bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 5503: Ultrahigh-plex spatial phenotyping of head and neck cancer tissue uncovers multiomic signatures of immunotherapy response
Authors: Pratapa Aditya , Hernandez Lydia , Cheikh Bassem Ben , Jhaveri Niyati , Kulasinghe Arutha 
Published: March 2024

Abstract
Background Targeted immune checkpoint inhibitors (ICI) with anti-PD-1/PD-L1 therapy offer durable treatment of mucosal head and neck squamous cell cancer (HNSCC), in both human papillomavirus-positive (HPV+) and negative (HPV-) patients. However, currently available biomarker signatures for targeted ICI therapies have limited predictive value. Our recent ultrahigh-plex profiling of HNSCC tissue with 100+ cancer hallmarks of tumor and immunobiology uncovered distinct spatial domains that serve as defining factors for clinical response and resistance.
Methods Our unbiased analysis of whole-slide metastatic HNSCC tumors is from a clinical cohort of patients treated with Pembrolizumab/Nivolumab. The cohort consisted of patients with a range of outcomes from complete vs partial vs progressive disease responses to ICI therapy. We first characterized the tumor microenvironment using our ultrahigh-plex protein panel with 100+ antibodies on the PhenoCycler®-Fusion platform. To expand upon our biomarker discovery, we included multiomic cancer hallmarks with a multimodal protein/RNA detection panel. Targeted spatial RNA detection was performed to complement and augment the microenvironment characterization achieved by our protein panel. To further consolidate the multiomic data, we leveraged MaxFuse, a state-of-the art computational framework that integrates multimodal spatial and single-cell expression data.
Results Our multiomic spatial phenotyping uncovered diverse tumor regions, each with distinct biomarker expression that is reflected across modalities including protein, RNA, and metabolic activity, indicating regions likely associated with resistance to immunotherapy. Our multiomic data integration also revealed spatial signatures associated with different tissue compartments, such as the tumor and non-tumor associated tertiary lymphoid structures.
Conclusions We demonstrate a multi-pronged approach that incorporated both novel experimental and computational techniques for elucidating tumor microenvironment in HNSCC tissue prior to ICI-based immunotherapy. Our multiomic approach provides deeper characterization of the HNSCC at the transcriptomic and proteomic level incorporating depth across the entire transcriptome and single-cell spatial resolution of key protein determinants for predicting and furthering our understanding of immunotherapy response to ICI therapy.
Citation Format: Aditya Pratapa, Lydia Hernandez, Bassem Ben Cheikh, Niyati Jhaveri, Arutha Kulasinghe. Ultrahigh-plex spatial phenotyping of head and neck cancer tissue uncovers multiomic signatures of immunotherapy response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5503.
Abstract 5523: granulocyte-colony stimulating factor secreted from cancer associated fibroblasts initiates tumorigenesis and metastasis in triple negative breast cancer
Authors: Gotoh Noriko , Tacheuchi Yasuto , Murayama Takahiko , Kashimura Risa , Ikeda Kazuhiro , Horie Kuniko , Inoue Satoshi , Okamoto Koji 
Published: March 2024

Abstract
Although cancer stem-like cells (CSCs) interact with cancer-associated fibroblasts (CAFs), it remains obscure how it occurs and what are the functional roles of this interaction. When patient-derived breast cancer cells (BCCs) were co-cultured with CAFs, significantly more spheroids were formed compared to those cells cultured alone. This suggests that CAFs produce soluble factors that increase the tumor-initiating ability of CSCs. Transcriptome analysis revealed that the expression of granulocyte colony stimulating factor (G-CSF) was highly upregulated in the conditioned medium of CAFs co-cultured with BCCs. Tumor-initiating ability was increased in the presence of G-CSF. Furthermore, G-CSF neutralizing antibody treatment suppressed tumorigenesis and bone metastasis in the patient-derived xenograft (PDX) model. These findings indicate that G-CSF secreted by CAFs induces CSCs to initiate tumors and metastasis. Inhibition of G-CSF would be a novel therapeutic target for breast cancer.
