bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 6769: Precise spatial multiplexing of protein biomarkers for immune profiling in tissue samples with chip cytometry
Authors: Kwarta Karen , Campbell Thomas , Northcutt Adam , Schwarz Spencer 
Published: April 2023

Abstract
Immunohistochemistry is the most widely used diagnostic technique in tissue pathology. However, IHC is associated with several limitations including the labeling of just a few markers per tissue section and limited quantification of cell populations. As a result of plex limitations, key insights about tumor biology are missed, which could be important for advancing our understanding of tumor biology and ultimately improving patient outcomes. Chip Cytometry is a novel image-based platform for precise spatial multiplexing that addresses these challenges by combining iterative immuno-fluorescent staining with high-dynamic range imaging to facilitate quantitative phenotyping with single-cell resolution. The platform enables simultaneous detection of dozens of markers on a single tissue section and enables accurate quantification of protein expression levels necessary to deeply profile single cells, understand interactions between key immune cells, and identify topographic biomarkers. Here we demonstrate how standard FCS files are generated from multichannel OME TIFF images, enabling identification of cellular phenotypes via flow cytometry-like hierarchical gating. Quantification of results reveal precise expression levels for each marker in the assay in each individual cell in the sample, while maintaining spatial information about each cell. Chip Cytometry has the potential to advance precision medicine in immuno-oncology and inform the discovery of novel biomarkers by enabling quantitative analysis of cellular phenotypes in the spatial context. The Chip Cytometry platform enables simultaneous detection of multiple protein markers on a single tissue section for deep immune cell profiling in the tumor microenvironment. Combined with the single-cell spatial information, such data sets provide an opportunity for the discovery of new complex multiplexed biomarker signatures to inform therapeutic development.
Citation Format: Karen Kwarta, Thomas Campbell, Adam Northcutt, Spencer Schwarz. Precise spatial multiplexing of protein biomarkers for immune profiling in tissue samples with chip 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 6769.
Abstract 6771: Interrogating the tumor-immune landscape with a novel automated RNAscope™ assay for multiplexed detection of RNA and protein
Authors: Dikshit Anushka , Basak Sayantani , Murlidhar Vasudha , Kim Ge-Ah , Yu Julia , Deshpande Sonali , Wang Li-Chong , Srinivasan Maithreyan 
Published: April 2023

Abstract
Understanding tissue heterogeneity is critical for elucidating cell-cell interactions with important implications in immuno-oncology, inflammation, and neuroscience. Tissue heterogeneity poses immense challenges to understanding underlying molecular mechanisms using techniques such as qRT-PCR or bulk sequencing. While single-cell RNA sequencing can provide information about precise cellular composition of tissues, data analysis can be cumbersome and spatial context is lost. With single-cell spatial platforms such as RNAscope, target gene and protein expression can be visualized to characterize cell types and tissue neighborhoods. Here, we demonstrate a novel method for the simultaneous detection of RNA and protein using a modified co-detection assay. This novel co-detection assay enables visualization of a combination of up to 12 RNA and/or protein targets on the same sample. We used a set of antibodies targeting key immune and tumor cell markers- PD1, CD3, CD4, CD8, CD68, FOXP3 and KRT17, along with RNA biomarkers to interrogate the tumor microenvironment (TME) in human FFPE tumor samples. Using a combination of RNA and protein targets, we characterized different cell types such as T cells, macrophages, and tumor cells in the TME. We also developed a novel method for visualizing intercellular interactions between PD1 and PD-L1, offering insights into popular checkpoint mechanisms that are targeted for therapeutic intervention in cancer treatment. The assay offers a powerful technique for visualizing target RNA biomarkers in specific cell-types identified by cell-marker protein expression. This is a valuable tool for multi-omic analysis and accurate interrogation of complex tissues to obtain insights into novel biomarkers and therapeutic targets.
Citation Format: Anushka Dikshit, Sayantani Basak, Vasudha Murlidhar, Ge-Ah Kim, Julia Yu, Sonali Deshpande, Li-Chong Wang, Maithreyan Srinivasan. Interrogating the tumor-immune landscape with a novel automated RNAscope™ assay for multiplexed detection of RNA and protein. [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 6771.
Abstract 6779: Spatial and single-nucleus transcriptomics of human glioblastoma
Authors: Hao Yue , Baker Angela , Hilbush Brian , Otero Marcos , Streck Chris , Fink Karen L. , Snipes George J. , Mickey Bruce E. , Berens Michael 
Published: April 2023

