bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 4339: Critical role of Dnmt3b catalytic activity in prevention of oncogene-induced leukemias and lymphomas
Authors: Lopusna Katarina , Nowialis Pawel , Haney Staci L. , Abraham Ajay , Opavska Jana , Opavsky Rene 
Published: August 2019

Abstract
Cytosine methylation is involved in a variety of biological processes, including development, X-chromosome inactivation, imprinting, and suppressing unwanted transcription. DNA methylation in mammalian cells is catalyzed by several DNA methyltransferases, including DNMT1, DNMT3A and DNMT3B. In addition to DNA methylation catalysis, these enzymes interact with a number of repressive proteins including HDACs, thereby repressing transcription in methylation-independent manner. The extent to which methylation-dependent and independent activities play roles in biological processes remains poorly understood. Here we examined the role of methyltransferase (MT) activity of Dnmt3b in normal mouse embryogenesis and in prevention of hematologic malignancies. Loss of Dnmt3b in mice is embryonically lethal between 10.5-12.5 dpc. Dnmt3b was also identified as tumor suppressor in murine models of lymphoid and myeloid malignancies. To address whether Dnmt3b’s catalytic activity is important for mouse embryogenesis and prevention of hematologic malignancies, we generated mice bearing a conventional Dnmt3bCI allele using CRISPR/Cas9 system. This catalytically inactive allele of Dnmt3b (Dnmt3bCI) was generated by a double amino acid substitution in enzyme active center (P656V and C657D) abolishing its ability to perform transfer of methyl group onto cytosine. Surprisingly, Dnmt3bCI/CI mice were born at similar ratios as wild-type littermates and lived over 12 months suggesting that Dnmt3b is dispensable for both pre- and post-natal development. Importantly, MYC-induced T-cell lymphomagenesis was accelerated in the absence of Dnmt3b’s methyltransferase activity in MYC;Dnmt3bCI/CI mice. Global gene expression and methylation profiling revealed a number of deregulated events specific for MYC;Dnmt3bCI/CI, resulting in activation of Pak, Fgfr and Igf2 signaling and downregulation of tumor suppressors (e.g. Lrp12, Dusp6 and Marcks). The lack of Dnmt3b catalytic activity also accelerated a development of acute myeloid leukemia induced by MLL-AF9 overexpression in mice. Altogether, our data suggest that Dnmt3b’s MT activity is dispensable for mouse development but critical to prevent hematologic malignancies.
Citation Format: Katarina Lopusna, Pawel Nowialis, Staci L. Haney, Ajay Abraham, Jana Opavska, Rene Opavsky. Critical role of Dnmt3b catalytic activity in prevention of oncogene-induced leukemias and lymphomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4339.
Abstract 4349: Predicting gene expression from plasma cell-free DNA using both the fragment length and fragment position
Authors: John John A. St , Gafni Erik , White Brandon , Kannan Ajay , Hansen Loren , Jaroszewicz Artur , Kundaje Anshul , Boley Nathan 
Published: August 2019

Abstract
The ability to use a blood sample to determine the transcriptional state of cells that are releasing DNA into the bloodstream of a patient may be helpful in a variety of clinical applications. Here we present a case study of a gene expression prediction model that uses cell-free DNA (cfDNA) fragment coverage data generated by high-throughput sequencing to predict which genes are highly or lowly expressed in the cells contributing to that cfDNA. We evaluated a number of models, including a convolutional neural network that takes cfDNA fragment information (the density of both fragment midpoint and length by genomic position) over a transcription start site (TSS) as input, and outputs a predicted probability of whether that gene is highly expressed in cfDNA-producing cells. When we trained the convolutional model on a set of 554 genes with TSSs that were either constitutively expressed or unexpressed across leukocyte samples from the NIH Roadmap Epigenome Mapping Consortium, we achieved ~0.97 AUC in cross validation. With other models and splits of the data, we observed AUCs ranging from 0.95 to 0.99 on this gene-expression task. Next, we were interested in whether this trained model could answer specific clinical questions. For example, we hypothesized that we should see an increased influence of colon gene expression profiles in colorectal cancer patients with a higher fraction of circulating tumor DNA. To test this hypothesis, we applied our models to a set of genes with colon-specific expression, which generated a list of probabilities of each gene being expressed in each sample. We then applied simple models on the these lists of probabilities to predict whether a patient had CRC or was healthy. This yielded cross validation AUCs between 0.85 and 0.95 across many of the models we tested in differentiating healthy patients from colorectal cancer patients with tumor fraction over 5%. These results suggest a path forward for modeling transcriptional states using cfDNA sequencing data, which will enable greater insights from cfDNA that could augment those provided by other analytes.
Citation Format: John A. St John, Erik Gafni, Brandon White, Ajay Kannan, Loren Hansen, Artur Jaroszewicz, Anshul Kundaje, Nathan Boley. Predicting gene expression from plasma cell-free DNA using both the fragment length and fragment position [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4349.
Abstract 4350: MAPK1
E322K somatic mutation promotes cell proliferation via positive feedback regulation of EGFR/RAF signaling
Authors: Zhang Jianqing , Brooke Dewey J. , Blair Jessica P. , Riby Jaques , Ojesina Akinyemi I. 
Published: August 2019

