leverages regulatory network analysis to (a) identify cognate models based on conservation of patient-specific Master Regulator (MR) proteins and (b) prioritize drugs based on their ability to invert the activity of MR proteins (MR-inverters), using drug perturbation profiles in cognate cell lines. As proof-of-concept, we applied OncoLoop to prostate cancer using a series of genetically engineered mouse models (GEMMs) that capture a broad range of phenotypes, including metastatic, castration-resistant and neuroendocrine disease. Indeed, >70% of patients in published cohorts had at least one high-fidelity matched GEMM. Drugs targeting shared Master Regulator dependencies of a patient and its cognate GEMM(s) were predicted using perturbational profiles of >300 drugs in MR-matched cell lines, resulting in an 80% validation rate in GEMM allografts and human xenografts. This network-based approach is highly generalized and can be applied to both cancer and non-cancer-related contexts.

Citation Format: Alessandro Vasciaveo, Min Zou, Juan M. Arriaga, Francisca Nunes de Almeida, Eugene F. Douglass, Michael Shen, Andrea Califano, Cory Abate-Shen. Accelerating clinically-translatable discoveries using a network- and RNA-based precision-oncology framework [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 1905.
Abstract 1906: Single cell precision oncology: A proof of principle
Authors: Sinha Sanju , Vegesna Rahulsimham , Schaffer Alejandro , Ruppin Eytan
Published: June 2022

A combination treatment designed to target the multiple clones of a patient’s tumor could decrease the likelihood of resistant emergence. The ability to learn and predict the response of a drug at a single-cell resolution could help to design such optimal combinations. A lack of large-scale patients’ datasets with single-cell (sc) expression hinders our ability to build such models.

To overcome this limitation, we built a precision oncology framework for personalized single-cell expression-based planning for treatments in oncology (PERCEPTION) that utilizes large-scale drug screens in cancer cell lines and matched bulk and single-cell transcriptome profiles to build response models that can be translated to patients.

We first showed that our predicted viability profile of multiple drugs with known mechanisms of action strongly correlates with the targeted pathway activity at a single-cell resolution, demonstrating our ability to predict at this resolution. We next predict response to monotherapy and combination treatment in three independent screens performed across cancer cell lines and patient-tumor-derived cell lines using their sc-expression profiles. Translating to the clinical context, we successfully stratify responders of combination therapy in a multiple myeloma clinical trial using the tumor’s sc-expression profile. For individuals in this trial, we next find the optimal combination treatments (pairs and triplets) from the existing FDA-approved drugs set, where the pair of gefitinib and niraparib, an EGFR and a PARP inhibitor, is one of the top candidates.

In sum, we provide a first-of-its-kind framework to utilize the tumor’s sc-expression to identify responders to combination therapy or to design an optimal combination for an individual patient.

Citation Format: Sanju Sinha, Rahulsimham Vegesna, Alejandro Schaffer, Eytan Ruppin. Single cell precision oncology: A proof of principle [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 1906.
Abstract 1930: Unsupervised sub-cellular segmentation of complex tissue and cell samples using highly multiplexed imaging-derived a priori knowledge
Authors: Kochetov Bogdan , Bell Phoenix D. , Raphael Rebecca , Raymond Benjamin J. , Leibowitz Brian J. , Tong Jingshan , Diergaarde Brenda , Yu Jian , Pai Reetesh K. , Schoen Robert E. , Zhang Lin , Singhi Aatur , Uttam Shikhar
Published: June 2022

Spatial context of heterocellular interactions within solid tumor microenvironments (TMEs) is important for deciphering the mechanistic underpinnings of malignant TME phenotypes and leveraging that knowledge to improve personalized and precision medicine. Recent development of highly multiplexed imaging approaches, such as co-detection by indexing (CODEX), cyclic immunofluorescence (cycif), and imaging mass cytometry (IMC) has, for the first time, allowed deep interrogation of this heterocellular spatial complexity. Proper quantitation of this complexity, however, requires the ability to easily and accurately segment and localize cells and their sub-cellular compartments within the spatial context of the tumor microenvironment. Seminal approaches based on semi-supervised and supervised learning methods, including deep learning techniques, have been developed to segment cells and their nuclei. However, generalization of these methods to segmenting heterogenous and complex cell and tissue samples with varying resolution, magnification, and dynamic range, remains a persistent bottleneck. In case of deep learning, the requirement of large and accurate annotated datasets further adds to the challenge of seamless integration of systems-based methods in pathology and cancer research. Here, we demonstrate that by leveraging cell-compartment specific a priori knowledge captured by these imaging modalities, we can segment cells in complex tissue and cell samples in an unsupervised manner, without requiring model training. We specifically show that using nucleus and cell-membrane markers, we can accurately segment sub-cellular compartments of a diversity of tissue samples imaged at different resolutions, magnifications and dynamic ranges, and cell samples at varying levels of confluency. We also demonstrate that our method is fast. Given its ease of use, accuracy, robustness, and no requirement of large, annotated datasets, our unsupervised segmentation method fills a much-needed gap toward integration of spatial systems biology and cancer research within the convergence science paradigm.

