tbuckley/cabot-search huggingface dataset:
Abstract 465: Effect of Epstein-Barr virus <i>lnc-BARTs</i> on EBV genome maintenance in EBV-associated tumors
Authors: Jiayan Liu, Bobo Wing-Yee Mok, Honglin Chen
Journal: Cancer Research (2024)

Abstract Most humans infected with Epstein-Barr virus (EBV) remain asymptomatic throughout the whole life. However, EBV is linked to several human cancers, including Burkitt's lymphoma, Hodgkin's disease, post-transplant lymphoproliferative disorder (PTLD), nasopharyngeal carcinoma (NPC), and gastric carcinoma. Among these EBV-associated tumors, EBV genome is present in 100% of NPC tumor cells. In NPC cells, EBV establishes a latent infection, expressing limited number of viral proteins but elevated levels of non-coding RNAs transcribed from the BamHI-A region of the EBV genome, also known as BamHI-A rightward transcripts (BARTs). The family of EBV BART RNAs includes BART-microRNAs (miRNAs) and long non-coding RNAs (lnc-BARTs). Although various functions of BART miRNAs have been identified, the role of EBV lnc-BARTs remains largely unknown. In this study, we provide evidence demonstrating that lnc-BARTs functions as a regulatory long non-coding RNA, referred to as lnc-BARTs. These lnc-BARTs play keys role in modulating the core networks that maintains EBV latency and promotes NPC oncogenesis through epigenetic mechanisms. Our study found that the apoptosis rate of NPC cells is significantly increased following the knockdown of EBV lnc-BARTs, indicating their anti-apoptotic role in EBV-associated tumors. Mass spectrometry analysis identified several host factors, including transcriptional regulators BRD4 and SC35’ interact with EBV lnc-BARTs in NPC cells. RNA-FISH assays showed lnc-BARTs co-localized with BRD4 and SC35 complexes in nuclear s peckles and such interaction were disrupted by JQ1, a BRD4 competitive inhibitor. Binding of lnc-BARTs to BRD4 RNA was confirmed using immunoprecipitation and pulldown assays. ATAC sequencing and transcriptome analyses showed that BART knockdown in EBV-harboring NPC cell line C666-1 led to reduced chromatin accessibility, downregulation of oncogenes, and decreased EBV episome replication and maintenance. Quantitative qPCR and DNA FISH analyses of cell samples treated with shRNA targeting lnc-BARTs or BRD4 reduced EBV copy numbers and EBNA1 RNA expression levels in EBV-infected NPC cells. Finally, ChIP sequencing analysis revealed that lnc-BARTs is critical for BRD4 binding to the oriP region of the EBV genome. These findings support a mechanism by which EBV lnc-BARTs epigenetically regulate host gene expression through functional interactions with elongation regulatory machinery and contribute to the maintenance of EBV latent genome by interaction with BRD4 complex. Citation Format: Jiayan Liu, Bobo Wing-Yee Mok, Honglin Chen. Effect of Epstein-Barr virus lnc-BARTs on EBV genome maintenance in EBV-associated tumors [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 465.
