bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 2250: Immuno-oncology study to profile the tumor microenvironment in multiple human cancers using high-plex imaging mass cytometry
Authors: Pfister Thomas D. , Lim Liang , Ouladan Shaida , Zabinyakov Nick , Raza Qanber , Loh Christina 
Published: April 2023

Abstract
Immune profiling of tumor tissues has become a key tool in understanding the complexity of the tumor microenvironment (TME), for predictive biomarker discovery, and in cancer treatment. The presence of tumor-infiltrating lymphocytes has been associated with benefit from therapy. Furthermore, the TME also contains immunosuppressive elements that can impede immune response. Imaging Mass Cytometry™ (IMC™) enables detailed assessment of cell phenotype and function using 40-plus markers simultaneously at subcellular resolution on a single slide without spectral overlap or background autofluorescence. High-plex IMC has enabled us to evaluate the TME in different cancer histologies including in highly autofluorescent tissue types like lung, hepatocellular carcinoma, and skin melanoma.
The Maxpar® Human Immuno-Oncology IMC Panel Kit (201508) was customized using antibodies from the Standard BioTools™ catalog to create panels for tissue-based immuno-oncology research. Data acquisition was performed using a Hyperion™ Imaging System. To facilitate cell segmentation, an IMC Cell Segmentation Kit (TIS-00001) was applied to enhance cell membrane boundaries. We applied a pixel classification approach and CellProfiler™ for single-cell segmentation. We used histoCAT™ for single-cell analysis to visualize protein expression in various cancer types via PhenoGraph clustering and t-SNE maps.
Our panels were applied to normal and cancer human tissue microarrays (TMAs) to phenotype and analyze cell populations in these tissues. We provide detailed analysis of the TME by classifying activation state of immune cell populations, epithelial-to-mesenchymal transition (EMT) progression, and composition of the extracellular matrix. In-depth single-cell analysis quantitatively evaluated the cellular makeup and immune cell component in the TME of cancer tissues and identified major tumor, immune, and stromal cell phenotypes. This work demonstrates the capability of IMC for quantitative and spatial identification of multiple immune parameters in the TME on a single slide of cancer patient samples (e.g. tumor microarray).
For Research Use Only. Not for use in diagnostic procedures.
Citation Format: Thomas D. Pfister, Liang Lim, Shaida Ouladan, Nick Zabinyakov, Qanber Raza, Christina Loh. Immuno-oncology study to profile the tumor microenvironment in multiple human cancers using high-plex imaging mass cytometry [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2250.
Abstract 2281: Dual immune checkpoint blockade induces analogous alterations in the dysfunctional CD8+ T cell and activated Treg compartment
Authors: van der Leun Anne M. , Traets Joleen J. , Vos Joris L. , Elbers Joris B. , Patiwael Sanne , Qiao Xiaohang , Machuca-Ostos Mercedes , Thommen Daniela S. , Haanen John B. , Schumacher Ton N. , Zuur Charlotte L. 
Published: April 2023

Abstract
Immune checkpoint blockade has shown clinical activity in a range of cancer types. To dissect the effect of neoadjuvant PD-1 and CTLA4 blockade on intratumoral T cells in head and neck squamous cell carcinoma, we analyzed immune infiltrates in tumor biopsies from responding and non-responding patients. At baseline, a higher ratio between active (4-1BB+) and inactive regulatory CD4+ T cells was associated with response to therapy. Furthermore, upon therapy, this active Treg population showed a profound decrease in responding patients. In an analogous process, intratumoral dysfunctional CD8+ T cells transitioned to a state of reduced activity and dysfunction in responding patients, while in non-responding patients, NK cells showed an increased cytotoxic transcriptional profile upon treatment. These data reveal the immunological changes in response to dual PD-1 and CTLA4 blockade, including a parallel remodeling of presumed tumor-reactive T cell compartments in responding patients, and indicate that the presence of an activated Treg compartment at baseline may predict response.
Citation Format: Anne M. van der Leun, Joleen J. Traets, Joris L. Vos, Joris B. Elbers, Sanne Patiwael, Xiaohang Qiao, Mercedes Machuca-Ostos, Daniela S. Thommen, John B. Haanen, Ton N. Schumacher, Charlotte L. Zuur. Dual immune checkpoint blockade induces analogous alterations in the dysfunctional CD8+ T cell and activated Treg compartment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2281.
Abstract 2314: Development of a 6-color multiplex Crystal Digital PCR assay for the detection of ESR1 and PIK3CA mutations in the plasma of metastatic breast cancer patients
Authors: Quillien Veronique , Corne Julien , Rouge Thibault De la Motte , Du Fanny Le , Godey Florence 
Published: April 2023

