bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 6830: Xenium in situ analysis and reproducibility study of multiple carcinomas for clinical studies
Authors: Cheung Elim , Zhang Baowen , Zhang Lutong , Lu Tong , Gakhar Rikita , Sundaram Vidyodhaya 
Published: March 2024

Abstract
10x Genomics’ Xenium is the newest in situ spatial transcriptomics platform offering sub-cellular resolution in frozen and FFPE tissue sections for a deeper study of cellular mechanisms and interactions. Mapping RNA targets at high specificity with fully customizable assays and quick workflow, it uses rolling circle amplification and interpretation-ready data is available immediately after the run. At BioChain Institute, Inc. (BioChain), we are conducting validation studies for reproducibility of results with the Xenium platform using BioChain’s oncology biospecimen.FFPE tissues from BioChain’s repository were screened by our pathologist for tumor content above 30%. Four carcinoma tissues from Breast, Colon, Lung, and Kidney with high DV200 scores were selected. An array was constructed with these tissues to fit the Xenium slide’s imageable area. Two serial sections were used for the Xenium run per 10x Genomics’ protocol. The Off-the-shelf Human Multi-Tissue and Cancer Panel was used for targeting 377 genes. H&E staining and imaging was performed, and the image was integrated with the data on the Xenium platform. The results were found to be reproducible between two different operators. For example, in the breast section, over 96,000 cells were detected and median transcripts per cell were 70 in both the runs. There were 20 clusters representing different cell types/states, 99% transcripts were within cells, and ~85% of the transcripts were found to be high quality. Furthermore, we are analyzing the expression of unique tumor type and immune transcripts to map the heterogeneity of the tissues, as well as sensitivity, and standard deviation between the runs. The Xenium platform is a powerful tool for the sub-cellular spatial transcriptomics study of tissues with targeted gene panels. However, one of the four tissues used here failed to show enough transcripts. Further investigation is underway to examine the issue and conclude best practices thereafter. Our future studies will include accuracy and concordance validation with Xenium run on different days and Visium whole transcriptome assay post- Xenium.
Citation Format: Elim Cheung, Baowen Zhang, Lutong Zhang, Tong Lu, Rikita Gakhar, Vidyodhaya Sundaram. Xenium in situ analysis and reproducibility study of multiple carcinomas for clinical studies [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 6830.
Abstract 6839: Comprehensive transcriptomic analysis of acquired resistance after immune-checkpoint inhibitors in non-small cell lung cancer
Authors: Joe Cheol Yong , Bang Yeong Hak , Park Sehhoon , Jung Hyun Ae , Sun Jong-Mu , Choi Yoon-La , Ahn Jin Seok , Ahn Myung-Ju , Lee Se-Hoon 
Published: March 2024

Abstract
Background: Treatment of lung cancer has changed dramatically with the use of immune checkpoint inhibitors (ICI). Nevertheless, most patients underwent drug resistance even though they initially showed a response to ICI, and there is an unmet need to delineate the mechanism.
Method: We analyzed RNA sequencing data of paired pre- and post-ICI samples from 31 NSCLC patients. Among them, we identified 17 patients who underwent acquired resistance (AR) who initially showed partial or complete response or stable disease lasting more than six months, and the remaining 14 patients who showed primary resistance (PR) to ICI. The analysis was performed using a tumor microenvironment (TME) classifier, classifying immune-enriched [IE], immune-enriched and fibrotic [IE/F], fibrotic [F] and immune-desert [D] subtype, and CIBERSORTx, the immune cell deconvolutional analysis tool.
Results: Most patients with AR were initially classified as IE or IE/F subtypes (N=12, 70.6%), but six out of 14 with PR (42.8%) showed IE or IE/F subtypes. Among 12 patients with initial IE or IE/F subtypes, seven (58.3%) patients turned into the D subtype after AR to ICI. Most patients initially classified as D or F subtypes (N=5, 29.4%) maintained their subtypes (N=4, 80%) after AR.When assessing the pre-ICI samples, memory B cell was enriched, and M2 macrophage and regulatory T cell were depleted in AR patients compared to PR. The memory B cell and resting memory CD4+T cell decreased, and M2 macrophage increased after AR to ICI. These immune cell composition changes were not observed in PR patients.
Conclusions: We observed differences in TME phenotype and immune cell composition before ICI between AR & PR patients. The TME change from immune-enriched to desert and cell composition change of increased M2 macrophages and decreased memory B and resting CD4+ T cells after AR to ICI could be significant mechanisms of AR to ICI.
Citation Format: Cheol Yong Joe, Yeong Hak Bang, Sehhoon Park, Hyun Ae Jung, Jong-Mu Sun, Yoon-La Choi, Jin Seok Ahn, Myung-Ju Ahn, Se-Hoon Lee. Comprehensive transcriptomic analysis of acquired resistance after immune-checkpoint inhibitors in non-small cell lung 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 6839.
Abstract 6840: Automated preparation of single nuclei from FFPE samples for snRNA-Seq
Authors: Jovanovich Stevan , Pereira Nate , Meyer Danielle , Snopkowski Catherine , Masilionis Ignas , Meškauskaitė Brigita , Takizawa Meril , Abou-Mrad Zaki , Yu Kenny , Tabar Viviane , Luckett Kathleen , Ganesh Karuna , Khan Nabiha , Chaligne Ronan 
Published: March 2024

