bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 2041: Research strategies for rare germline variants and cancer study
Authors: Kim Seokhyeon , Koh Youngil , Yoon Sung-Soo 
Published: April 2023

Abstract
Exploration of rare germline variants in cancer is the fields of ongoing research. So, we would like to suggest several considerations for the rare pathogenic germline variants studies. We confirmed the pathogenicity of each variant using ClinVar (https://www.ncbi.nlm.nih.gov/clinvar). In addition, we utilized in silico prediction tools such as Polyphen and SIFT. Even for the same variant, the report of the variant may vary depending on the database used. We conducted rare germline variants screening using ICGC (International Cancer Genome Consortium) PCAWG (Pan-Cancer Analysis of Whole Genomes) data. we filtered allele frequencies using the gnomAD (v2.1.1) exome database. We utilized several ClinVar versions to check the clinical significance of germline variants. Next, we have investigated some in silico tools that predict ClinVar pathogenic and benign variants well. We observed inconsistent variant reports across versions of ClinVar. Although the information on variants may change over time, there have been inconsistent changes in the clinical significance of variants reported as P (Pathogenic) or LP (Likely pathogenic). The clinical significance of the variants reported in the previous version was P or LP, but those in the updated version were changed to “Conflicting interpretations of pathogenicity”. It was confirmed that the variant report changes when at least one “Uncertain Significance” review is added. Among various prediction tools, we found that the predictive power of a tool called “MetaRNN” was useful. Compared with several tools, we confirmed that MetaRNN’s AUC (Area Under the ROC Curve) value was 0.985, which is the best performance. But, it is not enough to judge the pathogenicity of a variant only by the prediction result of the tool. And, prediction tools are also known to be more efficient in predicting missense variants than others. Therefore, it is necessary to examine the pathogenicity of germline variants using both the prediction tool and the clinical significance of ClinVar. In summary, for rare germline variants in cancer studies, it is necessary to observe variants compared to the previous versions of ClinVar. Moreover, if prediction tools are appropriately used, researchers will increase the possibility of finding a variant or gene with more crucial clinical significance to reveal the association between the rare germline variants and cancer development.
Citation Format: Seokhyeon Kim, Youngil Koh, Sung-Soo Yoon. Research strategies for rare germline variants and cancer study [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 2041.
Abstract 2183: Absolute quantification of PD-L1 gene expression in single cell on tissue for accurately predicting response to ICIs
Authors: Gerstenberg Amandine , Ponzoni Adele , Ramos Corinne , Stauber Jonathan 
Published: April 2023

Abstract
Background PD-L1 immunohistochemistry (IHC) has been traditionally used for predicting clinical responses to immune checkpoint inhibitors (ICIs). However, there are at least 4 different assays and antibodies used for PD-L1 IHC, each developed with a different ICI. Spatial transcriptomic analysis at the single cell level can be helpful for deeply characterize the complexity and heterogeneity of tumors. We set to test if in-situ hybridization-based RNA scope coupled to single cell quantification is a robust method to determine PD-L1 mRNA expression levels in each cell and furthermore efficacy of predicting response to ICIs as compared to routinely used standardized IHC procedures. Method FFPE sections from retrospectively collected surgically resected NSCLCs (adenocarcinoma and squamous cell carcinoma) tumor with progression disease or complete response from adjuvant pembrolizumab therapy were used. Target genes CD274 (PD-L1) and GZMB (Granzyme B) were assessed. For fluorescent detection, the label probe was conjugated to Opal 570 and 620 respectively. Tissues cells were counterstained with DAPI to detect the nuclei. A Digital pathology software QuPath was used for cell segmentation and dot’s detection for gene expression quantification and further classification. Results Difference in expression levels were seen between PD-L1 and GZMB across the tumor with PD-L1 staining mostly located in the tumoral area and Granzyme B in stromal area of the NSCLC tissue. This is consistent with the expected expression of PD-L1 on tumor epithelial cells and Granzyme B on T cells. This heterogeneity in the signal distribution specific to the analyzed tissue correspond to intra-tissue cells metabolism heterogeneity between cell types. This heterogeneity of expression was captured though a digital workflow capable of quantifying the number of cells expressing PD-L1 and GZMB. Among the cells expressing the markers, 96% were positive for PD-L1 for the tumor that did not respond to therapy with the threshold of positivity being set at 1 of dots, that corresponds to 1 transcript, per cell.
