tbuckley/cabot-search huggingface dataset:
Abstract 2943: Investigation of microsatellite instability in RNA compared to DNA, using microsatellite targeted, anchored multiplex PCR and NGS
Authors: Ryan Rogge, Taylor Patterson, Alicia Navetta, Dhruti Legare
Journal: Cancer Research (2024)

Abstract MSI measurements are typically made on DNA, but it would be useful to make similar measurements from RNA or total nucleic acid inputs (TNA), so that MSI determinations could be made in parallel to interrogation of the RNA. Doing so requires characterizations of microsatellite lengths from those which are transcribed and untranscribed, because both will be detected following cDNA creation. Microsatellite instability (MSI) occurs when small unit repeats of DNA undergo incorrect replication resulting in the growth or contraction of the number of repeats in the newly synthesized DNA. This accumulation of errors at microsatellite DNA is usually mitigated by the mismatch repair (MMR) pathway which can correct these errors. MSI is of interest because it serves as a phenotypic readout of the status of the MMR machinery, and MSI status can correlate to tumor progression and response to agents that regulate these cellular mechanisms. We investigated the status of microsatellites using Anchored Multiplex PCR (AMP™) targeted panels (RUO) and compared results from TNA inputs using an AMP MSI module and both VARIANTPlex™ chemistry to interrogate DNA, and FUSIONPlex™ chemistry to interrogate both RNA + DNA. Our results indicate differences in the diversity of lengths of microsatellites present in RNA, and the resulting stability calls which would be made at those sites. Microsatellite length diversity was highly dependent on the genomic context of the microsatellite. Microsatellites located within transcripts showed increased length diversity when examining the RNA + DNA results compared to DNA alone. Microsatellites located in intergenic regions, which are unlikely to be transcribed, showed no increase in diversity of lengths when comparing the RNA + DNA results to DNA alone. While these results suggest that MSI determinations could be made from RNA or RNA + DNA NGS data, the unique behavior of microsatellites in RNA is likely to require additional investigations and unique data analysis techniques to correctly categorize microsatellites as stable or unstable. Confidential - Company Proprietary Citation Format: Ryan Rogge, Taylor Patterson, Alicia Navetta, Dhruti Legare. Investigation of microsatellite instability in RNA compared to DNA, using microsatellite targeted, anchored multiplex PCR and NGS [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 2943.
Abstract 4308: Same-section spatial multiomic analyses using MICS technology for investigating the dynamics of the tumor microenvironment
Authors: Dongju Park, Emily Neil, Rebecca C. Hennessey, Michael DiBuono, Hanna Lafayette, Erica Lloyd, Hsinyi Lo, Julia Femel, Alex Makrigiorgos, Shaina Lu, John Lee, Sameh Soliman, Dominic Mangiardi, Paurush Praveen, Fabian Staubach, Ryan Hindman, Thomas Rothmann, Telma Santos, Stefan Borbe, Hansueli Meyer, Tanya Wantenaar, Jinling Wang, Werner Müller, Robert Pinard, Andreas Bosio
Journal: Cancer Research (2024)

Abstract The recent increase in image-based, spatially-resolved technologies enables researchers to profile the tumor microenvironment (TME) by capturing gene expression profiles within tissue sections. However, a significant limitation of these technologies is the lack of ability to resolve protein and RNA information in the same section, as well as conveniently analyze multimodal data sets. Here, we report a spatial RNA detection method, RNAsky, using Miltenyi Biotec’s MACSima™ Platform as an automated, multiomic approach. Our method integrates spatial proteomics and transcriptomics data to provide in-depth profiling with single-cell resolution on the same tissue section. We demonstrate these capabilities by characterizing key immune-oncology markers across normal and diseased tissues using our specialized MACS® iQ View analysis software. MACS iQ View provides fast segmentation and intuitive gating and clustering strategies to simultaneously assess protein and RNA data. We investigated the impact of clustering using protein, RNA, or the combination of both to evaluate the contribution of different information modalities on TME spatial dynamics. This cutting-edge approach will enable the identification of valuable parameters and new cell types, furthering the discovery and development of predictive and prognostic biomarkers. Citation Format: Dongju Park, Emily Neil, Rebecca C. Hennessey, Michael DiBuono, Hanna Lafayette, Erica Lloyd, Hsinyi Lo, Julia Femel, Alex Makrigiorgos, Shaina Lu, John Lee, Sameh Soliman, Dominic Mangiardi, Paurush Praveen, Fabian Staubach, Ryan Hindman, Thomas Rothmann, Telma Santos, Stefan Borbe, Hansueli Meyer, Tanya Wantenaar, Jinling Wang, Werner Müller, Robert Pinard, Andreas Bosio. Same-section spatial multiomic analyses using MICS technology for investigating the dynamics of the 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 4308.