Abstract
S2 Genomics developed the Singulator™ 100 and 200 Systems to automate the processing of fresh, frozen, or OCT tissues into single cell or single nuclei suspensions using disposable cartridges, reagents, and customizable protocols. The systems have been used to prepare cells or nuclei from a wide range of tissues and organisms, including human, mouse, chicken, insects, snails, zebrafish, and plants.
Formalin-fixed, paraffin-embedded (FFPE) tissues are the preferred format for pathologists and as many as one billion FFPE slides are in repositories. FFPE tissue samples have traditionally been difficult to study with molecular techniques due to the chemical modifications caused by the formalin fixation, which can lead to degradation and sequestration of RNA and DNA. Recent advances in single cell/nuclei RNA-Seq library preparation technology have made it possible to overcome these challenges and generate high-quality single cell or nuclei genomic data from FFPE samples. Protocols have been released for processing previously deparaffinized and rehydrated FFPE samples on the Singulator 100 or 200 into single nuclei.
We now report the development of a fully automated workflow for the deparaffinization and rehydration of FFPE tissues in about 40 min, with an optional enzymatic treatment of 45 min, and processing of FFPE tissues into singulated cells or nuclei on prototype Singulator 200 systems. Data will be presented for the optimization of process parameters for cell or nuclei recovery and RNA quality for six tissues. Finally, single nuclei sequencing data will be presented for snRNA-Seq libraries from healthy and cancerous human FFPE samples including glioblastomas and colorectal cancer. These data demonstrate the successful recovery of genomic materials from FFPE samples using an automated sample preparation system for single cell/nuclei transcriptomics.
Citation Format: Stevan Jovanovich, Nate Pereira, Danielle Meyer, Catherine Snopkowski, Ignas Masilionis, Brigita Meškauskaitė, Meril Takizawa, Zaki Abou-Mrad, Kenny Yu, Viviane Tabar, Kathleen Luckett, Karuna Ganesh, Nabiha Khan, Ronan Chaligne. Automated preparation of single nuclei from FFPE samples for snRNA-Seq [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 6840.
Abstract 6841: Mutation specific mechanisms of resistance to oncogenic KRAS inhibition
Authors: Barravecchia Ivana , Lasse-Opsahl Emily , Cavanaugh Sophia , Rober Lily , Baliira Rachael , Robotti Marzia , Hinshaw Rachael , Lee Jennifer M. , Zhang Yaqing , di Magliano Marina Pasca , Galbán Stefanie 
Published: March 2024