Citation Format: Noriko Gotoh, Yasuto Tacheuchi, Takahiko Murayama, Risa Kashimura, Kazuhiro Ikeda, Kuniko Horie, Satoshi Inoue, Koji Okamoto. granulocyte-colony stimulating factor secreted from cancer associated fibroblasts initiates tumorigenesis and metastasis in triple negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5523.
Abstract 5553: Glycan CA19-9 mediated immune modulation in the pancreatic tumor microenvironment
Authors: Hsu Jasper , Oh Tae Gyu , Peck Kristina L. , Rock Angelica E. , Bishop Garret , Okhovat Shira R. , Kaech Susan M. , Engle Dannielle D. 
Published: March 2024

Abstract
Pancreatic ductal adenocarcinoma (PDA) is an intractable common malignancy with a pro-tumorigenic and immunosuppressive microenvironment (ME) that often limits treatment efficacy. Only 10-15% of patients are eligible for surgical resection, which is the only cure for PDA. The glycan CA19-9 is used to follow treatment response in PDA patients, but its functional role in PDA remained unknown until recently because rodents lack the ability to produce this carbohydrate. CA19-9 elevation in a KRAS-mutant background results in increased tumor proliferation and ME remodeling in mice. The tumor ME is encompassed by hypovascularized stroma consisting of cancer associated fibroblasts (CAFs) and tumor associated macrophages (TAMs) that contribute to desmoplasia and immunosuppression. All prior work investigating the tumor ME in PDA mouse models was performed in CA19-9 negative context, potentially missing a key element of PDA biology. Elevation of CA19-9 in mice caused expansion of both antigen-presenting (ap)CAFs and TAMs. CA19-9 induction in KRAS-mutant organoids increased gene expression of M-CSF, IL1a, and TGFb and led to increased apCAF and TAM differentiation. This project aims to uncover the mediators of CA19-9-mediated ME remodeling. CA19-9-modified macrophage colony-stimulating factor (M-CSF) was identified via immunoprecipitation and mass spectrometry from KRAS-mutant CA19-9-inducible pancreatic organoids. CA19-9-M-CSF induced increased immunosuppressive TAM differentiation in vivo and in vitro using a novel Macrophage, Organoid, and Fibroblast (MOrF) co-culture platform. This project will identify the mechanisms by which CA19-9 directly contributes to PDA ME immune modulation and unveil essential molecular underpinnings of PDA biology that will inform effective therapies in the future.
Citation Format: Jasper Hsu, Tae Gyu Oh, Kristina L. Peck, Angelica E. Rock, Garret Bishop, Shira R. Okhovat, Susan M. Kaech, Dannielle D. Engle. Glycan CA19-9 mediated immune modulation in the pancreatic tumor microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5553.
Abstract 5556: An vascularized melanoma model for with unidirectional perfusion of circulating immune cells for advancing immune-oncology research
Authors: Torregrosa Manuel Caro , de Ruiter Sander , Burton Todd , Queiroz Karla , Allen Will , Komen Job , Trietsch Sebastiaan , Broek Lenie van den 
Published: March 2024

Abstract
Understanding the interactions between the tumor the vascular systems and circulating immune cells is crucial for elucidating mechanisms of immune cell recruitment in cancer and in exploring potential immunotherapeutic approaches. However, current in vitro models often lack the fidelity to replicate these intricate dynamics observed in vivo. The OrganoPlate Graft has been developed for perfusion of peripheral blood mononuclear cells (PBMCs) through a vascular bed with a melanoma monolayer (A375) to study aspects such as immune cell adhesion, extravasation and interaction with the tumor. The OrganoPlate Graft comprises 48 chips per plate, each designed to simulate the conditions of vascular beds. The device achieves flow through passive leveling, utilizing gravity to induce a pressure drop and unidirectional flow across the vascular bed in both positive and negative inclines. This approach avoids the complications and potential artifacts introduced by external pump, reduces complexity, and increases the throughput with up to 16 plates (768 chips) served by each OrganoFlow rocker. In experimental settings, formation of the vascular bed was seen to be consistent in plates and the introduction of the chemokine CXCL-12 led to the establishment of a gradient. Subsequently, PBMCs were observed to localize in clusters as a result of extravasation towards this gradient and the A375 monolayer. This behavior is consistent with known chemotactic responses in more complex in vivo environments. A notable observation was the sustained activity of PBMCs within the system. Cells continued to perfuse through the vascular bed for up to three days after seeding. In summary, the OrganoPlate Graft provides a platform for studying immune interactions in an immunocompetent vascular bed model. Its design and functionality allow for the exploration of immune cell behaviors in proximity to tumor cells, offering potential insights for immune-oncology research. The system's ability to mimic immune cell migration and extravasation in a controlled environment, and future potential to observe tumour killing makes it a valuable tool for advancing our understanding of immune-tumor interactions and may contribute to the development of novel immune-oncology therapeutic strategies.