Abstract
Glioblastoma (GBM) multiforme is the most aggressive type of brain cancer. These lethal brain tumors are characterized by the inter- and intra-tumor molecular heterogeneity and diverse cell plasticity. We sought to interrogate the immune landscape of GBM, tease out the distinct biological and therapeutic niches in GBM and to understand how the tumor microenvironments mediated the heterogeneity of GBM. We have collected six human GBM samples for spatial profiling and single-nucleus RNA sequencing. Multiple sets of spatial gene panels were designed to capture the cell identities (cancer stem cells, astrocytes, oligodendrocytes, microglia, macrophages, endothelial cells, etc.) and the spatially-resolved expression patterns of genes indicative of different functional states. We also aim to find altered neurovascular units by examining the spatial correlation between cells that highly express angiogenesis markers such as VEGFA with tumor-associated macrophages, which could be recruited to the angiogenic niche by GBM tumor cells. From the spatial RNA dataset of the first two samples, we observed close proximity of tumor-associated macrophages and endothelial cells that form the microvasculature. Our preliminary results from the single-nucleus RNA sequencing and spatial transcriptomics of two samples shed light on the complex cell landscape and the dynamic interaction between tumor cells and infiltrating or resident immune cells in the GBM tumor tissue.
Citation Format: Yue Hao, Angela Baker, Brian Hilbush, Marcos Otero, Chris Streck, Karen L. Fink, George J. Snipes, Bruce E. Mickey, Michael Berens. Spatial and single-nucleus transcriptomics of human glioblastoma [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 6779.
Abstract 6786: NT-I7 as an adjuvant to DNA neoantigen vaccination enhances and prolongs neoantigen-specific anti-tumor immunity
Authors: Chen Michael Y. , Chen Ina , Supabphol Suangson , Wolfarth Alexandra A. , Martinez Sara F. , Lee Byung Ha , Li Lijin , Zhang Xiuli , Goedgebuure Peter S. , Gillanders William E. 
Published: April 2023

Abstract
Background: IL-7 is an essential cytokine in the development and maintenance of antigen-specific T cells. NT-I7 (efineptakin alfa; NeoImmuneTech, Inc, Rockville, MD), is a long acting IL-7 composed of recombinant human IL-7 (rhIL-7) fused to a hybrid Fc antibody platform that has significantly improved in vivo stability and half-life compared to rhIL-7. DNA cancer neoantigen vaccines are a promising personalized cancer immunotherapy capable of generating strong anti-tumor immunity, but limited by a short-lived neoantigen-specific T cell response. We hypothesize NT-I7 as an adjuvant to a DNA neoantigen vaccine will enhance the magnitude and duration of neoantigen-specific anti-tumor immunity.
Methods: C57BL/6 mice were vaccinated with DNA vaccine encoding neoantigens present in E0771 murine breast cancer model on days 0, 3, and 6. NT-I7 (5 mg/kg) was administered intravenously on day 4 or 13 during T cell expansion or contraction phase respectively. Primary T cell responses to neoantigens were assessed by IFN-γ ELISPOT. Tumor protection was evaluated by inoculating mice with 5×105 E0771 cells subcutaneously after receiving DNA vaccine with or without NT-I7. Duration of neoantigen-specific CD8 T cell immunity was determined by in vivo CFSE killing assay.
Results: NT-I7 administered during the T cell contraction phase following the DNA vaccine increases the magnitude of neoantigen-specific T cell responses on day 20 compared to DNA vaccine alone. DNA vaccination and NT-I7 alone prior to tumor inoculation confers partial protection against tumor growth compared to control while DNA + NT-I7 during contraction phase rejects 100% of tumors. Compared to DNA vaccine alone, DNA vaccine + NT-I7 during contraction phase induces greater neoantigen-specific killing on day 41 (34.6% vs. 11.97%, p=0.03).
Conclusion: NT-I7 as an adjuvant to a DNA neoantigen vaccine increases the magnitude and duration of neoantigen-specific anti-tumor immunity in a murine model. Clinical application of NT-I7 may help overcome immunologic shortcomings of current neoantigen vaccines.
Citation Format: Michael Y. Chen, Ina Chen, Suangson Supabphol, Alexandra A. Wolfarth, Sara F. Martinez, Byung Ha Lee, Lijin Li, Xiuli Zhang, Peter S. Goedgebuure, William E. Gillanders. NT-I7 as an adjuvant to DNA neoantigen vaccination enhances and prolongs neoantigen-specific 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 6786.
Abstract 6790: The peptide vaccine revived in cancer immunotherpay: a novel peptide vaccine platform for effective cancer immunotherpay
Authors: Kim Dongho , Lee SeungHwan 
Published: April 2023

