bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 2536: Intracellular Ctla4 overexpression promotes melanoma progression and metastasis
Authors: Kazmi Hasan Raza , Mo Xuan , Zhou Bo , Alp Sarah Preston , Gross Scott , Wajeeh Hassaan , Merali Carmen , Elrod John , Soboloff Jonathan , Merali Salim , Zaidi M. Raza 
Published: April 2023

Abstract
Cytotoxic T Lymphocyte Antigen 4 (CTLA4) expressed on the surface of T cells is an important immunotherapeutic target in many cancers, including melanoma. However, we previously found highly upregulated expression of CTLA4 in BRAF/NRAS-mutant human melanoma cell lines and tissues. Although CTLA4 is almost entirely expressed intracellularly in melanoma cells, its intracellular functions have remained elusive. Ectopic expression of Ctla4 (Ctla4-ee) in mouse melanoma cell lines significantly promoted lung colonization in syngeneic mice as well as in immunocompromised mice, suggesting that Ctla4 had pro-tumorigenic effects independent of its extracellular immune checkpoint function. Proteomics analysis identified apoptosis to be a major affected pathway and we found that Ctla4 ectopic-expressing mouse melanoma cells (B2905-Ctla4-ee) were significantly resistant to doxorubicin-induced apoptosis as compared to empty vector (EV) controls. In a reciprocal experiment, knocking out CTLA4 in the Hs936T human melanoma cells, that exhibit high endogenous CTLA4 expression, showed significantly increased apoptosis than the parental cells. Moreover, significant upregulation of anti-apoptotic proteins (Bnip3, Birc6, Pak1, Mcl-1, Survivin, Rac1/Cdc42, Bcl-2, and Bnip3l) and downregulation of pro-apoptotic proteins (p53 and Bad) were observed in CTLA4-ee cells as compared to EV controls. CTLA4-ee cells also showed significantly higher invasion in Matrigel-coated Transwell assay. Interestingly, we also found that CTLA4 translocated to mitochondria, where it downregulated oxidative phosphorylation and increased glycolysis. These findings lead us to hypothesize that CTLA4 plays a significant role in regulating apoptosis and mitochondrial metabolic functions, leading to the promotion of melanoma progression and metastasis.
Citation Format: Hasan Raza Kazmi, Xuan Mo, Bo Zhou, Sarah Preston Alp, Scott Gross, Hassaan Wajeeh, Carmen Merali, John Elrod, Jonathan Soboloff, Salim Merali, M. Raza Zaidi. Intracellular Ctla4 overexpression promotes melanoma progression and metastasis [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 2536.
Abstract 2541: Heterogeneity of VDAC2-Bak/Bax mediated mitochondrial apoptosis can be exploited to develop effective and selective treatment against metastatic uveal melanoma
Authors: Mishra Piyush 
Published: April 2023

Abstract
Apoptosis, a form of programmed cell death, is an evolutionarily conserved and genetically regulated phenomenon that is pivotal in maintaining tissue homeostasis and is an important player in regulating carcinogenesis. Mitochondria along with its resident proteins are the central player in regulating apoptosis. In recent years, VDAC2, an Outer Mitochondrial Membrane (OMM) protein has been shown to be the key recruitment factor for Bak, a pro-apoptotic protein to the OMM and, therefore is crucial for tBid-induced OMM permeabilization. We have previously found that unexpectedly, hepatocellular carcinoma (HCC) cells are vastly more sensitive to tBid induced apoptosis compared to normal hepatocytes and this difference is owed to high abundance of VDAC2-Bak in HCC. These findings are in line with multiple datasets posted in Oncomine, and protein atlas websites and may have clinical relevance. Combination of S63845, a selective Mcl-1 inhibitor, with TRAIL was effective at reducing tumor growth in vivo, but only in tumors expressing VDAC2. We hypothesized that the liver metastases of some extrahepatic primary tumors might also show enhanced sensitivity to VDAC2-Bak mediated apoptosis as compared to the normal liver tissue. Testing this hypothesis is important for uveal melanoma (UM) that primarily metastasizes in the liver, and these metastases lack an effective treatment. Interestingly, on testing several UM cell lines and patient samples we observed that VDAC2-Bak are upregulated in UM liver metastasis as well as compared to normal liver tissue. As expected, high VDAC2 expressing cell lines were also more sensitive to tBid induced OMM permeabilization. We propose that these differences can be exploited to design an effective therapy for metastasized UM.
Citation Format: Piyush Mishra. Heterogeneity of VDAC2-Bak/Bax mediated mitochondrial apoptosis can be exploited to develop effective and selective treatment against metastatic uveal 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 2541.
Abstract 255: Isolation of unaltered sub-populations of immune cells using magnetic levitation
Authors: Travers Kevin , Wilson Nathan , Kale Abhijit 
Published: April 2023

