bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 2180: Deciphering the Warburg effect: Redox is the key to tumor differentiation
Authors: Haowen Jiang , Greathouse Rachel L. , He Bo , Li Yang , LI Albert M. , Forgo Balint , Banuelos Selene , Gruber Joshua , Shimada Hiroyuki , Chiu Bill , Ye Jiangbin 
Published: June 2022

Abstract
It was proposed by Warburg that the cause and consequence of the Warburg effect were the injury of respiration and cell dedifferentiation, respectively. However, the underlying mechanism was unclear due to limited understanding of metabolic control of epigenetics. Inhibition of mitochondrial electron transport chain (ETC) causes reduction of NAD+/NADH ratio. Recently it was discovered that this redox stress not only drives lactate production from pyruvate to enhance the Warburg effect, but also promotes the conversion of α-ketoglutarate (αKG) to 2-hydroxyglutarate (2HG), turning the substrate of DNA demethylase TET into an inhibitor of TET, suggesting a potential link between ETC inhibition and dysregulated DNA methylation in cancer. In this study we use a mitochondrial uncoupler niclosamide ethanolamine (NEN) to block the Warburg effect and remodel cancer epigenome. NEN treatment activates ETC and accelerates glutaminolysis to produce αKG, which promotes promoter CpG island demethylation. This epigenomic reprograming not only upregulates tumor suppressor genes such as p53, inhibits N-Myc expression, but also activates neuron differentiation markers to promote differentiation in neuroblastoma cells. Hypoxia is one common microenvironmental stress existing in all solid tumor. NEN treatment reduces 2HG generation from αKG under hypoxia, highlighting its application potential in preventing DNA hypermethylation in vivo. Associated with 2HG reduction, NEN treatment also represses HIF signaling under hypoxia. In addition, NEN treatment inhibits reductive carboxylation flux. Moreover, dietary supplementation with NEN reduces orthotopic neuroblastoma growth and N-Myc expression in vivo. Together, these results validated Warburg’s hypothesis that mitochondrial respiration is the key to maintain normal differentiation. Restoring ETC activity with mitochondrial uncoupler is an effective metabolic/epigenetic therapy against neuroblastoma (Jiang et al., BioRxiv 2021).
Citation Format: Jiang Haowen, Rachel L. Greathouse, Bo He, Yang Li, Albert M. LI, Balint Forgo, Selene Banuelos, Joshua Gruber, Hiroyuki Shimada, Bill Chiu, Jiangbin Ye. Deciphering the Warburg effect: Redox is the key to tumor differentiation [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 2180.
Abstract 2247: Prostate cancer-related mortality risk assessment in a cohort of southern Nigerian men
Authors: Okoye Jude O. , Ogbonnaya Vivian I. , Emeka Chiemeka M. , Obioma Okechi 
Published: June 2022

Abstract
Background: Overexpression of breast cancer susceptibility gene 2 (BRCA2) in patients with prostate cancer is associated with a high Gleason score at diagnosis, poorly differentiated tumors, poor prognosis, and disease recurrence. Such aggressive tumors possess high iron storage which promotes inflammation, angiogenesis, and cell proliferation. Expression of iron progressively increases with cancer grade and stage.
Purpose: This study evaluated the expression of BRCA2 protein and Iron expression in Gleason’s graded prostate cancer tissues, in a bid to determine the disease aggressiveness and mortality risk among Southern Nigerian men.
Methods: In this retrospective study, 86 formalin-fixed paraffin-embedded prostate cancer tissues (diagnosed in 2018 and 2019) were reviewed using Gleason’s grading system. Tissues stained for iron and BRCA2 proteins using histochemical and immunohistochemical staining techniques, respectively. Staining intensity was scored using a scale of 0, +1, +2, and +3. For BRCA2 and Iron expressions, score 0 and +1 were considered negative while score +2 and +3 were considered positive. Pearson’s chi-square test was used to determine the association between Gleason’s grade and expression of BRCA2 and iron.
Results: The prevalence of prostate cancer in the age groups of 50-59, 60-69, 70-79, 80-89, and 90-99 years was 10.8%, 32.4%, 40.5%, 13.5% and 2.7%, respectively. Using the Gleason’s grading pattern, the frequency of Grade (mean age in years) I, II, III, IV and V was 9.3% (70.25 ± 6.95), 16.3% (77.29 ± 6.23), 16.3% (75.57 ± 12.59), 25.6% (72.75 ± 7.80) and 32.6% (67.42 ± 9.76), respectively. Higher frequency of BRCA2 and Iron expression were observed in ≥G4 (37.5% and 72.7%) than in ≤G3 (versus 16.7% and 11.8%) at p= 0.191 and p&lt; 0.001, respectively. The prevalence of BRCA2 negative and positive tissues was 65.1% and 34.9%, respectively whereas the prevalence of iron negative and positive tissues was 48.7% and 51.3%, respectively. There was an inverse relationship between tumour grade and age (p= 0.108), and direct relationships between tumour grade and BRCA2 (p= 0.059), tumour grade and iron (p= 0.000), BRCA2 and Iron expressions (p= 0.027), BRCA2 expression and age (p= 0.019), and Iron and age (p= 0.281). Patients with prostate cancer who are within the age group of 50-59 years and those with ≥G4 require close monitoring for improved survival.
Conclusion: This study revealed a high prevalence of aggressive prostate cancer and suggests that there is a high mortality risk among Southern Nigerian men diagnosed with the disease.
Citation Format: Jude O. Okoye, Vivian I. Ogbonnaya, Chiemeka M. Emeka, Okechi Obioma. Prostate cancer-related mortality risk assessment in a cohort of southern Nigerian men [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 2247.
Abstract 2250: Eosinophil-to-lymphocyte ratio and cancer risk in the UK Biobank
Authors: Wang Jeanny , Engels Eric , Song Minkyo 
Published: June 2022

