bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 1672: PKC-ι and 14-3-3 are crucial regulators of c-Raf and the Erk pathway in human medulloblastoma
Authors: Lajmi Luke , Ratnayake Wishrawana S. , Palathinkal Joseph , Breedy Sloan , Todman Aaron , Acevedo-Duncan Mildred 
Published: March 2024

Abstract
Medulloblastoma is the second most common childhood cancer, behind leukemia, and the most common pediatric brain tumor, comprising 20% of all childhood brain cancers. Current treatment options are limited to radiation therapy, surgical resection, and chemotherapy, which are extremely invasive. This underscores the need for more targeted and effective therapeutic treatments to improve patient outcomes. The following study will focus on exploring the PKC-ι specific inhibitor 5-amino-1-((1R,2S,3S,4R)-2,3-dihydroxy-4-methylcyclopentyl)-1H-imidazole-4-carboxamide (ICA-1S) and its effects on medulloblastoma cell lines Daoy and ONS-76. Our in-vitro treatments showed that PKC-ι functions an oncogenic protein that is necessary for Daoy and ONS-76 cell proliferation and that ICA-1S was found to be cytostatic to both Daoy and ONS-76 cells. The inhibition of PKC-ι in both cell lines resulted in a decreased phosphorylation of PKC-ι as well as downregulation of 14-3-3 and crucial components of the c-Raf/Erk pathway including total and phosphorylated levels of c-Raf, Mek1/2, and Erk1/2. This comes as a result of ICA-1S blocking the association of PKC-ι with 14-3-3 while PKC-ι and c-Raf were not found to directly associate with each other, indicating indirect modulation of c-Raf by PKC-ι. Additionally, PKC-ι inhibition decreased its association with Stat3. Expression levels of Stat1, Stat3, c-Fos, and c-Myc transcription factors were significantly downregulated, which is likely the result of reduced transcriptional activation due to upstream inhibition of PKC-ι and Erk signaling. Treatment with ICA-1S was also shown to substantially decrease cellular invasion of Daoy and ONS-76 cells and induce apoptosis. Taken together, these data suggest that PKC-ι likely plays a critical role in the regulation of the c-Raf/Erk pathway, which controls the proliferation and invasion of human medulloblastoma.
Citation Format: Luke Lajmi, Wishrawana S. Ratnayake, Joseph Palathinkal, Sloan Breedy, Aaron Todman, Mildred Acevedo-Duncan. PKC-ι and 14-3-3 are crucial regulators of c-Raf and the Erk pathway in human medulloblastoma [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 1672.
Abstract 1689: CRISPR functional genetic screening for immune enhancers of inhibitor receptors in human primary CD8 T cells
Authors: Wang Ping , Giles Josephine R. , Huang Hua , Shi Junwei , Wherry E.John 
Published: March 2024

Abstract
The restrained efficacy of T cell therapies in cancer treatment is associated with T cell exhaustion (TEX), an impaired effector function state that is marked by distinct epigenetic landscape. These unique epigenetic features promoted the progression of TEX, hindered reinvigoration of TEX state and controlled the abnormal expression of inhibitor receptors (IRs), which could serve as target sites in cancer treatment. Thus, deciphering the regulatory elements in primary human T cells will deeply reveal the mechanism controlling TEX and provide novel therapeutic strategies to promote clinical response. However, how enhancers can be effectively applied in anti-cancer treatment is still poorly understood because high throughput identifying the functional enhancers of inhibitor receptors at scale is technically limited in human T cells. Here, we first developed a pooled screening platform that employs a compact CRISPRi system and enabled efficient one-step delivery of pooled screening libraries to primary human T cells. Leveraging this platform, we screened large genomic regions (~300kb) at saturation around key TEX genes, two IRs—PDCD1, HAVCR2 and one transcription factor (TF)—TBX21 to interrogate functional enhancers in human primary CD8 T cells. We identified two enhancers for PDCD1, three enhancers for HAVCR2 and three enhancers for TBX21, all of which are located over 12kb away from each gene’s transcription start sites. Then, to parse the essential sequences that fulfill enhancer function, we employed Cas9-based in-situ saturation mutagenesis screening to the identified enhancers of PDCD1 and HAVCR2. We found disrupt essential sequences impaired the entire enhancer function, quantitatively phenocopied the effect of targeting the entire enhancer with CRISPRi. Transcription factor motifs analyses of these sequences revealed potential regulation of ZFX for controlling PDCD1 expression and STAT for HAVCR2 expression. Finally, we explored the functional consequences of applying enhancers to anti-cancer treatment. Indeed, targeting the identified enhancers of PDCD1 and HAVCR2 in CAR T cells lead to enhanced cancer cell killing efficiency in vitro. Together, our study provides a platform and paradigm to interrogate functional enhancers in human T cells, illuminated the great potential of manipulating enhancers in T cell therapies.
Citation Format: Ping Wang, Josephine R. Giles, Hua Huang, Junwei Shi, E.John Wherry. CRISPR functional genetic screening for immune enhancers of inhibitor receptors in human primary CD8 T cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1689.
Abstract 1695: Genomic clustering tendency of transcription factors reflects phase-separated transcriptional condensates at cancer super-enhancers
Authors: Wang Zhenjia , Wang Shengyuan , Zang Chongzhi 
Published: March 2024