Citation Format: Bogdan Kochetov, Phoenix D. Bell, Rebecca Raphael, Benjamin J. Raymond, Brian J. Leibowitz, Jingshan Tong, Brenda Diergaarde, Jian Yu, Reetesh K. Pai, Robert E. Schoen, Lin Zhang, Aatur Singhi, Shikhar Uttam. Unsupervised sub-cellular segmentation of complex tissue and cell samples using highly multiplexed imaging-derived a priori knowledge [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 1930.
Abstract 2048: In vitro and in vivo characterization of non-oncolytic engineered arenavirus vectors for cancer immunotherapy
Authors: Raguz Josipa , Kleissner Theresa , Rosskopf Sandra , Habbeddine Mohamed , Lechner Katharina , Just Valentin , Edwards Donna , Matushansky Igor , Lampert Christoph , Orlinger Klaus K. , Lauterbach Henning
Published: June 2022

Cytotoxic CD8+ T cells are paramount for effective cancer immunotherapy. We engineered two distantly related arenaviruses, lymphocytic choriomeningitis virus (LCMV) and Pichinde virus (PICV), encoding the same non-oncogenic HPV16 E7E6 fusion protein to effectively mount and maintain tumor specific CD8+ T cell responses. The designated vectors, HB-201 (LCMV) and HB-202 (PICV), are currently in an ongoing Phase I/II open labelled clinical trial of HB-201 single vector therapy and HB-202/HB-201 alternating two-vector therapy in patients with treatment-refractory HPV16+ cancers (NCT04180215). To characterize the immunogenic properties of both vectors, we designed a comprehensive set of preclinical and translational experiments utilizing human PBMCs, artificial APCs and HPV16 E6 and E7 specific reporter T cells. This was done in conjunction with a preclinical model for HPV16 associated cancer (TC-1). HB-201 (LCMV) and HB-202 (PICV) surrogate vectors encoding GFP readily infected human monocytes, plasmacytoid dendritic, and conventional dendritic cells. In addition, HB-201 and HB-202 vectors successfully induced antigen presentation of E7 and E6 epitopes as evidenced by TCR reporter cells. Innate immune cell activation and cytokine responses to HB-202 were slightly lower compared to HB-201, findings which are consistent with different memory profiles of E7 specific CD8+ T cells in non-tumor bearing mice. In a therapeutic setting of the TC-1 tumor model, both vectors were comparably effective, showing major infiltration of CD8+ T cells into the tumor microenvironment, tumor growth delay and a significantly prolonged survival already after a single administration. In this data set we have confirmed the strong immunogenicity of the engineered arenavirus platform leading to efficient tumor control in a relevant mouse model for HPV16+ cancers, which further supports the clinical development of our novel arenavirus platform.

Citation Format: Josipa Raguz, Theresa Kleissner, Sandra Rosskopf, Mohamed Habbeddine, Katharina Lechner, Valentin Just, Donna Edwards, Igor Matushansky, Christoph Lampert, Klaus K. Orlinger, Henning Lauterbach. In vitro and in vivo characterization of non-oncolytic engineered arenavirus vectors for cancer immunotherapy [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 2048.
Abstract 2049: A novel, rapid, sensitive, and reproducible in vivo platform to assess efficacy and toxicity of bispecific antibodies
Authors: Yang Jiwon , Jiao Jing , Draheim Kyle , Cai Danying , Brehm Michael A. , Shultz Leonard D. , Greiner Dale L. , Cheng Mingshan , Keck James G.
Published: June 2022

A bispecific T-cell engager (BiTE) enhances the antitumor capabilities of T-cells by directing them to recognize a tumor-specific antigen. Several BiTEs are currently in clinical trials, and there is one FDA-approved BiTE for cancer therapy at the moment. However, one of the biggest challenges BiTE is currently facing is cytokine release syndrome (CRS). While most patients have mild flu-like symptoms, some patients experience a severe inflammatory syndrome, which could ultimately cause multi-system organ failure and death. Thus, the key is to accurately predict the risk-benefit ratio of each individual before starting the treatment. Unfortunately, there is no reliable in vitro or in vivo model to predict the toxicity and efficacy of BiTE at the moment. Additionally, one of the most challenging factors for pre-clinical evaluation of BiTEs for toxicity and efficacy is the inherent differences among patients’ immune systems. Here, we developed an in vivo PBMC-humanized mouse model that can evaluate both toxicity and efficacy of BiTE and other immune-oncology therapeutics in each individual mouse. The platform was validated using an anti-CD28 superagonist (TGN1412), which none of the pre-clinical in vitro assays and in vivo studies, including non-human primates, executed before clinical trials were able to predict the observed clinical toxicities. This model uses luciferase-tagged human B-cell lymphoma Raji tumor cells to allow the measurement of tumor burden and response to treatment, along with toxicity simultaneously. In addition, we showed that this platform can determine individual PBMC donor differences, and potential adverse drug combinations and drug dose-response with efficacy and safety on individual PBMC donors. The model we developed can potentially be used as a predictive and reproducible platform to identify patient, cancer, and therapy combinations at risk for developing CRS. This model will also help to optimize the therapeutic drug dose range to improve the safety profile of BiTE and other immune-oncology drugs. We believe this platform will greatly benefit not only the scientific community but potentially cancer patients as well.

