bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 227: Kethoxal-assisted single-stranded DNA sequencing (KAS-seq) reveals dynamic and temporal changes in transcription in response to UVB exposure
Authors: Wilkinson Emma A. , Wu Tong , Park Gayoung , Cui Yan-Hong , He Chuan , He Yu-Ying 
Published: June 2022

Abstract
Skin cancer is the most common form of cancer, with over 5 million cases reported in 2021. UVB exposure derived from sunlight is the major carcinogenic driver of skin cancer and poses a major public health risk. In response to UVB exposure, keratinocytes must activate DNA repair pathways to avoid mutagenesis. In addition to DNA repair pathways, cells initiate well-coordinated DNA damage response pathways to facilitate the repair process, including arresting global transcription. Here we report the use of kethoxal-assisted single-strand DNA-Sequencing (KAS-Seq) technology to profile the transcriptional dynamics that underlie the DNA damage response upon UVB exposure. Mechanistically, KAS-Seq involves the addition of an azide-tagged kethoxal group (N3-kethoxal) to DNA samples, which then reacts with guanines on single-stranded DNA (ssDNA). A “KAS signal” is therefore only obtained when DNA is unwound, allowing the N3-kethoxal reaction with accessible guanines to occur. Accordingly, in response to DNA damage, DNA can form ssDNA bubbles in order to facilitate DNA damage recognition and repair processes. KAS-Seq is therefore a suitable method to profile the transcriptional dynamics that occur in response to UVB-induced DNA damage. Here we show that UVB exposure in normal human keratinocytes (NHEK) cells induces a temporal and dynamic reprogramming in transcription using KAS-Seq. In terms of global transcription, our data show that the greatest loss of KAS signal occurs rapidly between 30mins and 3hrs post-UVB exposure, signifying transcriptional arrest. Interestingly, KAS signal is regained between 6-24hrs post-UVB, which is representative of a transition towards transcriptional recovery and induction of DNA damage processes. Furthermore, a more discrete and targeted analysis shows that the gain and loss of KAS signals primarily occur within the gene body, followed by promoter and intergenic regions. Overall, our data shows that transcriptional control in response to UVB-induced DNA damage is both dynamic and temporal. Further analysis is required to identify which transcriptional phenotype (transcriptional arrest or transcriptional recovery) is the most deleterious to the cell and DNA damage repair processes when disrupted. Additionally, we aim to further elucidate the molecular mechanisms that underlie these global changes in transcription, which will provide expanded insights into the wide-ranging oncogenic mechanisms that underlie UVB exposure.
Citation Format: Emma A. Wilkinson, Tong Wu, Gayoung Park, Yan-Hong Cui, Chuan He, Yu-Ying He. Kethoxal-assisted single-stranded DNA sequencing (KAS-seq) reveals dynamic and temporal changes in transcription in response to UVB exposure [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 227.
Abstract 2273: Unsupervised clustering of multi-omics molecular layers reveals consensus molecular subtypes showing potential therapeutic opportunities for pancreatic cancer
Authors: Lee Sung Hwan , Park Jiyeon 
Published: June 2022

Abstract
Introduction: Pancreatic cancer is a lethal disease showing dismal prognosis and therapeutic resistance. Previous molecular subtypes from genome or transcriptome did not show clinical relevance regarding precision strategy for optimal therapeutic options followed by precise patient classification. This study aims to uncover consensus molecular subtypes from cancer-specific multi-omics data showing clinically relevant therapeutic opportunities.
Methods: We performed comprehensive analyses using the dataset from the cancer dependency map (DepMap) project, including cancer-specific molecular characterization with multi-omics data, genome-wide loss-of-function screening using the CRISPR-Cas9 system, and cancer drug sensitivity. The subtype-specific molecular signatures were validated in independent translational cohorts (TCGA-PAAD; n=150, ICGC-PACA-AU; n=461, ICGC-PACA-CA; n=317).
Results: Integrative profiling of multi-omics molecular layers (Mutational signature, Copy number alteration, Transcriptome, MicroRNA, Chromatic profile, Proteome, and Metabolome) from pancreatic cancer cell lines (n=59) from the Cancer Cell Line Encyclopedia (CCLE) revealed a total of three cancer-specific molecular subtypes showing distinct tumor biology through all omics layer as well as clinical relevance with unique molecular dependency. Major molecular features of each subtype were reproducible in the validation cohorts. Subtype-specific molecular biomarkers, including mutational signature and metabolites, were identified. Finally, the target drug with subtype-specific genetic dependency was analyzed to provide precision strategy according to distinct subtypes’ molecular characterization.
Conclusions: Integrative profiling from multi-omics molecular layers revealed precision strategies based on cancer-specific molecular subtypes of pancreatic cancer in terms of tumor classification and discriminative therapeutic opportunities. Prospective translational studies companion with clinical trials based on cancer-specific molecular subtypes is mandatory to establish the precision strategy for managing pancreatic cancer.
Citation Format: Sung Hwan Lee, Jiyeon Park. Unsupervised clustering of multi-omics molecular layers reveals consensus molecular subtypes showing potential therapeutic opportunities for pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2273.
Abstract 2285: Co-expressed gene networks in CRC CMS1 subtype
Authors: Nunez Sha'Kayla K. , Young Corey D. , Griffen Ti'ara L. , Kopetz Scott , Lillard James W. 
Published: June 2022

