bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 189: Evaluating the influence of Lactobacillus rhamnosus-derived extracellular vesicles on calcium deposition in early breast cancer
Authors: Vuong Ngoc Bao , Alomia Melany , Alruwaili Intisar , Alsaab Fahad , Erickson James L. , Zhou Weidong , Luchini Alessandra , Van Hoek Monique , Espina Virginia , Hoefer Richard A. , Liotta Lance 
Published: June 2022

Abstract
Microcalcifications are an important mammographic feature of ductal carcinoma in situ (DCIS) and are detected in 85-90% of abnormal mammograms. Calcium transport and calcium channels regulate microcalcifications and are essential for breast cancer proliferation. The breast duct intraductal lumen, which is the origin of ductal carcinomas, has been shown to be a non-sterile environment. We hypothesize that the intraductal microbiome influences calcium handling and mineral deposition in breast cancer. Bacteria have been known to enhance the formation of mineral deposits, including calcium salts, in various non mammalian microenvironments via secreted factors or extracellular vesicle mediated nucleation. We performed a clinical study on a cohort of 150 women who received a suspicious mammogram and were subjected to a follow up biopsy, and we identified differences in calcium handling microbiota between patients who harbored a malignant disease with respect to benign controls. To mechanistically study the role of microbiota in breast cancer calcium handling, we developed a 3D spheroid model of ductal carcinoma in situ using the BT-474 cell line. When exposed to high concentrations of calcium in the culture medium (from 1.75 mM to 2.05 mM), spheroids developed calcium mineral deposits in a calcium dose dependent manner; deposits were identified in internal regions of the spheroid, which correspond to hypoxic areas of DCIS in vivo. Extracellular calcium deposition correlated with cell survival in face of a toxic calcium level. Spheroids were cultured under a continuous flow of Lactobacillus rhamnosus LMS2-1-derived EVs over the course of two weeks. EVs were isolated by sequential ultracentrifugation; the 100K fraction was retained and characterized in terms of size, concentration, and protein content. EV treatment induced increased calcium export and mineral deposition in a dose dependent manner. Our findings support the hypothesis that L. rhamnosus-derived extracellular vesicles influence calcium regulation and mineral deposition in the hypoxic breast cancer milieu. More studies will be undertaken in the future to unveil molecular mechanisms that underlie this interaction, both at the cancer cell and the microbiota level.
Citation Format: Ngoc Bao Vuong, Melany Alomia, Intisar Alruwaili, Fahad Alsaab, James L. Erickson, Weidong Zhou, Alessandra Luchini, Monique Van Hoek, Virginia Espina, Richard A. Hoefer, Lance Liotta. Evaluating the influence of Lactobacillus rhamnosus-derived extracellular vesicles on calcium deposition in early breast 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 189.
Abstract 1892: Expression of bacterial heme-sequestering proteins (HeSPs) in Pichia pastoris for effective treatment of lung cancer
Authors: Salamat Narges , Ashrafi Adnin , Wang Tianyuan , Akter Zakia , Gong Hanling , Zhang Li 
Published: June 2022

Abstract
Heme is a central biosynthetic molecule with important implications in diverse molecular and cellular processes, including oxygen utilization and metabolism. Heme carries out a vital role in mitochondrial energy generation through oxidative phosphorylation (OXPHOS) by acting as a cofactor or prosthetic group for complexes II, II, and IV in the electron transport chain. Lung cancer is the leading cause of cancer related death in the US. Our lab has previously shown that non-small cell lung cancer (NSCLC) cells exhibit an elevated heme flux characterized by elevated heme synthesis and import. This increased heme flux correlates with an enhanced oxygen consumption and ATP production. To target this elevated heme flux, we have engineered recombinant bacterial HasA hemophores as heme-sequestering proteins (HeSPs). HeSPs bind to and sequester heme with an extremely high (pM) affinity, thereby disrupting this elevated heme flux. HeSPs display potent anti-tumor activity in mouse models of NSCLC and triple-negative breast cancer (TNBC). Here, we utilized the Pichia pastoris expression platform to achieve high-yield expression. P. pastoris is a methylotrophic yeast that has minimal endogenous protein secretion and potentially high-yields for heterologous protein expression, due to a tightly regulated alcohol oxidase gene (AOX1). The P. pastoris expression platform is generally easier to handle and requires simpler fermentation conditions than mammalian cell cultures, making it an ideal candidate for expression of recombinant bacterial proteins without endotoxin contamination.We utilized a secretion signal to direct secretion of HeSP2 into the culture medium to allow for easier protein purification. Purification was performed through ion exchange chromatography. We utilized native PAGE and heme-binding spectrum to verify that these yeast-expressed HeSPs adopt a similar conformation to those expressed in bacteria and maintain their heme-binding activity. HeSPs expressed through this P. pastoris expression system demonstrated remarkable anti-cancer efficacy in proliferation assays on NSCLC cells and SCLC (small cell lung cancer) cells. Experiments are underway to test their anti-tumor efficacy in mouse models. These experiments may suggest a novel approach to generate effective anti-cancer agents.
Citation Format: Narges Salamat, Adnin Ashrafi, Tianyuan Wang, Zakia Akter, Hanling Gong, Li Zhang. Expression of bacterial heme-sequestering proteins (HeSPs) in Pichia pastoris for effective treatment of lung 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 1892.
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

Abstract
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, &gt;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 &gt;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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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.