bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 5643: Targeted RNA-seq of dried blood microsamples for convenient RNA biomarker monitoring
Authors: Kobzik Lester , Liu Tianbing , Makhanov Mikhail , Hu Dongfang , Ghias Khadija , Diehl Paul , Chenchik Alex 
Published: March 2024

Abstract
Microsampling lancet-induced blood drops enables frequent and comprehensive analysis of various metabolites, lipids, cytokines, and proteins. This approach holds promise for monitoring immunotherapy patients using RNA biomarkers, but a suitable method for processing RNA has been lacking.
In this study, we employed a targeted RNA-sequencing protocol, the DriverMap™ EXP assay, to process 30 ul of dried blood. We compared the gene expression profile in traditionally collected blood samples with that of blood absorbed onto a Mitra® microsampling device containing an RNA-stabilization reagent. Following endotoxin incubation, RNA was extracted from stimulated and unstimulated blood samples. Targeted PCR amplification of 274 immune/inflammatory genes using the DriverMap targeted RNA-Seq protocol demonstrated robust detection and high correlation (r = 0.94) between the two methods in both unstimulated and endotoxin-stimulated blood. Moreover, differentially expressed genes (DEGs) identified in standard and microsampling methods exhibited substantial overlap with publicly available datasets from similar experiments. Furthermore, we compared whole blood extracted from Tempus™ blood RNA tubes to Mitra microsamples pre- and post-immunization with the Pneumovax® vaccine using the DriverMap EXP genome-wide 19K panel for targeted RNA-sequencing. We observed approximately 90% overlap in the top 10K genes between Tempus and Mitra microsamples. Notably, microsamples stored at 4ºC for over a year exhibited similar expression profiles to more recently drawn whole blood samples.
Citation Format: Lester Kobzik, Tianbing Liu, Mikhail Makhanov, Dongfang Hu, Khadija Ghias, Paul Diehl, Alex Chenchik. Targeted RNA-seq of dried blood microsamples for convenient RNA biomarker monitoring [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 5643.
Abstract 566: The anticancer effects of polyisoprenylated cysteinyl amide inhibitors involves interaction with the KRAS chaperone calmodulin
Authors: Ofosu-Asante Kweku , Lazarte Jassy Mary , Burra Amarender , Lamango Nazarius S. 
Published: March 2024

Abstract
Pancreatic cancer is the third leading cause of cancer-related deaths with a 5-year survival rate of less than 10%. Approximately 90% of reported cases are driven by KRAS mutations. The mutant KRAS acquires its functional localization through interactions with chaperone proteins via its polybasic polyisoprenylated tail. Polyisoprenylated cysteinyl amide inhibitors (PCAIs) mimic this region possibly disrupting the polyisoprenylation-dependent interactions with chaperone proteins. Here, we determine the effect of newly developed PCAIs that were designed to be more water-soluble on cell viability, 3D spheroid invasion, spheroid degeneration and F-actin filaments on MIA PaCa-2 and PANC-1 cells. Of the seven new PCAIs analogs tested, NSL-AB-51 and NSL-AB-45 were the most potent, with EC50 values of 2.5 and 5.6 µM against MIA PaCa-2, and 1.7 and 4.5 µM against PANC-1 cells, respectively. At 5 and 10 µM, NSL-AB-51 decreased the invasion area of 3D spheroids by 98 and 99%, respectively. MIA PaCa-2 spheroids degenerated by 61% after 72 h treatment with 10 µM NSL-AB-51. Treatment with 1.0 μM NSL-AB-51 caused cell rounding and reduction of mean cell areas by 69% and F-actin filaments by 96%. Moreover, to identify the pharmacological target of the PCAIs, NSL-AB-45 was coupled to an epoxy-activated Sepharose resin for affinity trapping of PCAIs-interacting proteins. Affinity-analysis of supernatants and detergent membrane extracts from MIA PaCa-2 and PANC-1 cells revealed single Coomassie band of about 17 kDa that was identified as calmodulin by western blotting analysis. The calmodulin-PCAIs affinity interaction was found to be strongest in the presence of calcium and weakest in the presence of EDTA. These findings reveal that calmodulin is the likely target of PCAIs. Since calmodulin is the chaperone protein responsible for KRAS trafficking and localization to the inner surface of the plasma membrane, this finding strongly suggests, at least in part, an anticancer role for the PCAIs that involve disruption of KRAS functions.
Citation Format: Kweku Ofosu-Asante, Jassy Mary Lazarte, Amarender Burra, Nazarius S. Lamango. The anticancer effects of polyisoprenylated cysteinyl amide inhibitors involves interaction with the KRAS chaperone calmodulin [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 566.
Abstract 5667: Intratumoral heterogeneity in gastric cancer related with survival and tumor microenvironment
Authors: Gu Do-eon , Kwon Woo Sun , Rha Sun Young , Park Woong-Yang 
Published: March 2024