Abstract 5881: Upregulation of TET2 expression by DNA methyltransferase (DNMT) inhibitors is associated with resistance in DNMT1 knockout colorectal cancer cells
Authors: Angelo B. Laranjeira, Dat Nguyen, Lorraine C. Pelosof, James H. Doroshow, Sherry X. Yang
Journal: Cancer Research (2024)

Abstract Ten-eleven-translocation 2 (TET2) is a member of the TET family proteins (TET1-3) that convert 5-methylcytosine to 5-hydroxymethylcytosine (5-hmC) in DNA and causes site-specific DNA demethylation. The effects of DNMT1 on TET2 phenotype following DNMT inhibitor treatment is unclear in human cancer. In colorectal cancer HCT116 cells with DNMT1 gene intact (DNMT1+/+) and deletion (DNMT1−/−) status, we found that TET2 expression was robustly increased in DNMT1−/− cells after treatment with 0.5 µM and 5 µM decitabine for 72 h, 96 h, and 120 h. The augmentation in TET2 expression was accompanied by a dose-dependent re-expression of p16ink4A in DNMT1−/− cells. Particularly, TET2 upregulation was associated with resistance to DNMT inhibitors, showing a lack of induction of DNA damage, cell-cycle arrest and apoptosis after drug exposure in DNMT1−/− compared to DNMT1+/+ cells. The treatment with 4’-thio-5-aza-2’-deoxycytidine (aza-T-dCyd) only up-regulated TET2 and re-expressed p16ink4A at the lower dose of 0.5 µM, which was consistent with our previous findings that high dose of aza-T-dCyd at 5 µM predominantly eliminates the cancer cells with severe DNA damage by undergoing apoptosis and cell death (Scientific Reports, 13:5964, 2023). Moreover, both decitabine and aza-T-dCyd had minimal effects on TET2 upregulation and p16ink4A re-expression in cells with intact DNMT1 gene. The data suggest that the absence of DNMT1 gene made the cells prone to TET2 upregulation upon DNMT inhibitor challenges. Future study is needed to investigate the interactive relationship between DNMT1 and TET2 as well as demethylation, and its impact on cancer treatment with DNMT inhibitors. Citation Format: Angelo B. Laranjeira, Dat Nguyen, Lorraine C. Pelosof, James H. Doroshow, Sherry X. Yang. Upregulation of TET2 expression by DNA methyltransferase (DNMT) inhibitors is associated with resistance in DNMT1 knockout colorectal cancer 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 5881.
Abstract 2438: A retrospective pilot study to validate the utility of proteomic biomarkers in the blood for diagnosis of breast cancer
Authors: So-Youn Jung, Eun-Gyeong Lee, Jai Hong Han, Seeyoun Lee, Soyeon Shin, Ju Yeon Lee, Sung-Soo Kim, Yumi Kim, Dong-Young Noh
Journal: Cancer Research (2024)

Abstract Background: Previously, three-protein signature (Mastocheck®, Bertis Inc.) from plasma has been launched to overcome the limitation of low accuracy of mammography. In addition, nine-protein signature from serum was newly developed to improve the accuracy of three-protein signature as a blood-based diagnostic tool. This study aimed to validate the diagnostic utility for breast cancer of nine-protein signature with comparison with three-protein signature. Methods: A blood-based test using multiple reaction monitoring (MRM) by mass spectrometry to quantify nine proteins (APOC1, CHL1, FN1, VWF, PPBP, CLU, PRDX6, PRG4, and MMP9) in serum and three proteins (APOC1, CHL1, CA1; Mastocheck®) in plasma was investigated using blood of 30 health women and 30 breast cancer patients. Using the cut-off values confirmed by AI-based deep learning model, we evaluated the sensitivity, specificity, and accuracy of nine- and three-protein signature for detecting breast cancer. Results: Among 60 cases, the sensitivity and specificity of nine-protein signature was 87.9% and 80.7% for diagnosis of breast cancer. These values were 20% and 10% higher than those of three-protein signature, respectively (66.7% of sensitivity and 70.0% of specificity). The accuracy of nine-and three-protein signature was 83.3% and 68.3%. Conclusion: This study demonstrated that nine-protein signature could be a more accurate and effective tool for detecting breast cancer compare to three-protein signature). For a confirmatory study, we need to perform a large scaled validation study in future. Grants: This research was supported by Bertis, Republic of Korea (grant number: NCC 2341770-1) Citation Format: So-Youn Jung, Eun-Gyeong Lee, Jai Hong Han, Seeyoun Lee, Soyeon Shin, Ju Yeon Lee, Sung-Soo Kim, Yumi Kim, Dong-Young Noh. A retrospective pilot study to validate the utility of proteomic biomarkers in the blood for diagnosis of breast 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 2438.