Abstract
The production of tumor-specific T cells is essential for cancer immunotherapy. Due to the low cost and ease of CMC, peptide vaccines have been suggested as effective immunotherapy for cancer. A variety of peptide vaccines have been designed and tested in clinical trials for decades. However, most clinical trials of peptide vaccines have failed for several reasons. Poor stability of peptides, use of inappropriate adjuvants, lack of co-delivery of peptides and adjuvants, and immunosuppression by the tumor microenvironment. We tried to solve the problems that lead to failure and developed effective platform technologies for them. The first problem was the choice of vaccine adjuvants. Poly IC and its derivatives are known to induce antigen-specific Th1 and CTL responses. Since Th1-type immunity is essential for the elimination of intracellular pathogens or tumors, they may be suitable as the adjuvant for peptide vaccines. Despite several limitations of poly IC and its derivatives, such as high heterogeneity, inconsistent activity, poor stability, and unpredictable in vivo kinetics, they still serve as major adjuvants in numerous clinical trials. A novel and defined TLR3 agonist called NexaVant (NVT) was developed as an alternative to them. NVT induces a stronger anti-cancer efficacy compared to the known TLR agonists through multiple advantages of homogeneity, stability, and quantitative in vivo kinetics. Second, the stability of peptides was dramatically improved by a peptide/adjuvant complex formation. When a cationic peptide domain is introduced into the epitope together with an epitope processing domain, the peptide and adjuvant can form a nanocomplex by a simple charge interaction. And this complex improves the stability of the peptide which leads to improvement of the T cell immunity. Third, suppression of T cell immunity in cancer was mitigated by Treg modulation in the presence of a known chemotherapeutic drug. When this combination therapy of the vaccine and chemical was applied to various animal models, a strong anticancer effect was obtained by increasing T cell immunity and suppressing Treg. The same therapeutic effect was shown in several terminal stage tumor models with strong T cell memory regardless of whether the epitope was self or foreign originated.
Citation Format: Dongho Kim, SeungHwan Lee. The peptide vaccine revived in cancer immunotherpay: a novel peptide vaccine platform for effective cancer immunotherpay [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 6790.
Abstract 684: Nanovaccine displaying immunodominant T cell epitopes of fibroblast activation protein is effective against desmoplastic tumors
Authors: Shin Hocheol , Kim Yujin , Jon Sangyong 
Published: April 2023

Abstract
Cancer-associated fibroblasts (CAFs), which are dominant cell types in the tumor microenvironment (TME), support tumor growth by secreting cytokines and forming an extracellular matrix (ECM) that hampers penetration of chemical and biological therapeutics within the tumor and thereby limits their therapeutic efficacy. Here, we report a cancer nanovaccine targeting fibroblast activation protein alpha (FAP)-expressing CAFs as a potential pan-tumor vaccine. We predicted immunodominant FAP-specific epitope peptides and selected two candidate peptides after in vitro and in vivo screening for immunogenicity and antitumor efficacy. Next, we developed a nanoparticle-based vaccine that displays the two selected epitope peptides on the surface of lipid nanoparticles encapsulating CpG adjuvant (FAPPEP-SLNPs). Immunization with one of two FAPPEP-SLNP nanovaccines led to considerable growth inhibition of various tumors, including desmoplastic tumors, by depleting FAP+ CAFs and thereby reducing ECM production in the TME while causing little appreciable adverse effects. Furthermore, when combined with a chemotherapeutic drug, the FAPPEP-SLNP nanovaccine increased drug accumulation and resulted in a synergistic antitumor efficacy far better than that of each corresponding monotherapy. These findings suggest that our FAPPEP-SLNP nanovaccine has potential for use as an “off-the-shelf” pan-tumor vaccine applicable to a variety of tumors and may be a suitable platform for use in various combination therapies.
Citation Format: Hocheol Shin, Yujin Kim, Sangyong Jon. Nanovaccine displaying immunodominant T cell epitopes of fibroblast activation protein is effective against desmoplastic tumors [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 684.
Abstract 700: Induction of cancer-specific T-cell responses in patients immunized with P10s-PADRE vaccine
Authors: Lee John J. , Nounamo Bernice C. , Jousheghany Fariba , Makhoul Issam , Siegel Eric R. , Kieber-Emmons Thomas , Monzavi-Karbassi Behjatolah 
Published: April 2023