Abstract
Blood-based liquid biopsies have become a real asset for patient treatment management in the field of precision oncology over the past few years, as they allow quick and easy access to tumor genetic alterations of interest. The analysis of circulating tumor DNA (ctDNA) from these liquid biopsies is a particularly well-suited strategy for longitudinal monitoring of patients. In patients with HR+/HER2- metastatic breast cancer (MBC), early detection of ESR1 and PIK3CA mutations is a key element to better personalize disease management. Among the technologies currently used for liquid biopsies, digital PCR (dPCR) has the advantage of being among the fastest and least expensive, providing robust results along with unmatched sensitivity as compared to other methods. Until recently, however, dPCR has been previously limited by multiplex capability. The recent availability of the 6-color version of the naica® platform (Stilla Technologies) has allowed us to develop a single-well multiplexed assay that combines an 11 pathogenic mutation ESR1 assay with a 21 mutation PIK3CA assay, for a combined total of 32 ESR1 and PIK3CA mutations. Here we present data on this new high-plex dPCR panel. As ESR1 and PIK3CA analyses are often requested together, this new screening assay represents a significant saving of time and resources for the analysis of our MBC patients with a relative ease of implementation and analysis.
Citation Format: Veronique Quillien, Julien Corne, Thibault De la Motte Rouge, Fanny Le Du, Florence Godey. Development of a 6-color multiplex Crystal Digital PCR assay for the detection of ESR1 and PIK3CA mutations in the plasma of metastatic breast cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2314.
Abstract 2325: IRF1 displays opposing tumor cell-intrinsic and -extrinsic roles in anti-tumor immunity
Authors: Purbey Prabhat Kumar , Paul Manash K. , Iwamoto Keisuke S. , Daly Allison , Seo Joowon , Champhekar Ameya S. , Campbell Katie , Schaue Dorthe , McBride William H. , Dubinett Steven M. , Ribas Antoni , Smale Stephen T. , Scumpia Philip O. 
Published: April 2023

Abstract
Interferons (IFNs), including IFN-α/β and IFN-γ, are multifaceted cytokines critical for antitumor immunity but contribute to T cell exhaustion through immune checkpoints. Recently, tumor cell expression of IRF1 was shown to enhance antitumor immunity, but a comprehensive evaluation of how IRF1 regulates IFN responses in the tumor and host has not been performed. Here, we show that Irf1-/- mice display enhanced tumor growth of WT and Irf1-/- tumors, as they fail to recruit sufficient NK cells and cytotoxic T cell (CTL). However, Irf1-/- tumors in wild-type mice displayed rapid immunogenic control, expansion of intratumoral lymphoid cells with enhanced effector programs and diminished exhaustion programs when compared to WT tumors. Mechanistically, IRF1 positively regulates the expression of distinct subsets of anti-tumor immunity suppression genes including the CD274/PD-L1, TRAIL, and IDO-1 checkpoints but not the IFN-inducible chemokines CXCL9-11. Surprisingly, control of Irf1-/- tumors required host IFN-α/β signaling but not IFN-γ signaling, while PD-L1 overexpression only weakly restored tumor growth. Thus, IRF1 selectively regulates the effects of IFNs on tumor cells and the tumor microenvironment and may be targeted to boost anti-tumor immunity.
Citation Format: Prabhat Kumar Purbey, Manash K. Paul, Keisuke S. Iwamoto, Allison Daly, Joowon Seo, Ameya S. Champhekar, Katie Campbell, Dorthe Schaue, William H. McBride, Steven M. Dubinett, Antoni Ribas, Stephen T. Smale, Philip O. Scumpia. IRF1 displays opposing tumor cell-intrinsic and -extrinsic roles in anti-tumor immunity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2325.
Abstract 2331: Loss of LRRC15 in osteosarcoma cells disrupts extracellular matrix integration, intercellular communication, and differentiation
Authors: Mukherjee Sanjit , Jajoo Ankit , Zhu Jack , Pineda Marbin , Walker Robert , Purcell James , Helman Lee J , Meltzer Paul S. 
Published: April 2023

