bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 29: Characterization of a murine intestinal cancer homograft model for therapeutic evaluation
Authors: Wang Jinxi , Chen Leilei , Zhang Likun , Zhu Jingqian , Bourre Ludovic , Wang Jingjing 
Published: June 2023

Abstract
Introduction: Intestinal cancers are one of the most lethal malignancies and are responsible for a mass of cancer-related deaths. The discovery of new drugs and therapeutic strategies is underway, and to complement this, the development of superior animal models is required for preclinical studies. Genetically engineered mouse models (GEMMs) mimic de novo human tumor growth within an intact tumor microenvironment and are potent immunocompetent models for studying pathogenesis and immuno-oncology of intestinal cancers. GEMMs with dysfunctional DNA mismatch repair (MMR) genes, like MHL1 and MSH2, manifest intestinal tumors related to microsatellite instability (MSI). However, the low incidence and distinct latency among individuals hamper the application of these GEMMs in preclinical research. In this study, a murine intestinal cancer homograft from GEMMs with MMR deficiency is established to enroll larger cohorts of mice for preclinical studies.
Methods: MMR-deficient GEMMs were generated by knockout of Mlh1 gene with a CRISPR-Cas9 system. Intestinal cancer development was investigated in 16 GEMMs. The developed tumor in the intestine of GEMM was isolated by surgery and inoculated into C57BL/6 mice subcutaneously to establish a murine homograft model. The tumor homograft was passaged and expanded in vivo, and stable tumor growth was established over consecutive passages. Histopathological studies were conducted for both the original and passaged tumors. Genomic mutations and gene expression were analyzed by whole exome sequencing and RNA-sequencing, and tumor-infiltrating lymphocytes (TILs) were analyzed by flow cytometry. Therapeutic efficacy of chemotherapies and immune checkpoint inhibitors were evaluated in vivo for tumor growth inhibition.
Results: The intestinal tumors or lesions were observed in two of the sixteen Mlh1-KO mice with an incidence of 12.5%. A murine homograft model of small bowel adenocarcinoma was successfully established using the tumor located in jejunum of a Mlh1-KO mouse. This model was stably passaged in vivo with semblable pathological features as the original lesion in Mlh1-KO mice. The various degrees of TILs and response to treatments revealed the potential of this model for in vivo investigation of immune response.
Conclusion: Our murine intestinal cancer homograft model presented rapid and stable subcutaneous growth in immunocompetent mice, providing an efficient approach for intestinal cancer researchers and a superior preclinical model for new drug discovery.
Citation Format: Jinxi Wang, Leilei Chen, Likun Zhang, Jingqian Zhu, Ludovic Bourre, Jingjing Wang. Characterization of a murine intestinal cancer homograft model for therapeutic evaluation [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 29.
Abstract 2909: Genetically engineered Natural Killer cells as an immunotherapeutic approach for the treatment of neuroblastoma
Authors: Croom-Perez Tayler J. , Oyer Jeremiah L. , Hasan Md Faqrul , Robles-Carrillo Liza D. , Tullius Brian P. , Copik Alicja J. 
Published: June 2023