Abstract
The RAS-MAPK signaling cascade serves as the central node in the transduction of signals starting from the binding of the epidermal growth factor (EGF) ligand to the membrane receptors (EGFR) through to the nucleus. Recent studies suggested that different defined thresholds of RAS-MAPK activity are required for maintaining homeostasis as opposed to facilitating malignant transformation, and that Ras-oncogenic toxicity is quantitatively dictated by MAPK function. We and others have demonstrated that somatic MAPK1(E322K) mutations in MAPK1 occur in 8% of cervical squamous cell carcinoma (CSCC) and 3% of head and neck squamous cell carcinoma (HNSCC), suggesting that mutant MAPK1 may play an important part in tumorigenesis. To investigate the molecular mechanism involved in the effects of the mutated MAPK1, we transduced MAPK1 wild type and MAPK1(E322K) mutant as lentiviral constructs into the untransformed human embryonic kidney cell line HA1E. We found that cells expressing MAPK1(E322K) exhibited higher rates of proliferation and cellular mobility compared to the cells transduced with wild type MAPK1. However, the cells expressing wild type MAPK1 presented poor cell proliferation compared to the cells transduced with the empty lentiviral vector. Western blot analyses showed approximately two-fold increase phosphorylation of ERK (T202/Y204) following EGF treatment in the cells harboring the mutation compared to the cells expressing the wild type MAPK1. A similar pattern was observed with phospho-EGFR (T669, Y1148, Y1068, Y1148) phospho-cRaf (S259, S338, S289/296/301), phosphor-RSK1, phospho-AKT (S473, T389), phosphor-GSK3β (S9/21) and phospho-STAT5 (Y694), suggesting that MAPK1(E322K) mutation might reinforce the positive/negative feedback loop on EGFR and cRaf. Our data contributes to the understanding of the roles of MAPK1 in the RAS/RAF-MEK-MAPK1 signaling pathway and might help identifying possible therapeutic targets for HNSCC and CSCC patients with tumors harboring somatic MAPK1(E322K) mutations.
Citation Format: Jianqing Zhang, Dewey J. Brooke, Jessica P. Blair, Jaques Riby, Akinyemi I. Ojesina. MAPK1E322K somatic mutation promotes cell proliferation via positive feedback regulation of EGFR/RAF signaling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4350.
Abstract 4370: Knockdown of PKM2 induces autophagic cell death via Akt/mTOR pathway in human prostate cancer cells
Authors: Dey Prasanta , Kundu Amit , Lee Byung Mu , Kim Hyung Sik 
Published: August 2019