Abstract
Many transcription factors (TFs) have been shown to bind to super-enhancers, forming transcriptional condensates to activate transcription in various cellular systems including cancer. However, the genomic and epigenomic determinants of phase-separated transcriptional condensate formation remain poorly understood. Questions regarding which TFs tend to associate with transcriptional condensates and what factors influence their association are largely unanswered. Here we systematically analyzed 528 DNA sequence motifs across the human genome and 6,650 TF binding profiles across different cell types to identify the molecular features contributing to the formation of transcriptional condensates. We found that the genomic distributions of sequence motifs for different TFs exhibit distinct clustering tendencies. Notably, TF motifs with a high genomic clustering tendency are significantly associated with super-enhancers. TF binding profiles showing a high genomic clustering tendency are further enriched at cell-type-specific super-enhancers. TFs with a high binding clustering tendency also possess high liquid-liquid phase separation abilities. Compared to non-clustered TF binding, densely clustered TF binding sites are more enriched at cell-type-specific super-enhancers with higher chromatin accessibility, elevated chromatin interaction, and stronger association with cancer outcomes. Our results indicate that the clustered genomic binding patterns and the phase separation properties of TFs collectively contribute to the formation of transcriptional condensates at cancer super-enhancers.
Citation Format: Zhenjia Wang, Shengyuan Wang, Chongzhi Zang. Genomic clustering tendency of transcription factors reflects phase-separated transcriptional condensates at cancer super-enhancers [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 1695.
Abstract 171: Chemotherapeutic agent, cisplatin, influences the proportion of TREM2 (+) M2 macrophages in the TME of LUAD
Authors: Cha Yoon Jin , Park Min Kyung , Chang Yoon Soo 
Published: March 2024

Abstract
Background: Triggering receptor expressed on myeloid cells (TREM2) serves as an immune signaling hub that senses and interacts with a wide range of ligands arising from damaged tissues in pathologic conditions. Despite TREM2’s diverse role in casting immune suppressive environment, the effects of chemotherapy on tumor microenvironment (TME), TREM2 and their interactions are not well established. In this study, we aimed to investigate the characteristics of TREM2 (+) Mφ within the lung TME (Tu), focusing on the impact of chemotherapy on the immune dynamics of lung adenocarcinoma (LUAD).
Method: Changes in the number and distribution of Mφ subclusters in normal appearing lung tissue (NL) and Tu were examined using open-source single cell RNA sequencing (scRNA-seq) datasets and immunofluorescent staining of lung cancer-induced Kras-G12D mouse tissue. Clinical measures affecting the expression of TREM2 were explored using the TCGA-LUAD and -LUSC datasets, and the effects of anticancer drugs and the apoptotic cells on Mφ were observed by differentiating THP1 cells into M0, M1, and M2.
Results: scRNA-seq analysis on LUAD datasets showed that Mφ were the second most abundant cell population that constitutes the lung TME, and the proportion of Mφ in the Tu decreases compared to NL. Among the Mφ subclusters in Tu, a subcluster which specifically increased in Tu shows enrichment of apoptotic cell clearance gene sets, including TREM2. In lung cancer induced Kras-G12D mouse, compared to NL the Tu has an increase in M2 proportion, showing the characteristics of interstitial Mφ in addition with overexpression of TREM2 and enrichment of monocyte chemotaxis gene set enrichment. Among TCGA-LUAD, the high TMB group has low TREM2 expression, and the proportion of TREM2 (+) M2 in the Tu decreases in cisplatin-treated Kras-G12D mouse Tu, suggesting the expression of TREM2 in M2 is suppressed by either cisplatin treatment itself or active immunity in Tu. Additionally, we are going to observe the effect on TREM2 expression by adding cisplatin treated A549-GFP cells or cisplatin alone, to the THP-1 cells that were differentiated into M0, M1, or M2 state.
Conclusion: In addition to changes in the lung immune environment due to the tumor, anticancer treatment changes in the characteristics of M2 in TME, in terms of decrease in TREM2 (+) Mφ fraction. Considering that TREM2 plays a central inhibitory role in the tumor immune environment, the effect of anticancer chemotherapeutic agents should be considered in the development TREM2 targeting agents.
Citation Format: Yoon Jin Cha, Min Kyung Park, Yoon Soo Chang. Chemotherapeutic agent, cisplatin, influences the proportion of TREM2 (+) M2 macrophages in the TME of LUAD [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 171.
Abstract 1720: 53BP1 regulates heterochromatin through liquid-liquid phase separation (LLPS)
Authors: Geng Xinran , Zhang Youwei 
Published: March 2024