Abstract
In this study we test if knockout of DNAM-1 competing inhibitory receptors on Natural Killer (NK) cells improves cytotoxic response against neuroblastoma cell lines. Neuroblastoma and other peripheral nervous cell tumors account for 6% of all pediatric cancer. While the 5-year survival rate has greatly improved, the prognosis of children with high-risk neuroblastoma at diagnosis is less than 50%. Immune checkpoint therapy is a promising new application for pediatric oncology; however, neuroblastoma is often immunologically “cold” and current immune checkpoint targets are not abundant in pediatric solid tumors. To improve response to checkpoint blockade and directly target tumor cells for elimination, this study evaluated the use of NK cells. NK cells prime the immune system for successful response to cancer immunotherapy. NK cells activated with particle technology (PM21-NK cells) are highly cytotoxic, produce IFNγ and induce PD-L1 on cancer cells. Although highly cytotoxic, PM21-NK cells express inhibitory receptors that compete for ligands that trigger NK cell lysis, such as PVR, a ligand highly expressed on neuroblastoma cells. We knocked out expression of multiple PVR inhibitory receptors in PM21-NK cells to further enhance cytotoxicity and prevent exhaustion. Three inhibitory receptors on NK cells that bind PVR - TIGIT, CD96, and PVRIG were knocked out alone or in combination and effector functions of these edited NK cells tested. Cytotoxicity against 3D spheroids of the neuroblastoma cell line SK-NA-S cells was assessed and compared to wild type PM21-NK cells. Knockout (KO) of TIGIT enhanced NK cell killing compared to wildtype NK cells (72%±10 vs 55%±3% killing) as well as PVIRG KO (84±3% vs 46±6% killing) and CD96 KO (62%±9% vs 46±6% killing) at a 1:3 E:T ratio at 72 h. Double or triple KO of these receptors resulted in further increased killing of cancer cells. The knockouts of each of the receptors could affect cytokine production and cytokine responsiveness and this will be examined. Overall, PM21-NK cells show promise for therapeutic use against neuroblastoma and preventing the PVR-mediated inhibitory axis signaling enhances their function.
Citation Format: Tayler J. Croom-Perez, Jeremiah L. Oyer, Md Faqrul Hasan, Liza D. Robles-Carrillo, Brian P. Tullius, Alicja J. Copik. Genetically engineered Natural Killer cells as an immunotherapeutic approach for the treatment of neuroblastoma [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 2909.
Abstract 2916: CAR-NK cells generated with CAR-RNA-LNP express high cytotoxic activity against tumor cells
Authors: Golubovskaya Vita M. , Sun Jinying , Sienkiewicz John , Huang Yanwei , Zhou Hua , Deng Gongping , Harto Hizkia , Xu Shirley , Berahovich Robert , Wu Lijun 
Published: June 2023

Abstract
NK (natural killer) cells have several advantages compared to T cells such as no cytokine release syndrome (CRS), neurotoxicity and GVHD in allogenic setting to kill tumors. We developed CAR-NK platform using RNA-LNP (lipid-nanoparticles) technology. High expansion of NK cells (up to 2000-fold) was achieved using K562 feeder cells with stable expression of 4-1BBL and IL-21. We showed efficient encapsulation of BCMA and CD19-CAR RNA into LNP that resulted in up to 99% expression of CAR+ CD56+ NK cells after transfection. The BCMA-CAR-NK cells more effectively than NK cells killed MM1S, H929 and RPMI8226 multiple myeloma cells and secreted IFN-gamma in a dose-dependent manner. In addition, frozen BCMA-CAR-NK cells were viable and expressed similar cytotoxic activity to not frozen expanded CAR-NK cells. In addition, frozen-thawed BCMA-CAR-NK cells showed 93% CAR expression at 24 hours post-thaw which remained &gt;70% at 48 hours post-thaw. In a similar way, CD19-CAR-NK cells generated with CD19-CAR-LNP killed CD19-positive Raji and Daudi target cells and secreted high level of IFN-gamma. This, frozen/thawed CAR-NK cells demonstrated high in vitro cytotoxic activity against target cells. Manufacturing of NK cells using G-Rex system resulted in 1862-fold expansion at day 13 and 2450-fold expansion of 97% CD56+ NK cells at day 14. Transfection of BCMA-CAR RNA-LNP into 13 day expanded NK cells resulted in 95% BCMA-CAR-NK positive cells. Thus, CAR-NK cells generated with RNA-LNP technology can be used in future pre-clinical studies.
Citation Format: Vita M. Golubovskaya, Jinying Sun, John Sienkiewicz, Yanwei Huang, Hua Zhou, Gongping Deng, Hizkia Harto, Shirley Xu, Robert Berahovich, Lijun Wu. CAR-NK cells generated with CAR-RNA-LNP express high cytotoxic activity against tumor cells [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 2916.
Abstract 3107: Development of novel JAK2 inhibitors and PROTACs as chemical probes for the investigation of JAK2 inhibition and degradation
Authors: Humphrey Briley A. , li Bao , Ferreira Renan B. , Ranatunga Sujeewa R. , Rowsell Tegan M. , Sun Luxin , Lawrence Harshani R. , Schonbrunn Ernst , Reuther Gary , Lawrence Nicholas J. 
Published: June 2023

