bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 1977: Extending the capabilities of a high-parameter immunophenotyping assay with cytoplasmic staining applications for mass cytometry
Authors: Saederup Noah , Yao Huihui , Cohen Michael , Fung Leslie 
Published: June 2022

Abstract
Mass cytometry, empowered by CyTOF® technology, utilizes monoisotopic metal-tagged antibodies and a high-sensitivity mass cytometer to allow high-dimensional single-cell analysis in complex biological samples. The 30-marker panel Maxpar® Direct™ Immune Profiling Assay™ (Cat. No. 201325) for suspension mass cytometry provides an unprecedented sample-to-answer solution for detecting and analyzing 30 surface markers in a single experiment. With 18 open mass channels for additional biological markers, the Maxpar Direct Assay facilitates panel expansion and enables flexibility for higher multiplexity and applications. Among the potential complementary applications with the Maxpar Direct Assay, intracellular cytokine staining (ICS) is of particular interest as it may be used to assess infiltrating immune cell phenotypes in the tumor microenvironment. However, for the purpose of assessing cell viability in this workflow, the effectiveness of the Cell-ID™ Intercalator-Rh (Cat. No. 201103) that is included in the Maxpar Direct Assay is in question, since cell permeabilization during ICS can potentially damage the DNA-intercalator bondIn this study, we investigated the compatibility of the Cell-ID Intercalator-Rh (103Rh) with intracellular staining. To do this, we stained either human peripheral blood mononuclear cell (PBMC) or whole blood samples (FLDM-400287) with the Maxpar Direct Assay followed by intracellular staining for the detection of expressed cytokines. The intercalator was evaluated for its ability to discriminate live and dead cells when the sample undergoes surface antibody staining. The monoisotopic Cell-ID Cisplatin-194Pt (Cat. No. 201194) was used as the control to provide benchmark measurement of cell viability of the samples. For both sample types, known percentages of heat-killed PBMC were spiked into the samples in order to evaluate the influence of dead cells. We demonstrate that 103Rh provides equivalent functionality as a cell viability indicator during intracellular staining for cytoplasmic proteins compared to Cell-ID Cisplatin-194Pt. This work was designed to support the use of the Maxpar Direct Immune Profiling Assay in combination with additional intracellular markers. Overall, these findings expand the applicability of Cell-ID Intercalator-Rh (103Rh) to processes that involve cytoplasmic staining. For Research Use Only. Not for use in diagnostic procedures.
Citation Format: Noah Saederup, Huihui Yao, Michael Cohen, Leslie Fung. Extending the capabilities of a high-parameter immunophenotyping assay with cytoplasmic staining applications for mass cytometry [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 1977.
Abstract 2006: Preclinical evaluation of dual AURKA (LY3295668) and BCL2 (venetoclax) inhibition in neuroblastoma (NB)
Authors: Groff David , Casey Colleen , krytska Kateryna , Tsang Matthew , Acholla Christina , Maris John M. , Mosse Yael P. 
Published: June 2022

Abstract
Introduction: Deregulated expression of the MYCN oncogene is associated with the development of many neural-derived pediatric cancers including NB, medulloblastoma and atypical teratoid rhabdoid tumors. Amplification of the MYCN oncogene is present in over 40% of high-risk NBs that remain lethal in most patients, thus developing better therapies for these patients is essential. While direct therapeutic targeting of MYCN protein remains challenging, we previously demonstrated synergistic activity of dual targeting of BCL-2 (venetoclax) and AURKA (MLN8237) in MYCN-amplified NB (Ham Cancer Cell, 2016). With MLN8237 no longer being developed due to toxicities related to AURKB inhibition, testing of a highly selective AURKA inhibitor, LY3295668, is warranted.
Methods: LY3295668 (Chemie Tek) and venetoclax (Selleck Chem) were tested alone and in combination in six NB PDX models using 2-3 mice/arm. Five Patient Derived Xenograft (PDX) models tested (COG-N-424x, COG-N-453x, NB-1643, Obelix-Rx and Obelix-2x) were MYCN-amplified and one xenograft model (SK-N-AS) was MYCN-non-amplified. First, a comprehensive toxicity study, testing LY3295668 at 30mg/kg with venetoclax at 100mg/kg, 75mg/kg, 50mg/kg, and 25mkg/kg, was performed. Based on tolerability of combination, an optimal dose of 30mg/kg for LY3295668 and 50mg/kg for venetoclax was selected and administered once daily, seven days a week, via oral gavage for 60 days. These were the maximum tolerated doses when tested in combination, that did not result in weight loss greater than 15% or other overt signs of toxicity.