Abstract
The analysis and characterization of subsets of immune cells from heterogeneous samples, such as peripheral blood mononuclear cells (PBMCs), requires isolation and enrichment. Common methods for this enrichment step include fluorescence activated cell sorting and positive or negative selection with magnetic beads. However, these methods alter native cell phenotypes during the enrichment process by the application of pressure, binding of antibodies, extensive manipulation and centrifugation, among other perturbations. This results in altered gene expression, generating molecular profiles that are not representative of true biological significance. These alterations are prevented by using magnetic levitation cell isolation and enrichment. The LeviCellTM platform performs hands-free cell enrichment by utilizing magnetic fields to levitate viable, healthy cells away from dead cells and debris. Unlike other single cell separation methods, the enriched target cells are not subject to mechanical force, labeling, or staining to achieve viability enrichment. This results in a single cell suspension that is ready for immediate downstream analysis, producing molecular profiles free of isolation-induced gene expression artifacts.
We have developed reagents to extend the benefits of this technology to the immuno-oncology research market. These new reagents are used to target the enrichment of all T cells, the CD4+ or CD8+ subsets of T cells, or all B cells, with other target populations in development. In all cases, unwanted cells are captured within the levitation chamber, depleting them from the sample. These reagents leverage the magnetic field across the levitation chamber. Specifically-tagged, unwanted cells are pulled to the edges of the levitation chamber while the target cells undergo viable cell enrichment. The end result is a cell population that has been enriched and at higher viability. We have seen consistent depletion rates of &gt;98%, resulting in a final targeted population with 90% or higher purity in most cases. Here we demonstrate the performance of the LeviCell platform in the enrichment of targeted cell populations relevant to the immuno-oncology research community.
Citation Format: Kevin Travers, Nathan Wilson, Abhijit Kale. Isolation of unaltered sub-populations of immune cells using magnetic levitation [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 255.
Abstract 2557: Targeting the IGF1R signaling pathway inhibits cell growth and dissemination in BCOR mutant retinoblastoma
Authors: Lee Su-Chan , Alaali Lujain , Eberhart Charles G. 
Published: April 2023