Citation Format: Jiwon Yang, Jing Jiao, Kyle Draheim, Danying Cai, Michael A. Brehm, Leonard D. Shultz, Dale L. Greiner, Mingshan Cheng, James G. Keck. A novel, rapid, sensitive, and reproducible in vivo platform to assess efficacy and toxicity of bispecific antibodies [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 2049.
Abstract 2079: Tumor cell intrinsic inactivation of TREX1 increases type I IFN signaling and immune cell recruitment
Authors: Mathsyaraja Haritha , Wolf Benjamin , Cortez Chari , Kashishian Adam , Karst Alison , Cueva Madelyn , Wang Min , Keegan Kathleen S. , Cain Jennifer
Published: June 2022

Tumor cells employ mechanisms to evade anti-tumor immune responses that can include the downregulation or silencing of cytosolic nucleic acid sensing pathway components to dampen Type I IFN signaling. It has been documented that genomic instability and mitotic stress in malignant cells can lead to aberrant cytosolic DNA accumulation and activation of the cGAS-STING pathway. A key negative regulator of cytosolic DNA is the DNA exonuclease TREX1. TREX1 assists in removing DNA from the cytosol, in turn reducing cGAS-STING mediated type I IFN induction. Not surprisingly, TREX1 is overexpressed in several tumor types when compared to normal tissue. The functional importance of TREX1 in cytoplasmic nucleic acid surveillance is evidenced by inactivating TREX1 mutations having an association with Type I inteferonopathies such as Aicardi-Goutières syndrome and SLE. Specifically, most of these mutations impact the enzymatic function of TREX1, underscoring the importance of its exonuclease function. To directly assess TREX1 function in cancer, we inactivated TREX1 in a panel of tumor cell lines. Loss of TREX1 resulted in reduced proliferation and increased expression of the Type I IFN-stimulated gene CXCL10. This finding was validated with CRISPR knockout of TREX1, which also led to the activation of IRF3 and a Type I IFN associated gene signature. To characterize the role of TREX1 function in curbing anti-tumor immunity in vivo, we inactivated Trex1 in the murine syngeneic B16F10 melanoma model. TREX1 knockout together with PD1 blockade resulted in slower tumor growth when compared to PD1 blockade alone. This was accompanied by an increase in CD8+ T and NK cell infiltration in tumors. In addition, gene expression profiling of whole tumors revealed that TREX1 loss resulted in increased type I IFN signaling within the tumor microenvironment. In summary, our data strongly suggest a critical role for TREX1 in suppressing anti-tumor immunity and indicate it would be an attractive target for therapeutic intervention.

Citation Format: Haritha Mathsyaraja, Benjamin Wolf, Chari Cortez, Adam Kashishian, Alison Karst, Madelyn Cueva, Min Wang, Kathleen S. Keegan, Jennifer Cain. Tumor cell intrinsic inactivation of TREX1 increases type I IFN signaling and immune cell recruitment [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 2079.
Abstract 208: Peposertib-induced senescence primes irradiated p53 wild-type cancer cells for clearance by both immune cells and senolytic drugs
Authors: Carr Michael , Sun Qing , Lee Chien-Fei , Zenke Frank T. , Blaukat Andree , Vassilev Lyubomir T.
Published: June 2022

Peposertib (previously known as M3814) is a potent and selective DNA-PK inhibitor in early-stage clinical development. It effectively blocks the non-homologous end-joining pathway for repair of DNA double-strand breaks (DSB) and has shown strong synergy with ionizing radiation (IR) and DSB-inducing chemotherapy. We recently reported that M3814 overactivates the ATM/p53 signaling axis, reinforces cell cycle checkpoint arrest, and promotes durable premature senescence in irradiated p53 wild-type cancer cells. This unique property of peposertib permits to turn the bulk of irradiated cancer cells into nearly uniform senescent cell population. Using this experimental model, we examined the immunological effects and potential therapeutic applications of IR+peposertib induced senescence. Gene expression analyses of IR+peposertib treated A549 cells showed activation of multiple immune-related genes in the senescent cells, consistent with a strong STING-driven inflammatory response. Multiple secreted cytokines were found substantially elevated in culture media compared to IR controls. Co-culture of IR+peposertib induced senescent cells with PBMCs from healthy volunteers coupled with FACS analyses and live imaging revealed stimulation of the T-cell compartment and killing of senescent but not control cells. Further co-culture experiments with isolated NK cells showed accelerated killing of the senescent IR+peposertib treated A549 cells as compared to controls. These results indicated that IR+peposertib induced inflammatory signaling in senescent A549 cells can stimulate an immune response in vitro, resulting in the effective elimination of both treated and naive A549 cells. We also explored a pharmacological "two-hit" approach. Viability assays and time-lapse imaging showed that the senescent, IR+peposertib treated A549 cells were sensitive to several reported senolytic agents. Of those, the BCL-XL inhibitor A-1331852 was most effective at killing peposertib-promoted senescent A549 cells. Our experiments revealed that selective inhibition of DNA-PK in irradiated p53 wild-type cancer cells provides a powerful mechanism for induction of senescent cancer cells with an immunostimulatory secretory phenotype in vitro. In addition, these cells can be selectively targeted by senolytic agents, suggesting that triple combination radiotherapy with DNA-PK inhibitors and senolytics could offer a potential new approach to the treatment of locally advanced tumors.

