bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 3817: A single-cell, spatial multiomics atlas and cellular interactome of all major skin cancer types
Authors: Grice Laura , Ni Guiyan , Jin Xinnan , Tran Minh , Killingbeck Emily , Gregory Mark , Mulay Onkar , Teoh Siok-Min , Kulasinghe Arutha , Leon Michael , Murphy Sarah , Warren Sarah , Kim Youngmi , Nguyen Quan 
Published: June 2022

Abstract
Skin cancer is by far the most common cancer, encompassing squamous cell carcinoma (SCC), basal cell carcinoma (BCC), and melanoma. The diversity of cell types and tissue organisation in skin cancer remains poorly understood yet is required to improve diagnosis and treatment. In this work, we integrated six imaging and sequencing technologies to build the first spatial single cell reference for all three major skin cancer types and create a comprehensive skin cancer interactome. Using single-cell RNA-Seq (RNA) of &gt;100,000 cells from 11 paired patient biopsies, we identified 28 SCC cell types, including 10 immune cell types, and found core suites of 39 cancer genes and 222 healthy genes shared across ≥80% patient samples. Using independent Nanostring Digital Spatial Profiling (RNA, protein), we validated most immune cell types and gene markers at protein and RNA levels. The enrichment of an immune signalling signature in SCC was further revealed by spatial Nanostring Single Molecular Imaging - SMI (RNA). Strikingly, we found the high consistency in mapping cell types in scRNAseq data and the independent SMI data, for example, the distribution of the three keratinocyte layers (basal, cycling and differentiated). This observation suggested the power of combining scRNAseq data with spatial SMI data. Furthermore, we implemented three approaches to validate the spatial distribution and cell type co-localisation by both Visium Spatial Transcriptomics (RNA), SMI (RNA) and Opal Multiplex Polaris (protein). Finally, cell-cell interactions were inferred at the global level using scRNAseq data (no spatial information) and Visium data (with spatial dimension), which were then validated at high throughput (517 ligands/receptors) and single-cell resolution using SMI. These in situ interaction maps were built across all three cancer types to create a comprehensive spatial interaction atlas of skin cancer. We also used targeted approaches with Polaris (protein) and RNAScope (RNA) to confirm and visualise clinically-important ligand-receptor pairs, including checkpoint inhibitor drug targets PD-1 and PD-L1. By integrating six distinct yet complementary spatial and single cell technologies, this study highlights the power of a spatial multi-omics approach for understanding cell types and their activities in cancer tissues.
Citation Format: Laura Grice, Guiyan Ni, Xinnan Jin, Minh Tran, Emily Killingbeck, Mark Gregory, Onkar Mulay, Siok-Min Teoh, Arutha Kulasinghe, Michael Leon, Sarah Murphy, Sarah Warren, Youngmi Kim, Quan Nguyen. A single-cell, spatial multiomics atlas and cellular interactome of all major skin cancer types [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 3817.
Abstract 3825: Germline modifiers of the tumor immune microenvironment reveal drivers of immunotherapy response
Authors: Pagadala Meghana , Wu Victoria , Pérez-Guijarro Eva , Kim Hyo , Castro Andrea , Talwar James , Gonzalez-Colin Cristian , Cao Steven , Schmiedel Benjamin J. , Sears Timothy , Goudarzi Shervin , Kirani Divya , Salem Rany M. , Morris Gerald P. , Harismendy Olivier , Patel Sandip P. , Mesirov Jill P. , Zanetti Maurizio , Day Chi-Ping , Fan Chun C. , Thompson Wesley K. , Merlino Glenn , Gutkind J. Silvio , Vijayanand Pandurangan , Carter Hannah 
Published: June 2022

Abstract
With the continued promise of immunotherapy as an avenue for treating cancer, understanding how host genetics contributes to the tumor immune microenvironment (TIME) is essential to tailoring cancer risk screening and treatment strategies. Using genotypes from over 8,000 European individuals in The Cancer Genome Atlas and 137 heritable tumor immune phenotype components (IP components), we identified and investigated 532 TIME-SNPs. Focusing on 77 variants that were relevant to cancer risk, survival, or treatment response, we explored their potential to reveal novel targets for immunotherapy. Many variants overlapped regions with histone marks indicating active transcription, and influenced gene activities in specific immune cell subsets, such as macrophages and dendritic cells. TIME-SNPs implicated genes such as LAIR1, TREX1, CTSS, CTSW and LILRB2 were differentially expressed between responders and non-responders to immune-checkpoint blockade (ICB) in preclinical studies. Of these, LILRB2 and LAIR1 have already been identified as putative targets for immunotherapy. Here we found that inhibition of CTSS led to better tumor control and survival in murine models, alone or in combination with anti-PD-1. Collectively we show that through an integrative approach, it is possible to link host genetics to TIME characteristics, informing novel biomarkers for cancer risk and target identification in immunotherapy.