Abstract
Retinoblastoma is the most common intraocular cancer of childhood, with approximately 8,000 new cases each year worldwide. While survival rates are relatively high in developed countries, death can occur in up to half of children in some regions. In addition, blindness is common in patients who survive, and improved therapies are clearly needed. While loss of RB gene function is essential for the initiation of almost all retinoblastoma, additional molecular changes driving their growth and dissemination are poorly understood. Improved understanding of the molecular pathways driving retinoblastoma growth and dissemination may allow us to develop more effective and less toxic therapies. Alterations leading to BCL-6 corepressor (BCOR) loss of function are the second most common mutations in retinoblastoma after changes affecting the RB locus, and are found in more aggressive tumors. BCOR mutations are also associated with metastasis and poor prognosis in other types of pediatric cancer, suggesting that targeting it will represent a new therapeutic approach for aggressive retinoblastoma. Here, we found that BCOR knockdown or knockout in two retinoblastoma cell lines with high baseline levels of protein caused significantly increased invasion/migration, proliferation and clonogenicity. In contrast, overexpression of BCOR in retinoblastoma cells with low/no baseline expression showed opposite effects. In orthotopic xenograft models, BCOR knockout dramatically increased the size and spread of retinoblastoma xenografts as compared to parental controls. In order to determine the molecular pathways modulated by BCOR, we used RNA sequencing and found that loss of function induces IGF1 transcription, resulting in activation of IGF1R and the ERK signaling pathway. Pharmacological inhibition of IGF1/IGF1R signaling using Lincitinib or AEW541 inhibited proliferation and migration in BCOR knockout retinoblastoma cells in vitro, and Lincitinib dramatically slowed xenograft growth in vivo, suggesting that induction of IGF1 represents an important downstream effector following BCOR loss. Our studies support a functional role for BCOR mutations in aggressive retinoblastoma, and suggest that this is mediated at least in part by increased IGF1R signaling, which represents a new therapeutic target for these malignant childhood tumors of the eye.
Citation Format: Su-Chan Lee, Lujain Alaali, Charles G. Eberhart. Targeting the IGF1R signaling pathway inhibits cell growth and dissemination in BCOR mutant retinoblastoma [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 2557.
Abstract 2589: TROP2 gene copy number variations are a hallmark of glioblastoma and MEN-2A cancers
Authors: Alberti Saverio , Trerotola Marco , Moschella Antonino , Guerra Emanuela 
Published: April 2023

Abstract
TROP2 mutations are not required to trigger activation of tumor growth and metastasis. However, expression of Trop-2 is affected by DNA methylation in choriocarcinomas, i.e. trophoblast-derived malignancies, and in lung adenocarcinomas, suggesting that loss of TROP2 expression may provide a selective advantage in specific tumor types. Intriguingly, amplification of the TROP1/EPCAM and TROP2/TACSTD2 genes was found to be driven by alterations of DNA methylation, with parallel LOH in sister cell clones. Consistent, mutations of TP53 were shown to induce amplification of TROP genes through loss of DNA methylation. Hence, we investigated whether LOH/DNA methylation of the TROP2 gene and gene amplification are selectively associated with specific tumor types. Our findings indicate that TROP2 amplification occurs in a subgroup of aggressive glioblastomas (15.7%, n=3/19), suggesting impact on malignant progression. On the other hand, TROP2 LOH was shown to occur in the majority of low-grade gliomas (80%, n=4/5). Investigation on the TROP2 gene in MEN-2A revealed that LOH of TROP2 was somatically acquired in 25% of phaechromocytomas and medullary thyroid carcinomas (n=6/24), but did not appear as a heritable trait in the germline. TROP2 gene copy number variations were rarely detected in other cancer types, suggesting tumor subtype-specific impact.
Citation Format: Saverio Alberti, Marco Trerotola, Antonino Moschella, Emanuela Guerra. TROP2 gene copy number variations are a hallmark of glioblastoma and MEN-2A cancers [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 2589.
Abstract 26: BaF3 RAS cell panel, a powerful cell model for Ras inhibitor discovery and development
Authors: YAO PENG , Wang Yu , Liu Chang , Wang Na , Meng Wei , Ning Jinying , Hao Feng 
Published: April 2023