Abstract
Colorectal cancer (CRC) is a heterogenous disease driven by dysregulated Wnt, Ras-Raf-MAPK, TGF-β, and PI3K-Akt signaling, which leads to an upregulation of proliferative and survival signals from the tumor microenvironment. Molecular and genomic alterations, immune signatures and gene mutations contribute to the progression of CRC. The consensus molecular subtype (CMS), an RNA-based classification system with four classes, is used to better understand CRC heterogeneity. CMS1 is the immunogenic subtype, enriched with MSI; CMS2-CMS3 has epithelial characteristics; and CMS4 is characterized by mesenchymal transitions associated gene expression. CMS1 tumors display immune infiltration, hypermethylation and microsatellite instability, and are known to have a poorer prognosis. We investigated gene signatures and associated coding mRNAs, which are co-expressed by CMS1 CRC. We acquired CRC primary tumor samples from The Cancer Genome Atlas (TCGA). CXCL13, CXCR5, IL10, PIK3R5, PIK3AP1, CCL19 and other co-expressed genes were identified to be positively correlated with CMS1. The canonical pathways and their upstream regulators of this co-expressed network were analyzed using Gene Ontology (GO). The co-expressed network associated with CMS1 was significantly and positively correlated with PI3K, WNT, ERK1 and ERK2 activation. This network was also positively correlated to right-sided tumors, microsatellite instability, chemokine-mediated signaling pathways, and immune responses. Our findings have confirmed and identified new gene signatures significantly correlated with CMS1, which in no doubt activate key pathways associated with CRC progression.
Citation Format: Sha'Kayla K. Nunez, Corey D. Young, Ti'ara L. Griffen, Scott Kopetz, James W. Lillard. Co-expressed gene networks in CRC CMS1 subtype [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2285.
Abstract 2301: Targeting the MUVB complex or downstream G2/M proteins potentiates CDK4/6 inhibitor efficacy in breast cancer
Authors: Cuellar-Vite Leslie , Weber-Bonk Kristen , Keri Ruth A. 
Published: June 2022

Abstract
Uncontrolled progression through the cell cycle sustains the growth and progression of cancer. The cell cycle is comprised of 4 phases that are tightly regulated by two key transcriptional modulators, RB-E2F and MUVB complexes that regulate gene expression during the G1/S and G2/M cell cycle transitions, respectively. Target transcriptomes of both complexes overlap, suggesting that maximal inhibition of cell cycle progression, requires targeting both. Inhibitors that regulate the RB-E2F signaling axis have been FDA approved for treatment of a subset of breast cancers. These drugs specifically inhibit two kinases involved in the cell cycle known as CDK4 and CDK6. Palbociclib and abemaciclib, CDK4/CDK6 inhibitors (CDK4/6i), decrease cell proliferation by inducing a G1 cell cycle arrest. In contrast to CDK4/6, we previously reported that the activity of MUVB complex can be repressed using inhibitors of BET proteins, including the tool compound, JQ1. We hypothesized that dual targeting of MUVB and CDK4/CDK6 will synergize in breast cancer models to further decrease growth. To test this hypothesis, we assessed the impact of growth by adding JQ-1 to CDK4/6i in multiple intrinsically resistant cell lines. We found that addition of JQ-1 reduced IC50 of CDK4/6i by 60-75% and that the combination displayed synergistic growth suppression. Mechanistically, analysis of mRNA and protein expression revealed that the combination had greater ability to suppress expression of proteins that are MUVB target genes, G2/M, compared to single agents. We found through genetic and pharmacological approaches that inhibition of G2/M proteins Aurora Kinase A and NEK2 mediated CDK4/6i inhibitor response. Preclinical xenograft models confirmed that combined inhibition of CDK4/6 and MUVB, NEK2, or Aurora Kinase A can synergistically suppress tumor growth. Together, these results indicate that dual targeting of distinct phases of the cell cycle should be a more efficacious approach for suppressing breast cancer growth and provide a potential approach for blocking the acquisition of resistance to CDK4/6 inhibitors, a major clinical challenge for the treatment of luminal breast cancer.
Citation Format: Leslie Cuellar-Vite, Kristen Weber-Bonk, Ruth A. Keri. Targeting the MUVB complex or downstream G2/M proteins potentiates CDK4/6 inhibitor efficacy in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2301.
Abstract 2318: Real-time quantitative PCR based analysis of transcriptional effects of CDK8/Cyclin C inhibitors
Authors: Jordt Laura M. , Totzke Frank , Lauterwasser Joachim , Ehlert Jan E. , Hekking Koen , Aerts Bas , Obodozie Cynthia , Weber Holger , Müller Gerhard , Kubbutat Michael H. 
Published: June 2022