Conclusion Our results demonstrate that PD-L1 was highly expressed in a tumor context that was not responding to PD-1 ICI inhibitor. Measurement of mRNA expression at the single cell level on tissue provides another layer of PD-L1 detection which can be exploited to predict tumor response to ICI suggesting that moving forward with this technology is a viable approach for this dynamic biomarker.
Citation Format: Amandine Gerstenberg, Adele Ponzoni, Corinne Ramos, Jonathan Stauber. Absolute quantification of PD-L1 gene expression in single cell on tissue for accurately predicting response to ICIs [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 2183.
Abstract 2192: Potential of galectin-7 as differentiating biomarker of lung cancer subtypes
Authors: Funkhouser Avery T. , Shealy Jonah C. , Kesic Alexandra E. , Blair Bailey B. , Martin Julie C. , Arthur Connie M. , Funk Christopher R. , Edenfield W. Jeffery , Blenda Anna V. 
Published: April 2023

Abstract
Background. Lung cancer is the leading cause of cancer-related death in both men and women in the United States. Non-small Cell Lung Cancer is the most prevalent and includes adenocarcinoma (AD), and squamous cell lung cancers. The unique cellular biology of these cancers could potentially allow for serological detection and identification via tissue specific protein markers. Galectins are a group of β-galactoside binding proteins which are known to be alternatively expressed in cancers and are being studied for their biomarker potential. Galectin-7 is expressed in epithelial tissues as well as in all layers of the epidermis as it is normally highly expressed by squamous cells. Purpose. We are evaluating potential of galectin-7 to be used as a serum biomarker and delineator of several lung cancer subtypes.
Methods. The serum concentrations of galectin-7 were measured in 96 cancer patients using ELISA. Twenty-eight samples were from adenocarcinoma lung cancer patients, 25 were from squamous cell lung carcinomas patients, 19 were from all other types of lung cancer, and 28 were from other squamous cell carcinomas of non-pulmonary origin. The serum galectin-7 concentrations in cancer patients were compared amongst themselves by their histological subtypes. One-way analysis was performed using Student’s t-test for pairwise comparisons.
Results. Galectin-7 concentrations were significantly elevated in serum samples from squamous cell lung cancer patients (n=25; mean, 1.91 ng/mL) relative to adenocarcinoma lung cancer patients (n=24; mean, 1.02; p-value, 0.0149). Additionally, levels of galectin-7 in samples of squamous cell lung carcinomas were higher than samples of squamous cell carcinomas of non-pulmonary origin (n=28; mean, 0.33 ng/mL, p-value, &lt;0.0001). These results show that serum galectin-7 is increased in patients with squamous cell lung cancer compared to adenocarcinoma lung cancer.
Conclusion. Potential clinical applications of this study include the measurement of galectin-7 in blood samples of cancer patients to aid in cancer screening and tumor type identification. Further explorations comprise measuring serum concentrations of galectin-7 by stage of squamous cell lung cancer and histological subtype (keratinizing, non-keratinizing, and basaloid) to determine a more nuanced understanding of the tumor molecular biology.
Citation Format: Avery T. Funkhouser, Jonah C. Shealy, Alexandra E. Kesic, Bailey B. Blair, Julie C. Martin, Connie M. Arthur, Christopher R. Funk, W. Jeffery Edenfield, Anna V. Blenda. Potential of galectin-7 as differentiating biomarker of lung cancer subtypes [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 2192.