Abstract
RAS, abbreviated from Rat sarcoma virus, is composed of three small GTPase proteins, HRAS, KRAR and NRAS. Over-activation of these genes due to different mutation were found in up to 20% of all human cancers and about 90% in pancreatic cancer. The identification of RAS mutation, especially KRAS-G12S or G12D mutation, as cancer diver genes has recently led to rapid development of anti-tumor therapeutics agents such as sotorasib (AMG 510), adagrasib (MRTX-849) and MRTX1133, but there are still no good drugs for the cancer patients with other RAS mutations. Ba/F3 line is a popular cell model for studying both kinases and their inhibitors, because some kinases can render the growth of Ba/F3 cells to be depended on the over-activation of the kinases instead of exogenous IL-3 supplement, while their inhibitors can antagonize these effects. Our group has generated a Ba/F3 RAS cell panel with 29 KRAS, 11 HRAS and 20 NRAS different single or double mutants for RAS inhibitor screening and development, all of these lines were well validated with PCR sequencing, Western Blot and KRAS G12C and G12D inhibitors. In addition to use the cell lines for in vitro assays, the transformed Ba/F3 lines can grow well in immune-deficient mice as in vivo models. Our data indicate that the cell line panel of Ba/F3 is a powerful system for new RAS inhibitor discovery and development.
Citation Format: PENG YAO, Yu Wang, Chang Liu, Na Wang, Wei Meng, Jinying Ning, Feng Hao. BaF3 RAS cell panel, a powerful cell model for Ras inhibitor discovery and development [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 26.
Abstract 260: Long RNA and DNA sequencing reveals HEK293 diversity between commercial sources
Authors: Blum Laura , Sexton Brittany , Sanford Jonathan C. , Janzen Evan , Sun Luo , Koetsier Paul A. , Krishnan Keerthana , Apone Lynne , Langhorst Bradley W. 
Published: April 2023

Abstract
HEK293 cells are used extensively in cancer research, with more than 4800 articles between 2017 and 2022 (PubMed search “cancer[MeSH Major Topic] and hek293”). Studies involving transfection to overexpress, knock down, or modify proteins in these cells are common. While HEK293 cells are relatively easy to grow and maintain, early use of high throughput sequencing Yao-Cheng et. al. identified genomic variability between different sources of cell lines and revealed unexpected details about their developmental lineage (likely adrenal, not kidney)[1]. Genomic or transcriptomic reorganization may complicate interpretation of results from targeted intervention experiments. Here, we evaluate HEK293 cells from various commercial sources using long read sequencing technology. Oxford Nanopore direct cDNA profiling was used to compare isoform usage and examine gene fusions. Long DNA libraries were prepared using a high molecular weight isolation method, sequenced on Oxford Nanopore, and assembled to produce long contiguous fragments. Genome assemblies generated from long read sequencing support the genomic diversity reported by Yao-Cheng et.al, though the specific copy number variants are distinct from those previously reported. Assembled genomes and transcriptomes for these specific lots of HEK293 cells will be available at NCBI. Given the plastic nature of HEK293 cells, we recommend confirmation of genomic and transcriptomic structure of the specific cells in use before and after intervention.
[1] Lin, Yao-Cheng, Morgane Boone, Leander Meuris, Irma Lemmens, Nadine Van Roy, Arne Soete, Joke Reumers, et al. “Genome Dynamics of the Human Embryonic Kidney 293 Lineage in Response to Cell Biology Manipulations.” Nature Communications 5, no. 1 (September 3, 2014): 4767. https://doi.org/10.1038/ncomms5767.
Citation Format: Laura Blum, Brittany Sexton, Jonathan C. Sanford, Evan Janzen, Luo Sun, Paul A. Koetsier, Keerthana Krishnan, Lynne Apone, Bradley W. Langhorst. Long RNA and DNA sequencing reveals HEK293 diversity between commercial sources [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 260.
Abstract 2604: Functional analysis of p53 codon 72 polymorphism with cysteine substitution in cancer cells
Authors: Zhang Shengliang , El-Deiry Wafik S. 
Published: April 2023

