bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 5617: A novel DNA double-strand breaks biosensor based on fluorescence resonance energy transfer
Authors: Suh Jung-Soo , Kim Tae-Jin 
Published: April 2023

Abstract
Revealing the spatiotemporal behavior of DNA double-strand breaks (DSBs) is crucial for understanding the processes of DNA damage and repair. Traditionally, γH2AX and DNA damage response (DDR) factors have been used to detect DSBs using classical biochemical assays, such as antibody-based immunostaining. However, a reliable method to visualize and assess DSB activity real-time in living cells is yet to be established. Herein, we developed a novel DNA double-strand breaks biosensor (DSBS) based on fluorescence resonance energy transfer (FRET) by employing the H2AX and BRCT1 domains. By applying FRET imaging with DSBS, we show that DSBS specifically reacts to drug- or ionizing radiation (IR)-induced γH2AX activity, allowing for the quantification of DSB events at high spatiotemporal resolutions. Taken together, we provide a new experimental tool to evaluate the spatiotemporal dynamics of DNA double-strand breaks in response to cancer therapies. Ultimately, our biosensor can be useful for elucidating the molecular mechanisms underlying DNA damage and repair processes and applying for cancer therapies.
Citation Format: Jung-Soo Suh, Tae-Jin Kim. A novel DNA double-strand breaks biosensor based on fluorescence resonance energy transfer. [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 5617.
Abstract 5620: Radiogenomic analysis in the patients with primary brain tumor using dual time point 18F-FET PET/CT
Authors: Lee Dong Yun , Song Sang Woo , Lee Seungjoo , Oh Minyoung , Oh Jungsu S. , Kim Jaeseung 
Published: April 2023

Abstract
Purpose: To evaluate the association between genomic data and imaging features of dual time point 18F-FET PET/CT in patients with primary brain tumor for radiogenomic mapping.
Methods: From June 2021 to July 2022, we prospectively enrolled the patients under suspicious of de novo primary brain tumor in Asan Medical Center. Prior to the surgery, contrast-enhanced MRI and 18F-FET PET/CT scans were routinely performed. Twenty minutes after the post-injecting (p.i.) approximately 5 mCi of 18F-FET, patients underwent early PET/CT acquisition (20-40 min p.i.). Delay PET/CT (80-100 min p.i) was subsequently obtained after 40-minute break. SUVmax, maximum tumor-to-brain ratios and PET-positive volumes using different isocontours of SUVmax (I30, I60, I90%) in tumor were calculated in each sum images. Histopathologic results were made based on 2016 WHO classification and, isocitrate dehydrogenase (IDH) mutation, O6-methylguanine-DNA methyltransferase (MGMT) methylation, telomerase reverse transcriptase (TERT) mutation and co-deletion of 1p19q status were investigated as well. Spearman’s correlation coefficient (r), logistic regression and AUC-ROC analysis were employed using aforementioned radiomics information.
Results: A total of 42 patients (median age 55.5 yrs, range 21-84; M:F=31:11) were recruited and, 29 patients had glioblastoma with grade IV. Except TERT mutation (n=25), IDH mutation (n=11), MGMT methylation (n=19) and co-deletion of 1p19q (n=8) had statistically significant correlation each other (IDH vs. MGMT, r=0.55; IDH vs. 1p19q, r=0.53; MGMT vs. 1p19q, r=0.42). Early scan of I60% was closely related with IDH mutation (positive, 3.92 ± 3.04 vs. negative, 7.96 ± 5.36; p=0.005) meanwhile delay scan of I30% had significant association with co-deletion of 1p19q (present, 34.16 ± 18.67 vs. absent, 71.99 ± 38.79; p=0.01). The accuracy of logistic regression and the corresponding AUC-ROC values for IDH/MGMT/TERT/co-deletion of 1p19q status were 0.86/0.73/0.78/0.85, and 0.88/0.76/0.78/0.91, respectively.
Conclusion: Although this is a preliminary and interim analysis during our prospective study being slated to enroll the patients until December 2023, we suggest that the information acquired from both genetics and 18F-FET could be integrated into better characterization of primary brain tumor.