Results: LY3295668 (30mg/kg) and venetoclax (50mg/kg) were well tolerated as monotherapy, and when administered in combination showed a maximum weight loss of 13%. Single agent therapy resulted in minimal if any growth delay. Four of five MYCN-amplified PDX models demonstrated maintained complete responses and one showed significant tumor growth delay. No effect was observed in the MYCN-non-amplified model with single agent or combination treatment compared to vehicle.
Conclusions: Dual targeting of AURKA and BCL2 with LY3295668 and venetoclax is tolerable and demonstrates compelling anti-tumor activity in MYCN-amplified NB PDX models, validating our earlier findings (Ham et al). These preclinical results provisionally support clinical development of this combination for NB patients with MYCN amplification. Assessment of additional PDX models is currently ongoing and will be reported.
Citation Format: David Groff, Colleen Casey, Kateryna krytska, Matthew Tsang, Christina Acholla, John M. Maris, Yael P. Mosse. Preclinical evaluation of dual AURKA (LY3295668) and BCL2 (venetoclax) inhibition in neuroblastoma (NB) [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 2006.
Abstract 2010: Transcriptional antagonism by CDK8 inhibition improves therapeutic efficacy of MEK inhibitors
Authors: Malone Clare F. , Kim Minjee , Alexe Gabriela , Forman Alexandra B. , Robichaud Amanda , Conway Amy Saur , Goodale Amy , Hatcher John M. , Gray Nathanael S. , Piccioni Federica , Stegmaier Kimberly 
Published: June 2022

Abstract
Mutations in the RAS/MAPK pathway are frequent drivers of oncogenesis. Clinically approved MEK inhibitors are effectively used to target RAS-pathway driven cancers in combination with RAF inhibitors in BRAF mutant cancers such as melanoma and non-small cell lung cancer. However, single agent treatment with MEK inhibitors is not typically sufficient for clinical benefit. Therefore, combination therapy approaches will be required for maximal efficacy in most advanced cancers. Here, we sought to identify MEK inhibitor-based combination therapy approaches in the setting of RAS-mutant neuroblastoma. Neuroblastoma is a cancer that arises in the developing peripheral nervous system. Children with low-risk disease frequently benefit from therapy, but 50-60% of children with high-risk disease will ultimately relapse, and relapsed disease is generally incurable. We performed genome-scale functional genomic drug modifier screens and identified mediator kinase module members CCNC and CDK8 as two genes that when lost sensitize RAS-mutant NBL to MEK inhibition. We used small molecule inhibitors of CDK8 and found that combined inhibition of MEK and CDK8 leads to an improved therapeutic response in vitro and in vivo in a xenograft model of neuroblastoma. Using transcriptional profiling, we established that CDK8 loss and MEK inhibition induce opposite transcriptional signatures. When combined, CDK8 loss prevents the compensatory upregulation of the pro-growth gene expression program induced by MEK inhibition, while the downregulation of MAPK signaling is maintained. Finally, we show that this combination is effective in a subset of other RAS-mutant cancers including pancreatic and lung cancers. Together these data suggest that the mediator kinase module is critical for the adaptive pro-survival transcriptional response induced by MEK inhibition in RAS-mutant neuroblastoma and other RAS-driven malignancies, and that the addition of a CDK8 inhibitor may improve clinical response to MEK inhibitors. Our data supports a model where agents with antagonistic transcriptional programs can have synergistic therapeutic effects when combined, which may be a broadly relevant approach in combination therapies.
Citation Format: Clare F. Malone, Minjee Kim, Gabriela Alexe, Alexandra B. Forman, Amanda Robichaud, Amy Saur Conway, Amy Goodale, John M. Hatcher, Nathanael S. Gray, Federica Piccioni, Kimberly Stegmaier. Transcriptional antagonism by CDK8 inhibition improves therapeutic efficacy of MEK inhibitors [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 2010.