Citation Format: Meghana Pagadala, Victoria Wu, Eva Pérez-Guijarro, Hyo Kim, Andrea Castro, James Talwar, Cristian Gonzalez-Colin, Steven Cao, Benjamin J. Schmiedel, Timothy Sears, Shervin Goudarzi, Divya Kirani, Rany M. Salem, Gerald P. Morris, Olivier Harismendy, Sandip P. Patel, Jill P. Mesirov, Maurizio Zanetti, Chi-Ping Day, Chun C. Fan, Wesley K. Thompson, Glenn Merlino, J. Silvio Gutkind, Pandurangan Vijayanand, Hannah Carter. Germline modifiers of the tumor immune microenvironment reveal drivers of immunotherapy response [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 3825.
Abstract 383: ONCR-021 as a systemic intravenous synthetic RNA virus immunotherapy for the repeat treatment of cancer
Authors: Bryant Jeffrey , Denslow Agnieszka , Hewett Jacqueline , Cong Lingxin , De Almeida Ana , Lee Jennifer , Jacques Judy , Feau Sonia , Wambua Daniel. , Yanez Adrienne , Wang Pam Shou-Ping , Deterling Jessica , Scott Matthew , Auer Jason , Haines Brian B. , Quéva Christophe , Lerner Lorena , Kennedy Edward M. 
Published: June 2022

Abstract
Oncolytic viruses (OV) have shown great potential to improve clinical outcomes when dosed intratumorally, however, their therapeutic efficacy when intravenously administered is likely limited by the rapid emergence of neutralizing antibodies. To overcome this limitation, we developed Synthetic RNA viruses consisting of a replication competent viral genomic RNA (vRNA) encapsulated within a lipid nanoparticle (LNP) for IV administration. Upon dosing and delivery of this infectious RNA payload, the vRNA initiates viral replication and virus production in neoplastic cells leading to oncolysis and tumor destruction. This formulation enables repeat intravenous dosing of a replication competent oncolytic virotherapy even in presence of circulating neutralizing antibody to the virus. Here we present ONCR-021, an LNP formulation of Coxsackievirus A21 (CVA21) vRNA. ONCR-021 vRNA encodes a novel ICAM1-dependent strain of CVA21 that results in greater in vitro and in vivo oncolysis compared to the previously described CVA21 Kuykendall strain. ONCR-021 is broadly oncolytic in cancer cell lines in vitro and is intended for clinical development in NSCLC, RCC, and HCC based upon the viral tropism. IV-administration of ONCR-021 vRNA results in rapid initiation of viral replication, oncolysis, and potent anti-tumor efficacy, even in the presence of circulating CVA21 neutralizing antibodies. This efficacy is principally driven by CVA21 amplification in situ after delivery to tumor cells and we demonstrate viral replication, virion production and spread within the tumor after dosing. We also observe only modest and transient production of CVA21 in healthy tissues of transgenic mice expressing the CVA21 entry receptor human ICAM1. Consistent with these findings, high doses levels of ONCR-021 were well-tolerated in this model. Altogether, these preclinical data support the development of ONCR-021, a novel synthetic oncolytic virus designed to overcome the challenges of repeat intravenous administration of viral immunotherapy for the treatment of disseminated cancers.