Abstract
Inhibition and, more recently, degradation of protein kinases is an important therapeutic strategy to modulate disregulated signaling pathways in the cell cycle. Janus kinase 2 (JAK2) is a protein kinase involved in the JAK/STAT pathway which is one of the 12 core cancer pathways; thus, the regulation of JAK2 is important in the maintenance of normal cell function. A fragment-based drug discovery approach was taken to synthesize novel JAK2 inhibitors based using building blocks suitable for PROTAC development. Small molecule inhibitors were analyzed through computational analysis to probe the binding interactions in the hinge region of the ATP active site of JAK2. PROTACs were designed to investigate the degradation of JAK2 based on small molecule ligands with high binding affinity to JAK2. Pyrrolopyrimidine and pyrimidine scaffolds were used to probe the hydrogen bonding interactions in the hinge region to investigate binding affinity. Modification of A-ring and B-ring fragments of the inhibitors and PROTACs were used to develop SAR through data obtained by functional assays, including differential scanning fluorimetry and 33P HotSpot™ kinase assay, in addition to in-vivo cell viability assays as models for myeloproliferative neoplasms. Several key pyrrolopyrimidine and pyrimidine core containing inhibitors and PROTACs bind strongly to JAK2 and modulate JAK2 activity in appropriate cancer cell lines.
Citation Format: Briley A. Humphrey, Bao li, Renan B. Ferreira, Sujeewa R. Ranatunga, Tegan M. Rowsell, Luxin Sun, Harshani R. Lawrence, Ernst Schonbrunn, Gary Reuther, Nicholas J. Lawrence. Development of novel JAK2 inhibitors and PROTACs as chemical probes for the investigation of JAK2 inhibition and degradation [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 3107.
Abstract 3117: Molecular and clinical correlates of genetic ancestry in a diverse, admixed cancer dataset
Authors: Postel Mackenzie D. , Teer Jamie K. , Eschrich Steven A. , Dutil Julie , Siegel Erin M. , Cress William D. , Carpten John D. , Craig David W. 
Published: June 2023

Abstract
The objective of this study is to determine whether genetic ancestry analysis can provide additional insight into the genetic determinants of cancer disparities distinct from socially constructed variables like self-reported race and ethnicity. The Oncology Research Information Exchange Network (ORIEN) “Avatar” project is a diverse dataset of extensive, longitudinal clinical and molecular data from 18 cancer centers across the U.S.; the ORIEN Intermember Ancestry Project cohort described in this study is a subset of the larger dataset. Using paired tumor/germline whole exome sequencing data from ORIEN, the Genome Aggregation Database (gnomAD) dataset of ancestry reference individuals, and the software tools ADMIXTURE and RFMix, we have estimated genetic ancestry for cancer cases from both ORIEN and The Cancer Genome Atlas (TCGA). The ORIEN dataset has 2.6X greater representation of self-reported Hispanic/Latinos than does TCGA, with Hispanic/Latinos making up 9% of the ORIEN dataset vs. 4% in TCGA. As expected, individuals of Hispanic/Latino ethnicity are heterogeneous in their admixture proportions of Indigenous American, African, and European ancestries. We performed statistical analyses in R to identify molecular and clinical correlations with ancestry. This study highlights the clinical utility of genetic ancestry analysis as an approach to understand the genetic contributions to cancer disparities in diverse, admixed populations.
Citation Format: Mackenzie D. Postel, Jamie K. Teer, Steven A. Eschrich, Julie Dutil, Erin M. Siegel, William D. Cress, John D. Carpten, David W. Craig. Molecular and clinical correlates of genetic ancestry in a diverse, admixed cancer dataset [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 3117.
Abstract 3166: CanSig: De novo discovery of shared transcriptional states in cancer single cells
Authors: Yates Josephine , Barkmann Florian , Czyz Pawel Piotr , Kraft Agnieszka , Beerenwinkel Niko , Boeva Valentina 
Published: June 2023