Abstract 2276: Spatiotemporal analysis of metastatic melanoma reveals mechanisms of resistance to immune checkpoint blockade
Authors: Wei Shiyou , Lee Jinho , Labrie Marilyne , Betts Courtney , Liu Lunxu , Coussens Lisa , Herlyn Meenhard , Boland Genevieve , Mills Gordon , Zhang Gao 
Published: April 2023

Abstract
The treatment of metastatic melanoma has been revolutionized with the introduction of immune checkpoint blockade (ICB) therapies in the last decade. Despite durable responses exhibited by a subgroup of patients, most of patients do not respond to ICB therapies and the vast majority (60%-90%) of patients experience disease progression within five years. Molecular mechanisms of primary and acquired resistance to ICB are still widely unknown, which warrants further mechanistic investigation. Towards that goal, we used a holistic approach driven by integrated genomic tools to molecularly profile 35 longitudinal tumor specimens at pre-, on-, and post-treatment time points which were derived from seven patients with metastatic melanoma who progressed on sequential ICB therapies, including three responders and four non-responders. We integrated analyses of data generated from RNA sequencing, Whole-exome Sequencing (WES), NanoString nCounter vantage 3D, Cyclic Immunofluorescence (CyCIF), NanoString Digital Spatial Profiling (DSP) and Multiplex Immunohistochemistry (mIHC) platforms to elucidate evolutionary trajectories that occurred in both the tumor and the tumor immune microenvironment (TiME) that may have orchestrated response and resistance to ICB therapies. Simultaneous analyses conducted on genomic, transcriptomic and proteomic levels identified the re-activation of the MAPK pathway as a potential mechanism of resistance to ICB therapies. Spatially-resolved, image-based immune monitoring analysis at single cell resolution revealed that response to ICB is associated with infiltration of immune cells accompanied by induced activities of myeloid, T cells and macrophages in the TiME. In summary, integrated analyses allow us not only to reveal the dynamic co-revolution of both tumor and immune cells in TiME following sequential ICB therapies but also to provide a comprehensive perspective to molecular mechanisms of response and resistance to ICB therapies. A deeper understanding and elucidation of the evolution of mechanisms of response and resistance to ICB therapies will point us to generate hypothesis-driven, potential salvage therapies to overcome resistance to ICB therapies.
Citation Format: Shiyou Wei, Jinho Lee, Marilyne Labrie, Courtney Betts, Lunxu Liu, Lisa Coussens, Meenhard Herlyn, Genevieve Boland, Gordon Mills, Gao Zhang. Spatiotemporal analysis of metastatic melanoma reveals mechanisms of resistance to immune checkpoint blockade [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 2276.
Abstract 228: Recurrent mitochondrial mutations in thyroid cancer
Authors: Hopkins Julia F. , Fleischmann Zoe , Jin Dexter X. , Killian Jonathan Keith , Montesion Meagan 
Published: April 2023

Abstract
Despite the importance of mitochondrial function on the bioenergetics and metabolism of the cell, understanding the functional impact of somatic mitochondrial mutations has been difficult. Additionally, small cohorts, as used in previous studies, lack the power to estimate the prevalence of specific recurrent mutations.
We evaluated 177540 advanced cancer patients, across 84 different tumor types, who were sequenced as part of routine clinical care on the FoundationOne®CDx platform. Off-target sequencing reads were mapped to the mitochondrial genome (rCRS) and variant calling was performed. We had a median read depth of 18 and filtering by allele frequency (&lt;= 95% and &gt;= 5%) led to the identification almost 400,000 predicted somatic mitochondrial variants. Over 80% of patients had at least one mitochondrial variant detected, with an average of 2.2 mitochondrial variants detected per patient.
We next assessed each recurrent mitochondrial short variant to look for associations with specific cancers. The alteration with the strongest enrichment was G3224A, a mutation in the mitochondrial leucine tRNA gene (MT-TL1), which had a prevalence of 3.6% (51/1426) in thyroid cancer samples, as compared to 0.05% (85/176114) in all other disease types (OR=76.8, P&lt;2.2e-16). The G3244A mutation has been previously identified as occurring in thyroid cancer, specifically Hurthle cell carcinomas, as well as in the mitochondrial disease MELAS (mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes). Thyroid cancer samples in our dataset with G3244A were found to be associated with thyroid follicular carcinomas (7/124, 5.6%) and Hurthle cell carcinomas (7/57, 12.2%). Additional recurrent MT-TL1 mutations were identified in the thyroid cancer cohort at positions 3242 (9/1426) and 3248 (5/1426).