Abstract
Gastric cancer (GC), often diagnosed at an advanced stage, poses a significant therapeutic challenge due to its resistance to treatment. The understanding of intratumoral heterogeneity, crucial for tumor cell survival, remains limited in GC. We conducted a comprehensive analysis of three patient groups (intraperitoneal metastasis [IM], hematogenous metastasis [HM], and both metastasis [HIM]) undergoing immunotherapy (IO) and chemotherapy. Utilizing single-cell RNA sequencing and TCR sequencing, we examined 11 adjacent normal, 10 HM, 8 IM, and 5 HIM primary GC samples. In epithelial cells, three distinct tumor clusters (Tumor_1, Tumor_2, and Tumor_3) were identified. Trajectory analysis revealed the differentiation of chief cells into Tumor_1, subsequently dividing into more malignant cell types, Tumor_2 and Tumor_3. Tumor_2 was enriched in IM, while Tumor_1 was enriched in HM and HIM. Patients grouped by Tumor_1, 2, 3 levels showed varying survival outcomes. Surprisingly, high Tumor_2 levels correlated with increased survival, attributed to elevated HLA and PDL1 expression, promoting immune cell recruitment and robust response to IO therapy. Conversely, Tumor_3 high patients exhibited worse survival, with enrichment in metabolic pathways associated with glycolysis and hypoxia, linking to metastasis. We observed the proportion of T cells that increased presence of CD8 effector cells among patients exhibiting high levels of Tumor_1 and Tumor_2. Through TCR analysis, we found heightened clonality in both CD8 effector cells and exhausted T cells in patients with elevated Tumor_1 and Tumor_2 levels. This suggests that the activated CD8 effector T cells in these patients may enhance their ability to effectively target and attack cancer cells. In summary, this study provides a comprehensive picture of intratumoral heterogeneity in GC can impact the survival and tumor microenvironment. The unexpected high survival in Tumor_2 patients emphasizes the potential of targeting specific pathways for improved therapeutic outcomes. Additionally, the observed T cell dynamics and clonality in Tumor_1 and 2 underscore the importance of understanding the immune microenvironment for effective cancer attack.
Citation Format: Do-eon Gu, Woo Sun Kwon, Sun Young Rha, Woong-Yang Park. Intratumoral heterogeneity in gastric cancer related with survival and tumor microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5667.
Abstract 5674: Characterizing Cellular Heterogeneity and Identifying Potential Biomarkers in Esophageal Squamous Cell Carcinoma (ESCC) Using Single-Cell RNA Sequencing
Authors: Hsiao Tzu-Hung , Lin Chih-Hung , Wu Ting-Shuan , Lee Li-Wen , Hsu Chung-Ping 
Published: March 2024

Abstract
Esophageal squamous cell carcinoma (ESCC) exhibits significant cellular heterogeneity, rendering it susceptible to developing radioresistance and recurring tumors. Single-cell RNA sequencing (scRNA-seq) is an advanced technique that allows for the exploration of distinct gene expression profiles in individual cells. To investigate cellular heterogeneity in ESCC, scRNA-seq analysis was performed on tumor tissues from ten ESCC patients, as well as adjacent non-malignant esophageal tissues. The cellular composition revealed 19 distinct cell clusters, further categorized into seven cell populations: 69.31% Fibroblast, 15.36% T cell, 5.30% Monocytes, 5.26% Endothelial cells, 2.68% plasma cell, 1.91% Epithelial cells, and 0.18% ambiguous. Notably, Fibroblast and Endothelial cells were more prevalent in non-malignant tissues, while the remaining cell types were enriched in tumor tissues. Differential gene expression analysis identified 49 genes with higher expression in tumor cells and 37 genes with lower expression. Gene Set Enrichment Analysis (GSEA) revealed the top three most relevant GO Biological Processes pathways: positive regulation of immune response, regulation of T cell activation, and positive regulation of cell migration. Furthermore, in post-treatment follow-up, four patients were observed to develop metastasis within one year. Comparative analysis between metastatic and non-metastatic patients unveiled 9 Differentially Expressed Genes (DEGs), including KRT6A and AKR1B10, which exhibited specific expression in Epithelial cells and were highly expressed in tumor tissues. Additionally, IGLC2, IGHG4, and IGHG1 demonstrated specific expression in plasma cells, with elevated expression in tumor tissues. These findings suggest that KRT6A, AKR1B10, IGLC2, IGHG4, and IGHG1 may serve as potential biomarkers for predicting post-chemotherapy metastasis in ESCC patients.
Citation Format: Tzu-Hung Hsiao, Chih-Hung Lin, Ting-Shuan Wu, Li-Wen Lee, Chung-Ping Hsu. Characterizing Cellular Heterogeneity and Identifying Potential Biomarkers in Esophageal Squamous Cell Carcinoma (ESCC) Using Single-Cell RNA Sequencing [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 5674.
Abstract 5696: Exploring the association between miR-9-5p levels and the mTORC1/mTORC2 pathway in laryngeal cancer cell lines
Authors: Gobin Christina , Chang Matthew , Lattimore Chayil C. , Fredenburg Kristianna M. 
Published: March 2024