Citation Format: Dong Yun Lee, Sang Woo Song, Seungjoo Lee, Minyoung Oh, Jungsu S. Oh, Jaeseung Kim. Radiogenomic analysis in the patients with primary brain tumor using dual time point 18F-FET PET/CT. [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 5620.
Abstract 5727: Identification of synthetic lethal vulnerabilities in cancers with loss of function mutations in NOTCH
Authors: Hong Deli , Booker Matthew A. , Anjum Sidrah , Li Yixiang , Thai Tran C. , Wang Michelle Y. , Barbie David A. , Tolstorukov Michael Y. , Qi Jun , Oser Matthew G. 
Published: April 2023

Abstract
Loss of Function (LOF) mutations in the NOTCH receptors are found in several different cancers most notably in small cell lung cancer (SCLC) and squamous cell carcinomas (SCC). We previously developed genetically engineered mouse models (GEMM) of SCLC using CRISPR/Cas9 engineered to be NOTCH1-Mutant, NOTCH2-Mutant, and NOTCH-WT. Synthetic lethality provides a paradigm for targeting cancers with LOF mutations in tumor suppressor genes. In applying this paradigm, one looks for specific vulnerabilities that are created upon loss of the gene of interest. Using 6 cell lines developed from these CRISPR-based SCLC GEMMs which are isogenic to NOTCH, we performed CRISPR/Cas9 LOF negative selection screens (using an sgRNA library enriched in druggable enzymes) to identify synthetic lethal interactors with LOF NOTCH mutations. Our CRISPR/Cas9 screen identified TRIM28 (Tripartite Motif Containing 28, or KAP1) as a highly significant synthetic lethal interactor with NOTCH1 or NOTCH2. We validated the synthetic lethal interaction between NOTCH1/2 and TRIM28 using both human and mouse NOTCH-isogenic cell lines. Interestingly, RNA-sequencing of NOTCH2-Mutant or NOTCH-WT SCLC cell lines after TRIM28 CRISPR inactivation showed robust increases in endogenous retroviral (ERV) expression and the MDA5/RIG-I/MAVS RNA-sensing machinery leading to hyperactivation of the TBK1/IRF3/7 innate immune signaling pathway and the pro-inflammatory cytokine CXCL10 selectively in cells with NOTCH inactivated. Notably, inactivation of TBK1 activity or JAK-STAT activity using specific small molecule inhibitors of TBK1 or JAK completely reversed the synthetic lethality between NOTCH and TRIM28 suggesting that the synthetic lethality phenotype is a consequence of hyperactivation of innate immune signaling, which is known to be cytotoxic. Together our findings uncover a novel vulnerability in SCLCs with LOF NOTCH mutations and perhaps other cancers with LOF NOTCH mutations and suggest a strategy that could also potentiate anti-tumor immunity by increasing innate immune signaling in tumor cells.
Citation Format: Deli Hong, Matthew A. Booker, Sidrah Anjum, Yixiang Li, Tran C. Thai, Michelle Y. Wang, David A. Barbie, Michael Y. Tolstorukov, Jun Qi, Matthew G. Oser. Identification of synthetic lethal vulnerabilities in cancers with loss of function mutations in NOTCH. [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 5727.
Abstract 5739: Targeting WEE1 to improve the therapy of KRAS G12C mutant non-small cell lung cancer
Authors: Yamamoto Gaku , Tanaka Kosuke , Kamata Ryo , Mori Shunta , Liu Jie , Yamauchi Toyohiro , Sakae Yuta , Ohashi Akihiro , Kobayashi Susumu S. 
Published: April 2023

Abstract
Background: While sotorasib is the first clinically approved small-molecule inhibitor of KRAS G12C in non-small-cell lung cancer (NSCLC), efficacy of sotorasib alone is limited, presumably due to adaptive resistance mechanisms in cancer cells. To expand therapeutic potential of sotorasib, combination strategies need to be developed. In this study, we conducted a large-scale screening to identify novel combination candidates with sotorasib. In addition, molecular mechanisms of synergistic effects were investigated in multiple preclinical models.