Abstract
CDK8 has been identified as being frequently upregulated in various types of human cancer such as colorectal cancer, certain sub-types of breast cancer and acute myeloid leukemia. In different tumor cell lines RNA interference mediated knockdown of CDK8 results in significant inhibition of tumor cell growth in vitro and in vivo. CDK8, therefore, represents an interesting target for the development of novel anti-cancer drugs.
Various compounds targeting CDK8/Cyclin C with high potency in low nanomolar range have been reported. These compounds differ with respect to their binding modes, but all of them show high potency in biochemical assays, inhibition of tumor cell growth, and for many in vivo activities in different tumor cell xenograft models have been demonstrated.
CDK8 binds to Cyclin C resulting in the active protein kinases complex. CDK8/Cyclin C interacts with MED12 and MED13, two proteins that regulate CDK8/Cyclin C activity and its interaction with the mediator complex. Mediator consists of 26 subunits and the interaction of the CDK8/Cyclin C/MED12/Med13 complex with mediator enables CDK8/Cyclin C to regulate gene transcription via C-terminal phosphorylation of RNA-polymerase II. This mechanism mediates an indirect regulation of transcription factors such as ß-catenin. In addition of its function via phosphorylation of RNA-polymerase II, CDK8/Cyclin C can also directly regulate the activity of transcription factors by phosphorylation. Best known examples are STAT1 and STAT5 which are phosphorylated by CDK8/Cyclin C on serine 727 and Serine 726, respectively. Recent data indicates that mutations of MED12 can result in a reduced sensitivity of CDK8/Cyclin C towards certain published CDK8/Cyclin C inhibitor in a cellular context. In this study we performed real-time quantitative PCR (qPCR) analyses to characterize the effect of different type I and type II CDK8/Cyclin C inhibitors on the cellular expression of selected genes controlled by two CDK8/Cyclin C dependent pathways, namely the WNT/ß-catenin- and the STAT-pathway. Furthermore, results of qPCR analyses of tumors derived from human xenograft in vivo models treated with type I and type II CDK8/Cyclin C inhibitors will be presented.
Citation Format: Laura M. Jordt, Frank Totzke, Joachim Lauterwasser, Jan E. Ehlert, Koen Hekking, Bas Aerts, Cynthia Obodozie, Holger Weber, Gerhard Müller, Michael H. Kubbutat. Real-time quantitative PCR based analysis of transcriptional effects of CDK8/Cyclin C inhibitors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2318.
Abstract 2326: Preclinical characterization of MTB-9655, a first-in-class, clinical stage ACSS2 inhibitor
Authors: Goutopoulos Andreas , Amanati Iris , Fattaey Ali , Hay-Koren Avital , Nakache Philippe , Erez Omri , Kovalerchik Dimitri , Paz Dikla , Botti Simone , Oppenheimer Hannah , Fainer Irit 
Published: June 2022