Abstract
Background: We previously demonstrated that differing levels of miR-9-5p could predict chemosensitivity to cisplatin, and that miR-9-5p is a regulator of potential chemotherapeutic target MAP1B. As the mTOR/PIK3CA pathway has been implicated in the pathogenesis of laryngeal squamous cell carcinoma (LSCC), we sought to determine an association between differing miR-9-5p levels, mTOR pathway mediators including MAP1B, and methylation.
Methods: UM-SCC-98, UM-SCC-12, UM-SCC-11A, UM-SCC-10A (obtained from the University of Michigan) laryngeal cancer cell lines were used in this study. We previously showed UM-SCC-98 and UM-SCC-12 to have significantly lower miR-9-5p levels as compared to UM-SCC-11A and UM-SCC-10A (Northern blot analysis). The IC50 of an mTORC1 inhibitor (Rapamycin) and an mTORC1/C2 inhibitor (AZD-8055) were evaluated using the Cell Titer Blue Viability assay. Cells were treated with the de-methylating agent, 5-Azacytidine (1μM). Gene expression of mTOR pathway mediators- miR-9-5p, PTEN, EGFR, PIK3CA, and MAP1B- were determined in each cell line pre-and post-treatment via qPCR.
Results: All cell lines were resistant to treatment with Rapamycin (IC50 &gt; 60μM) with the UM-SCC-12 cell line yielding the highest IC50 (&gt; 150μM). Conversely, decreased cell proliferation was detected with AZD-8055. This was significantly associated with their miR-9-5p levels– a higher AZD-8055 IC50 was associated with cell lines UM-SCC-98 (~40μM) and UM-SCC-12 (~23μM) compared to UM-SCC-10A (~16μM) and UM-SCC-11A (~8μM). Following demethylation treatment, miR-9-5p levels were significantly increased in UM-SCC-12 only (2-fold), and this corresponded to a significant decrease in MAP1B gene expression (2-fold) but not with EGFR, PIK3CA, and PTEN gene expression.
Conclusion: In conclusion, our study suggests that miR-9-5p may regulate MAP1B gene expression via the mTORC2 pathway. In addition, methylation may play a role in the regulation of the miR-9-5p gene and its downstream targets in laryngeal cancer tumorigenesis. Future studies will involve exploring epigenetic mechanisms of miR-9-5p inhibition and defining the role of key mediators of the mTOR pathway in LSCC.
Citation Format: Christina Gobin, Matthew Chang, Chayil C. Lattimore, Kristianna M. Fredenburg. Exploring the association between miR-9-5p levels and the mTORC1/mTORC2 pathway in laryngeal cancer cell lines [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 5696.
Abstract 5697: MILIP drives triple-negative breast cancer through complexing with transfer RNAs to promote protein production
Authors: Feng Yuchen , Zheng Simin , Zhao Xiaohong , Zhang Yuanyuan , Xu Ran , Xu Liang , Preiss Thomas , Jin Lei , Gao Jinnan , Zhang Xu Dong 
Published: March 2024