Abstract
Introduction: HR+/HER2− breast cancer is the most common form of breast cancer in the United States. HR+/HER2− tumors are known for a low number of tumor-infiltrating lymphocytes (TILs) and considered less immunogenic than other breast cancer subtypes. We have demonstrated that vaccination with P10s-PADRE, a carbohydrate-mimetic-based peptide, cancer vaccine in combination with standard-of-care chemotherapy in HR+/HER2− breast cancer patients led to an increase in TILs and stromal CD3+ T cells. The current study was performed to determine the vaccine specificity and anti-tumor functionality of T cells in treated patients.
Methods: Peripheral blood mononuclear cells (PBMCs) collected at the baseline and after vaccination were used in T-cell assays by multi-color ELISpot, examining Th1, Th2, and cytotoxic responses. PBMCs were also interrogated for the vaccine-induced changes in immune gene expression by next-generation RNA-seq analysis.
Results: We observed a significant increase in IFN-g, but not in IL-5 or IL-10, responses in post-immune PBMCs after stimulation with P10s, P10s-PADRE and polyclonal stimulation of T cells by anti-CD3/CD28 antibodies. Stimulation with cancer cell lysate resulted in a strikingly high IFN-g response in post-immune samples. Determining the trio of IFN-g, GzB, and IL-2 together with CD4/CD8 cell proliferation assays of consequent post vaccination specimens established the dynamics of effector T-cell populations. RNA-seq data clearly distinguished post-treatment samples by the increase in immune cell activation, cytokine response, and antigen presentation.
Conclusions: The data indicate that immunization of HR+/HER2− breast cancer patients with P10s-PADRE in combination with chemotherapy leads to specific activation of T-cells that recognize breast cancer cells. Improving immunogenicity of such immunologically cold tumors could increase the effectiveness of standard therapeutic approaches.
Citation Format: John J. Lee, Bernice C. Nounamo, Fariba Jousheghany, Issam Makhoul, Eric R. Siegel, Thomas Kieber-Emmons, Behjatolah Monzavi-Karbassi. Induction of cancer-specific T-cell responses in patients immunized with P10s-PADRE vaccine [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 700.
Abstract 704: MDSC-targeted TFF2-MSA suppresses tumor growth and increases survival in anti-PD-1 treated MC38 and CT26.wt murine colorectal cancer models
Authors: Daugherty Bruce L. 
Published: April 2023