Citation Format: Michael Carr, Qing Sun, Chien-Fei Lee, Frank T. Zenke, Andree Blaukat, Lyubomir T. Vassilev. Peposertib-induced senescence primes irradiated p53 wild-type cancer cells for clearance by both immune cells and senolytic drugs [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 208.
Abstract 2081: Poly ADP-ribose polymerase inhibition enhances T cell cytotoxicity and anti-tumor function by altering NAD+ levels
Authors: Dean Matthew J. , Zheng Liqin , Philbrook Phaethon , Ochoa Augusto C. , Boulares A. Hamid
Published: June 2022

Poly ADP-ribose polymerase (PARP) is an NAD-dependent DNA repair enzyme. Inhibition of PARP in BRCA-mutant cancers has been a clinically approved therapy for several years. While the PARP inhibitor, olaparib, has been approved for the treatment of BRCA-mutant breast and ovarian cancers, it has not been used in other cancers because its mechanism of action relies on synthetic lethality. We have found that olaparib may also have use in other cancers due to its ability to modulate the immune system directly. Specifically, we have found that olaparib is able to increase the proliferation, activation, and cytotoxicity of T cells in vitro and reduce tumor growth in vivo at low doses. Recent papers have proposed that olaparib is able to enhance T cell function through the stimulator of interferon genes (STING) pathway by enhancing antigen presenting cell activity and resulting in more granzyme B expression and enhanced tumor killing. Using purified T cells from both wild type and STING knockout mice, we have shown that olaparib can also cause an increase in granzyme B and perforin expression, an increase in T cell proliferation, and enhanced tumor cell killing in a STING-independent manner. Because PARP is an NAD-consuming enzyme, we examined the role of NAD+ in the activation T cells and the production of granzyme B and perforin. By using an inhibitor of NAD+ recycling, FK866, we show that T cells have reduced NAD+ levels, reduced granzyme B and perforin expression, and even fail to activate in the presence of CD3 and CD28 when NAD+ is limited; however, adding olaparib to these cells rescues the effects of FK866 and allows proliferation and granzyme B production. In vivo we can see that even at olaparib doses that are significantly below those which induce synthetic lethality of tumor cells, olaparib is able to inhibit tumor growth in models of both colorectal and breast cancer. This suggests that olaparib can modulate the activity of T cells directly and has implications for enhancing the anti-tumor activity of these cells both alone and in combination with other forms of immunotherapy.

Citation Format: Matthew J. Dean, Liqin Zheng, Phaethon Philbrook, Augusto C. Ochoa, A. Hamid Boulares. Poly ADP-ribose polymerase inhibition enhances T cell cytotoxicity and anti-tumor function by altering NAD+ levels [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 2081.
Abstract 2095: Selective inhibition of the STAT3 pathway suppresses K-ras mutant lung tumorigenesis
Authors: Clowers Michael J. , Chou Cody , Yuan Bo , Velasco Walter V. , Zarghooni Melody , Peng Stephen , Eckols T Kris , Kadara Humam , Tweardy David J. , Moghaddam Seyed Javad
Published: June 2022

K-ras mutant lung adenocarcinoma (KM-LUAD) is a difficult-to-drug cancer subtype characterized by a chronic inflammatory tumor microenvironment (TME). Resistance to therapies, including immune checkpoint blockade (ICB), necessitates therapies that target this inflammatory TME. A major transcription factor that mediates chronic inflammation in KM-LUAD is signal transducer and activator of transcription 3 (STAT3). Inhibiting STAT3 may attenuate pro-tumor inflammation. Moreover, STAT3 modulates PD-L1 transcription, so STAT3 inhibitors in conjunction with ICB may increase ICB response rates. Here, we tested the anti-tumor ability of TTI-101, a selective STAT3 inhibitor, in a STAT3 addicted lung cancer cell line (MDA-F471) and in a transgenic mouse model of KM-LUAD (CCSPCre/LSL-KrasG12D, CC-LR). For in vivo experiments, CC-LR mice were treated daily with 50 mg/kg TTI-101 by oral gavage from 10 to 14 weeks of age to model a preventative regimen or from 14 to 18 weeks of age to survey the treatment effect on established tumors. TTI-101 was compared to anti-PD-1 ICB, with 200 μg injected intraperitoneally 3 times per week. In MDA-F471 cells, TTI-101 treatment decreased cell viability, with an IC50 of ~ 20 μM. In mice treated from 10 to 14 weeks of age, TTI-101 therapy significantly reduced the tumor burden compared to ICB. TTI-101 also reduced the number of proliferating cells within tumors. Mice in the 14-18-week group displayed similar trends, but these experiments are ongoing, as are combination TTI-101 and ICB treatment regimens. Our studies show that TTI-101 can reduce K-ras driven tumor cell proliferation in vitro and in vivo, suggesting STAT3 inhibition as an alternative preventive and therapeutic modality for KM-LUAD. The ongoing combination treatments and the 14-18-week cohorts will elucidate the timing of treatments as well as reveal if by targeting the inflammatory TME we are able to improve response to ICB. Funded by: R01 grant from NIH/NCI (R01CA225977)