Abstract
Despite the progress in endocrine therapy, targeted therapy and immunotherapy, the treatment of triple-negative breast cancer (TNBC), one of the most aggressive types of breast cancer, is challenging. This is closely associated with the lack of effective molecular targets in TNBC cells for therapeutic intervention. Here we report that the long noncoding RNA (lncRNA) MILIP drives TNBC cell survival, proliferation and tumorigenicity through complexing with transfer RNAs (tRNAs) to promote protein production, and thus represents a potential therapeutic target in TNBC.
MILIP was expressed at high levels in TNBC cells that commonly harbor loss-of-function mutations of the tumor suppressor p53, yet MILIP silencing diminished TNBC cell viability and retarded TNBC xenograft growth, indicating that MILIP functions distinctively in TNBC beyond its well-established role in repressing p53 in other types of cancers. Mechanistical investigations revealed that MILIP interacted with eukaryotic translation elongation factor 1 alpha 1 (eEF1α1) and formed an RNA-RNA duplex with tRNALeu and tRNASer, type II tRNAs, through their variable loops, thus facilitating the binding of eEF1α1 to these tRNAs. Disrupting the interaction between MILIP and eEF1α1 or tRNAs diminished protein production and cell viability, with therapeutic potential revealed where targeting MILIP using Gapmers inhibited TNBC growth and cooperated with the clinically available protein synthesis inhibitor omacetaxine mepesuccinate in vivo.
Collectively, these results identified MILIP as an RNA translation elongation factor to promote protein production in TNBC cells and demonstrated that experimental therapy with MILIP Gapmers inhibits TNBC growth, indicating MILIP targeting is a potential avenue for developing improved TNBC treatment through blocking protein synthesis.
Citation Format: Yuchen Feng, Simin Zheng, Xiaohong Zhao, Yuanyuan Zhang, Ran Xu, Liang Xu, Thomas Preiss, Lei Jin, Jinnan Gao, Xu Dong Zhang. MILIP drives triple-negative breast cancer through complexing with transfer RNAs to promote protein production [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 5697.
Abstract 5708: Silence exportin 7 sensitizes esophageal squamous cell cancer to CDK4/6 inhibition through block the cell cycle coresectory
Authors: Wu Zhong , Xu Lin , Jiang Chuang , Bass Adam , Zhou Jin 
Published: March 2024

Abstract
Introduction: There is a lack of effective target therapies for esophageal squamous cell cancer. Our previous studies have demonstrated that CDK4/6 is a potency target for ESCC and combination with ERBB inhibitors is sufficient to achieve durable response. The aim of the current study is to prospectively map the landscape of sensitivity and resistance to CDK4/6 inhibition and develop novel combination therapies in ESCC.
Experimental Procedures: We performed a genome-wide functional genetic screening and mini-pool designed CRISPR screen approaches to identify the modulators whose depletion sensitize CDK4/6 inhibition or confer resistance to the CDK4/6 inhibitor Palbociclib and elucidate new therapeutic strategies.
Results: Our screen identified RB as the most enriched sgRNA, while guides targeting CCNE1 and CDK2 as the most depletion sgRNAs after CDK4/6 inhibition. These results validates our experimental approach as RB loss and CCNE1/CDK2 reactivation is the main mechanisms of CDK4/6 resistance. After gathering potential candidates from both screens, we found that genetically ablation of Exportin 7, a nuclear export factor, strongly sensitize CDK4/6 inhibition both in vitro and in vivo. RNAseq revealed a further repression of transcriptional activity of E2F and G2M by addition of XPO7depletion under CDK4/6 inhibitor treatment. To increase our insight in the molecular mechanism that could explain the synergy between XPO7 and CDK4/6, we further performed proteomics of nuclear and cytoplasm in ESCC lines with or without CDK4/6 inhibition. We found that silence XPO7 result in nuclear accumulation of mitosis-regulated genes such as CENPM, KIF4A and WEE1. Combined CDK4/6 inhibition with XPO7 depletion results in further downregulate of CENPM and KIF4A expression in nucleus, abrogating compensatory activation of cell cycle regulation and promote the cytostatic effect in ESCC. We further validated that CENPM and KIF4A depletion also sensitize CDK4/6 inhibition, and consequentially use WEE1 inhibitor after CDK4/6 inhibitor also effectively block the growth of ESCC lines.
Conclusion: Overall, our comprehensive functional genetic screening approach revealed modulation of sensitive and resistance to the inhibition of CDK4/6 in ESCC. XPO7 was identified as a driver to change cell cycle landscape and merits as a therapeutic target combined with CDK4/6 inhibition in ESCC, which is beneficial to provide a novel treatment strategy.
Citation Format: Zhong Wu, Lin Xu, Chuang Jiang, Adam Bass, Jin Zhou. Silence exportin 7 sensitizes esophageal squamous cell cancer to CDK4/6 inhibition through block the cell cycle coresectory [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 5708.
Abstract 5716: CDK7 as a drug target in advanced stage uveal melanoma
Authors: Waltrich Francis J. 
Published: March 2024