Abstract
Background: Leucine rich repeat containing 15 (LRRC15) is a 581 amino acid type 1 transmembrane protein that contains 15 leucine rich repeats. Cysteine clusters flank the LRR domain that functions as the collagen binding domain. LRRC15 has been found to be upregulated during osteogenic differentiation of mesenchymal stem cells, induced by TGFβ, and highly expressed in multiple solid tumors, notably in osteosarcoma (1). Antibody drug conjugates targeting LRRC15 have shown promising activity in pre-clinical studies (2).
Results: To investigate the function of LRRC15 in the osteosarcoma microenvironment, we generated inducible shRNA knockdown (KD) derivatives targeting 3’UTR and ORF regions of LRRC15 of four osteosarcoma cell lines. Using these models, we characterized the biological properties of LRRC15 knockdown under 2-D and 3-D growth conditions. We found that LRRC15 KD in 2-D culture resulted in reduced adhesion to extracellular matrix (ECM) components and impaired cell migration. In 3-D spheroid culture, LRRC15 KD severely impacted scaffold-free spheroid compaction and invasion of spheroids embedded in Matrigel. Dysregulation of multiple ECM, cell adhesion and communication pathways were revealed by transcriptomic analysis from samples collected at time points during the LRRC15 KD. Of interest, several key transcription factors including RUNX2, CTNNB1, and SP7 were downregulated in LRRC15 deficient cells.
Conclusion: Our comprehensive results establish the importance of LRRC15 as a critical cell-adhesion molecule essential for the maintenance of the osteogenic intercellular communication, invasion and differentiation revealing novel aspects of osteosarcoma cell-biology.
Reference:1.Purcell JW, Tanlimco SG, Hickson J, Fox M, Sho M, Durkin L, et al. LRRC15 Is a Novel Mesenchymal Protein and Stromal Target for Antibody-Drug Conjugates. Cancer Res 2018;78:4059-4072.2.Slemmons KK, Mukherjee S, Meltzer P, Purcell JW, Helman LJ. LRRC15 antibody-drug conjugates show promise as osteosarcoma therapeutics in preclinical studies. Pediatr Blood Cancer 2020:e28771.
Citation Format: Sanjit Mukherjee, Ankit Jajoo, Jack Zhu, Marbin Pineda, Robert Walker, James Purcell, Lee J Helman, Paul S. Meltzer. Loss of LRRC15 in osteosarcoma cells disrupts extracellular matrix integration, intercellular communication, and differentiation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2331.
Abstract 2380: Fluorescence labeling of human gastric cancer using novel tumor specific near infrared labeled antibodies
Authors: Cox Kristin E. , Turner Michael A. , Amirfakhri Siamak , Lwin Thinzar M. , Ghosh Pradipta , Obonyo Marygorret , Kelly Kaitlyn M. , Hoffman Robert M. , Yazaki Paul J. , Bouvet Michael 
Published: April 2023

Abstract
Introduction: Gastric cancer has a global incidence of ~1 million cases per year. Currently, complete surgical resection is the only opportunity for cure for patients. Bright labeling of tumor margins with tumor specific markers could improve outcomes. This report demonstrates the advantages of targeting gastric cancer with humanized anti-CEA and TAG-72 antibodies in mouse models.
Methods: A cell line of human gastric cancer, MKN45, and a patient-derived tumor, KG8, were used to create xenograft models. To establish orthotopic models for each, ~1mm tumor fragments were harvested from subcutaneous models of these lines and sutured to the lesser curvature of the stomach. Humanized versions of TAG-72 (huCC44) and CEA (M5A) were conjugated to the near infrared dye IRDye800CW. IgG was conjugated to IRDye800CW and used as a control. For CEA-IR800 and IgG-IR800, mice received 50 µg IV and were imaged after 72 hours. For Tag72-IR800, mice received 75 µg IV and were imaged after 96 hours. Fluorescence imaging was performed on the mice using the LI-COR Pearl Imaging System. A tumor to background ratio (TBR) was calculated by dividing mean fluorescence intensity of the tumor versus normal gastric tissue.
Results: Humanized anti-CEA and TAG-72 brightly labeled multiple mouse models of human gastric cancer (Table 1). The TBR for TAG-72 labeling of KG8 was 2.777. CEA had a superior TBR of 3.528 compared to 0.606 for the control (IgG) in KG8 models. In MKN models labelled with CEA, an excellent average TBR of 7.407 were seen compared to 0.668 for the control.
Conclusion: Humanized anti-CEA and TAG-72 antibodies conjugated to near-infrared fluorescent dyes provide specific labeling of gastric cancers in orthotopic models. These tumor-specific fluorescent antibodies are promising potential clinical tools for visualization of gastric cancer margins at the time of surgical resection and improved surgical outcomes.
Orthotopic Model Antibody Tumor to Background Ratio KG8 anti-TAG-72 2.777 KG8 anti-CEA 3.528 KG8 Control 0.606 MKN anti-CEA 7.407 MKN Control 0.668
Citation Format: Kristin E. Cox, Michael A. Turner, Siamak Amirfakhri, Thinzar M. Lwin, Pradipta Ghosh, Marygorret Obonyo, Kaitlyn M. Kelly, Robert M. Hoffman, Paul J. Yazaki, Michael Bouvet. Fluorescence labeling of human gastric cancer using novel tumor specific near infrared labeled antibodies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2380.
Abstract 2485: RAB31 interacts with AGR2 to respond to oxaliplatin resistance and epithelial-mesenchymal transition in colorectal cancer cells via the EGFR-independent pathway
Authors: Chen Chi-Long , Hsiao Michael 
Published: April 2023