Citation Format: Michael J. Clowers, Cody Chou, Bo Yuan, Walter V. Velasco, Melody Zarghooni, Stephen Peng, T Kris Eckols, Humam Kadara, David J. Tweardy, Seyed Javad Moghaddam. Selective inhibition of the STAT3 pathway suppresses K-ras mutant lung tumorigenesis [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 2095.
Abstract 2096: Natural killer cells inhibit CD4+ T cell mediated IL-9 production in head and neck Cancer
Authors: Crist McKenzie , Lehn Maria , Takiar Vinita , Wise-Draper Trisha
Published: June 2022

Head and neck squamous cell carcinoma (HNSCC) is the 6th most common cancer in the world, yet 5 year survival remains poor for those with recurrence despite advances in treatment such as immunotherapy. Checkpoint blockade substantially improved survival in ~20% of recurrent and/or metastatic HNSCC patients. However, given the lack of efficacy in most patients, and the known immunosuppressive nature of HNSCC, exploring other potential immune cell therapeutic targets is of interest. Decreased natural killer (NK) as well as increased immunosuppressive CD4+ regulatory T cells (Tregs) in both peripheral blood and the tumor microenvironment are associated with a poor prognosis in HNSCC. We discovered that the anti-diabetes drug, metformin, which is also known to improve immune cell function, not only increases peripheral NK cells in HNSCC patients to the level of healthy controls, but also suppresses IL-9 secretion from NK cells. IL-9 has been implicated as a driving factor in allergic disease, a poor prognosis factor in hematologic malignancies, and an enhancer of T-reg immunosuppressive abilities. However, the function of IL-9 in solid tumors is poorly understood. Interestingly, upon depletion of CD56+ NK and NKT cells from peripheral blood mononuclear cells (PBMCs), there was a significant increase of IL-9 secretion. This effect was negated upon depletion of CD4+ T cells suggesting that NK cells may directly or indirectly inhibit CD4+ T cell IL-9 production. In order to understand potential consequences of IL-9 overproduction, we subjected HNSCC cell lines, which we demonstrated express IL9 receptor, to exogenous IL-9 which resulted in enhanced proliferation. We also found that IL-9 plasma levels are high in HNSCC patients compared to healthy controls corroborating a potential tumorigenic role for IL-9. In order to elucidate potential mechanism(s) by which NK/NKT cells regulate CD4+ T cell production, we performed single-cell RNAseq on PBMCs upon NK and NKT cell depletion. We also performed flow cytometry to identify specific CD4+ cell types responsible for increased IL-9 production and the consequential changes in other immune cell phenotypes upon the absence of NK/NKT cells. Understanding the role of IL-9 in HNSCC will be important for utilizing IL-9 as a potential marker for HNSCC prognosis as well as a possible target for future immunotherapy approaches.

Citation Format: McKenzie Crist, Maria Lehn, Vinita Takiar, Trisha Wise-Draper. Natural killer cells inhibit CD4+ T cell mediated IL-9 production in head and neck Cancer [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 2096.
Abstract 2108: ScRNA-Seq and imaging mass cytometry analyses unveil iNKT cells-mediated anti-tumor immunity in pancreatic tumor liver metastasis
Authors: Wang Jie , Yi Qijun , Liu Tingting , Yao Yi , Loveless Ian , Subedi Kalpana , Adrianto Indra , Crawford Howard , Zhou Li , Mi Qing-Sheng
Published: June 2022

Background: Liver metastasis is a common feature of pancreatic tumor and associated with a poor outcome. Invariant natural killer cells (iNKT) are innate-like T cells that are important regulators of innate and adaptive immune responses in cancer and is the largest subset of lymphocytes within liver. However, the role of iNKT cells in pancreatic tumor liver metastasis (PTLM) is still not clear. Hypothesis: activated liver iNKT cells could play a role in PTLM.

Method: We established a PTLM mouse model by hemi-spleen murine pancreatic tumor cells (CF1242) injection. We combined single-cell RNA sequencing, flow cytometry analysis, and imaging mass cytometry analysis to landscape the immune profile of tumor microenvironment during PTLM with or without iNKT cell activator α-galactosylceramide (αGC) treatment.

Results: αGC treatment significantly blocked PTLM development based on liver weight compared to control group(P<0.001). We sequenced total 6,728 CD45+ infiltrating immune cells in PTLM with/without αGC treatment and identified total 12 immune subpopulations that were present in both samples at different frequencies. Post αGC treatment, activated iNKT cells in liver appeared robust population expansion and enriched in cytotoxic signaling pathway. Alternatively, activated iNKT cells promoted infiltrating CD4 T cells to a Th1 profile shift, and promoted infiltrating CD8 T cells toward an effector/memory phenotype (upregulation of the CD44, T-bet, and IFN-γ; P<0.001), and increased NK cell cytotoxic activity (P<0.001). In addition, we observed that aGC treatment blocked infiltrating CD8 T cell exhaustion by downregulating the immune checkpoint TIGIT, Lag3, and PD-1 (P<0.001). Analysis of tumor-infiltrating myeloid clusters revealed that macrophage skewed to M1 phenotype compared to the control group(P<0.05).