Citation Format: Jeffrey Bryant, Agnieszka Denslow, Jacqueline Hewett, Lingxin Cong, Ana De Almeida, Jennifer Lee, Judy Jacques, Sonia Feau, Daniel. Wambua, Adrienne Yanez, Pam Shou-Ping Wang, Jessica Deterling, Matthew Scott, Jason Auer, Brian B. Haines, Christophe Quéva, Lorena Lerner, Edward M. Kennedy. ONCR-021 as a systemic intravenous synthetic RNA virus immunotherapy for the repeat treatment of 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 383.
Abstract 3835: Kindlin-2 complexes containing α6β1 integrin are responsive to hypoxia
Authors: Hernandez-Cortes Daniel , Gard Jaime M.C. , Knudsen Beatrice S. , Warfel Noel A. , Cress Anne E. 
Published: June 2022

Abstract
The laminin-binding integrins are mechanosensory receptors critical for cell adhesion and structural organization that link the extracellular matrix (ECM) to the cytoskeleton. Integrin α6β1 is associated with prostate cancer (PCa) migration, invasion, metastasis, and decreased cancer-specific survival. Kindlin-2 (FERMT2) is a β1 integrin adaptor and mechanosensory focal adhesion (FA) protein that activates and clusters integrins in response to structural ECM alterations in the tumor microenvironment. Our goal was to determine if integrin-kindlin-2 adhesion complexes (kindlin-2:α6β1) were responsive to hypoxia, a physiologically relevant and altered microenvironment in PCa progression. Five different endpoints were tested including the biochemical analysis of kindlin-2 complexes, qRT-PCR, immunoblotting, immunocytochemistry, and electric cell impedance sensing (ECIS). Using DU145 prostate cancer cells grown under hypoxia (1% O2) for up to 16 hours, the results showed a reversible increase in kindlin-2:α6β1 complexes with maximal assembly within 4 hours and disassembly starting by 8 hours. Notably, kindlin-2:α6β1 complexes were found exclusively within membrane projections and were not observed within hypoxia-inducible paxillin (PXN)-containing FAs. The hypoxia induced kindlin-2:α6β1 complexes and classical FAs were dependent on kindlin-2 as determined by CRISPR-Cas9 heterozygous deletion of FERMT2. Protein co-localization of α6 integrin and PXN with kindlin-2 within membrane projections and FAs, respectively, was also induced under hypoxia. Further, non-invasive ECIS measurements in live cells confirmed functional cell-cell and cell-ECM dynamics driven by hypoxia and requiring kindlin-2. Our results indicate that the kindlin-2:α6β1 complexes are uniquely associated with FA-independent membrane projections induced by hypoxia, a tumor microenvironment associated with aggressive prostate cancer. The novel kindlin-2:α6β1 complexes may represent an actionable pharmacological target for blocking escape of organ confined disease and metastasis promoting steps of human prostate cancer.
(Partially supported by NIH grants CA P30 23074, DOD W81XWH-19-1-0455, and NCI R01 CA242226).
Citation Format: Daniel Hernandez-Cortes, Jaime M.C. Gard, Beatrice S. Knudsen, Noel A. Warfel, Anne E. Cress. Kindlin-2 complexes containing α6β1 integrin are responsive to hypoxia [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 3835.
Abstract 3836: Mapping the interactome of the endogenous metalloproteinase inhibitor TIMP2 using extracellular proximity labeling (ePL)
Authors: Peeney David , Gurung Sadeechya , Liu Yueqin , Lazaroff Carolyn , Richie Christopher , Stetler-Stevenson William G. 