Abstract 1458: Anti tumoral role of PDX1 on pancreatic ductal adenocarcinoma aggressiveness
Authors: Jimena Mosna, Federico Garde, Marcelo Stinson, Candela Pastore, Pablo Sanchis, Abel Carcagno
Journal: Cancer Research (2024)

Abstract Pancreatic ductal adenocarcinoma (PDAC) represents a very aggressive type of pancreatic cancer (9% survival rate at 5 years). PDX1 is an important transcription factor for embryonic development of the pancreas, endocrine lineage differentiation and the maintenance of mature beta cells. Notably, in PDAC patients, the expression of PDX1 is downregulated in tumor cells compared to adjacent non-tumoral tissue. Interestingly, increasing tumor PDX1 expression has been shown to enhance the overall survival rate in PDAC patients. Therefore, our aim was to analyze the role of PDX1 on tumor aggressiveness of PDAC cells. To induce PDX1 expression, PANC1 cells were treated with BRD7552 (a PDX1 inducer) for 9 days. Overexpression of PDX1 was confirmed by Western Blot analysis and no cytotoxic effects were observed by MTT or Trypan Blue exclusion assays on treated cells compared to control. Wound healing and transwell migration assays showed a significant reduction in the migration rate compared to the control group. A higher proportion of cells in G1 phase was observed in treated cells compared to control by propidium iodide staining followed by flow cytometry assay. Furthermore, the cell confluence assay showed a significant reduction in proliferation rate in treated cells compared to control, but no differences were observed on the proportion of KI67+ and PH3+ cells by immunostaining. To assess the in ovo effects of BRD7552, treated PANC1 cells were implanted onto the chorioallantoic membrane of chick embryos and tumor growth was measured at different stages observing a significant reduction in tumor growth in PANC1 cells compared to control between days 3 and 8 post implantation. No significant differences in morphology or color were observed between treated and control implanted cells. Hematoxylin-eosin staining showed reduced invasion of treated cells into the chorioallantoic membrane compared to control. In conclusion, the overexpression of PDX1 affects cell cycle, reduces proliferation rate and inhibits migratory potential in vitro. Moreover, in an in ovo model this overexpression diminished tumor growth and invasion in PANC1 cells. In conclusion, the overexpression of PDX1 induced by BRD7552 drives pancreatic ductal adenocarcinoma to a less aggressive tumoral phenotype. Citation Format: Jimena Mosna, Federico Garde, Marcelo Stinson, Candela Pastore, Pablo Sanchis, Abel Carcagno. Anti tumoral role of PDX1 on pancreatic ductal adenocarcinoma aggressiveness [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 1458.