Conclusion: αGC treatment can expand and activate liver iNKT cells, which may directly increase tumor cell killing ability, recruit immune cells to tumor sites, and orchestrate the anti-tumor function through boost both innate and adaptive tumor immunity to inhibit PTLM. Our results indicate that iNKT cells may serve as a new immunotherapeutic target for PTLM. (Funded by HFCI and NIH/NIAID)

Citation Format: Jie Wang, Qijun Yi, Tingting Liu, Yi Yao, Ian Loveless, Kalpana Subedi, Indra Adrianto, Howard Crawford, Li Zhou, Qing-Sheng Mi. ScRNA-Seq and imaging mass cytometry analyses unveil iNKT cells-mediated anti-tumor immunity in pancreatic tumor liver metastasis [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 2108.
Abstract 2155: PMR-116, a novel inhibitor of ribosome biogenesis with antitumor activity in preclinical models of prostate cancer
Authors: Huglo Alisee , Rebello Richard , Lawrence Mitchell , Risbridger Gail , Drygin Denis , Haddach Mustapha , Hannan Katherine , Hannan Ross , Furic Luc
Published: June 2022

Advanced prostate cancer is characterised by mutations and amplifications of genes involved in regulating protein synthesis. PTEN-loss stimulates activity of the mTOR pathway, while amplification of MYC leads to increased ribosome biogenesis and elevated mRNA translation rate. Our previous work has demonstrated the efficacy of co-targeting ribosome biogenesis, via inhibition of RNA Pol I activity, and 4E-BP1 phosphorylation to suppress prostate cancer growth in vivo in GEMM of PCa and in patient-derived xenografts (Rebello et al., Clinical Cancer Research, 2016; Lawrence et al., European Urology, 2018).

In a collaboration with Pimera Inc., we investigated the efficacy of their new lead RNA Pol I inhibitor PMR-116 in models of prostate cancer. PMR-116 is well tolerated in vivo in mice and can be given at 300mg/kg weekly. Using the Hi-MYC mouse model of PCa we show that dosing 6 month old mice once weekly for 4 weeks can decrease the incidence of invasive lesions by up to 85% compared to vehicle control while reverting glands to patterns of low grade intraepithelial neoplasia. PMR-116 rapidly inhibits proliferation in the Hi-MYC model with a 50% decrease in Ki67 observed 12 hours after oral administration. Conversely, PMR-116 showed minimal anti-tumour efficacy in the PTEN-null model of PCa suggesting that elevated MYC signalling may be required for optimal response.

To further validate our promising GEMM results in more clinically relevant human-derived models, we used patient-derived xenografts lines we established from multidrug-resistant, metastatic PCa (Lawrence et al, European Urology, 2018). PMR-116 treatment decreased tumour volume in all PDX tested including complete response in a line in which tumour volume decreased by ~90% compared to baseline.

We believe this new RNA Pol I inhibitor shows promising results in a wide range of preclinical models and may exert higher efficacy in tumours expressing high levels of MYC. PMR-116 is currently in Phase I dose escalation trial in patient with solid tumours (ACTRN12620001146987).

Citation Format: Alisee Huglo, Richard Rebello, Mitchell Lawrence, Gail Risbridger, Denis Drygin, Mustapha Haddach, Katherine Hannan, Ross Hannan, Luc Furic. PMR-116, a novel inhibitor of ribosome biogenesis with antitumor activity in preclinical models of prostate cancer [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 2155.
Abstract 2176: NADPH production and redox homeostasis regulate acinar to ductal metaplasia
Authors: Radyk Megan D. , Nelson Barbara S. , Halbrook Christopher J. , Shan Mengrou , Alektiar Jonathan , Crawford Howard C. , Shah Yatrik M. , Lyssiotis Costas A.
Published: June 2022

Activating mutations in KRAS reprogram cellular metabolism to support continuous growth, proliferation, and survival in pancreatic cancer. However, there is little information on how KRAS-dependent alterations in metabolism change precancerous states and cancer initiation. Acinar cells can give rise to pancreatic tumors through acinar-to-ductal metaplasia (ADM), a reversible cell state that persists and progresses to neoplasia and cancer with oncogenic KRAS. During ADM, acinar cells transdifferentiate to duct-like cells, a process we hypothesized was mediated by metabolic rewiring. We performed transcriptomic analysis on acinar cells undergoing ADM and found metabolic programs are globally enhanced. Indeed, we and others have demonstrated how inhibiting metabolic pathways necessary for ADM can prevent transdifferentiation and tumorigenesis. A detailed analysis of our data revealed that the transcripts for NADPH-producing enzymes, Glucose-6-phosphate dehydrogenase (G6pd) and Malic enzyme 1 (Me1), were significant enriched during ADM. Following these results, we obtained G6pd-mutant mice and generated Me1flox/flox mice and bred them into the KC (KrasLSL-G12D/+;Ptf1aCre/+) line, resulting in KCG (KrasLSL-G12D/+;Ptf1aCre/+;G6pdmut/mut) and KCM (KrasLSL-G12D/+;Ptf1aCre/+;Me1flox/flox) mice. Interestingly, KCG and KCM mice develop ADM and neoplasia faster than their KC counterparts. We also observe that acinar cells and ADM in KCG cells have higher levels of lipid peroxidation and reactive oxygen species (ROS) both in vivo and using primary ex vivo acinar cell cultures. Thus, increased ROS levels may underlie ADM acceleration in this system. In primary acinar cell culture, we can rescue the accelerated ADM phenotype in KCG cells with the addition of antioxidants. Furthermore, we find that treatment of wild type acinar cells with buthionine sulphoximine (BSO) to deplete glutathione levels and increase ROS also accelerates ADM in culture. These results suggest that NADPH and glutathione pools are important for regulating redox levels during ADM, and that reducing these pools leads to accelerated tumorigenesis. Together, this work demonstrates new metabolic pathways driving pancreatic cancer initiation.