Abstract
Tumor heterogeneity is regarded as a significant obstacle to successful personalized cancer medicine. Specifically, multiple cancer types have been shown to exhibit heterogeneity in the transcriptional states of malignant cells even within the same tumor. Some of these specific transcriptional states of malignant cells have been linked to cancer relapse and resistance to treatment. However, today there is no universal and easy-to-use computational method to extract information about shared transcriptional states from single-cell RNA sequencing measurements (scRNA-seq).
To reliably identify shared transcriptional states of cancer cells, we propose a novel computational tool, CanSig. CanSig automatically preprocesses, integrates, and analyzes cancer scRNA-seq data from multiple patients to provide novel signatures of shared transcriptional states; it also associates these states to known and potentially targetable biological pathways. CanSig jointly analyzes cells from multiple cancer patients while correcting for batch effects and differences in gene expressions caused by genetic heterogeneity. For this, CanSig automatically infers copy number variations in malignant cells and trains a deep learning architecture based on conditional variational autoencoders integrating scRNA-seq measurements.
In our benchmarks, CanSig shows state-of-the-art performance in data integration and reliably re-discovers known transcriptional signatures on four previously published cancer scRNA-seq datasets. For instance, CanSig re-discovers four main cellular states of glioblastoma cells previously reported by Neftel et al., Cell, 2019.
We further illustrate CanSig’s investigative potential by uncovering signatures of novel transcriptional states in several cancer types; some of the novel signatures are linked to such cancer hallmarks as cell migration and proliferation and are enriched in more advanced tumors. We also uncover signatures associated with specific genomic aberrations such as gene copy number gains.
In conclusion, CanSig detects shared transcriptional states in tumors using as input scRNA-seq data for cells with different genetic backgrounds and possibly exhibiting strong batch effects. It can significantly facilitate the analysis of scRNA-seq cancer data and efficiently identify transcriptional signatures linked to known biological pathways. The CanSig method implemented in Python is available at https://github.com/BoevaLab/CanSig
Citation Format: Josephine Yates, Florian Barkmann, Pawel Piotr Czyz, Agnieszka Kraft, Niko Beerenwinkel, Valentina Boeva. CanSig: De novo discovery of shared transcriptional states in cancer single cells [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 3166.
Abstract 3263: Implications for cancer viroimmunotherapy: a new adenovirus capsid sensor
Authors: Gillard Andrew Gregg , Shin Dong Ho , Laspidea Virginia , Jiang Hong , Xuejun Fan , Yi Yanhua , Alonso Marta M. , Fueyo Juan , Gomez-Manzano Candelaria 
Published: June 2023

Abstract
The median survival for glioblastoma (GBM) patients is 12-15 months, with a five-year survival rate of less than 10% despite aggressive treatment with surgery, radiotherapy, and chemotherapy. Oncolytic virotherapy is emerging as a promising approach to reprogramming the immunosuppressed microenvironment of GBMs and restoring anti-tumor immunity. Delta-24-RGD is an oncolytic adenovirus that has shown favorable results in phase I clinical trials (NCT00805376; NCT03178032). However, immune responses functionally cleared the virus within weeks of administration, limiting anti-cancer efficacy to a subset (~20%) of patients. A better understanding of the innate immune response against adenoviruses may provide the rationale for developing improved anticancer approaches. Using bulk RNA sequencing, we have examined the transcriptome of normal lung fibroblasts infected with wild-type adenovirus. Ingenuity pathway analysis (IPA) showed upregulation of several immune response-related pathways, including interferon response factor 3 (IRF3). Interestingly, these analyses also showed an unexpected upregulation of the Non-POU Domain Containing Octamer Binding (NONO) pathway during adenoviral infection. In fact, upstream regulators analyses showed a 7-fold increase in the NONO pathway in two different cell lines. Increases in NONO expression changes in response to adenovirus treatment were validated by western blot. Furthermore, co-immunoprecipitation assays showed that NONO binds to adenoviral capsid proteins during infection and to the foreign DNA sensor cyclic GMP AMP synthase (cGAS), which is critical for the activation of the innate immunity, via IRF3. In our proposed model, NONO protein binds to the adenoviral capsid protein and associates with the sensor cGAS in the nucleus to enable sensing of viral nucleic acid. In conclusion, we uncovered a new mechanism for detecting adenovirus infection that involves the interaction of adenoviral capsid proteins with members of the NONO pathway in the nucleus of the infected cell. Further studies are in progress to examine to which extent adenoviruses unable to bind NONO may persist longer in the infected tumors than unmodified adenoviruses and whether the persistence of the virus in the tumor correlates with enhanced anti-glioma effect.
Citation Format: Andrew Gregg Gillard, Dong Ho Shin, Virginia Laspidea, Hong Jiang, Fan Xuejun, Yanhua Yi, Marta M. Alonso, Juan Fueyo, Candelaria Gomez-Manzano. Implications for cancer viroimmunotherapy: a new adenovirus capsid sensor [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 3263.
Abstract 3265: Temozolomide combined with ipilimumab + nivolumab enhances T cell killing of MGMT-expressing, MSS colorectal cancer cells
Authors: Gonzalez Zenovia , Carlsen Lindsey J. , El-Deiry Wafik S. 
Published: June 2023