Abstract
Pyruvate kinase M2 (PKM2) is crucial for aerobic glycolysis that is highly expressed in the various cancer tissues. Although high expression of PKM2 is observed in prostate tumor tissues, its functional role against affecting cancer metabolism is not clearly understood. Herein, we investigate its role in regulating autophagy and its associated pathways. In the current study, various PKM2-siRNA constructs were used to knockdown the PKM2 expression and observed its cellular pathways on autophagy. Cell viability was significantly reduced in PKM2-siRNA transfected prostate cancer cells, DU145. Acridine orange staining and immunoblotting analysis showed that downregulation of PKM2 markedly increased autophagy cell death. In addition, immunoblotting analysis exhibited the blocking the protein kinase B (Akt) and mTOR1 pathways, which subsequently down-regulated the expression of glycolytic enzymes lactate dehydrogenase A (LDHA) and Glucose transporter 1 (GLUT1). To the best of our knowledge, this is the first study that inhibition of PKM2 changes in cancer cell metabolism and induces autophagy, thus, providing new perspectives into the mechanism of its anticancer activity against prostate cancer, DU145.
Citation Format: Prasanta Dey, Amit Kundu, Byung Mu Lee, Hyung Sik Kim. Knockdown of PKM2 induces autophagic cell death via Akt/mTOR pathway in human prostate cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4370.
Abstract 4373: Lack of FGF21 promotes NASH-HCC transition via exosome-mediated carcinogenetic signaling
Authors: Yu Youxi , Martin Robert C. , Zheng Qianqian , Shi Xiaoju , Liu Xingkai , Guo Wei , Li Suping , Zhang Ping , Li Yan 
Published: August 2019

Abstract
Background: Nonalcoholic steatohepatitis (NASH) is the most severe form of non-alcoholic fatty liver disease (NAFLD) and a potential precursor of hepatocellular carcinoma (HCC). FGF21, with its metabolic benefits, was reported as the liver safeguard to protect from obesity, diabetes, and NAFLD. Recent study showed an exosome based FGF21 inhibition via organs communication to regulate hepatic metabolism. However, the role of the exosome-FGF21 axis in NASH-HCC has never been studied.
Aim: To study the exosome based FGF21 metabolic regulation during NASH-HCC carcinogenetic transformation.
Methods: NASH-HCC model was induced in FGF21 knockout (KO) mice and wild type (WT) control using methionine-choline-deficient diets (MCD) and diethylnitrosamine (DEN). The exosomes releasing, miRNA and protein contents were analyzed in the primary cultured hepatocytes from the liver tissues of NASH-HCC mice (KO and WT) as well as benign controls. FGF21 was knockdown (KD) by shRNA in a mouse hepatoma cell line (Hepa1-6) and a benign mouse hepatocyte cell line (FL83B) to investigate the potential carcinogenetic signaling related to exosome-FGF21 axis.
Result: NASH-HCC model was successfully established with confirmation of the metabolic disorders and liver cancer development. Early HCC detection and increased HCC incidence were found in the KO-MCD mice (P&lt;0.05 versus KO-CD and WT controls). The collected exosomes from primary cultured hepatocytes and cell lines were identified using the antibodies of Tsg101, CD63 and cytochrome C by western blotting and immunofluorescent staining. In the KO-MCD mice, exosomes retained in the cytosol of benign hepatocyte but released increasingly from cancer cell. Similar results were showed in the Hepa1-6KD cells and the FL83BKD cells. Aberrant EMT, and p53 and Wnt signaling was found in the KO-MCD mice as well as Hepa1-6KD cells challenged with free fatty acid.
Conclusion: lack of FGF21 plays critical role for the exosome retention in hepatocytes of NASH mice but not in HCC mice. Abnormal traffic of exosomes contribute to the carcinogenetic signaling. This work was supported by an Institutional Development Award (IDeA) from the NIGMS of the National Institutes of Health under grant number P20GM113226.
Citation Format: Youxi Yu, Robert C. Martin, Qianqian Zheng, Xiaoju Shi, Xingkai Liu, Wei Guo, Suping Li, Ping Zhang, Yan Li. Lack of FGF21 promotes NASH-HCC transition via exosome-mediated carcinogenetic signaling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4373.
Abstract 4390: Dietary soy isoflavone equol promotes breast cancer progression via regulation of protein synthesis initiation
Authors: Cruz-Collazo Ailed M. , Parra Columba De la , Schneider Robert , Dharmawardhane Suranganie 
Published: August 2019