Abstract
Aims: Myeloid-derived suppressor cells (MDSCs) in the tumor microenvironment are a potential therapeutic target in immune checkpoint cancer therapy, but MDSC-targeted therapies have yet been shown to improve survival. Trefoil factor family 2 (TFF2), a secreted anti-inflammatory peptide, can suppress MDSC expansion and activate tumor immunity in part through agonism of the CXCR4 receptor. The aim of this study is to investigate whether a novel TFF2 - albumin fusion peptide (TFF2-MSA) can improve survival in anti-PD-1 treated syngeneic colorectal cancer (CRC) mouse models.
Methods: Two syngeneic colon carcinoma mouse models were developed using cell lines grafted subcutaneously into mice. MC38 CRC cells were engrafted into C57BL/6 mice while CT26.wt CRC cells were implanted into BALB/C mice We generated a recombinant fusion protein, designated TFF2-MSA, which contains murine TFF2 fused to murine serum albumin (MSA), for the purpose of increasing half-life and reducing dose frequency. Mice subsequently received either TFF2-MSA or anti-PD-1 antibody (clone 29F.1A12) or both, and tumor volume, and survival were measured. At the endpoint, flow cytometry was performed to examine treatment-induced effects on immune profiles.
Results: In the MC38 model, administration of TFF2-MSA suppressed tumor growth (TGI 38%), the combination of TFF2-MSA and anti-PD-1 had an additive effect and suppressed tumor growth dramatically (TGI 74%). The combination also exhibited a survival rate of 90% after 50 days, while vehicle and single TFF2-MSA therapy were 30% and 65%, respectively. The percentage of exhausted CD8+ T cells was markedly reduced in the draining lymph node by the combination treatment, as measured by flow cytometry using antibodies against LAG3, TIM3 and PD-1. In the CT26.wt model, administration of TFF2-MSA alone exhibited little effect, but the combination of anti-PD-1 and TFF2-MSA showed a profound effect. In the CT26.wt model, administration of TFF2-MSA suppressed tumor growth (TGI 17%), anti-PD-1 alone (TGI 43%) and the combination of TFF2-MSA and anti-PD-1 (TGI 54%).
Conclusion: Targeting MDSCs using TFF2-MSA fusion protein synergizes well with PD-1 blockade therapy in advanced and metastatic syngeneic mouse models of colorectal cancer. In a separate abstract, additive effects between TFF2-MSA and anti-PD-1 antibody were also demonstrated in a separate ACKP (Atp4b-Cre; Cdh1-/-; LSL-KrasG12D; Trp53-/-) gastric cancer model, suggesting combination therapy may also be applicable to gastric cancer.
Citation Format: Bruce L. Daugherty. MDSC-targeted TFF2-MSA suppresses tumor growth and increases survival in anti-PD-1 treated MC38 and CT26.wt murine colorectal cancer models [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 704.
Abstract 720: Implementation and evaluation of a mental health app with comedy content for women living with advanced cancer
Authors: Rothberg Saranne , Grill Katherine B. , Wheeler Claire 
Published: April 2023

Abstract
Introduction: Metastatic cancer patients report elevated stress levels and unique stressors compared to other adults. This study tested the feasibility and efficacy of a mental health app with comedy content delivered to women living with advanced cancer (WLAC).
Methods: The mental health platform Neolth was used as a self-guided intervention for WLAC, ages 18+ years. WLAC were recruited by The Comedy Cures Foundation through a press release, social media posts, an email newsletter, and a video call for participants on the foundation’s website. No compensation was provided to participants. After using the Neolth platform, which included watching comedy content for eight weeks, researchers evaluated engagement, and stress levels using The Perceived Stress Scale -10 (PSS-10), self-efficacy using The New General Self-Efficacy Scale (GSES), and anxiety and depression using The Hospital Anxiety and Depression Scale (HADS-A and HADS-D).
Results: 54 WLAC (M = 52.2 years, R = 31-74) from 10 countries and 24 states participated by completing the baseline questionnaire. 20.5% identified as BIPOC and 33.0% had previous experience with a mental health app. 57.4% (N=31) completed the study surveys at Week 4 and Week 8. At Week 8, HADS-D scores decreased 18.1%, PSS-10 scores decreased 15.1%, HADS-A scores decreased by 9.7%, and GSES scores increased 7.6%. Participants spent an average of 116 minutes per week on Neolth with an average of 3.15 logins per week. 43.6% of time spent was completing self-guided relaxation practices and 17.2% watching Comedy Cures Foundation videos from cancer survivor Saranne Rothberg. The 30-day retention on Neolth was 100%, with 60-day retention 83%.
Conclusion: This study demonstrated the ability of a mental health app with comedy content to engage and support the mental health of WLAC, presenting a cost-effective intervention. Further examination with a larger sample size is needed to conduct multivariate analyses for enhanced understanding of the role of mobile apps and comedy content in reducing stress, anxiety, and depression for WLAC.
Citation Format: Saranne Rothberg, Katherine B. Grill, Claire Wheeler. Implementation and evaluation of a mental health app with comedy content for women living with advanced cancer [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 720.