Abstract
ACSS2 is a nucleo-cytoplasmic enzyme that converts acetate into Acetyl-CoA. In many tumor types ACSS2 is dramatically upregulated in response to the hypoxic and lipid-depleted conditions often encountered in the tumor microenvironment. In these conditions, ACSS2 allows tumor cells to switch to acetate as key carbon source to meet their anabolic and energetic needs and thereby they become dependent on both acetate and ACSS2. MTB-9655 is a novel, potent and selective ACSS2 inhibitor discovered at Metabomed. It is currently in Phase I clinical investigation on patients with tumors with high levels of ACSS2. The antitumor effect of MTB-9655 was characterized in a number of PDX models across various tumor types. PDX tumors that exhibit over 50 TPM copies of ACSS2 mRNA showed significant sensitivity to ACSS2 inhibition in vivo. TCGA analyses suggests that most GU tumors, such as hepatocellular, gastric, colorectal show high frequency of ACSS2 upregulation and therefore present an opportunity for treatment with MTB-9655. In addition, PDX studies revealed a significant combination effect with cisplatin and gemcitabine. This opens opportunities for combination treatments of several GU cancers expressing high levels of ACSS2, such as ovarian and breast cancers.As a potential PD biomarker assay, 11C acetate PET imaging was explored preclinically in tumor-bearing mice as a way to assess inhibition of acetate flux in the presence of ACSS2 inhibitor. MTB-9655 resulted in robust inhibition of 11C acetate uptake in tumors in a dose-dependent manner opening the possibility of using 11C acetate PET as a clinical PD biomarker.
Citation Format: Andreas Goutopoulos, Iris Amanati, Ali Fattaey, Avital Hay-Koren, Philippe Nakache, Omri Erez, Dimitri Kovalerchik, Dikla Paz, Simone Botti, Hannah Oppenheimer, Irit Fainer. Preclinical characterization of MTB-9655, a first-in-class, clinical stage ACSS2 inhibitor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2326.
Abstract 2342: Quinolinate promotes alternatively activated macrophage-induced immune tolerance in glioblastoma through the NMDA/PPARy signaling axis
Authors: Kesarwani Pravin , Kant Shiva , Prabhu Antony , Buelow Katie L. , Miller C. Ryan , Chinnaiyan Prakash 
Published: June 2022

Abstract
There has been considerable scientific effort dedicated to understanding the biologic consequence and therapeutic implications of aberrant tryptophan metabolism in brain tumors and neurodegenerative diseases. An overwhelming majority of this work has focused on the upstream metabolism of tryptophan, however, this has not resulted in clinical application. Using global metabolomic profiling of patient-derived brain tumors, we identify the downstream metabolism of tryptophan and accumulation of quinolinate (QA) as a metabolic node in glioblastoma and went on to demonstrate its critical role in promoting immune tolerance. QA acts as a “metabolic checkpoint” in glioblastoma by inducing NMDA receptor activation and Foxo1/PPARγ signaling, resulting in amplification of immune suppressive macrophages. Using a genetically-engineered mouse model designed to inhibit production of QA, we identify kynureninase as a promising therapeutic target to revert the potent immune suppressive microenvironment in glioblastoma. These findings offer the scientific community an opportunity to revisit the biologic consequence of this pathway as it relates to oncogenesis and neurodegenerative disease and a framework for developing new immune modulatory agents to further clinical gains in these otherwise incurable diseases.
Citation Format: Pravin Kesarwani, Shiva Kant, Antony Prabhu, Katie L. Buelow, C. Ryan Miller, Prakash Chinnaiyan. Quinolinate promotes alternatively activated macrophage-induced immune tolerance in glioblastoma through the NMDA/PPARy signaling axis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2342.
Abstract 2344: BRAF inhibitor resistant thyroid cancer cells exhibit altered cellular energetics
Authors: Bolf Eric , Schweppe Rebecca 
Published: June 2022