Abstract
In the process of colonic epithelial carcinogenesis, the epithelial-mesenchymal transition may occur and bring metastatic ability and drug resistance. These events will affect patient outcomes and clinical treatment strategies. To this end, we investigated differentially expressed genes between several chemotherapy regimens in colon cancer cells through available transcriptomics datasets. We identified a member of the Rab family, RAB31, which is overexpressed after oxaliplatin treatment, while the other option is not (Irinotecan). We confirmed that RAB31 can enhance resistance to oxaliplatin in some overexpression models and that RAB31 has the ability to promote exocytosis and vesicle trafficking. Using shRNA as complementary models, we observed consistent trends when RAB31 function was discarded. Moreover, our evidence determined epithelial-mesenchymal transition (EMT)-related molecules responsive in the RAB31 bidirectional models, including CDH2, SNAI1, SNAI2 and TWIST1. The expression of RAB31 has an independent prognostic value in patients with colon cancer and is significantly positively correlated with mesenchymal markers. Furthermore, the interactome analysis selected RAB31 and AGR2 to form a direct protein interaction. This result differs from previous studies that did not rely on EGFR binding and signaling. Taken together, our study found that RAB31 can modulate oxaliplatin sensitivity and EMT status, which are additional chemotherapeutic strategies and independent prognostic factors for the treatment of colorectal cancer.
Citation Format: Chi-Long Chen, Michael Hsiao. RAB31 interacts with AGR2 to respond to oxaliplatin resistance and epithelial-mesenchymal transition in colorectal cancer cells via the EGFR-independent pathway [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2485.
Abstract 2487: Metastasis: Cancer cells that have turned on a Yamanaka-like pluripotency program
Authors: Bamdad Cynthia C. , Smagghe Benoit J. , Carter Mark G. , Grant Trevor J. , Reale Laura M. , Nash Michael J. , Walkley Danica M. , Nash Jac-Leen S. , Yi Kevin R. , Stewart Andrew K. 
Published: April 2023