Abstract
The p53 codon p72 polymorphism with proline (p53P72)/arginine (p53R72) substitution is associated with cancer incidence. Cysteine(C) substitution at p53 codon 72 polymorphism (p53C72) is rarely studied in cancer patients. A patient who developed AML and who carries p53C72 was described (El-Deiry, 2022 WIN Symposium). The patient’s family has high rates of cancer susceptibility in the women some of whom carry FANCC alterations and other alleles. To examine the functional characteristics of different p53 alterations at codon 72, we generated plasmids expressing p53C72, p53 R72 or p53P72. The variants of p53 were overexpressed in p53-null cancer cells by transient transfection of the plasmids. We tested functions of the p53 codon 72 polymorphisms (p53C72, p53R72 and p53P72) in two cancer cell lines (Soas-2 and HCT116 p53 null) with different expression levels of the p53 variants at different time points. To examine the effect of codon 73 variants on p53 transactivation, we performed a PG13-Luciferase reporter assay and examined the endogenous p53 targets at the protein level. The luciferase-reporter assay showed that all the three variants of the p53 codon p72 variants increased PG-13 luciferase expression at early time points. The Western blot assay showed that the p53C72, the p53R73 and the p53P72 increased endogenous p21, DR5, puma and MDM2 at the protein levels at different time points. The p53C72 increased the p53 targets and PG13-driven luciferase expression much higher than the p53R72 and the p53P72. These results suggest that the p53 codon 72 variants (C72, R72 and P72) retain wild-type activity for p53-mediated transcription, and p53C72 has the highest potency among them. We examined the effect of the p53 variants on cell growth and death. PARP cleavage (a marker of cell apoptosis) was induced in cells overexpressing all the three p53 codon 72 variants. We observed a lesser potency of p53C72 to induce PARP cleavage compared to p53R72 and p53P72. Colony formation assay showed a suppressive effect of p53C72, p53R72 and p53P72 on cancer cell growth. Our studies demonstrate some differences of in wild-type functions of p53 p53C72, p53R72 and p53P72 alleles.
Citation Format: Shengliang Zhang, Wafik S. El-Deiry. Functional analysis of p53 codon 72 polymorphism with cysteine substitution in 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 2604.
Abstract 2625: KRAS activity-mediated mechanism of castration-resistant prostate cancer progression
Authors: Kamijima Taiki , Izumi Kouji , Kadono Yoshifumi , Mizokami Atsushi 
Published: April 2023

Abstract
Purpose: Prostate cancer is highly androgen-dependent, and androgen receptor (AR) signaling is suppressed by treatment. However, there are cases in which disease progresses rapidly at the end of treatment even after AR suppression, suggesting that the disease progresses by mechanisms different from AR. The aim of this study is to investigate the KRAS signaling pathway as one of the mechanisms.
Methods: We used the hormone-sensitive prostate cancer (HSPC) cell line LNCaP and the castration-resistant prostate cancer (CRPC) cell line DU145. We performed KRAS knockdown by si-RNA and activation of KRAS signaling by EGF stimulation. To examine KRAS signaling, PCR and Western blotting were performed. The changes in proliferation and migration due to inhibition and activation of KRAS signaling were confirmed.
Results: RT-PCR showed a fusion gene of ubiquitin-conjugating enzyme UBE2L3 and KRAS (UBE2L3-KRAS) in DU145. Western blotting showed increased phosphorylation of ERK and p38 downstream of KRAS in DU145. KRAS knockdown inhibited proliferation and migration in DU145 but not in LNCaP. In EGF-stimulated activation of KRAS signaling, Western blotting showed activation of downstream KRAS signaling in LNCaP, but no change in proliferation and migration in fetal bovine serum (FBS)-added medium. In contrast, EGF stimulation of DU145 further activated downstream KRAS signaling and promoted proliferation and migration. The AR-dependent LNCaP showed almost no effect of KRAS signaling activation on cancer progression, whereas DU145 showed that KRAS signaling is involved in cancer progression.
Conclusion: While HSPC is highly AR-dependent and does not show any effect of KRAS on cancer progression, KRAS may be involved in cancer progression in some CRPCs.
Citation Format: Taiki Kamijima, Kouji Izumi, Yoshifumi Kadono, Atsushi Mizokami. KRAS activity-mediated mechanism of castration-resistant prostate cancer progression [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 2625.