Citation Format: Manuel Caro Torregrosa, Sander de Ruiter, Todd Burton, Karla Queiroz, Will Allen, Job Komen, Sebastiaan Trietsch, Lenie van den Broek. An vascularized melanoma model for with unidirectional perfusion of circulating immune cells for advancing immune-oncology research [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5556.
Abstract 5572: Microneedle-guided lymphatic delivery of a natural immune modulator toxin for enhanced cancer immunotherapy
Authors: Lim Su Yeon , Kim Byung Deok , LIU PIN , Shin Ju hwa , Jeong Ji Hoon 
Published: March 2024

Abstract
Cancer immunotherapy has demonstrated significant potential as a cancer treatment by enhancing the immune system's ability to recognize and eliminate cancer cells. However, its efficacy can be limited by factors such as tumor heterogeneity, immunosuppressive tumor microenvironments, and systemic toxicities. Recent advances in drug delivery systems have facilitated the development of more targeted and personalized cancer therapies. Microneedles have emerged as a promising platform for non-invasive and highly localized drug delivery, directly administering drugs, vaccines, and other therapeutic agents to the skin. In this study, we designed dissolving microneedles (dMN) based on a biocompatible amphiphilic tri-block copolymer, which enables the self-assembly of nano-micelles containing hydrophobic drugs when applied to the skin. We used the dMN technology to formulate SKKU-06, a hydrophobic natural immune modulator toxin derived from fungi, which exhibits anti-cancer and immunomodulatory properties in melanoma (SKKU-06@dMN). After intratumoral application of SSKU-06@dMN to skin tumors, the drug-loaded nano-micelles can migrate to tumor-draining lymph nodes (TDLN). The dMN-guided delivery of SKKU-06 to skin tumors and TDLN induced immunogenic cell death and stimulated the activation and maturation of antigen-presenting cells (APCs), promoting the development of humoral and cellular anti-tumor immunity. Furthermore, the immunomodulatory effects of SSKU-06@dMN were enhanced when combined with anti-PD-1 treatment, impacting the tumor microenvironment through increased intratumoral CD8+ T cell infiltration and reduced Treg populations. This resulted in efficient growth inhibition of established skin cancer and metastatic cancer, as well as prolonged survival. The dMN-guided lymphatic delivery of SKKU-06 demonstrates the potential for treating metastatic solid tumors and improving cancer immunotherapy efficacy by modulating the tumor microenvironment.
Citation Format: Su Yeon Lim, Byung Deok Kim, PIN LIU, Ju hwa Shin, Ji Hoon Jeong. Microneedle-guided lymphatic delivery of a natural immune modulator toxin for enhanced cancer immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5572.