Abstract 2012: A humanized anaplastic lymphoma kinase (ALK)-directed antibody-drug conjugate (ADC) demonstrates potent cytotoxicity in neuroblastoma (NBL) and fusion positive rhabdomyosarcoma (FP RMS)
Authors: Guerra Alberto D. , Kennedy Annie , Adams Cynthia , Shraim Rawan , Weiner Amber K. , Chen Chuan , Krytska Kateryna , Larmour Colleen , Matkar Smita , Dimitrov Dimiter , Jelev Dontcho V. , Mossé Yael P. 
Published: June 2022

Abstract
Introduction: ALK is a lineage restricted oncoprotein expressed on the cell surface of NBL as wild-type (WT), mutated, or amplified, and recently shown to be overexpressed in FP RMS. Small molecule inhibitors have shown potent efficacy in NBL with ALK mutations or amplifications, but is limited to a minority of the high-risk population and have demonstrated conferred resistance. We have previously shown the potential of an ADC approach for WT ALK-expressing NBL with a chimeric ALK-directed ADC CDX-0125.
Methods: A highly specific humanized ALK antibody KTN0239 was developed with site-specific conjugation of an amine-azido linker conjugated to pyrrolobenzodiazepine (PBD) dimers or duocarmycin using click chemistry. ALK surface expression in ALK amplified (NB-1), WT non-amplified (IMR-32), mutant (Felix, SH-SY5Y, Kelly, NB1-643), and WT null (SK-N-AS) cell lines were quantified with flow cytometry using the primary KTN0239 antibody. Internalization kinetics of KTN0239 were measured using Incucyte® Fabflour-pH labeling. In vitro ADC IC50 values and viability rescue were assessed with a CellTiter-Glo® assay with ADC concentrations ranging from 10 fM to 10 nM. Western blot was used to elucidate cytotoxic mechanism of the ADC.
Results: ALK surface protein molecule expression was 21,820 in NB-1 cells, 3,708 in Felix, and 1,426 in SK-N-AS cells. KTN0239 was internalized into NB1 cells with a logarithmic trend, with &gt;65% of antibody internalized within 8 hours.
NB-1 cell line viability was rescued to &gt;80% when 2.5 nM of KTN0239 was in competition with the PBD-conjugated ADC at the IC50 concentration. The ADC induced activation of PARP, caspase-3, and γH2AX without attenuation of ALK signaling in NB-1 cells.
Conclusions: ADCs directed to ALK-expressing cancers are a promising therapeutic approach. The efficacy of the ADCs are currently being tested in NBL and FP RMS mouse models, and will be reported.
Mean IC50 values (pM) of ADCs with a drug antibody ratio (DAR) of 6 in NBL cell lines ADC: PBD-conjugated Duocarmycin-conjugated NB-1 14 71 IMR-32 12 741 Felix 51 110 NB-1643 6.6 1,196 Kelly 517 34,700 SH-SY5Y 693 3,024 SK-N-AS 533 1,420
Citation Format: Alberto D. Guerra, Annie Kennedy, Cynthia Adams, Rawan Shraim, Amber K. Weiner, Chuan Chen, Kateryna Krytska, Colleen Larmour, Smita Matkar, Dimiter Dimitrov, Dontcho V. Jelev, Yael P. Mossé. A humanized anaplastic lymphoma kinase (ALK)-directed antibody-drug conjugate (ADC) demonstrates potent cytotoxicity in neuroblastoma (NBL) and fusion positive rhabdomyosarcoma (FP RMS) [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 2012.