Abstract
Mechanisms of resistance to inhibitors against mutant KRAS are linked to the remodeling of the tumor microenvironment (TME). Understanding this remodeling process during intervention and tumor recurrence will likely guide the development of future therapeutic treatment paradigms with long-term responses. 56% of never-smokers with non-small cell lung cancer have KRASG12D mutant cancer and respond little to immune checkpoint therapy (ICI) compared to smokers, who often have mutations in KRASG12C. Our analysis of the TME in a unique KrasG12D inducible and reversible mouse model of NSCLC using single cell RNA sequencing data shows KrasG12D-dependent control of the TME, particularly of the expression of PDL1 in a subset of myeloid cells. PDL1 expression was found to be KrasG12D dependent as it was reduced significantly when KrasG12D was turned ON in mouse lungs. Interestingly, when KrasG12D was turned OFF, the expression of PDL1 increased, indicating mechanisms of resistance. Furthermore, the cytokine expression and secretion of IL6, a known regulator of PDL1 expression, increased in lung tissue and lung cancer cells derived from this model upon genetic and chemical (MRTX1133) Kras inhibition. Moreover, the mechanisms of resistance to oncogenic Kras inhibition appear to be mutant specific. Transcriptome and secretome analyses in human and murine KrasG12D or KrasG12C mutant lung cancer cells show distinct cytokine regulation upon KRAS inhibition. Identification of mechanisms of resistance like the induction of PDL1 expression upon KrasG12D inhibition may provide a strong rationale for co-treatment of KRAS inhibitors with ICI for KrasG12D never-smokers with NSCLC.
Citation Format: Ivana Barravecchia, Emily Lasse-Opsahl, Sophia Cavanaugh, Lily Rober, Rachael Baliira, Marzia Robotti, Rachael Hinshaw, Jennifer M. Lee, Yaqing Zhang, Marina Pasca di Magliano, Stefanie Galbán. Mutation specific mechanisms of resistance to oncogenic KRAS inhibition [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 6841.
Abstract 6892: Murine ex vivo platform: A powerful tool for biomarker assessment and high throughput screening of translationally relevant in vivo tumor models for PD and efficacy studies
Authors: Bachawal Sunitha , Leung Janet , Mandawe Remie , Garza Malia , ly Kimberly , Stefanson Ofir , Lohre Jack , Kamali Diba , Doan Ngan , King Benjamin , Kim Elliot , Hegde Ganapathi , Liao Xiaoyun , Liu Scot , Kim Jeong , Vigdal Amanda Mikels , Mukhopadhyay Anandaroop 
Published: March 2024

Abstract
Ex vivo model systems using tumor biopsies from patients are often utilized to develop predictive biomarkers. However, these readouts are often proximal and do not inform on downstream mechanisms (distal pharmacodynamics) and their relationship to anti-tumor efficacy. In vivo murine models represent a powerful tool to bridge this gap. However, selection of an appropriate translationally relevant murine model can often be a time-consuming process given that the complexity of the tumor microenvironment (TME). Additionally, in vivo models are generally not amenable to high throughput screening. Here, we demonstrate that ex vivo mouse tumor platforms can be used for rapid screening of treatment responsive and translationally relevant tumor models. These models can be used to interrogate the impact of a therapeutic on anti-tumor efficacy in a long-term in vivo study, thus allowing for the establishment of biomarker/response relationships in a rational and rapid manner. To operationalize this platform, ex vivo cultures of dissociated tumor cells (DTC) or tumor tissue slices (histoculture) were first optimized for maximum viability and/or preservation of tissue architecture. To allow for high throughput screening, feasibility of freezing DTCs or tumor chunks prior to sectioning was also explored. Finally, both ex vivo tumor cultures and in vivo tumors were treated with a Innate agonist as a proof of concept to demonstrate functional equivalency. In conclusion, this work provides a novel way of screening responsive, translationally relevant murine tumor models in a high throughput and cost-effective manner. These efforts have the potential benefits of saving time and animal usage, while also maximizing the probability of successfully evaluating a therapeutic’s benefit.
Citation Format: Sunitha Bachawal, Janet Leung, Remie Mandawe, Malia Garza, Kimberly ly, Ofir Stefanson, Jack Lohre, Diba Kamali, Ngan Doan, Benjamin King, Elliot Kim, Ganapathi Hegde, Xiaoyun Liao, Scot Liu, Jeong Kim, Amanda Mikels Vigdal, Anandaroop Mukhopadhyay. Murine ex vivo platform: A powerful tool for biomarker assessment and high throughput screening of translationally relevant in vivo tumor models for PD and efficacy studies [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 6892.
Abstract 6900: Patient-derived xenografts from circulating cancer stem cells and their potential utility in personalized medicine of pancreatic cancer
Authors: Pizon Monika , Schott Dorothea , Ettner-Sittner Andreas , Wagner Benedikt J. , Pachmann Katharina , Aung Thiha , Hackl Christina , Haerteis Silke 
Published: March 2024