Abstract 5578: Multi-omics approach reveals a SMAD4-deficiency signature, translational reprogramming and synthetic lethality in esophageal adenocarcinom
Authors: Milne Julia V. , Fujihara Kenji , Kusnadi Eric , Pechlivanis Maree , Thio Niko , Cabalag Carlos , Gulati Twishi , Gotovac Jovana , Simpson Kaylene , Duong Cuong , Furic Luc , Phillips Wayne , Clemons Nicholas 
Published: March 2024

Abstract
Esophageal adenocarcinoma (EAC) is a cancer of high mutation burden with negligible recurrent and druggable driver genes and, therefore, a paucity of options for targeted therapy. Mutation or loss of the tumor suppressor gene SMAD4 occurs in up to 20% of EAC cases, and we have previously shown that loss of SMAD4 is sufficient to promote EAC tumorigenesis in an in vivo xenograft model. The present study aimed to delineate the role of SMAD4 in EAC tumorigenesis and identify synthetic lethal interactions in SMAD4-deficient cancers as a novel approach for treating EAC.
Our multi-omics methodology integrated RNA-sequencing, proteomics, polysome-sequencing, reverse-phase protein arrays, and genome-wide CRISPR-Cas9 screening to unveil a SMAD4-deficiency signature and new therapeutic avenues for EAC. These data reveal a complex interplay between SMAD4 loss and regulation of mTOR signaling, with specific downstream effects to reprogram translation. SMAD4-deficient cells express decreased levels of 4E-BP1, the inhibitory binding partner of EIF4E, which is the rate-limiting component of the cap-dependent translation initiation complex. This was accompanied by increased mTOR activity, including phosphorylation and inactivation of 4E-BP1. We found that SMAD4-deficient cells exhibit vastly different polysome traces compared to their wildtype counterparts and preferentially upregulate cap-dependent translation, acquiring an addiction to translation of oncogenic mRNAs. Furthermore, perturbation of additional negative regulators of mTOR signaling in combination with SMAD4 knockout exacerbated these effects and accelerated tumorigenesis in vivo and growth of patient-derived organoids in vitro.
This work advances our knowledge of EAC tumorigenesis, provides new mechanistic insights into SMAD4-driven transformation as well as novel potential therapeutic avenues for SMAD4-deficient EAC.
Citation Format: Julia V. Milne, Kenji Fujihara, Eric Kusnadi, Maree Pechlivanis, Niko Thio, Carlos Cabalag, Twishi Gulati, Jovana Gotovac, Kaylene Simpson, Cuong Duong, Luc Furic, Wayne Phillips, Nicholas Clemons. Multi-omics approach reveals a SMAD4-deficiency signature, translational reprogramming and synthetic lethality in esophageal adenocarcinom [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5578.
Abstract 560: IGF1 induces the expression of CYR61 in metastatic prostate cancer
Authors: Ortiz Hernandez Greisha L. , Walker Mya , Woods-Burnham Leanne , Kittles Rick A. , Casiano Carlos A. , Neuhausen Susan 
Published: March 2024

Abstract
The cysteine-rich angiogenic inducer 61 (CYR61) is a member of the cellular communication network (CCN) protein family that can be induced by growth factors. CYR61-specific functions are dependent on cellular context. In prostate cancer (PCa), CYR61 contributes to cell growth and survival through its interactions with extracellular ligands, such as integrins avb3 and a6b4, in the extracellular matrix space. Interestingly, CYR61 contains an insulin-like growth factor-binding protein domain suggesting that it may interact with insulin-like growth factor-I (IGF1). High serum levels of IGF1 are directly linked to PCa development and recently have been studied as a predictor of metastatic disease. Given the important roles that IGF1 and CYR61 play in PCa and their potential interaction, it is critical to investigate their molecular interplay. The correlation between PCa aggressiveness and circulating levels of CYR61 and IGF1 is poorly studied. Our goal was to assess the contribution of CYR61-IGF1 interaction to PCa cell proliferation. Their combined role may explain a proportion of aggressive PCa. This study was designed to characterize the role of IGF1-induced expression of CYR61 in metastatic PCa cellular models and to determine if this interaction contributes to aggressive tumor properties (e.g., proliferation, migration, tumorsphere formation). Using immunoblotting, we demonstrated that CYR61 is upregulated in the metastatic cell line PC3. Furthermore, optimized knockdown of CYR61 using siRNA significantly reduced PC3 cell proliferation, viability, and prostasphere formation. To examine the underlying mechanisms associated with IGF1 signaling, we assessed the activation of either the PI3/Akt and MAPK pathways in PC3 cells with CYR61 silencing. CYR61 siRNA-mediated knockdown decreased activation of the PI3/Akt pathway but did not affect the MAPK pathway. In addition, we found that IGF1 induces protein expression of CYR61 in a time-dependent manner, validated by both immunoblotting and confocal microscopy. In conclusion, these data provided evidence that CYR61 expression is induced by IGF1, and its inhibition decreased the capacity of metastatic PCa cells to proliferate, indicating a potential utilization of CYR61 inhibition in the therapy of metastatic PCa.