Abstract 2018: Therapeutic benefit of dual ALK and FAK inhibition in neuroblastoma
Authors: Chugh Seema , Tien Jean C. , Hon Jennifer , Bawa Pushpinder Singh , Kenum Carson , Li Chi Chiang , Cheng Yunhui , Delekta Andrew D. , Choi Jae Eun , Mannan Rahul , Qiao Yuanyuan , Mody Rajen , Chinnaiyan Arul 
Published: June 2022

Abstract
Neuroblastoma (NB) is the most common extracranial pediatric tumor, and accounts for approximately 12% of cancer-related deaths in children. Though several genomic drivers have been identified, the development of targeted therapy for treating this aggressive pediatric malignancy has yet to be realized. Thus, there exists an urgent need to develop alternative therapeutic strategies for treating aggressive and metastatic NB. One novel approach is to therapeutically target anaplastic lymphoma kinase (ALK) and focal adhesion kinase (FAK), which are multi-functional tyrosine kinases implicated in neural development and play an important role in growth and metastasis of several cancers. Genomic aberrations of ALK such as overexpression, amplifications, and mutations, have been reported in NB. The role of FAK has also been delineated in NB as well as associated with disease metastasis. Using in silico analysis of sequencing data from NB patients procured from Pediatric MI-ONCOSEQ (precision oncology program), we found a cohort of patients that express high ALK and FAK expression. Given the potential roles of ALK and FAK in NB, we evaluated the efficacy of a novel compound ESK440, which is a dual ALK and FAK inhibitor. ESK440 has passed Phase 1 clinical trials in adult patients with solid tumors. It is capable of crossing the blood brain barrier and binds to several mutated forms of ALK, thus making ESK440 an attractive therapeutic candidate for treating NB. A wide panel of NB cancer cell lines were screened with ESK440, and a CellTiter-Glo® Luminescent Cell Viability Assay was used to determine the IC-50s. Our results revealed that NB cells with ALK genomic aberrations (mutations and amplifications) showed low IC-50 values. Further, treatment with ESK440 inhibited ALK and FAK associated signaling pathways. We also observed decreased expression of MYCN. Intriguingly, ESK440 studies in NB xenograft model (NB-1) resulted in tumor regression in treated animals. Altogether, our study has discovered the therapeutic potential of dual ALK and FAK inhibitor in NB, and our findings may provide the foundation for initiating clinical trials targeting this disease in pediatric patients.
Citation Format: Seema Chugh, Jean C. Tien, Jennifer Hon, Pushpinder Singh Bawa, Carson Kenum, Chi Chiang Li, Yunhui Cheng, Andrew D. Delekta, Jae Eun Choi, Rahul Mannan, Yuanyuan Qiao, Rajen Mody, Arul Chinnaiyan. Therapeutic benefit of dual ALK and FAK inhibition in neuroblastoma [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 2018.
Abstract 2117: IFN-γ signaling in myeloid cells regulates pancreatic cancer growth and progression
Authors: Ivleva Elena , Andreeva Natalia , Grivennikov Sergei 
Published: June 2022

Abstract
Pancreatic ductal adenocarcinoma (PDAC) is characterized by low survival, early metastasis, and rapidly emerging resistance to therapy. Interferon gamma (IFN-γ) signaling pathway is one of the key regulators of the tumor microenvironment in numerous cancer settings and its possible key role in myeloid cells is suggested. Here we investigated the IFN-y signaling in myeloid cells during PDAC development, progression, and metastasis using mice with conditional ablation of IFNgR2 in myeloid cells (IFNgR2-Delta-Mye). We performed an orthotopical injection of cells derived from conditional murine pancreatic model (Pdx1Cre-Kras-P53, or “KPC” cells) into IFNgR2-LysMCre (IFNgR2-Delta-Mye) mice. Ablation of IFN-γ signaling in myeloid cells led to a higher tumor burden compared to controls. Subsequent RNA sequence analysis demonstrated that IFN-γR2 deficiency in myeloid cells resulted in increased TGFβ1 gene expression as well as changes in metabolic and growth factor pathways in macrophages isolated from tumor tissue. Immunofluorescent analysis demonstrated that IFN-γR2 deletion in myeloid cells led to changes in cancer cell differentiation, resulting in a loss of characteristic epithelial histological pattern and shifting it towards more aggressive phenotype, possible via TGFβ1 dependent mechanism. Using murine model of liver metastasis, we found that loss of IFN-γR2 in myeloid cells leads to increased metastatic outgrowth of PDAC KPC cells. This effect was partially dependent on the gut microbiota, as shown by “separated and co-housed mice” experiments. Deficiency of IFN-γR2 in myeloid cells resulted in increased recruitment and infiltration of monocytes in normal and tumor/metastatic liver tissues. Our data identifies myeloid cell type specific IFN-γ signaling pathway as an important regulator of pancreatic cancer progression and metastasis, that can be potentially exploited as a novel immunooncology target.
Citation Format: Elena Ivleva, Natalia Andreeva, Sergei Grivennikov. IFN-γ signaling in myeloid cells regulates pancreatic cancer growth and progression [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 2117.