Abstract 1838: Advancing cancer research with Next-Generation Protein Sequencing™ on Platinum™ by Quantum-Si 
Authors: Khanh Dinh Nguyen
Journal: Cancer Research (2024)

Abstract Protein sequencing has the potential of playing a crucial role in advancing cancer research by providing insights into the specific proteins involved in cancer pathways. New discoveries from protein sequencing advance our understanding of cancer and potential targeted therapies. Here, we demonstrate the power of next-generation protein sequencing™ using the insight-generating Platinum™ platform. Individual peptides are digested from proteins and immobilized on a semiconductor chip and probed by dye-labeled N-terminal amino acid (NAA) recognizers, followed by subsequent aminopeptidase cleavage to expose each NAA in the peptide for recognition. By recording and analyzing fluorescent intensity, lifetime, and binding kinetics of each NAA binding event, we can decipher single amino acid substitutions and modifications. To demonstrate the versatility of this methodology across proteins associated with cellular biology, we sequenced a series of interleukins: IL4, IL6, IL7, IL13, IL20, and IL34. Interleukins, a group of cytokines that play a vital role in cancer by modulating immune responses, promoting inflammation, and influencing tumor microenvironment, impacting tumor growth and the efficacy of treatments. We have successfully sequenced all the mentioned interleukins individually or within protein mixtures. Furthermore, we were able to sequence IL6 that was enriched through immunoprecipitation from human serum. Finally, we demonstrated the unique potential of Platinum in detecting post-translational modifications (PTMs) relevant to cancer, as exemplified by the successful identification of arginine citrullination in vimentin, an onco-protein that promotes cancer cell mobility and invasion into surround tissues. These results demonstrate the transformative potential of next-generation protein sequencing using Platinum™ in enabling the identification of proteins in complex mixtures and biofluids, as well as the detection of critical PTMs implicated in human pathophysiology, offering valuable insights into cancer research. Citation Format: Khanh Dinh Nguyen. Advancing cancer research with Next-Generation Protein Sequencing™ on Platinum™ by Quantum-Si [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 1838.
Abstract 244: Patient-derived organoids: A pre-clinical model to assess infection and killing capacity of viral vectors for cancer therapy
Authors: Francisco Morales-Rodriguez, Maria Stella Sasso, Taya Bezhaeva, Samantha Bailey-Bucktrout, Ka Wai Lai, Foteini Gkogkou, Sylvia Boj
Journal: Cancer Research (2024)

Abstract HUB’s patient-derived organoids (PDOs) are in vitro models that preserve tissue morphology and original cellular complexity. Additionally, PDOs are compatible with (high) throughput screening methods, enabling informed decision-making early in the drug development pipeline and significantly improving the odds of positive outcomes in clinical trials. Akamis Bio has developed experimental viral vector-based tumour gene therapies that have the potential to treat a variety of solid tumours by driving the expression of immunologically active biomolecules and therapeutic proteins hampering tumour immune evasion. These vectors are based on a replication competent, chimeric group B adenovirus backbone that selectively replicates and expresses transgene payloads in tumor cells, and additionally exerts oncolytic activity. To evaluate the efficacy of such a virus-based gene delivery strategy, HUB set up a proof-of-concept study to assess the propagation capability of Akamis Bio’s viral vectors in tumour PDOs. Intact PDOs from primary pancreatic tumours were infected with several viral loads, ranging from 0.1 viral particles per cell (PPC) to 100 PPC. The viral vector encoded a GFP reporter gene to identify infected cells using fluorescence imaging. The cultures were imaged daily for 14 days, allowing the assessment of cytotoxicity and infection efficiency and dynamics. Independently of PPC, infections always started in the exterior of PDOs in a few GFP-positive cells. The gradual increase over time in GFP-signal toward the interior of PDOs suggests the high likelihood of secondary infection events. Crucially, GFP intensity was correlated with cell death in PDOs, as evidenced by morphological features detected in brightfield images. Moreover, the infection dynamics were dose-dependent, as the GFP intensity peak arose later with decreasing PPC. These results show the capacity of HUB PDOs to study the infection dynamics of Akamis viral vectors. This pre-clinical platform permits rapid and efficient screening and dose evaluation for oncolytic virotherapies. Unique access to extensive tumour PDO biobanks with characterized genomic landscapes allows best-in-class stratification of treatment response based on tumour type and genetic heterogeneity. Citation Format: Francisco Morales-Rodriguez, Maria Stella Sasso, Taya Bezhaeva, Samantha Bailey-Bucktrout, Ka Wai Lai, Foteini Gkogkou, Sylvia Boj. Patient-derived organoids: A pre-clinical model to assess infection and killing capacity of viral vectors for cancer therapy [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 244.