Published: June 2022

Abstract
Tissue inhibitors of metalloproteinases (TIMPs) are a family of endogenous proteins that were initially defined by their ability to inhibit the enzymatic activity of matrix metalloproteinases (MMPs), the major mediators of ECM breakdown and turnover. TIMPs are important regulators of ECM structure, function and homeostasis. Since their original discovery, additional MMP-independent functions have been attributed to TIMP family members leading to their designation as multifunctional proteins with discrete functional domains. TIMP2 is a unique family member, with a broad expression profile that is expressed in both normal and diseased tissues, even in those with minimal metalloproteinase activity. Understanding the functional transformation of matrisome regulators, like TIMP-2, during the dynamic evolution of tissue microenvironments associated with disease progression is essential to the development of ECM targeted therapeutics. This knowledge may also garner understanding of therapeutic resistance and the failure of conventional and next-generation cancer therapies. Interactome studies are predominantly performed in non-living systems, and very rarely performed in complex culture systems such as 3D spheroids/co-cultures. To investigate the TIMP-2 interactome in complex biological systems we recently developed carboxyl- and amino-terminal fusion genes of TIMP-2 with the promiscuous biotinylating peptides BioID2 and TurboID. Packaged for retroviral delivery, this system gives us great flexibility in assessing the TIMP-2 interactome in simple versus complex 3D co-culture systems. We show, for the first time, that conditions can be optimized to support proximity labeling reactions in the extracellular milieu, representing an important technical resource for extracellular matrix biologists. Using this method, we identify novel interacting partners for TIMP-2 that provide insight into the tissue-specific actions of this protein in both healthy and diseased tissues.
Citation Format: David Peeney, Sadeechya Gurung, Yueqin Liu, Carolyn Lazaroff, Christopher Richie, William G. Stetler-Stevenson. Mapping the interactome of the endogenous metalloproteinase inhibitor TIMP2 using extracellular proximity labeling (ePL) [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 3836.
Abstract 3857: A novel microfluidic platform for understanding the role of PDAC stroma in immune response
Authors: Geyer Marlene , D'Agosto Sabrina , Lanz Henriëtte , Corbo Vincenzo , Joore Jos , Queiroz Karla S. 
Published: June 2022

Abstract
Pancreatic Ductal Adenocarcinoma (PDAC), the most common pancreatic cancer type is estimated to become the second leading cause of cancer-related deaths by 2030 with mortality rates of up to 93%. PDAC is characterized by high-density stroma and an immunosuppressive tumor microenvironment that lead to a lack of efficacy of immunotherapeutic strategies. Those facts highlight the urgent need for more relevant PDAC in vitro models that support the discovery of novel (immuno-)therapies. Here, we describe the establishment of a multiple cell type culture in a microfluidic platform that will be applied for modeling immune and stroma cell interplay in PDAC. Microfluidic platforms such as the OrganoPlate® support 3D growth and inclusion of different cell types cultured under flow conditions. The aim of this project was to determine the involvement of stromal cells such as endothelial cells and pancreatic stellate cells in immune cell recruitment in pancreatic cancer. In order to generate a more relevant culture set up, supporting cells and PDAC organoids were used in the 3-lane OrganoPlate® to study immune cell recruitment. Migration of fluorescently labelled peripheral blood mononuclear cells from vasculature through the stromal compartment to the PDAC organoids was tracked for 72h using confocal microscopy. Migration of immune cells to the tumor cell compartment was significantly inhibited by the stromal compartment, thus confirming in vivo immune responses, as the stroma seems to form both a physical as well as a chemical barrier for immune cells to reach the active tumor site. Interestingly, PDAC organoid conditioned medium efficiently attracts immune cells into the tumor compartment, indicating that secreted factors play a relevant role in immune cell recruitment. Despite the positive effect on recruitment and immune-tumor cell interaction, a lack of tumor cell killing is observed. The co-culture of PDAC organoids with stromal and immune cells grown on-a-Chip as described in this study indicates the suitability of microfluidic platforms for generating complex models and its use for dissecting complex cellular interplay and processes involved in the lack of anti-tumor immune responses in PDAC.
Citation Format: Marlene Geyer, Sabrina D'Agosto, Henriëtte Lanz, Vincenzo Corbo, Jos Joore, Karla S. Queiroz. A novel microfluidic platform for understanding the role of PDAC stroma in immune response [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 3857.