Abstract 3674: Blood-based differentiation of malignant and benign pancreatic lesions using analysis of fragmentation patterns in cell-free DNA
Authors: Clayton T. Marcinak, Michelle D. Stephens, Bradon R. McDonald, Nabeel Merali, Stephanie M. McGregor, Sharon M. Weber, Adam E. Frampton, Shivan Sivakumar, Rebecca M. Minter, Muhammed Murtaza
Journal: Cancer Research (2024)

Abstract Pancreatic ductal adenocarcinoma (PDAC) remains lethal, with a five-year survival rate of less than 10%. For patients with pancreatic cystic lesions (PCL), analysis of DNA from cyst fluid has shown promise in determining the risk of malignant transformation. However, obtaining cyst fluid requires an invasive procedure. We recently developed an approach for blood-based cancer detection by analyzing fragmentation characteristics in plasma cell-free DNA (cfDNA). In this study, we evaluate the performance of this method in differentiating between patients with malignant and benign pancreatic lesions. We collected plasma samples from 81 patients at the time of endoscopic evaluation or surgical resection of a PCL. We simultaneously obtained plasma samples from 209 PDAC patients and 56 healthy individuals. Using plasma cfDNA whole genome sequencing data from patients with PDAC and healthy individuals, we trained and cross-validated an ensemble machine learning model based on 10 genomic features capturing plasma cfDNA fragmentation patterns. This model was applied to sequencing data from patients with PCL for independent evaluation of diagnostic performance. In training and cross-validation, the model demonstrated an area under the receiver operating characteristic curve (AUROC) of 0.90 for differentiating PDAC samples from healthy individuals. Of the 81 PCL patients, ten patients (12.3%) were found to have a malignant PCL, with either high-grade dysplasia or invasive carcinoma. The trained model showed an AUROC of 0.78 for differentiating malignant from benign lesions, achieving 50% sensitivity and 62.5% positive predictive value at 95% specificity. Our results are a novel demonstration that a peripheral blood test based on plasma cfDNA analysis can enable differentiation between malignant and benign pancreatic lesions. This approach may improve risk-stratification and clinical decision-making regarding the necessity for surgical resection. Larger studies and clinical trials to validate these results and evaluate their impact on outcomes are warranted. Citation Format: Clayton T. Marcinak, Michelle D. Stephens, Bradon R. McDonald, Nabeel Merali, Stephanie M. McGregor, Sharon M. Weber, Adam E. Frampton, Shivan Sivakumar, Rebecca M. Minter, Muhammed Murtaza. Blood-based differentiation of malignant and benign pancreatic lesions using analysis of fragmentation patterns in cell-free DNA [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 3674.
Abstract 1421: The HDAC6-specific inhibitor AVS100 (SS208) blocks M2 polarization of tumor associated macrophages and potentiates immunotherapy in preclinical tumor models
Authors: Damian Kovalovsky, Satish Noonepalle, Manasa Suresh, Dileep Kumar, Michael Berrigan, Anelia Horvath, Allen Kim, David Quiceno-Torres, Karthik Musunuri, Alejandro Villagra
Journal: Cancer Research (2024)

Abstract Inhibition of HDAC6 was associated with an increased proinflammatory tumor microenvironment and an antitumoral response. Here, we show that a highly specific HDAC6 inhibitor AVS100 (SS208), blocks M2 polarization in murine and human macrophages while partially affecting M1 polarization. AVS100 effects were observed as blocked upregulation of M2-related gene signature under M2 polarizing conditions and blocked generation of CD206+ and Arg1+ macrophages. Oral administration of AVS100 had an antitumoral effect in SM1 melanoma and CT26 colon cancer models and increased the efficacy of anti-PD1 treatment, leading to complete remission in melanoma and increased response in colon cancer. Flow cytometry and scRNAseq analysis of tumor-infiltrating immune cells revealed an increase of proinflammatory/anti-inflammatory ratio in tumor-associated macrophages as well as an increase of intratumoral CD8 effector T-cells after AVS100 treatment. Interestingly, cured mice didn’t relapse and became resistant to a subsequent tumor challenge, suggesting acquired antitumoral T-cell immunity. T-cell repertoire analysis of effector/memory T-cells in cured mice revealed a higher number of immunodominant T-cell clones after AVS100 treatment, indicating increased T-cell expansion. Finally, AVS100 has demonstrated no mutagenicity and a strong safety profile in rats and dogs, leading to its recent U.S. FDA clearance of an Investigational New Drug (IND) application and planned initiation of Phase Ia/b clinical trials targeting locally advanced or metastatic solid tumors in the first half of 2024. Altogether, we have performed the preclinical characterization of a novel small molecule inhibitor targeting HDAC6 for solid cancers. AVS100 had an antitumoral effect as single agent and improved the efficacy of immune checkpoint inhibition by blocking the immunoregulatory tumor microenvironment and increasing T-cell immunity. Citation Format: Damian Kovalovsky, Satish Noonepalle, Manasa Suresh, Dileep Kumar, Michael Berrigan, Anelia Horvath, Allen Kim, David Quiceno-Torres, Karthik Musunuri, Alejandro Villagra. The HDAC6-specific inhibitor AVS100 (SS208) blocks M2 polarization of tumor associated macrophages and potentiates immunotherapy in preclinical 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 1421.