Citation Format: Megan D. Radyk, Barbara S. Nelson, Christopher J. Halbrook, Mengrou Shan, Jonathan Alektiar, Howard C. Crawford, Yatrik M. Shah, Costas A. Lyssiotis. NADPH production and redox homeostasis regulate acinar to ductal metaplasia [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 2176.
Abstract 2216: Impact of EXO1 (K589E) single nucleotide polymorphism on breast cancer risk in Bangladeshi women
Authors: Rahman Md. Mustafizur , Kabir Md. Mahmudul , Rahman Md. Abdur , Hossain Amir , Hossain Md. Golam
Published: June 2022

Background and aim: Exonuclease 1 (EXO1) is an essential member of the RAD2 nuclease family which is involved in mismatch repair system and contributes to the maintenance of genomic stability, modulation of DNA recombination and cell cycle arrest mediation. Potential polymorphism in EXO1 may have the ability to control cancer risks by influencing the repair activity. K589E (rs1047840) is a potentially functional polymorphism in EXO1 gene and we hypothesized that it might be associated with risk of breast cancer in Bangladesh.

Method: We designed a case-control study consisting of 184 subjects with breast cancer and 200 healthy controls to identify the effect of K589E polymorphism on breast cancer susceptibility and clinicopathological features in Bangladeshi women. Genotype determination was performed by PCR-RFLP method.

Results: After the adjustment of age and weight, a significant association was found between EXO1 K589E alleles and genotypes and risk of breast cancer. The frequencies of the three genotypes G/G, G/A, and A/A were 49, 42, and 9% in cases whereas 69, 27.5, and 3.5% in controls, respectively. The heterozygote G/A genotype and combined G/A+A/A genotypes showed 2.12-fold (OR=2.12, 95% CI=1.3733 - 3.2822 p=0.0007) and 2.27-fold (OR=2.27, 95% CI=1.5001 - 3.4493, p=0.0001) increased risk of breast cancer, respectively when compared with homozygous G/G genotypes. The variant A allele also was associated with increased risk of breast cancer (OR= 3.46, 95% CI=1.3720 - 8.7571, p=0.0086). Analysis of clinicopathological characteristics and genotype distribution also showed a significant correlation.

Conclusion: Our results revealed that EXO1 K589E polymorphism could be a potential predisposing risk factor in genetic susceptibility to breast cancer in Bangladesh.

Citation Format: Md. Mustafizur Rahman, Md. Mahmudul Kabir, Md. Abdur Rahman, Amir Hossain, Md. Golam Hossain. Impact of EXO1 (K589E) single nucleotide polymorphism on breast cancer risk in Bangladeshi women [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 2216.
Abstract 2260: Non-alcoholic fatty liver disease polygenic risk score and risk of hepatocellular carcinoma in an East Asian population
Authors: Thomas Claire E. , Diergaarde Brenda , Kuipers Allison L. , Adibi Jennifer J. , Luu Hung N. , Chang Xuling , Dorajoo Rajkumar , Heng Chew-Kiat , Khor Chiea-Chuen , Wang Renwei , Jin Aizhen , Koh Woon-Puay , Yuan Jian-Min
Published: June 2022

Purpose: It is difficult to identify people with non-alcoholic fatty liver disease (NAFLD) who are at high risk for the development of hepatocellular carcinoma (HCC). A polygenic risk score (PRS) for hepatic fat derived from non-Asians has been reported to be associated with HCC risk in European populations. However, population level data of this risk in non-European populations are lacking.

Methods: Utilizing resources from the Singapore Chinese Health Study (SCHS), we examined the relationship between the previously published hepatic fat PRS (HFC-PRS) and HCC risk. We also constructed and evaluated a NAFLD-related PRS (NAFLD-PRS); the final version included SNPs in similar gene regions as the HFC-PRS but weighted by effect estimates for NAFLD among those with East Asian ancestry. Cox proportional hazards models were used to estimate hazard ratios (HRs) and 95% confidence intervals (95% CIs) of HCC incidence with both HFC-PRS and NAFLD-PRS.

Results: The HFC-PRS and NAFLD-PRS were highly correlated (Spearman r = 0.79, P < 0.001). The highest quartiles of both the HFC-PRS and the NAFLD-PRS were associated with significantly increased risk of HCC with HR of 2.39 (95% CI 1.51, 3.78) and 1.77 (95% CI 1.15, 2.73), respectively, compared to their respective lowest quartile.