Abstract
Colorectal cancer (CRC) is the third most frequently diagnosed cancer and third-deadliest cancer globally. Approximately 95% of patients with metastatic CRC have tumors that are microsatellite stable (MSS) and do not respond to immune checkpoint inhibitors (ICI). Results from the 2022 MAYA clinical trial suggest that the DNA-damaging agent temozolomide (TMZ), which is usually used to treat glioblastoma (GBM), sensitizes patients with MSS, MGMT-silenced CRC to ipilimumab + nivolumab ICI. The benefit of adding ipilimumab + nivolumab to TMZ and the impact of MGMT silencing remain unclear. Here, we aimed to determine in a controlled in vitro system if adding ICI to TMZ enhances T cell killing of MSS CRC cells. We also aimed to determine the role of MGMT in this response. MGMT protein expression was measured by western blot in CRC (n=4) and GBM (n=4) cell lines. Cell viability assays were conducted to measure sensitivity to TMZ. CRC and GBM cells were co-cultured with TALL-104 cells -/+ TMZ and -/+ ICI to measure TALL-104-mediated cell death. Western blot analysis indicated that CRC cells had significantly elevated MGMT expression as compared to GBM cells likely due to MGMT promoter methylation in GBM cells. In line with this, CRC cells were slightly more resistant to TMZ (IC50=100-150 µM) compared to GBM cells (IC50=10-90 µM) after five days of treatment. TMZ + ICI sensitized MGMT-expressing, MSS CRC cells to T cell killing. TMZ alone did not enhance T cell killing of MSS or MSI CRC cells but did enhance T cell killing of T98G GBM cells. Our results indicate that TMZ sensitizes MSS, MGMT-expressing CRC cells to ipilimumab + nivolumab ICI. Importantly, this suggests that TMZ-mediated sensitization to ipilimumab + nivolumab is independent of MGMT status and the patient cohort that may benefit TMZ + ipilimumab + nivolumab may be expanded to CRC patients with MGMT-expressing, MSS tumors.
Citation Format: Zenovia Gonzalez, Lindsey J. Carlsen, Wafik S. El-Deiry. Temozolomide combined with ipilimumab + nivolumab enhances T cell killing of MGMT-expressing, MSS colorectal cancer cells [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 3265.
Abstract 3347: Characterization of extracellular POTE-2 protein in liver cancer
Authors: Lopez Samantha , Doxtater Kyle D. , Anilkumar Adithya , Leslie Sophia , Sanchez Amayrani , Ezell Kristopher , Chauhan Subhash , Tripathi Manish K. 
Published: June 2023

Abstract
Liver cancer is projected to be the 5th and 7th leading cause of mortality in males and females in 2022. The top two forms of liver cancer diagnosed are hepatocellular carcinoma and cholangiocarcinoma, with a percentage of 75% and 11%. In recent years, Texas has had the highest incidence, with a rate of 11.6 per 100,000, with the Hispanic population having one of the highest rates. In South Texas, the Rio Grande Valley contains a high Hispanic population and faces multiple health disparities leading to a higher prevalence of liver cancer. These factors and the insufficient diagnostic methods for liver cancer lead to a need to identify faster and early biomarkers. Recently, we have identified an extracellular cancer-testis antigen, POTE-2, which belongs to the POTE gene family. Our preliminary data show that POTE-2 has an increased expression in liver cancer and can be associated with cancer progression. In this study, we will discuss the characterization of the extracellular face of POTE-2 in liver cancer. Lentiviral plasmids created an overexpressing and a knockdown POTE-2 cell line. The exosomes and conditioned media were collected from the cell lines to analyze POTE-2 protein expression through immunoblotting and ELISA. Antibodies targeting varying protein regions were produced and characterized for use in extracellular characterization. Exosome isolation and collection of conditioned media showed the expression of extracellular POTE-2 protein. Using varying antibodies targeting different regions determined the protein domain cleaved through secretion. These studies will aid in discovering novel characteristics of POTE-2 protein function and further explore its potential in liver cancer progression.
Citation Format: Samantha Lopez, Kyle D. Doxtater, Adithya Anilkumar, Sophia Leslie, Amayrani Sanchez, Kristopher Ezell, Subhash Chauhan, Manish K. Tripathi. Characterization of extracellular POTE-2 protein in liver 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 3347.