Abstract 5892: SCUBE3 promotes therapy resistance in triple negative breast cancer
Authors: Deepika Singh, Daisy Medina, Benjamin Onyeagucha, Rahul Mojidra, Panneerdoss Subbarayallu, Alex Taylor, Dongwen Lyu, Santosh Timilsina, Prabhakar Pitta Venkata, Saif S R Nirzhor, Shahad M. Abdulsahib, Trong Phat Do, Yidong Chen, Ratna Vadlamudi, Manjeet K. Rao
Journal: Cancer Research (2024)

Abstract Introduction: The development of novel targeted therapies is urgently required for improving the outcome of triple negative breast cancer (TNBC) patients. Chemotherapy is the common treatment option for TNBC. However, resistance and tumor relapse remain the major obstacles hindering the effectiveness of chemotherapeutic agents in cancer patients. Therefore, identifying genes/factors that sensitize breast cancer cells to chemotherapeutic agents could improve treatment outcome in patients. Here we report Signal peptide CUB domain EGF-like 3 (SCUBE3) genes as a novel therapeutic adjuvant that can improve the efficacy of doxorubicin, a chemotherapeutic agent commonly used in treating breast cancer patients. Methods: Unbiased high-throughput loss of function genomic screen was performed on breast cancer cells in the presence or absence of doxorubicin. Breast cancer cells lines (MDA-MB-231 and MDA-MB-468) were purchased from the American Type Culture Collection and cultured in standard medium. Breast cancer cells were transfected either with SCUBE3 overexpression plasmid or shRNA specific to SCUBE3. These overexpression/knockdown breast cancer cells were analyzed for cell viability, migration, invasion, colony formation, cell cycle, apoptosis assays, western blotting, and in vivo tumor xenograft study. Results: Our finding demonstrated that SCUBE3 promotes breast cancer cell progression as knockdown of SCUBE3 inhibited the ability of breast cancer cells to form colony, migrate, and invade, while overexpression of SCUBE3 promoted tumor growth in preclinical mouse models. Our results revealed that SCUBE3 mediates its protumor effects by regulating genes involved in growth and survival in the MAPK pathway, DNA damage surveillance pathway including RAD51 and FOXM1, and apoptotic pathway including Mcl-1. We demonstrated that SCUBE3 promotes tumor growth and progression by interacting with and activating several oncoproteins. Conclusions: Overall, our data suggests that SCUBE3 can be a potent therapeutic target for treating TNBC patients. Citation Format: Deepika Singh, Daisy Medina, Benjamin Onyeagucha, Rahul Mojidra, Panneerdoss Subbarayallu, Alex Taylor, Dongwen Lyu, Santosh Timilsina, Prabhakar Pitta Venkata, Saif S R Nirzhor, Shahad M. Abdulsahib, Trong Phat Do, Yidong Chen, Ratna Vadlamudi, Manjeet K. Rao. SCUBE3 promotes therapy resistance 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 5892.