Abstract 2129: Spatial charting of single cell transcriptomes in tissues
Authors: Wei Runmin , He Siyuan , Bai Shanshan , Sei Emi , Hu Min , Thompson Alastair , Chen Ken , Krishnamurthy Savitri , Navin Nicholas 
Published: June 2022

Abstract
Single cell RNA sequencing (scRNA-seq) methods can profile the transcriptomes of single cells but cannot preserve spatial information. Conversely, spatial transcriptomics (ST) assays can profile spatial regions in tissue sections but do not have single cell genomic resolution. To address this issue, computational approaches (e.g., cell2location, RCTD) have been designed to deconvolute ST spots into proportions of different cell types. However, the spatial deconvolution method has the following limitations, 1) it can only infer cell type proportions of each spot and cannot reach higher granular "cell states" mapping; 2) it only predict categorical labels and cannot infer continuous cell information (e.g., lineage trajectories, gene signatures, continuous phenotypes) at a spatial resolution.
Here, we developed a computational approach called CellTrek that combines these two datasets to achieve single cell spatial mapping. Using a machine learning-based metric learning approach, CellTrek learned a cell-spot graph and then transfer spatial coordinates to cells. The CellTrek toolkit also provides two downstream analysis modules, including SColoc for spatial colocalization analysis and SCoexp for spatial co-expression analysis.
We benchmarked CellTrek using a simulation and two in situ datasets. We then applied CellTrek to reconstruct cellular spatial structures in existing datasets from normal mouse brain and kidney tissues. We also performed scRNA-seq and ST experiments on two ductal carcinoma in situ (DCIS) tissues and applied CellTrek to identify subclones that were restricted to different ducts, and specific T cell states adjacent to the tumor areas.
Our data shows that CellTrek can accurately map single cells in diverse tissue types to resolve their spatial organization into cellular neighborhoods and tissue structures. This method provides a new paradigm that is distinct from ST deconvolution, enabling a more flexible and direct investigation of single cell data with spatial topography.
Citation Format: Runmin Wei, Siyuan He, Shanshan Bai, Emi Sei, Min Hu, Alastair Thompson, Ken Chen, Savitri Krishnamurthy, Nicholas Navin. Spatial charting of single cell transcriptomes in tissues [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 2129.
Abstract 2193: Subsets of cancer cells expressing CX3CR1 are endowed with metastasis-initiating properties and resistance to chemotherapy
Authors: Zhang Jieyi , DiNatale Anthony , Kaur Ramanpreet , Chen Qian , Marchioli Michael , Ipe Darin , Castelli Maria , McNair Christopher , Kumar Gaurav , Meucci Olimpia , Fatatis Alessandro 
Published: June 2022

Abstract
Metastasis-initiating cells (MICs) display stem cell-like features, cause metastatic recurrences and defy chemotherapy, which leads to patients’ demise. Here we show that prostate and breast cancer patients harbor contingents of tumor cells with high expression of CX3CR1, OCT4a (POU5F1) and NANOG. Impairing CX3CR1 expression or signaling hampered the formation of tumor spheroids by cell lines from which we isolated small subsets co-expressing CX3CR1 and stemness-related markers, similarly to patients’ tumors. These rare CX3CR1High cells show transcriptomic profiles enriched in pathways that regulate pluripotency and endowed with metastasis-initiating behavior in murine models. Cancer cells lacking these features (CX3CR1Low) were capable of re-acquiring CX3CR1-associated features over time, implying that MICs can continuously emerge from non-stem cancer cells. CX3CR1 expression also conferred resistance to docetaxel, and prolonged treatment with docetaxel selected CX3CR1High phenotypes with de-enriched transcriptomic profiles for apoptotic pathways. These findings nominate CX3CR1 as novel marker of stem-like tumor cells and provide conceptual ground for future development of approaches targeting CX3CR1 signaling and (re)expression as therapeutic means to prevent or contain metastasis initiation.
Citation Format: Jieyi Zhang, Anthony DiNatale, Ramanpreet Kaur, Qian Chen, Michael Marchioli, Darin Ipe, Maria Castelli, Christopher McNair, Gaurav Kumar, Olimpia Meucci, Alessandro Fatatis. Subsets of cancer cells expressing CX3CR1 are endowed with metastasis-initiating properties and resistance to chemotherapy [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 2193.