Abstract
We previously reported that dietary daidzein, a soy isoflavone, increased breast cancer progression in a nude mouse model of breast cancer metastasis. Further studies indicated that equol, a metabolite of the soy isoflavone daidzein is responsible for the cancer promoting effects of soy isoflavones in breast cancer cells in vitro. We reported that equol increases the expression of the eukaryotic protein synthesis initiation factor eIF4G1, and the transcription factor c-Myc. Increased eIF4G in response to equol resulted in the non-canonical protein synthesis of pro-cancer molecules such as Cyclin D, Bcl-XL, p120, matrix metalloproteinases, etc., as confirmed by ribosome profiling and eIF4G1 knockdown studies. This study tested the hypothesis that equol promoted breast cancer progression via eIF4G1 upregulation. Immunocompromised nude mice were used to establish mammary fatpad tumors from human metastatic breast cancer cells expressing eIF4G1 knockdowns via a Tetracycline-inducible promoter. Oral gavage of 50 mg/kg BW Doxycycline 3X a week for 4 weeks was enough to knockdown eIF4G1 expression by ~80%. Therefore, one week following tumor establishment, the mice were treated with vehicle (90% corn oil, 10% ethanol), equol, Doxycycline or, equol and Doxycycline. Data show that as expected, equol treatment increased tumor growth relative to vehicle treatment. Moreover, eIF4G1 knockdown abolished the effect of equol on tumor growth. Interestingly, the effect of eIF4G1 knockdown on mammary tumor growth was not evident until 55 days of doxycycline treatment. Therefore, we tested the cell and tumor lysates for potential expression of the eIF4G1 isoform Dap5 when eIF4G1 is knocked out. Dap5 protein was expressed in eIF4G1 knockdown cells and was increased by equol treatment, indicating that Dap5 may compensate for eIF4G1 knockdown by inducing alternative cap-mediated protein synthesis. In conclusion, the cancer promoting effect of equol is abolished in breast tumors where eIF4G1 expression was stably knocked down, thus, validating our hypothesis that equol increases breast cancer progression via upregulation of eIF4G1 dependent protein synthesis initiation.
Citation Format: Ailed M. Cruz-Collazo, Columba De la Parra, Robert Schneider, Suranganie Dharmawardhane. Dietary soy isoflavone equol promotes breast cancer progression via regulation of protein synthesis initiation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4390.
Abstract 4401: Implications of STAG2 loss in Ewing sarcoma
Authors: Gorthi Aparna 
Published: August 2019

Abstract
Ewing sarcoma is an aggressive pediatric bone and soft tissue cancer that is driven by a translocation event, predominantly involving the RNA binding protein EWSR1 and the transcription factor FLI1. The resultant fusion transcription factor EWSR1-FLI1 is a potent oncogene and drives dramatic changes in the transcriptional landscape of Ewing sarcoma. Our previous work demonstrated that EWS-FLI1 drives aberrant accumulation of R-loops, increases replication stress and suppresses homologous recombinational repair in Ewing sarcoma. Similar phenotypes were also observed with the loss of wildtype EWSR1. However, surprisingly, Ewing tumors have highly stable genomes. The most common mutation is in the STAG2 gene, a component of the cohesin ring complex.
It was recently reported that STAG2-cohesin complexes not only participate in maintaining chromatin architecture but also play a key role in directing tissue-specific gene expression by interacting with transcription factors. In the present study, we evaluate the STAG2 function in R-loop metabolism, replication and repair and attempt to identify the reason for its selective loss in Ewing sarcoma. Using biochemical and biophysical experimental strategies, we observed that STAG2 and EWSR1 both bind R-loop structures with high affinity and are protective against RNaseH-mediated degradation of R-loops to significantly different degrees. We also examine the effect of STAG2 loss on R-loop accumulation and replication stress in Ewing and non-Ewing cell lines. Finally, we evaluate the correlation between STAG2 binding sites and R-loops. We propose that loss of STAG2 alleviates some of the genomic stresses experienced in Ewing sarcoma.
Note: This abstract was not presented at the meeting.
Citation Format: Aparna Gorthi. Implications of STAG2 loss in Ewing sarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4401.
Abstract 4404: E-p-Methoxycinnamoyl-α-l-rhamnopyranosyl ester (MCR) increases Nrf2 stability by inhibiting ubiquitination in HaCaT cells
Authors: Jeong Jiwon , Wahyudy Lilik D. , Yang Heejung , Kim Jung-Hwan 
Published: August 2019