Abstract
Uveal melanoma (UM) metastasizes predominantly to the liver, and most metastatic UM are BAP1-deficient. Targeted therapies, such as MEK inhibitors, have failed clinically. There are few FDA-approved therapies for metastatic UM, but these therapies are limited to only a subset of patients and have modest survival benefits. Hence, there is a need to identify novel and effective treatment strategies. Due to the low mutational burden in UM, targeting transcriptional may be an effective strategy. Here, we identified Cyclin Dependent Kinase 7 (CDK7), a key regulator of transcription, as an essential and druggable target in UM. CDK7 directly phosphorylates RNA polymerase II and is expressed in all UMs. siRNA-mediated knockdown of CDK7 decreased the growth of three BAP1-deficient UM cell lines. We tested a clinically relevant, highly specific CDK7 inhibitor, SY-5609, developed by Syros Pharmaceuticals and similarly showed that the cell lines were sensitive to the growth inhibitory effects of SY-5609. Furthermore, we observed synergistic effects on cell growth inhibition when combined with a MEK inhibitor (Trametinib). We performed RNA sequencing and identified several Hallmark Genesets to be positively enriched, including interferon-gamma response, TGF-beta signaling, and NFκB signaling after treatment with SY-5609. These results are validated using a multi-omic approach, utilizing Reverse Phase Protein Array (RPPA) data to validate transcriptome to proteome expression of these enriched pathways. Overall, our studies indicate that targeting CDK7 in uveal melanoma is a potential treatment strategy for BAP1-deficient UM and enhances MEK inhibitor efficacy.
Citation Format: Francis J. Waltrich. CDK7 as a drug target in advanced stage uveal melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5716.
Abstract 5724: Preclinical evaluation of a novel CHK1 inhibitor encapsulated within the liposome, SMP-3124, for the treatment of solid cancer
Authors: Kumagai Yuka , Inagaki Ryosaku , Shimizu Kana , Hirose Wataru , Shimada Naoaki , Hayashi Kento , Fukuoka Yoshiko , Matsuoka Makoto , Kamioka Seiji , Ban Hitoshi , Umehara Hiroki , Sawayama Yusuke 
Published: March 2024

Abstract
Checkpoint kinase 1 (CHK1) is a serine/threonine kinase which plays a critical role for DNA damage responses (DDR) throughout the cell cycle in human cells. CHK1 is mainly activated by replication stress resulting in single-stranded DNA breaks induced by chemotherapeutic agents or mutations in DNA repair related genes. These kinds of stresses are reported to increase the dependency on DDR pathway molecule including CHK1. Therefore, targeting CHK1 is promising strategy for drug discovery. In fact, CHK1 inhibition induces S phase arrest and inhibits cell growth in wide range of cancer cell lines. Recently, a number of drugs in this pathway are tested in clinical trials. Although some of them showed obvious clinical responses in both monotherapy and combination therapy, their efficacies are limited because of their toxicities. To maximize the efficacy, we utilized CHK1 inhibitor with liposomal formulation which changes drug distribution to achieve longer drug retention in plasma and accumulation in tumor. Here, we generated SMP-3124, a novel and selective CHK1 inhibitor encapsulated within the liposome. SMP-3124 showed durable pharmacodynamic response due to the liposomal accumulation in the tumor in xenograft model. We confirmed potent anti-tumor activities of SMP-3124 in multiple subcutaneous xenografted models without severe side effects. In addition, SMP-3124 showed prolonged overall survival in both peritoneal dissemination and orthotopic model using human ovarian cancer cells. SMP-3124 synergistically inhibited tumor growth in combination with gemcitabine without additional hematological toxicities induced by gemcitabine. We are planning to an investigational new drug application in 2024.
Citation Format: Yuka Kumagai, Ryosaku Inagaki, Kana Shimizu, Wataru Hirose, Naoaki Shimada, Kento Hayashi, Yoshiko Fukuoka, Makoto Matsuoka, Seiji Kamioka, Hitoshi Ban, Hiroki Umehara, Yusuke Sawayama. Preclinical evaluation of a novel CHK1 inhibitor encapsulated within the liposome, SMP-3124, for the treatment of solid cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5724.