Methods: To identify novel combination partners of sotorasib, we conducted high-throughput screening using a kinase inhibitor library containing 1,400 chemical compounds. Anti-proliferative and apoptotic effects in vitro were assessed by ATP-based cell viability assay and/or clonogenic assay, and caspase 3/7 assay and/or Annexin V assay, respectively. Synergistic effects were evaluated by calculating the BLISS index and visualized by SynergyFinder Plus. Immunoblotting was performed using antibodies against pCDK1 (Tyr15), pERK, pAkt, MCL1, BIM, PUMA, BCL2, or BCL-xL. In vivo efficacy studies were performed using a KRAS G12C mutant H358 xenograft nude mouse model.
Results: Through the large-scale unbiased combination screening of -1,400 kinase inhibitors, we identified a WEE1 inhibitor (AZD1775), a G2/M checkpoint abrogator in clinical-stage development, as a promising combination partner of sotorasib in KRAS G12C mutant NSCLC. The synergistic effects in vitro were broadly observed in multiple KRAS G12C mutant NSCLC cell lines, regardless of single-agent sensitivity to sotrasib or co-occurring oncogenic mutation profiles. The combination treatment upregulated pro-apoptotic protein BIM, leading to apoptosis. In vivo efficacy studies in H358-xenografted models also demonstrated remarkable tumor regression and durable response in mice treated with sotorasib and AZD1775 compared to ones with a single agent alone.
Conclusion: We identify AZD1775, a WEE1 inhibitor, as a novel combination candidate, which enhanced the anti-tumor activity of sotorasib both in vitro and in vivo preclinical models. These findings can lead to a novel therapeutic strategy for KRAS G12C mutant NSCLC.
Citation Format: Gaku Yamamoto, Kosuke Tanaka, Ryo Kamata, Shunta Mori, Jie Liu, Toyohiro Yamauchi, Yuta Sakae, Akihiro Ohashi, Susumu S. Kobayashi. Targeting WEE1 to improve the therapy of KRAS G12C mutant non-small cell lung 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 5739.
Abstract 574: Depletion of regulatory T cells without interruption of IL-2 signaling by antibody against CD25 for enhancing antitumor immunity
Authors: Gao Yuxuan , He Feng , Peng Hao , Wu Kefei , Zhao Hui , Feng Yanpeng , Hao Feng , Wu Guojin , Ning Jinying 
Published: April 2023

Abstract
Depleting regulatory T cells from the tumor microenvironment is an attractive strategy for enhancing immunotherapy. Here we developed a humanized antibody against CD25 (H11E11-2V1) with Treg-biased binding. This antibody has a medium affinity to CD25 (KD=8.9nM), weaker than Daclizumab (KD=1.5nM) and RG6292 (KD=4.5nM). Primary T cells activated with CD3 and CD28 beads had increased CD25 expression. H11E11-2V1 bound to Treg (CD4+Foxp3+) with a concentration as low as 0.07nM, similar to RG6292, while it has no detectable binding to activated Teff (CD4+Foxp3-) with a concentration below 2nM (vs. RG6292 below 0.7nM). In addition, H11E11-2V1 did not block IL-2 signaling in NK-92 cells, which expressed CD25 on the cell surface, while Daclizumab blocked the IL-2 signaling. Daclizumab inhibited T cell proliferation (ki67+%) and activation (Granzyme B+%), but not by RG6292 and H11E11-2V1. In vitro cytotoxicity assay indicated that H11E11-2V1 with modified Fc to enhance ADCC specifically depletes Treg from activated primary T cells at a minimal concentration of 0.07nM (vs. RG6292 at 0.14nM) while leaving 90% of Teff intact. In the in vivo MC38 murine tumor model with mice whose CD25 was replaced with human CD25, H11E11-2V1 given by I.P. injection suppressed tumor growth with higher efficiency than RG6292. These results suggested that H11E11-2V1 was an excellent candidate therapeutical antibody against CD25 for cancer therapy.