Abstract
As compacted DNA, heterochromatin represses abnormal gene expression by inhibiting DNA transcription and maintains genome integrity by protecting aberrant chromosome segregation. Therefore, abnormalities in heterochromatin function are commonly found in cancer. However, how exactly heterochromatin preserves the genome integrity remains poorly understood due largely to the complex structure of heterochromatin. Recently, increasing evidence suggests that heterochromatin factors, including HP1α, KAP1, and SUV39H1/2, could drive the soluble heterochromatin into phase-separated droplets/condensates to promote gene silencing, which is referred to as liquid-liquid phase separation (LLPS). TP53-binding protein 1 (53BP1) has traditionally been a critical factor in DNA double-strand break (DSB) repair. We recently reported an unexpected finding that under normal growth conditions, 53BP1 regulates heterochromatin function through LLPS, which is independent of its DSB repair function. Our studies reveal a new paradigm in studying 53BP1, heterochromatin, and genome stability. However, an important question remains unanswered: how 53BP1 is recruited to heterochromatin to undergo LLPS and the associated broad biological impact. To address this question, we performed a special crosslinking coupled mass spectrometry to uncover potential factors in the 53BP1 condensates assembled on heterochromatin. We identified many factors associated with DNA methylation and histone modification, which are the two main steps in restoring heterochromatin epigenetic modification. Their interactions with 53BP1 at heterochromatin were confirmed by different approaches. We further focused on one of the key factors, PCNA, and carried out a detailed analysis of the interaction between PCNA and 53BP1 and the role of such interaction in 53BP1 LLPS, DSB repair, and heterochromatin function. These findings reveal the previously uncharacterized function of 53BP1 at heterochromatin during normal DNA replication.
Citation Format: Xinran Geng, Youwei Zhang. 53BP1 regulates heterochromatin through liquid-liquid phase separation (LLPS) [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 1720.
Abstract 1737: METTL3-mediated m6A modification promotes tumor progression in upper tract urothelial carcinoma
Authors: LIN LI-JIE , PENG PEI-HUA , HSU KAI-WEN 
Published: March 2024