Abstract
Thyroid cancer is the most commonly diagnosed endocrine malignancy. Although prognosis for patients is positive overall, dedifferentiated thyroid tumors and invasive thyroid tumors are difficult to treat. There is one FDA approved targeted therapy in use for in BRAF mutant, highly dedifferentiated anaplastic thyroid cancer, a combination of the BRAF inhibitor dabrafenib and the ERK inhibitor trametinib. While this treatment improves outcomes, resistance is of great concern. In other cancers driven by BRAF mutations, particularly melanoma, a known driver of BRAF inhibitor resistance is enhanced oxidative phosphorylation. We therefore investigated the energetics of thyroid cancer cells to determine whether metabolic changes can drive resistance in thyroid cancer. We have previously determined sensitivity to dabrafenib by area under the curve to classify cell lines as sensitive or resistant (Hicks HM et al, 2021). We used CUTC5 cells as our primary model of intrinsically sensitive cells and CUTC60 cells to model intrinsic resistance. We observed both cell lines had similar basal oxygen consumption rates (OCR), however dabrafenib treatment reduced this in the sensitive CUTC5 cells and did not in the resistant CUTC60 cells. Additionally, maximum OCR was reduced in the CUTC5 cells with as little as 10 nM dabrafenib. In a preliminary experiment, CUTC60 cells were co-treated with dabrafenib and rotenone, an inhibitor of the electron transport chain, and synergistic inhibition of proliferation was observed. We further investigated energetics in the dabrafenib sensitive cell line KTC1 and KTC1-VA7, which are derived from KTC1 and BRAF-inhibitor resistant (Danysh BP et al, 2016). Unlike the other cells evaluated these cells did not have spare respiratory capacity. Additionally, dabrafenib treatment did not alter basal OCR except at the highest doses. Although, we did observe a reduction in glycolysis in the parental KTC1 upon dabrafenib treatment, which was not observed in the KTC1-VA7 cells. Sensitive CUTC5 cells also exhibited a greater decrease in glycolysis than resistant CUTC60 cells. From this, we conclude that glycolysis may contribute to dabrafenib resistance and merits further investigation. With regards to oxidative metabolism, we only observed a reduction in OCR in a dabrafenib sensitive cell line and there was synergistic inhibition in the resistant CUTC60 cells treated with both dabrafenib and rotenone, suggesting that oxidative metabolism aids the cells in tolerating BRAF inhibition. Further screening of dabrafenib sensitive and resistant cells is necessary to determine if this is a function of dabrafenib sensitivity.
Citation Format: Eric Bolf, Rebecca Schweppe. BRAF inhibitor resistant thyroid cancer cells exhibit altered cellular energetics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2344.
Abstract 2345: Specificity of catechol-O-methyltransferase (COMT) for hydroxyestrogens favors 2-OHEs over 4-OHEs
Authors: Krzizike Daniel D. , Clapper Margie L. , Andrews Andrew J. 
Published: June 2022

Abstract
The contribution of estrogen receptor-mediated signaling to cancer progression and metastasis has been well documented. However, much less attention has been given to the role of estrogen metabolism in carcinogenesis. Parent estrogens are metabolized to 2- and 4-hydroxyestrogens (2-OHEs and 4-OHEs) that can retain their estrogenic activity, form reactive quinones that cause DNA damage, or become inactivated primarily by the rate-limiting conjugation enzyme catechol-O-methyltransferase (COMT). The ability of 4-OHEs to induce genomic instability and the malignant transformation of human breast epithelial cells has been reported. Glucuronidation or sulfation of methylated hydroxyestrogens, produced by COMT, increases their solubility and facilitates their excretion via urine or feces. The extent to which catechol estrogens are methylated dictates, in part, their ability to initiate carcinogenesis verses protect against tumor formation. COMT is a ubiquitous polymorphic enzyme that is expressed in humans in both peripheral tissues (soluble, s-COMT) and the central nervous system (membrane-bound). The goal of the present study was to compare the rate at which human wild type (WT) s-COMT and its major polymorphic variant (V108M s-COMT) transfer the methyl group from S-adenosylmethionine to 2-OHE and 4-OHE. This was accomplished by expressing COMT in E. coli, followed by protein purification and steady state Michaelis-Menten kinetics. Production of methylated hydroxyestrogens (2-MeOEs and 4-MeOEs) was quantified using LC-MS/MS methodology. The resulting data indicate that WT s-COMT methylates catechol estrogens more efficiently than V108M s-COMT. In addition, the specificity constant (kcat/KM) of WT s-COMT for methylation of 4-OHE2 was 12-fold greater than that of V108M s-COMT. The kcat/KM of V108M s-COMT was 4-fold greater for 2-OHE2 vs. 4-OHE2. Based on the enhanced catalytic efficiency of WT s-COMT in converting 2-OHEs to 2-MeOEs, 4-OHEs may have greater potential to cause DNA damage. Additional studies are needed to determine if the V108M s-COMT variant contributes to increased risk for cancer. These data provide novel insight into the potential mechanism by which 4-OHEs promote hormone-induced carcinogenesis.
This work was supported by an In Vino Vita Award from Fox Chase Cancer Center.
Citation Format: Daniel D. Krzizike, Margie L. Clapper, Andrew J. Andrews. Specificity of catechol-O-methyltransferase (COMT) for hydroxyestrogens favors 2-OHEs over 4-OHEs [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2345.