We also identified a mutation in the NADH dehydrogenase subunit MT-ND1. G3380A has been previously shown to occur in thyroid and colorectal cancer and results in a R25Q mutation that is thought to affect ND1 function. G3380A was identified in 26/1426 (1.8%) of thyroid cancer patients. The majority of G3380A variants occurred in thyroid anaplastic carcinomas 23/26 (88.5%).
Our dataset has allowed us to identify and determine the prevalence of rare mitochondrial short variant alterations in cancer. Further research is needed to investigate associations of these alterations with other clinical features.
Citation Format: Julia F. Hopkins, Zoe Fleischmann, Dexter X. Jin, Jonathan Keith Killian, Meagan Montesion. Recurrent mitochondrial mutations in thyroid 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 228.
Abstract 2280: BG34-200 immunotherapy of advanced melanoma
Authors: Roche Veronique P. , Sandoval Victor , Senders Zachary , Lyons Joshua , Wolford Claire , Zhang Mei 
Published: April 2023

Abstract
Background: High levels of myeloid derived cells are characteristic of tumor microenvironment (TME) of advanced melanoma. These cells work with the tumor cells to suppress host development of anti-tumor immune responses, regulate tumor metastasis, and drive cancer drug resistance to virtually all types of therapy. Therefore, methods to disrupt tumor-associated myeloid cell function are actively being sought to find a cure.
Goals: Our team has recently developed a plant-derived carbohydrate molecule, BG34-200, that modulates tumor-associated myeloid cells by targeting the cell surface receptor CD11b. In this study, we investigated the immune activation induced by BG34-200-CD11b engagement in the context of advanced melanoma and use the knowledge to develop BG34-200-based combination immunotherapy.
Methods: Wild type B57Bl6/J mice were injected with 1.5million B16F10 cells and treated intravenously with BG34-200. Tumor volume and animals survival were monitored, and whole blood was drawn for FACS analysis.
Results: We found that BG34-200 IV administration could significantly inhibit tumor growth and improve survival in B16F10 mice with advanced melanoma. Our data supported a model that the entry of BG34-200 into circulating melanoma tumor-associated inflammatory monocytes (TAIMs) could trigger a sequential immune activation: the BG34-200+ TAIM subsets migrated to tumor and differentiated into monocyte-derived dendritic cells (mo-DCs); then, the BG34-200+ mo-DCs migrated to tumor draining lymph nodes where they triggered the generation of tumor antigen specific T cells. Based upon these results, we combined BG34-200 treatment with adoptive transfer of TdLN-derived T-cell to treat advanced melanoma, which significantly improved animal survival and helped tumor-free survivors be resistant to a second tumor cell challenge.
Conclusions: The scientific findings from this study will allow us to develop new technology to apply BG34-200-based immunotherapy to patients with advanced melanoma who have not responded to current standard of care therapies with and without immunotherapy.
Citation Format: Veronique P. Roche, Victor Sandoval, Zachary Senders, Joshua Lyons, Claire Wolford, Mei Zhang. BG34-200 immunotherapy of advanced melanoma [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 2280.