Abstract
Upper tract urothelial carcinoma (UTUC), comprising 5% of urothelial neoplasms, is a rare malignancy arising from the transitional epithelium of the renal pelvis and ureter. Its rarity and diverse histology pose diagnostic and therapeutic challenges, often lead to delayed diagnoses. The absence of targeted therapies, coupled with a limited understanding of molecular pathogenesis, underscores the ongoing research in urological oncology for effective UTUC management. N6-methyladenosine (m6A) is the predominant RNA methylation in mammalian cells, with its inscription primarily orchestrated by METTL3, a crucial methyltransferase. METTL3 has been implicated in various cancers, affecting critical processes like proliferation, migration, and tumor progression. However, the specific mechanisms and biological function of how METTL3/m6A regulates the progression of UTUC remain unclear. In our study, we found that m6A modification and METTL3 expression were elevated in aggressive UTUC, both are negatively correlated with unfavorable clinical outcomes and poor patient survival. By overexpressing METTL3 in less aggressive UTUC cell lines BFTC909 and KTCC28, the abilities of cell proliferation, migration, invasion, and colony formation increased. Notably, overexpression of METTL3 also increased tumor growth and metastasis in the in vivo orthotopic mouse model. In contrast, knockdown of METTL3 decreases tumor progression in a highly aggressive UTUC cell line KTCC28M. Furthermore, our comparative analysis of RNA-seq and m6A MeRIP-seq datasets unveiled the regulation of 1660 genes by METTL3. This diverse set includes genes associated with tumor growth and metastasis (such as MYC, JAK2, and STAT3), as well as RNA processing-related genes which their critical roles in modulating mRNA stability and splicing (such as GEMIN5 and PABPC1L). Together, we noticed METTL3/m6A is a crucial protagonist in the oncogenic landscape of UTUC, which suggested that it can be used as a target for novel therapeutic strategy for UTUC treatment.
Citation Format: LI-JIE LIN, PEI-HUA PENG, KAI-WEN HSU. METTL3-mediated m6A modification promotes tumor progression in upper tract urothelial carcinoma [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 1737.
Abstract 1767: Molecular subclassification of gastrointestinal stromal tumors by genomic backgrounds
Authors: Yamamoto Hideki , Nakada Eiji , Kawano Seiji , Kato Fumino , Fukano Chika , Futagawa Mashu , Urakawa Yusaku , Ohsumi Risa , Ueno Sayaka , Yanai Hiroyuki , Hirasawa Akira 
Published: March 2024

Abstract
Gastrointestinal stromal tumors (GISTs) are the most common gastrointestinal mesenchymal tumors. While about 10% of GISTs are known to be developed from the KIT or PDGFRA gain-of-function mutations, the rest, which is the majority of GISTs, is so-called as wild-type GISTs. There are attempts to make subclassification of wild-type GISTs in syndromic or non-syndromic group as promising for understanding of heterogeneity or treatment strategy. Genomic states of succinate dehydrogenase B (SDHB) and neurofibromatosis type 1 (NF1) have been raised as candidates for subclassification of wild-type GISTs. In this presentation, we will discuss our recent three cases of wild-type GISTs, carrying germline pathogenic variants in SDHB or NF1. Two cases with SDHB germline pathogenic variants showed stomach GISTs with good clinical course, the maintained performance status and long survival nevertheless of the recurrence. The other case with an NF1 germline pathogenic variant showed multiple GISTs in small intestine which was controlled surgically and the late onset of other clinical symptoms of NF1. These cases might clinically suggest potential prognostic and predictive markers in genomic alterations of SDHB or NF1 for the cases with wild-type GISTs.
Citation Format: Hideki Yamamoto, Eiji Nakada, Seiji Kawano, Fumino Kato, Chika Fukano, Mashu Futagawa, Yusaku Urakawa, Risa Ohsumi, Sayaka Ueno, Hiroyuki Yanai, Akira Hirasawa. Molecular subclassification of gastrointestinal stromal tumors by genomic backgrounds [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 1767.
Abstract 1834: Discovery of a novel and highly selective PARP7 inhibitor for cancer immunotherapy
Authors: Liu Xiaohui , Wang Ying , Xia Dongliang , Zhang Wei , Tian Shijie , He Yan , Feng Xuerong , Yang Xia , Zhang Qi , Jiang Shiyi , Wu Meifeng , Deng Jianfeng , Wang Yeye , Su Yuxi , Yao Min , Yuan Weijiao , You Xuedan 
Published: March 2024