Abstract
Background: Pancreatic cancer carries a poor prognosis in the majority of patients, with an overall 5-year survival rate of less than 10%. Therefore, the development of new therapies and preclinical models is crucial and urgently needed. Circulating cancer stem cells (cCSCs) are a subset of circulating cancer cells that have stem cell-like properties and play a significant role in tumor progression, metastasis, and treatment resistance. Patient-derived xenografts (PDX) reflect the genotypic and phenotypic landscape of patients' cancers and are useful for drug screening, biomarker development, and preclinical evaluation of personalized medicine strategies. In this study, we describe a fast, simple, and cost effective method to generate PDX on Chorioallantoic Membrane (CAM) from circulating cancer stem cells.
Methods: In this study, primary cultures from circulating cancer stem cells were established using sphere-forming assays from 30 patients with newly diagnosed pancreatic cancer. Subsequently, tumorspheres were transplanted onto the CAM membrane of fertilized chicken eggs to form patient- derived xenografts.
Results: For the identification of cCSCs from peripheral blood of pancreatic cancer patients, an innovative in vitro sphere-forming assay was established. The number of tumorspheres was correlated with clinicopathological parameters like tumor size, lymph node involvement and grading status of the primary tumor. Implantation of tumorspheres onto the CAM was successful in ~90 % of the applied samples. The histological analysis suggests that the PDX tumors were morphologically and pathologically identical to primary tumor tissue.
Conclusions: The number of tumorspheres was associated with clinicopathological parameters. Further follow-up is needed to evaluate the prognostic significance of tumorsphere detection in pancreatic cancer. Generation of PDX from cCSCs on CAM has a high success rate and may become an integral part of the drug development arena, including drug screening and biomarker development.
Citation Format: Monika Pizon, Dorothea Schott, Andreas Ettner-Sittner, Benedikt J. Wagner, Katharina Pachmann, Thiha Aung, Christina Hackl, Silke Haerteis. Patient-derived xenografts from circulating cancer stem cells and their potential utility in personalized medicine of pancreatic 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 6900.
Abstract 693: The effect of butyrophilin 1A1 blockade in combination with radiation treatment in tumor models
Authors: Li Nan , Braun Chen , Kim Young-Seung , Park Andrew , Yoo Stephen S , Lin Steven H. 
Published: March 2024

Abstract
Expression of radiation-induced immune escape molecules, including PD-L1, contributes to the efficacy of cancer immunotherapy. We used an unbiased in vivo gene knockdown screen in naïve T-cells and introduced them into irradiated host tumors to identify novel immunosuppressive genes activated during radiation. From the screen, we found that butyrophilin 1A1 (BTN1A1) knockdown causes T-cell expansion in irradiated tumors. This points to the potential immune checkpoint role of BTN1A1. We validated that BTN1A1 expression is inducible in activated T-cells and that blocking BTN1A1 contributes to T-cell activation. We tested an anti-mouse BTN1A1 antibody (STC109) in mouse colon tumor models (CT26 tumors), we observed partial anti-tumor efficacy using single agent STC109, which was enhanced by the combination of STC109 with radiation. We also got similar result in in mouse lung tumor models (LLC tumors) using anti-mouse BTN1A1 antibody, and the combination treatment showed an improved suppression of tumor growth and lung metastasis compared to single agent. Moreover, our data shown that knockout of BTN1A1 in 4T1 tumor models shown dramatic defect of tumor growth, and the BTN1A1 ko tumors are more sensitive to radiotherapy. These findings indicate the role of BTN1A1 in tumor immune response from radiation stress, and that anti-BTN1A1 has strong potential to enhance efficacy of radiotherapy for cancer treatment.
Citation Format: Nan Li, Chen Braun, Young-Seung Kim, Andrew Park, Stephen S Yoo, Steven H. Lin. The effect of butyrophilin 1A1 blockade in combination with radiation treatment in tumor models [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 693.
Abstract 6960: Lysosome inhibition suppress collective cell migration through caveolin-1 mediated E-cadherin stabilization in colon cancer cells
Authors: Ching Yu-Chien , Chen Hui-Chun , Wang Yu-Chun , Cheng Chun-Pu , Ku Chia-En , Lee Shin-Ru , Chao Wei-Ting 
Published: March 2024