Abstract 1122: Inhibition of HDAC6 enhanced radiation therapy induced antitumor response in melanoma
Authors: Xintang Li, Manasa Suresh, Hawa Coulibaly, David Quiceno-Torres, Nithya Gajendran, Karen Tan, Satish Noonepalle, Scott Grindrod, Anatoly Dritschilo, Alejandro Villagra
Journal: Cancer Research (2024)

Abstract Patients with advanced melanoma are often treated with radiation therapy (RT) in combination with immunotherapies. Immunogenic tumor cell death induced by radiation is known to activate innate and adaptive immunity. Macrophage activity in the irradiated tumor microenvironment (TME) has been implicated to play a critical role in post-RT innate immune responses. However, tumor-associated macrophages (TAMs) due to their phenotypic plasticity convert from initial antitumor M1 phenotype to protumor M2 macrophages resulting in relapse and metastasis of any surviving tumor cells. Therefore, strategies regulating tumor macrophages post-radiation can enhance the therapeutic effectiveness of radiation therapy. Here, we report targeting HDAC6 function with a novel selective inhibitor (SP-2-225) as a potential therapeutic candidate for combination with RT. When administered intraperitoneally at a dose of 25mg/kg, SP-2-225 resulted in significant tumor suppression in the immunocompetent SM1 murine melanoma model. Phenotyping of tumor immune infiltrate indicated a profound decrease in M2 macrophages resulting in an M1/M2 macrophage ratio and an increase in CD8 effector memory T-cells. Further, in-vitro co-culture studies using trans-well assays indicated that irradiated tumor cells attract M2 macrophages, and treatment with SP-2-225 abrogated the M2 macrophage migration but did not alter M1 macrophage migration. In addition, 24 hours post-RT, intratumor administration of SP-2-225 treated M1 macrophages as adoptive cell therapy resulted in diminished tumor growth. The combination of conditioned M1 macrophages with an irradiated tumor microenvironment resulted in an increased M1/M2 ratio and infiltration of effector memory and central memory CD8 T-cells underscoring the influence of transplanted macrophages on the local antitumor immunity. Therefore, our findings demonstrate the ability of HDAC6 inhibitors to regulate macrophage function and phenotype as a cell therapy for use in combination with radiation therapy. Citation Format: Xintang Li, Manasa Suresh, Hawa Coulibaly, David Quiceno-Torres, Nithya Gajendran, Karen Tan, Satish Noonepalle, Scott Grindrod, Anatoly Dritschilo, Alejandro Villagra. Inhibition of HDAC6 enhanced radiation therapy induced antitumor response in melanoma [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 1122.
Abstract 730: Leveraging microdissection for proteogenomic analysis of histological sections to advance drug development
Authors: Ik Jae Shin, Michael Tangrea, Michael R. Emmert-Buck, Donald J. Johann
Journal: Cancer Research (2024)

Abstract Background: Combining proteogenomics with laser capture microdissection (LCM) in cancer research offers a targeted way to explore the intricate interactions between tumor cells and the tumor microenvironment. This is especially important for immuno-oncology (IO) research where improvements in the predictability of patient response to IO-based drugs is sorely needed. An improved understanding of the spatial relationships involving tumor cells proper, stromal cells, blood supply and immune cell interactions may help to inform drug development and improve the indicators of success for IO-based drug regimens. Methods: LCM is used to isolate and obtain distinct histological cell types from fresh frozen tissue. Once cells have been captured, nucleic acids and proteins are extracted for in-depth multi-modality molecular profiling assays involving multiple genomic modalities and a customized solution-based mass spectrometry proteomics approach for samples or specimens with a limited amount of tissue. Results: Optimizing analysis of minute tissue quantities from LCM captured cells is challenging. Following the isolation of nucleic acids, RNA-seq may be performed for gene expression and DNA sequencing performed for the discovery and analysis of actionable mutations, copy number variation, and methylation profiles. Regarding genomic-based studies, commercial kits are often utilized for these steps due to their general availability, rapid innovation, and the robust performance of these products. However, this kit-based adaptive approach is not true for proteomics. There remains a need for highly sensitive proteomic methods targeting small-sized samples. A significant part of our proteogenomics approach is focused around an enhanced liquid chromatography mass spectrometry (LC-MS) analysis of micro-scale and/or nano-scale tissue sections. This is achieved with a silver-stained one-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis (1D-SDS-PAGE) approach developed for LC-MS analysis of fresh-frozen tissue specimens obtained via LCM. This includes an in-gel digestion method adjusted and specifically designed to maximize the proteome coverage from amount-limited LCM samples to better facilitate in-depth molecular profiling. Conclusions: Reported here is a proteogenomic approach that is leveraging from microdissected fresh frozen tissue. The methodology may also be applicable to other types of specimens having limited nucleic acids, protein quantity, and/or sample volume. Citation Format: Ik Jae Shin, Michael Tangrea, Michael R. Emmert-Buck, Donald J. Johann. Leveraging microdissection for proteogenomic analysis of histological sections to advance drug development [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 730.