Abstract 3250: LNA gapmer to gastrin inhibits growth and metastases of human pancreatic cancer in mice
Authors: Godhanjali Chekuri, Wenqiang Chen, Narayan Shivapurkar, Hong Cao, Ruvanthi N. Kularatne, Stephan Stern, Jill P. Smith
Journal: Cancer Research (2024)

Abstract Background: Pancreatic cancer has a poor prognosis and novel strategies are needed to improve the survival. Gastrin stimulates growth of pancreatic cancer by an autocrine mechanism and RNAi techniques that decrease gastrin expression have been shown to inhibit growth of this malignancy in vitro. Locked nucleic acid (LNA) Gapmers are antisense oligonucleotides (ASO) that have long half-life and stability in vivo, hence represent a potential method to deliver RNAi for cancer therapeutics. We developed an LNA Gapmer that selectively downregulates gastrin expression in pancreatic cancer cells in culture. The goal of this project was to test this anti-gastrin Gapmer in vivo as a novel therapy for pancreatic cancer. Methods: The anti-gastrin LNA Gapmer was modified using thiol-click chemistry to conjugate a peptide to the 5’ end and render the Gapmer target-specific with the ability to bind selectively to the cholecystokinin-B receptor that is over-expressed in pancreatic cancer. Forty athymic nude mice with established AsPC-1 human pancreatic orthotopic tumors were divided into four groups of equal tumor size. Mice (N=10 per group) were treated with PBS (controls), an untargeted LNA-Gapmer, the CCK-BR targeted Gapmer (60nM), and the CCK-BR targeted Gapmer (120nM) intraperitoneally twice a week for 4 weeks. Growth was monitored by luciferase IVIS imaging. At necropsy, tumors were excised, and metastases counted. Results: Mean tumor mass was 43% smaller in mice treated with the targeted Gapmer-120nM (P=0.0007). Untargeted and targeted Gapmer 60nM slightly decreased tumor mass but this difference was not significant. Compared to PBS control-treated mice, metastases were significantly less in mice treated with the untargeted Gapmer by -39% (p=0.01); in the targeted Gapmer-60nM by -44% (p=0.003), and with the targeted Gapmer-120nM by -72% (p&amp;lt;0.0001). Gastrin mRNA analysis of the tumors by qRT-PCR confirmed downregulation of gastrin. Conclusion: Novel LNA Gapmers that downregulate gastrin mRNA expression decrease growth and metastases of pancreatic cancer in a dose-related fashion. Citation Format: Godhanjali Chekuri, Wenqiang Chen, Narayan Shivapurkar, Hong Cao, Ruvanthi N. Kularatne, Stephan Stern, Jill P. Smith. LNA gapmer to gastrin inhibits growth and metastases of human pancreatic cancer in 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 3250.