Citation Format: Yuxuan Gao, Feng He, Hao Peng, Kefei Wu, Hui Zhao, Yanpeng Feng, Feng Hao, Guojin Wu, Jinying Ning. Depletion of regulatory T cells without interruption of IL-2 signaling by antibody against CD25 for enhancing antitumor immunity [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 574.
Abstract 575: Brain delivery of clinically suitable nanobioconjugates to inhibit glioblastoma growth through extracellular matrix-immune cell crosstalk
Authors: Ljubimov Alexander V. , Patil Rameshwar , Ding Hui , Israel Liron , Holler Eggehard , Ljubimova Julia Y. , Sun Tao , Black Keith L. 
Published: April 2023

Abstract
Introduction: Tumor growth, invasion, and escape from immune surveillance largely depend on cancer microenvironment. Laminins are trimeric proteins and essential components of glioblastoma (GBM) microenvironment/extracellular matrix (ECM). In brain glioma samples from 230 patients, we found a correlation between the overexpression of tumor ECM protein laminin-411 (α4β1γ1) and faster tumor recurrence with shorter patient survival. Laminin-411 is produced by endothelial cells, neutrophils, monocytes, platelets, lymphocytes, and glioma cells and can modulate the immune system. Novel nanotechnology approach to block trimeric laminin-411 and activate of brain local immune system with brain delivery of PD-1 checkpoint inhibitor was developed for future translational application.
Methods: Nanobioconjugates (NBC) based on poly (β-L-malic acid, P), were synthesized, characterized and used to intravenously treat mice with intracranial syngeneic GL261 or CT-2A GBM. The lead NBCs P/PEG/LLL(40%)/AON(α4β1)(2.0%)/AP-2(2%) and P/PEG/LLL(40%)/AP-2(2%)/αPD-1(0.2%) contained antisense to laminin-411 α4 and β1 chains, or αPD-1 antibody as well as trileucine (LLL) peptide for endosomal escape and AP-2 peptide for BBB crossing and tumor cell targeting. CRISPR/Cas9 constructs were used to knockdown α4 and β1 laminin chains in GBM ex vivo. Flow cytometry and RNA-seq analyses were performed to evaluate treatment.
Results: Laminin-411 depletion with CRISPR/Cas9 and multifunctional NBC in vivo treatment equally suppressed GBM growth and significantly prolonged animal survival. The brain privileged immune system was activated upon treatment with a significant increase of CD3+, CD8+ T cells, NK, IFNγ+ NK cells, and M1 macrophages. RNA-sec analyses after treatment with a combination of NBC suppressing laminin-411 and checkpoint PD-1 showed enhanced anti-tumor effect with upregulation of genes coding for apoptotic Caspase 3 and IFNγ, and reduction of proliferation markers EGFR, c-Myc and Ki-67.
Conclusion: Study describes novel GBM treatment strategy via NBCs crossing blood-brain barrier and targeting critical ECM and immune components of tumor microenvironment largely independent of heterogeneous genetic mutations in glioblastoma.
Citation Format: Alexander V. Ljubimov, Rameshwar Patil, Hui Ding, Liron Israel, Eggehard Holler, Julia Y. Ljubimova, Tao Sun, Keith L. Black. Brain delivery of clinically suitable nanobioconjugates to inhibit glioblastoma growth through extracellular matrix-immune cell crosstalk [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 575.
Abstract 5754: Determining the regulatory logic of breast cancer cells using single-cell multi-omics
Authors: Regner Matthew J. , Thennavan Aatish , Garcia-Recio Susana , Wisniewska Kamila , Spanheimer Philip M. , Parker Joel S. , Perou Charles M. , Franco Hector L. 