Abstract
Poly-ADP-ribose polymerase 7 (PARP7) is a member of the wider PARP enzyme family that modulate protein function by using nicotinamide adenine dinucleotide (NAD+) as a substrate to transfer an ADP-ribose monomer onto specific amino acid acceptor residues of target proteins. PARP7 acts as a key repressor of type I interferon (IFN) signaling. Its inhibition combats tumor regression by enhancing antitumor immunity that depends on STING pathway. Therefore, PARP7 is emerging as a promising drug target for new immunotherapy. Using structure-based drug design and optimization, we discovered a novel PARP7 inhibitor, HSN002066, with high inhibitory potency (Enzyme assay IC50 = 0.96 nM) and high selectivity for PARP7 over PARP1/2/12/5A/5B/10 (IC50 =163.4/4.7/345.2/1790/110.2/&gt;10000 nM, respectively). In addition, HSN002066 has excellent ADMET profiles with CYPs inhibition, IC50 &gt;10 μM, human LMS T1/2 &gt; 60 min, hERG inhibition, IC50 &gt; 30 μM,mouse oral bioavailability (F) 98.1%. Notably, HSN002066 and RBN-2397, the only PARP7 inhibitor currently in Ph 1/2 clinical development, displayed differentiated antiproliferative activities in cell line NCI-H1373 (IC50 are 387.8 nM and 15.2 nM, respectively). However, HSN002066 revealed remarkable antitumor effects as monotherapy (TGI 77% at 100 mg/kg) or combination with PD-1 antibody in CT-26 allograft model.
The structure of HSN002066 was not presented and will not be disclosed at the time of presentation at AACR meeting.
Citation Format: Xiaohui Liu, Ying Wang, Dongliang Xia, Wei Zhang, Shijie Tian, Yan He, Xuerong Feng, Xia Yang, Qi Zhang, Shiyi Jiang, Meifeng Wu, Jianfeng Deng, Yeye Wang, Yuxi Su, Min Yao, Weijiao Yuan, Xuedan You. Discovery of a novel and highly selective PARP7 inhibitor for cancer immunotherapy [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 1834.
Abstract 184: M1-like macrophage infiltration, CD8+ T cell activation, and increased cancer cell apoptosis in immunologically cold Lewis lung carcinoma treated with tumor-trophic Salmonella Typhimurium expressing anticancer proteins in immunocompetent C57BL/6 mice
Authors: He Qiuhong , Brncick Lindsay R. , Gong Boxi , Flowers Julia L. 
Published: March 2024

Abstract
Immunotherapy has revolutionized cancer treatment with Immune checkpoint inhibitors (ICIs) and genetically engineered T-Cells expressing chimeric antigen receptors (CARs). CAR-T treatment of hematologic malignancies has achieved outstanding patient response rate. CAR T therapy, however, is thwarted in solid tumor treatment due to two major factors: the immune-suppressive tumor microenvironment that Inhibits T-cell infiltration and T-cell function. In addition, cancer resistance to ICIs treatment also limits the solid tumor response rate. This research aims to activate proinflammatory anticancer immune responses in immunologically cold solid tumors using the genetically engineered Salmonella typhimurium VNP20009 strains that express anticancer proteins. Previously, we have shown that the Salmonella Typhimurium VNP20009 strain expressing methioninase (METase) and/or Tumor Necrosis Factor (TNFα) caused rapid tumor destruction of cold Lewis Lung Carcinoma (LLC) grown on immunocompetent C57BL/6 mice. In this investigation, several mechanisms of this tumor tropic anti-cancer bacteria were studied including the innate and adaptive immune system responses and cancer cell apoptosis. In a pilot study, we selected eight tumor tissues treated with several different bacteria strains and performed histological analysis to observe the effectiveness of each. We found that in the tumor tissues treated with VNP20009_rMETase_TNFα, there was infiltration and activation of CD8+ T cells coupled with reduced amounts of T regulatory cells, as well as an increased ratio of M1-like to M2-like macrophages. We also observed increased tumor apoptosis associated with an elevated detection of an apoptosis biomarker and a suppressed amount of the Ki67 tumor growth signal. These findings indicate that VNP20009_rMETase_TNFα anticancer bacteria can disrupt the tumor microenvironment in the cold LLC tumors and active innate and adaptive anti-cancer immune response in immunocompetent mice. Further, we are investigating additional cold solid mouse tumor models to validate our findings and how this can apply to bacteria-based immunotherapy.
Citation Format: Qiuhong He, Lindsay R. Brncick, Boxi Gong, Julia L. Flowers. M1-like macrophage infiltration, CD8+ T cell activation, and increased cancer cell apoptosis in immunologically cold Lewis lung carcinoma treated with tumor-trophic Salmonella Typhimurium expressing anticancer proteins in immunocompetent C57BL/6 mice [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 184.