Citation Format: Greisha L. Ortiz Hernandez, Mya Walker, Leanne Woods-Burnham, Rick A. Kittles, Carlos A. Casiano, Susan Neuhausen. IGF1 induces the expression of CYR61 in metastatic prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 560.
Abstract 5647: Investigating the role of AP-2α in melanomagenesis
Authors: Bartschat Nicholas , Chang Jeremy , Suraju Mohammed , Nagel Ryan , Li Zhijie , White Jeffrey , Kenny Colin , Weigel Ronald 
Published: March 2024

Abstract
Introduction: Transcription factor AP-2α (encoded by the TFAP2A gene) is a protein involved in the early development of multiple tissues, particularly the neural crest. Melanocytes are derived from the neural crest and their development appears to rely on AP-2α and its paralogues, along with master regulator MITF. Prior studies have indicated that AP-2α is a crucial regulator of melanoma metastasis. However, it is unclear if AP-2α plays a role in melanomagenesis. We sought to understand the role of AP-2α in melanomagenesis, hypothesizing that knock out (KO) of TFAP2A would suppress malignant potential in vitro and downregulate genetic pathways linked to malignant transformation.
Methods: TFAP2A KO was generated with a single-guide RNA CRISPR/Cas9 system targeting exon 3 of the gene in the human melanoma cell line A375. Tumorigenesis phenotype was assessed by evaluating contact-independent colony formation with the in vitro soft agar assay. To identify downstream regulatory programs controlled by TFAP2A, we then utilized RNA-seq and Gene Set Enrichment Analysis (GSEA, San Diego). RNA-seq was performed on four clones each for wildtype and TFAP2A KO samples and the resulting data was processed using GSEA to identify gene sets modified after TFAP2A KO.
Results: Targeting of TFAP2A with CRISPR/Cas9 effectively knocked out AP-2α protein expression in the A375 melanoma cell line. Colony formation on soft agar assay was significantly decreased after TFAP2A KO (P &lt; 0.01). RNA-seq revealed significant differential expression of 11,195 genes after TFAP2A KO. Gene sets with negative enrichment after TFAP2A KO included those overall higher in tumors versus normal tissue (FWER P = 0.003) and multiple signaling pathways related to malignant transformation such as TGF-β (FWER P = 0.003), MYC (FWER P = 0.009), KRAS (FWER P = 0.03), and Notch (FWER P = 0.043).
Conclusions: Our data suggests that TFAP2A plays a role in cutaneous melanomagenesis. TFAP2A may represent a therapeutic target for melanoma, though further pre-clinical studies are needed. We plan to further test this hypothesis in a melanoma mouse model with conditional TFAP2A KO under the control of inducible Cre recombinase driven by the mouse tyrosinase gene promoter.
Citation Format: Nicholas Bartschat, Jeremy Chang, Mohammed Suraju, Ryan Nagel, Zhijie Li, Jeffrey White, Colin Kenny, Ronald Weigel. Investigating the role of AP-2α in melanomagenesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5647.