Published: April 2023

Abstract
Cancer cells rewire regulatory elements scattered throughout the genome (such as enhancers) to drive aberrant gene expression. Thus, deconvoluting the regulatory mechanisms that contribute to oncogenic gene expression in cancer cells is key to understanding tumor biology. To this end, we have charted the transcriptional and epigenetic landscape of breast cancer at single-cell resolution to quantitatively link variation in chromatin accessibility to gene expression across malignant and non-malignant cell types. Our comprehensive dataset profiles the chromatin landscape (scATAC-seq) in concert with the transcriptional profiles (scRNA-seq) of 4 breast cancer cell lines, 12 primary breast tumors, and 4 normal mammary reduction tissue specimens collected and processed immediately after surgical resection. This dataset, encompassing over 250,000 individual cells, allowed us to define the regulatory logic of cancer cells by 1) revealing how the epigenome underlies cellular heterogeneity of these tumors in comparison to normal mammary tissue, 2) defining how malignant cells hijack enhancer elements to drive key transcriptional programs in a subtype-specific manner, and 3) annotating which cancer-specific enhancer-to-gene connections portend a worse outcome in patients. Notably, we discovered that cancer cells acquire de novo non-coding enhancer elements to modulate hallmark cancer pathways that were previously hidden using bulk genomics approaches. This highlights the potential for cancer-specific enhancers to serve as markers with diagnostic and prognostic potential, or even serve as tractable targets for therapeutic intervention. Together these data enable the annotation of the cellular composition, transcriptional, and epigenetic landscape of breast tumors to help pinpoint clinically relevant mechanisms of tumorigenesis.
Citation Format: Matthew J. Regner, Aatish Thennavan, Susana Garcia-Recio, Kamila Wisniewska, Philip M. Spanheimer, Joel S. Parker, Charles M. Perou, Hector L. Franco. Determining the regulatory logic of breast cancer cells using single-cell multi-omics. [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 5754.
Abstract 5777: Race as a predictive confounder in the rate of transdifferentiation and drug response in human pancreatic acinar ductal metaplasia
Authors: Perkins Corey Melissa , Jiang Jinmai , Hakimjavadi Hesam , Brant Jason , Zhang Zhongyue , Lee Ji-Hyun , Quashie David , Mao Yating , Ali Jamel , Kim Sarah , Campbell-Thompson Martha , Schmittgen Thomas 
Published: April 2023

Abstract
Pancreatic diseases (chronic pancreatitis, type 2 diabetes, pancreatic cancer) disproportionately affect the Black/African American (AA) community in comparison to non-White Hispanics and Whites. Acinar to ductal metaplasia (ADM), the process by which pancreatic acinar cells transdifferentiate into ductal epithelial cells, is believed to be an initiating event of pancreatic ductal adenocarcinoma. Our lab has developed a 3D organoid assay to display ADM using primary, human pancreatic acinar cells to study the rate of transdifferentiation amongst these three different races. Preliminary data shows that the rate of ADM is occurring significantly faster (p &lt; 0.05) in Blacks/AAs (White=16, Hispanic=11, Black/AA=5), which may explain the disproportionately behind the incidence and mortality rates for this race in pancreatic cancer. A sigmoid Emax function best captured the longitudinal changes in the percentage of ADM in nonlinear mixed effects modeling analysis performed in Monolix. Covariate analysis on top of the selected model demonstrated that race was the only covariate affecting the individual trajectories in the percentage of ADM. We additionally use nanoparticles to study the biomechanical properties (I.e., viscoelasticity, storage modulus) of the ADM microenvironment which shows a stiffer microenvironment in Blacks/AAs than for the other races (White=4,Hispanic=4, Black/AA=1). Furthermore, we have used a histone deacetylase (HDAC) inhibitor in reversing the process of ADM, which has consequently shown race-related outcomes, with Blacks/AAs displaying a significant chemoresistance (p &lt; 0.05) to HDAC treatment (White=6,Hispanic=6, Black/AA=3) by utilizing an ADM reversal index (ADMRI). Through further analysis, the plan is to continue procuring human samples from these three races to isolate an ADM-specific biomarker in relation race and drug reversal by studying the expression/activity of pancreatic associated genes by bulk-RNA and single-cell sequencing.
Citation Format: Corey Melissa Perkins, Jinmai Jiang, Hesam Hakimjavadi, Jason Brant, Zhongyue Zhang, Ji-Hyun Lee, David Quashie, Yating Mao, Jamel Ali, Sarah Kim, Martha Campbell-Thompson, Thomas Schmittgen. Race as a predictive confounder in the rate of transdifferentiation and drug response in human pancreatic acinar ductal metaplasia. [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 5777.