Abstract
In tumor nest growth and collective cell migration, the dynamics of E-cadherin is critical, and been shown to be regulated by cell vesicle traffic system. Caveolin-1 is the vesicle protein to regulate caveolae associated endocytosis, many of the membrane receptors are shown been regulated by caveolin-1 in cancer progression, however, the role is still controversial. This study demonstrated the effect of lysosome inhibition in caveolin-1 mediated E-cadherin turnover in the cell cohort of colon cancer cells. HT-29 colon cancer cells were used in this study, the cells were treated with chloroquine to inhibit lysosome activity. The cell spheroid from HT-29 cells were also collected according to cell adhesion ability. Caveolin-1 and E-cadherin were immuno-stained and revealed by confocal microscopy. In the result of immunostaining, caveolin-1 was showed the co-localization with E-cadherin at cell-cell contacts. When cells were treated with chloroquine, the lysosome inhibitor, the collective cell migration of HT-29 cells were suppressed, and stable caveolin-1 distribution was found accumulated on the cell-cell contacts., meanwhile, chloroquine has no effect on clathrin distribution at either cell-cell contacts or cell leading edge. Furthermore, the distribution of caveolin-1 at cell-cell contacts on cell spheroid that derived from HT-29 cells was decreased. The results of these study suggested lysosome plays important role in mediating caveolin-1 regulated E-cadherin dynamics in collective cell migration, but not in the cell spheroid formation. The results of these study demonstrated chloroquine can be the potential inhibitor for collective cell migration in colon cancer cells through caveolin-1 mediated vesicle transport.
Citation Format: Yu-Chien Ching, Hui-Chun Chen, Yu-Chun Wang, Chun-Pu Cheng, Chia-En Ku, Shin-Ru Lee, Wei-Ting Chao. Lysosome inhibition suppress collective cell migration through caveolin-1 mediated E-cadherin stabilization in colon cancer cells [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 6960.
Abstract 6969: Determining the role of obesity in breast cancer progression
Authors: Perlman Alexandra , Piekny Alisa , Kuzmin Elena , Santosa Sylvia 
Published: March 2024

Abstract
Breast cancer, especially triple negative breast cancer, impacts a large proportion of the female population. Approximately ten to fifteen percent of all breast cancer diagnoses will be triple negative. Triple negative breast cancer lacks receptors that are used as therapeutic targets for other forms of breast cancer and has the poorest prognosis. Notably, the age of onset has also decreased, which correlates with the rise in prevalence of obesity. In addition, past studies revealed that maintaining a high BMI from childhood correlates with higher cancer mortality in adulthood. However, the mechanisms by which obesity contributes to cancer progression are not clear. Adipose tissue from different locations (visceral vs. subcutaneous, abdominal vs. femoral) and from patients with obesity from childhood rather than as adults could have different molecular characteristics. Further, depending on the genetic background, different profiles may be more susceptible to environmental cues that could drive their progression. To address this, we are using conditioned media collected from tissues that reflect these differences and determining how they affect TNBC cell lines with distinct genetic profiles. Preliminary data revealed that adipose tissue from both the abdominal and femoral regions of high BMI individuals caused an increase in the proliferation rate of TNBC cell lines. To determine if the adipocytes vs. other cell types in the adipose tissue drive this growth, we are co-culturing mature adipocytes from these tissues with the TNBC cell lines. Recent studies by other groups showed that adipocyte-derived extracellular vesicles could drive the expression of EMT genes in cancer cells. We will purify EVs from the adipocytes and characterize differences in their molecular signatures for different patients to determine which factors cause the change in TNBC progression and correlate this with different fat depots and/or age of onset. We will also measure the effect of adipose tissue and/or adipocytes on other cancer hallmarks including metastasis (migration and invasion) and changes in metabolism. These studies should reveal how adipocytes confer changes in TNBC progression, and how to consider obesity in different treatment regimes.
Citation Format: Alexandra Perlman, Alisa Piekny, Elena Kuzmin, Sylvia Santosa. Determining the role of obesity in breast cancer progression [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 6969.