Abstract
Purpose: To develop therapeutics to treat metastasis of solid tumor cancers. To overcome obstacles to developing anti-metastasis treatments by: 1) developing an animal model that reproducibly mimics cancer metastasis and does so within a reasonable timeframe; and 2) figuring out the basic science that drives metastasis.
Experimental: We discovered that all pluripotent human stem cells express a MUC1 cleavage product called MUC1* (muk 1 star). All MUC1 cleavage stops with the onset of differentiation and MUC1 goes back to its quiescent state. Over 75% of solid tumor cancers also express MUC1*. Overexpression of MUC1*, as well as enzymes that cleave MUC1 to MUC1* are predictors of poor prognosis. NME1 is a ligand of MUC1* that is secreted by both embryonic stem cells and cancer cells. As a dimer, NME1 dimerizes the MUC1* extra cellular domain to activate the MAP kinase growth pathway. In an embryo, the more stem cells there are, the more NME1 is secreted and it goes from the active dimer to an inactive hexamer (doesn’t bind MUC1*). The paradox was, “How do stem cells limit self-replication, but cancer cells do not?” Answer: A primitive growth factor, NME7AB, looks like a single chain dimer of NME1, so is always active, is expressed in the earliest, naïve stem cells and in metastatic cancer cells.
Unpublished Results: Growing cancer cells in recombinant NME7AB for 10 days transforms them into metastatic cells: 1) become non-adherent; 2) enter dormancy; 3) upregulate metastatic markers by 200-fold; 4) form sub-cu tumors in mice from as few as 50 cells; iv injection leads to total metastasis in 10 days; 5) the percent of injected tumor cells that were first grown in NME7AB determines the growth of the entire tumor. We developed a monoclonal antibody that blocks interaction of NME7AB and MUC1*. This antibody reverses established metastasis of breast cancers in animals. NME7AB should be turned off early in embryogenesis, but is aberrantly re-activated in metastatic cancers. Yamanaka factors OCT4, SOX2 and NANOG bind to the promoters of NME7, MUC1 and MMP16, an enzyme that cleaves MUC1 to MUC1* and exposes the cryptic binding site for NME7AB.
Conclusions: Primitive growth factor, NME7AB, drives metastasis of solid tumor cancers. Antibody that disrupts NME7AB-MUC1* interaction reverses metastasis in animals.
Citation Format: Cynthia C. Bamdad, Benoit J. Smagghe, Mark G. Carter, Trevor J. Grant, Laura M. Reale, Michael J. Nash, Danica M. Walkley, Jac-Leen S. Nash, Kevin R. Yi, Andrew K. Stewart. Metastasis: Cancer cells that have turned on a Yamanaka-like pluripotency program [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2487.
Abstract 251: Identification of therapeutic vulnerabilities by genome-wide CRISPR knockout library screening of colon cancer organoids
Authors: Buckhaults Phillip J. , Khalili Sana , Banister Carolyn , Gokare Prashanth R. , Pocalyko Dave , Bachman Kurtis 
Published: April 2023

Abstract
The promise of precision medicine is based on the idea that genetic alterations present only in tumor cells create vulnerabilities that can be targeted for therapeutic intent. In some instances, somatically mutated driver genes such as KRAS, BRAF or PIK3CA can be targeted with small molecule inhibitors specific for mutant oncoproteins. In other cases therapeutic vulnerability is an indirect consequence, such as response to immune checkpoint inhibitors caused by somatic inactivation of mismatch repair genes and subsequent creation of neo-antigens in tumors. Synthetic lethal vulnerabilities dependent on common somatic alterations would be highly specific therapeutic targets applicable to a large number of cancer patients. We sought to identify potential therapeutic vulnerabilities for colon cancer by performing a genome wide CRISPR knockout screen in a colon cancer organoid in both TP53-Wild-Type and TP53-Knockout backgrounds. We identified 1784 gene knockouts with TP53-dependent effects on Darwinian fitness. Examples include MDM2 and PPM1D knockouts, both of which selectively harmed the TP53 WT organoids. 250 gene knockouts selectively harmed the TP53 KO organoids and represent novel avenues for development of TP53 synthetic lethal targeted therapeutics. We also identified ~1000 gene knockouts under significant negative Darwinian selection in both TP53 WT and TP53 KO organoids which are not known to be common essential genes. Several of these organoid model specific vulnerabilities are in pathways that are downstream of the somatic mutations present in the tumor and are therefore candidates for highly-specific targeted therapeutic intervention. Examples include Werner’s pathway dependencies (WRN, EME1, MUS81) which are known to result from mismatch repair deficiency, WNT pathway dependencies (CTNNB1, PORCN) which result from RNF43 inactivating somatic mutation, and BRAF dependency resulting from its own activating oncogenic somatic mutation. In summary, genome-wide CRISPR knockout library screening of human colon cancer organoids can provide a comprehensive overview of dependencies interacting with either natural or engineered mutations and are a promising novel platform for discovering personalized or pathway based therapeutic targets. Future work will focus on target validation and additional primary screens using our biobank of tumor-normal organoid pairs.
Citation Format: Phillip J. Buckhaults, Sana Khalili, Carolyn Banister, Prashanth R. Gokare, Dave Pocalyko, Kurtis Bachman. Identification of therapeutic vulnerabilities by genome-wide CRISPR knockout library screening of colon cancer organoids [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 251.