Abstract 3234: A new vulnerability to BET inhibition due to enhanced autophagy in <i>BRCA2</i>-deficient pancreatic cancer
Authors: Suyakarn Archasappawat, EunJung Lee, Keely Ji, Jocelyn Pena, Virneliz Fernandez Vega, Ritika Gangaraju, Nitin Sai Beesabathuni, Martin Jean Kim, Qi Tian, Priya Shah, Louis Scampavia, Timothy Spicer, Chang-Il Hwang
Journal: Cancer Research (2024)

Abstract Pancreatic ductal adenocarcinoma (PDAC) is the third leading cause of cancer-related deaths in the United States, with the lowest five-year survival rate of all cancers. Around 10% of pancreatic cancer diagnoses are thought to be familial pancreatic cancer (FPC). BRCA2 pathogenic variants have been identified to be closely associated with FPC. Personalized medicine approaches that are tailored to FPC patients based on their mutation profiles could improve patient outcomes and minimize adverse effects. This study aims to identify novel potential drug candidates for BRCA2-deficient PDAC and dissect its underlying molecular mechanisms. To discover new vulnerabilities for BRCA2-deficient pancreatic cancer, we performed high-throughput drug screening (HTS) using isogenic murine Brca2 knockout (KO) and control PDAC cells. The HTS assay revealed that JQ1, a small molecule inhibitor of the bromodomain and extra-terminal domain protein (BET) family, selectively induced cytotoxicity in Brca2 KO cells. JQ1 significantly decreased the cell viability of Brca2 KO cells in vitro and suppressed the growth of Brca2 KO tumors in vivo compared to the controls. The transcriptomic analyses showed that JQ1 treatment resulted in upregulation of the gene sets associated with macroautophagy. Multi-orthogonal autophagy assays, including live cell imaging of fluorescence-based autophagy reporter, also supported that Brca2 KO cells had a constitutively higher basal level of autophagic activities compared to the controls, and JQ1 further induced autophagic flux in Brca2 KO cells. Moreover, blocking the autophagy process by pharmacological inhibition or knocking down essential autophagy genes rescued JQ1-induced cell death in Brca2 KO cells, indicating that the increased autophagy is responsible for JQ1-mediated cell death in Brca2 KO cells. In conclusion, we found that BRCA2 deficiency elevated autophagic flux, and extensive autophagy was further activated by BET inhibition, culminating in autophagy-dependent cell death in Brca2-deficient pancreatic cancer cells. Our findings suggest that BET inhibition could be a promising therapeutic strategy for treating BRCA2-deficient pancreatic cancer. Citation Format: Suyakarn Archasappawat, EunJung Lee, Keely Ji, Jocelyn Pena, Virneliz Fernandez Vega, Ritika Gangaraju, Nitin Sai Beesabathuni, Martin Jean Kim, Qi Tian, Priya Shah, Louis Scampavia, Timothy Spicer, Chang-Il Hwang. A new vulnerability to BET inhibition due to enhanced autophagy in BRCA2-deficient pancreatic 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 3234.
Abstract 1667: The role of CCN1 in mutant K-RAS addiction in pancreatic cancer
Authors: Anjali Kambhampati, Archana De, Inamul Haque, Snigdha Banerjee, Sushanta K. Banerjee
Journal: Cancer Research (2024)

Abstract Mutant K-RAS addiction of pancreatic ductal adenocarcinoma cells (PDAC) coordinates their transformation, proliferation, and survival. Therefore, initially, it had an impression that targeting mutant K-RAS could be an ideal strategy to treat PDAC. However, after decades of studies, no effective RAS inhibitors reached the clinic, indicating that RAS-oncoprotein is an undruggable target in PDAC. Thus, identifying a new target linked with K-RAS signaling was most needed. Using genetically engineered cell lines and K-RAS-driven genetically engineered mouse models (KC or KPC) with or without pancreas-specific CCN1 conditional knockout background, we identified a positive feedback circuit between CCN1 and mutant K-RAS expression. Moreover, blocking this feedback via conditional knockout of CCN1 in the pancreas significantly reduced invasive phenotypes, PDAC growth, and metastasis in the lung in KC and KPC mice. Mechanistically, we found that the K-RAS-CCN1 feedback circuit is regulated by microRNA miR-145 via a feedforward mechanism. Collectively, these studies highlight the clinical potential of targeting CCN1 in PDAC. (VA Merit Grant supports this work) Citation Format: Anjali Kambhampati, Archana De, Inamul Haque, Snigdha Banerjee, Sushanta K. Banerjee. The role of CCN1 in mutant K-RAS addiction in pancreatic 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 1667.