Abstract 3871: Solid tumor analytical validation of a T-regulatory immunohistochemistry multiplex for clinical studies
Authors: Gérus-Durand Marie , Baranova Elena , Tliba Maroua , Iglesias Sabine , Motte Manon , Burrer Renaud , Finan-Marchi Amanda 
Published: June 2022

Abstract
While classic, chromogenic immunohistochemistry (IHC) remains a mainstay in clinical diagnostics, it can be limiting in the era of immuno-oncology. In the field of immuno-oncology, where access to tissue samples may be limited, there is a need for an accurate interpretation of the sociology and in-depth phenotyping of the cells in the tumor microenvironment that requires a higher level of targets to investigate. Cytotoxic T cells are the main effector cells against tumors. Conversely, T-regulatory cells play a more pro-tumor role by suppressing cytotoxic T cell activation. The importance of the balance and tumor infiltration of these two cell populations has repeatedly been demonstrated in the literature. Due to this, Cerba Research was driven to develop an immunofluorescent multiplex to allow cytotoxic and regulatory T cells detection on the same tissue section for use in solid tumor clinical trials. Following our standard workflow, we developed a CD3-CD8-FoxP3 IHC multiplex (Histoprofile®- T-reg light). This panel allows for analysis of cytotoxic T-cells (CD3+/CD8+/FoxP3-), T helper cells (CD3+/CD8-/FoxP3-) and T regulatory cells (CD3+/CD8-/FoxP3+). Then following our standard process, we performed an analytical validation on a range of formalin fixed paraffin embedded solid tumors (including but not limited to Non Small Cell Lung Cancer, Head and Neck Squamous Cell Carcinoma, Colorectal Cancer and Breast Cancer). Specificity was verified by a pathologist on control tonsil tissue. The robustness of the protocol on a range of solid tumors was verified by the pathologist on tissue blocks and tumor microarrays. Precision tests (intra- and inter-assay) demonstrated a high level of panel reproducibility in solid tumor tissues - CD3 (CV 21.24%), CD8 (CV 19.5%), FoxP3 (CV 13.13%). Using Halo® software (Indica Labs), spatial analysis of the populations of interest can be appreciated in the tumor and stroma compartments. Cerba Research’s Histoprofile®- T-reg light panel passed all the analytical validation criteria for use in clinical studies. Cerba Research can provide this off the shelf panel in solid tumor clinical studies, allowing an elevated analysis of multiple immune biomarkers on a single tissue slide.
Citation Format: Marie Gérus-Durand, Elena Baranova, Maroua Tliba, Sabine Iglesias, Manon Motte, Renaud Burrer, Amanda Finan-Marchi. Solid tumor analytical validation of a T-regulatory immunohistochemistry multiplex for clinical studies [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 3871.
Abstract 3872: Overexpression of miR-200 in cancer-associated fibroblasts suppresses the migration and invasion of cancer cells in co-culture systems
Authors: Cheon Inyoung , Lee Sieun , Ahn Young-Ho 
Published: June 2022

Abstract
Cancer-associated fibroblasts (CAFs) promote cancer progression and metastasis in the tumor microenvironment. CAFs are regulated by diverse processes including regulation by microRNAs (miRNAs). To profile miRNAs involved in the regulation of CAF activation, we performed the NanoString nCounter® assay in mouse CAFs and normal lung fibroblasts (LFs). Among the miRNAs differentially expressed between CAFs and LFs, miR-200 family members were significantly downregulated in CAFs. Overexpression of miR-200 in CAFs suppressed the migration and invasion of lung cancer cells in co-culture systems (transwell migration and spheroid invasion assays). Next, we tried to identify novel miR-200 target genes based on RNA sequencing data obtained from control and miR-200-overexpressed CAFs, lung adenocarcinoma TCGA data, and TargetScan. We are now studying on these candidates to see whether they are involved in the interaction between CAFs and cancer cells.On the basis of these findings, we conclude that miR-200 suppresses the interaction between CAFs and lung cancer cells in the tumor microenvironment.
Keywords: cancer-associated fibroblasts, miR-200, lung cancer, tumor microenvironment, invasion
Citation Format: Inyoung Cheon, Sieun Lee, Young-Ho Ahn. Overexpression of miR-200 in cancer-associated fibroblasts suppresses the migration and invasion of cancer cells in co-culture systems [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 3872.