Abstract 2339: Exploration of multiple immunotherapy modalities in ostesarcoma
Authors: Ismail Aliaa A. , Patton Daniel J. , Higgins Theresa A. , Sandey Maninder , Smith Bruce F. , Agarwal Payal 
Published: April 2023

Abstract
Osteosarcoma (OS) is the most common primary bone malignancy affecting long bones in children and the third most frequent in adults in the United States. It is highly invasive and metastatic. The survival rates over the last 20 years are unchanged. Therefore, it is essential to develop novel, targeted therapeutic approaches to treat OS. In pursuit of that goal, novel models are needed. Due to the high similarity in cancer genetics, the spontaneous occurrence of tumors, and the presence of an intact immune system, dogs are deemed an excellent cancer immunotherapy model. OS is also the most common malignant bone tumor (80%) in dogs. Monotherapies like oncolytic viruses and immune checkpoint inhibitors have been shown to be insufficient for effective cancer treatment. Therefore, we propose a combination of immune checkpoint inhibition and oncolytic virotherapy to target osteosarcoma tumor cells. In this combined therapy, the oncolytic virus will serve to both stimulate an inflammatory response and transmit the checkpoint inhibitor, which in turn will block PD-1-directed down-regulation of T cells, allowing the adaptive immune system to respond better to tumors. In order to evaluate this approach in the canine model, we have developed an oncolytic virus (CAV2-AU-M2) based on canine adenovirus type 2 and armed with an immune checkpoint inhibitor, an anti-canine PD1 single domain camelid antibody (sdAb). Four canine osteosarcoma cell lines, D17, D22, MCKOS, and CF11, were cultured in two-dimensional (2D) and three-dimensional (3D) cultures and were infected with CAV2-AU-M2 to analyze the infective and lytic effects of the virus. CAV2-AU-M2 infected and lysed the cells in 2D. The virus also produced anti-PD1 sdAb upon infecting the cells. Similarly, results were evident in 3D cultures. The virus infected the spheroids in the outer layers on Day 4 and slowly diffused towards the core in 7 days. The spheroids infected started showing some cell death on day 4, which progressed significantly by Day 7. This approach to oncolytic virotherapy makes the tumor more visible to the immune system and abrogates tumor-induced immune suppression.
Citation Format: Aliaa A. Ismail, Daniel J. Patton, Theresa A. Higgins, Maninder Sandey, Bruce F. Smith, Payal Agarwal. Exploration of multiple immunotherapy modalities in ostesarcoma [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 2339.
Abstract 2390: Claudin-4 probe identifies triple negative breast cancer using multispectral optoacoustic tomography
Authors: Parsons Laycee , MacCuaig William M. , McNally Lacey R. 
Published: April 2023

Abstract
Background: Triple negative breast cancer (TNBC) is the most aggressive subtype of breast cancer. The cancer is known for the lack of estrogen and her2 receptors. TNBC has a 5-year survival rate of 77% as for the other breast cancers averaging out at 93%. The CL-750 probes are made to identify the claudin-4 that is expressed in TNBC, making it easy to identify the cancer quickly so we can treat quickly.
Methods: TNBC, aggressive pancreatic and kidney cancer cell lines were used to assess the expression of claudin-4 via western blot. Based upon the C-terminal fragment of Clostridium perfingens, we synthesized a 30 aa peptide. CL peptide was conjugated to amine reactive HiLite 750 nm fluorescent dye. The CL-750 probes were purified using dialysis to remove unattached dye. MDA-MB-468 (TNBC), MDA-MB-231 (TNBC), S2VP10 (pancreatic), and 293 (kidney) cells were incubated with CL-750 probes for 30 minutes and evaluated with near infrared-fluorescence using Odyssey imaging software. Using the treated cells were then scraped into agar tissue mimicking phantoms, the probes were assessed for optoacoustic activity using the MSOT (Multispectral optoacoustic tomography).
Results: Using western blot to show expression of claudin-4 within cell lines the S2VP10 pancreatic (positive control) showed the most expression of claudin-4, while the 293 kidney cells showed a lesser amount. Both MDA-MB-468 and MDA-MB-231 TNBC cells showed the lowest amount of claudin-4 nonetheless both showed enough to continue with experiments. Cell line S2VP10 showed an extreme amount of binding to probe, while as the probe also bound to both smaller amount of claudin positive breast cancer cell line (MDA-MB-231) and larger amount of claudin breast cancer cell line (MDA-MB-468). Both CL-Short-750 and CL-Long-750 showed signal using MSOT. The CL-Long-750 showed 2x as much signal as CL-Short-750 making the Cl-long-750 probe more efficient in identifying claudin positive cell TNBC (p&lt;0.05).
Conclusion: Both CL-750-probes have the capability of identifying claudin-4 positive cell lines, but CL-Long-750 was more effective and had greater binding.
Citation Format: Laycee Parsons, William M. MacCuaig, Lacey R. McNally. Claudin-4 probe identifies triple negative breast cancer using multispectral optoacoustic tomography [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 2390.