Abstract
The nuclear factor erythroid-derived 2-related factor 2 (Nrf2) is a key regulator of gene expression during oxidative stress and drug detoxification. Thus, identifying Nrf2 activators to protect from possible cell damage is necessary. In this study, we investigated whether E-p-methoxycinnamoyl-α-l-rhamnopyranosyl ester (MCR), a phenylpropanoid isolated from Scrophularia buergeriana, can activate Nrf2 signaling in human keratinocytes (HaCaT). First, we determined the dose- and time-dependent effects of MCR on the expression and activity of Nrf2. The antioxidant response element-luciferase reporter assay and western blot analysis results showed that MCR markedly induced Nrf2 activity and its protein expression, respectively. Further, MCR increased both the mRNA and protein levels of heme-oxygenase-1, one of the Nrf2 target genes, in the cells. Interestingly, we found that Nrf2 stability was remarkably enhanced by MCR. Furthermore, ubiquitin-dependent proteasomal degradation of Nrf2 was significantly reduced by MCR. Thus, MCR might afford skin protection by enhancing Nrf2 stability or by blocking its proteasomal degradation.
Citation Format: Jiwon Jeong, Lilik D. Wahyudy, Heejung Yang, Jung-Hwan Kim. E-p-Methoxycinnamoyl-α-l-rhamnopyranosyl ester (MCR) increases Nrf2 stability by inhibiting ubiquitination in HaCaT cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4404.
Abstract 4405: Acetylation of KLF5 controls the cell fate of basal progenitors during postnatal development and regeneration of mouse prostates
Authors: Zhang Baotong , Dong Jin-Tang 
Published: August 2019

Abstract
Adult stem cells are responsible for lineage specification in epithelial homeostasis, and thus are essential for both postnatal development and tissue regeneration. Genetic changes in adult stem cells have been revealed to promote cancer development. Dissecting the underlying regulators is critical for understanding the intrinsic mechanisms that regulate adult stem cell function, yet whether PTM of a single molecule determines cell fate of adult stem cells during organ development has not been well established, particularly for glandular organs. Using the androgen-dependent mouse prostate as an experimental system, an ideal system for understanding epithelial hierarchy, we examined the Krüppel-like factor 5 (Klf5) transcription factor and its acetylation for their roles in postnatal development and regeneration. The absence of KLF5 eliminated basal progenitor activities in both human and mouse prostate epithelial cells, as indicated by a compromised sphere and organoid formatting capabilities, downregulation of basal cell markers, and decreased basal cells. Klf5 was also necessary for basal progenitor cells to maintain their luminal differentiation capacity, as loss of Klf5 also decreased basal progenitor-derived luminal cells and their proliferation in mouse prostates. Interestingly, the progenitor activity of Klf5 was restricted to deacetylated Klf5 (deAc-Klf5), as indicated by in vitro and in vivo assays. On the other hand, acetylated Klf5 (Ac-Klf5) was essential for proper formation and maintenance of luminal structures in mouse prostates, as deacetylation of Klf5 interrupted the formation of normal luminal structures, almost eliminated the castration resistance in basal progenitor-derived luminal cells, and attenuated the luminal regeneration after a castration-regeneration cycle, even though deAc-Klf5 promoted basal-to-luminal differentiation and the proliferation of luminal cells during postnatal development. Mechanistically, deacetylation of Klf5 increased Notch signaling activity. These findings indicate that Klf5 and its acetylation control the cell fate of prostatic basal progenitors, which have a distinct contribution to postnatal development and regeneration of the prostate. Considering that androgen deprivation therapy (ADT) is currently a major therapeutic strategy in the treatment of prostate cancer, our findings also provide a potential mechanism for prostate cancer progression, i.e., interruption of Klf5 acetylation could sensitize castration-resistant prostate cancer to ADT or slow the recurrence of prostate cancer after ADT.
Citation Format: Baotong Zhang, Jin-Tang Dong. Acetylation of KLF5 controls the cell fate of basal progenitors during postnatal development and regeneration of mouse prostates [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4405.