Conclusion: The HFC-PRS and the NAFLD-PRS may both be useful in stratifying Asian populations according to their risk of HCC. In addition, the association between the NAFLD-PRS, derived from East Asians, and HCC risk suggests a potential causal role for NAFLD in the development of HCC in this population.

Citation Format: Claire E. Thomas, Brenda Diergaarde, Allison L. Kuipers, Jennifer J. Adibi, Hung N. Luu, Xuling Chang, Rajkumar Dorajoo, Chew-Kiat Heng, Chiea-Chuen Khor, Renwei Wang, Aizhen Jin, Woon-Puay Koh, Jian-Min Yuan. Non-alcoholic fatty liver disease polygenic risk score and risk of hepatocellular carcinoma in an East Asian population [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 2260.
Abstract 2263: The role of E-Cadherin mediated cell division in promoting collective colon cancer cell migration
Authors: Li Yu-Lin , Weng Yu-Cheng , Winarso Viriya Adhiguna , Lu Yi-Wen , Koo Hui Min , Hou Xiang-Ling , Tseng Kai-Yu , Chao Wei-Ting
Published: June 2022

Collective cell migration is the cell cohort migrates toward the direction. Other than single cell migration, collective cell migration requires cell-cell connection with E-cadherin, however, E-cadherin is the epithelial marker in epithelial mesenchymal transition and acts as tumor suppressor function. Therefore, the role of E-cadherin in collective cell migration is still under investigated. In the collected cells, cell migration and cell division are coordinated for the cohort motility, the mechanism is still not clear. This study is to investigate the role of E-cadherin orientation in cell division dependent collective cell migration. Colorectal cancer cell line HT29 with epithelial morphology were used and treated with Cetuximab and Dasatinib to inhibit EGFR and Src activity. Cells were also incubated on fibronectin to monitor the matrix dependent environment. The polarity of E-cadherin distribution and cell contact inhibition were defined and detected by Immunofluorescence. The molecular expression of p-FAK, CDK4, and cell proliferation marker, Ki67 were revealed by Immunofluorescence confocal microscopy and Western blot. The collective cell migration is analyzed and compared by wound healing and transwell assay. In the results, the polarized distribution of E-cadherin in leading cells which revealed pFAK expression on the cell membrane was associated with Ki67 and CDK4 positive proliferated cells. When cells were grown on fibronectin, the proliferated cells in the leading were decreased. When cells were treated with cetuximab, the E-cadherin distribution were not changed and had fewer effect on cell migration. However, dasatinib treatment can modulate E-cadherin orientation and suppress cell proliferation and cell migration. These results suggested modulate E-cadherin orientation such as Src inhibition can be the potential treatment strategy in colon cancer

Citation Format: Yu-Lin Li, Yu-Cheng Weng, Viriya Adhiguna Winarso, Yi-Wen Lu, Hui Min Koo, Xiang-Ling Hou, Kai-Yu Tseng, Wei-Ting Chao. The role of E-Cadherin mediated cell division in promoting collective colon cancer cell migration [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 2263.
Abstract 2271: Patient-specific visualization of cancer pathways
Authors: Swaminathan Padmapriya , Williams Casey B. , Meissner Tobias
Published: June 2022

​Introduction: Analysis of whole transcriptomics datasets to quantify gene expression and determine differentially expressed genes has provided valuable information for precision medicine. Evaluating enrichment of specific gene groups and pathways, and visualizing these results is an important step to obtain inferences about patient treatment outcomes, overall survival, drug resistance and therapeutic targets.

However, pathway analysis of cancer patient samples in a N-of-1 setting without their respective control (normal) samples remains to be challenging. There is a crucial need for methods and tools to conduct and visualize pathway analysis results in this setting.

Methods and Results: Our method focuses on a visualization technique showing patient-specific pathway activation relative to reference populations from The Cancer Genome Atlas (TCGA) and The Genotype-Tissue Expression (GTEX). Patient-specific pathway activity scores are displayed within the respective percentiles and averages of the TCGA and GTEX cohorts to visualize a patient's individual pathway activation profile within the TCGA tumor and GTEX normal reference population. Patient-specific pathway scores are derived from an individual patient's transcriptomic profile and transformed into activity scores for each of 14 cancer pathways. This allows for the comparison of an individual patient’s pathway activation profile with reference samples from TCGA and GTEX. We used PROGENy (Pathway RespOnsive GENes for activity inference) to calculate activity scores for the 14 cancer related pathways.

The pathway activity scores of each new tumor sample are scaled using the parameters of scaled pathway activity scores obtained from TCGA and GTEX gene expression data of all cancer tissue types. Finally we visualized the pathway activity scores of each patient sample.

Conclusion: Our visualization method is expected to unravel the activation patterns of each of the 14 cancer pathways in our patient samples. Specific pathway genes can then be evaluated in the patient samples to identify causal mutations and their associations with the pathway activity scores hence aid in treatment selection and in the further development of precision medicine therapeutic solutions.

Citation Format: Padmapriya Swaminathan, Casey B. Williams, Tobias Meissner. Patient-specific visualization of cancer pathways [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 2271.