Abstract
Background: Eosinophils exhibit anti-tumor cytotoxic responses in the tumor microenvironment. Some atopic diseases, characterized by elevated peripheral eosinophils, are inversely associated with cancer risk. The balance of atopy and immunity may be estimated by an eosinophil-to-lymphocyte ratio (ELR). This study aims to understand the role of ELR as a biomarker in carcinogenesis.
Methods: We evaluated 445,404 adults aged 37-73 years at baseline in a prospective cohort study, the UK Biobank, who were cancer-free at initial assessment, had more than one year of follow-up, and had baseline white blood cell (WBC) count and differential measurements. ELR was categorized into quartiles. Incident cancers were ascertained from cancer registries from 2006-2015. Multivariable Cox regression was used to estimate per quartile ELR hazard ratios (aHRs) separately for 52 cancer sites, adjusted for age (quartiles), sex, race (white, non-white), smoking/alcohol (never, past, current), body mass index (&lt;25, 25-30, ≥30 kg/m2) and total WBC (quartiles). Multiple comparisons were considered by a Bonferroni-corrected threshold (p&lt;0.00096).
Results: Over a median follow-up time of 6.9 years from baseline, 22,853 incident cancers were diagnosed. The median ELR was 0.07 (interquartile range=0.05-0.12). Higher ELR was inversely associated with overall cancer risk (aHR 0.98, 95%CI: 0.97-0.99; p-trend=0.0001) and chronic lymphocytic leukemia (0.50, 0.44-0.56; &lt;0.0001). We also observed suggestive inverse ELR associations with other lymphocytic leukemia, acute and other myeloid leukemia, myeloma, melanoma and cancers of the nose/middle ear, tongue, prostate (aHR range: 0.63-0.97; p-trend&lt;0.05). Per quartile increase of ELR was suggestively associated with increased risk of diffuse large B-cell lymphoma (aHR 1.13, 95%CI: 1.03-1.25; p-trend=0.01).
Conclusion: We observed inverse associations between ELR and cancer risk in a large general population. Our findings suggest that atopy may be protective against cancer. Future research is warranted to elucidate the relationship between atopy and immunity in tumor surveillance.
Impact/Significance: ELR presents a cost-effective and routinely accessible biomarker that may have implications for carcinogenesis, and may be leveraged to inform early detection of certain cancers.
Citation Format: Jeanny Wang, Eric Engels, Minkyo Song. Eosinophil-to-lymphocyte ratio and cancer risk in the UK Biobank [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 2250.
Abstract 2288: A novel enzymatic fragmentation library preparation chemistry that greatly reduces sequencing artifacts
Authors: Jaafar Zane , Haimes Josh , Harrison Thomas , Peterkin Lindsay , Ranik Martin , Scott Kristin , Kudlow Brian A. 
Published: June 2022

Abstract
After a decade of NGS technology and workflow innovation, personalized medicine is starting to become a reality. DNA fragmentation is still a critical bottleneck during library preparation. Sonication methods have been the gold standard for consistent fragmentation and uniform GC coverage, but are associated with a high upfront investment, expensive consumables, and are prone to oxidative DNA damage. On the other hand, enzymatic fragmentation methods hold the potential to be scalable, automation-friendly workflows that minimize DNA damage. Yet, typical enzymatic fragmentation methods have been shown to introduce systematic hairpin artifacts, exhibit suboptimal uniformity, and have a narrow range of input mass compatibility. We have developed a novel enzymatic fragmentation-based library preparation technology which, together with our high-fidelity library amplification module, effectively overcomes many of the key limitations of related chemistries. Libraries generated using our workflow reduced chimeric reads and terminal hairpin artifacts 10-fold compared to other enzymatic methods, and reached comparable levels of mechanically sheared DNA controls. Furthermore, we observed consistently even coverage uniformity and low sequence-specific bias for human whole genome sequencing. Fragmentation was tested across a broad sample input range from 100 pg to 500 ng. Library insert sizes were highly tunable from 150 bp to 550 bp and consistent across the input titration. High quality libraries with minimal adapter dimer were prepared from as little as 1 picogram of gDNA by adjusting the post amplification clean up conditions. Taken together, this enzymatic fragmentation and library preparation workflow avoids library preparation artifacts that convolute variant calling, is highly scalable, and suitable for ultra-low input samples.
Citation Format: Zane Jaafar, Josh Haimes, Thomas Harrison, Lindsay Peterkin, Martin Ranik, Kristin Scott, Brian A. Kudlow. A novel enzymatic fragmentation library preparation chemistry that greatly reduces sequencing artifacts [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 2288.
Abstract 2298: OTUD6B is a dependency in multiple myeloma that drives S-phase entry via MYC activation
Authors: Spallek Ria , Paulmann Carmen , Karpiuk Oleksandra , Zecha Jana , Klaeger Susan , Schaeffer Isabell , Öllinger Rupert , Engleitner Thomas , Krönke Jan , Wirth Matthias , Keller Ullrich , Rad Roland , Kuster Bernahrd , Bassermann Florian 
Published: June 2022

Abstract
Multiple myeloma (MM) is the second most common hematological malignancy and remains incurable, thus demanding for new therapeutic targets. While the pathophysiology of MM is poorly understood, the substantial responsiveness of MM patients to proteasomal inhibitors (PIs) like bortezomib or carfilzomib hints towards a central role of the ubiquitin proteasome system (UPS). Deubiquitylases (DUBs) are therapeutically targetable components of the UPS, whose inhibition can destabilize oncoproteins. However, the identities of oncoprotein-regulating DUBs remain largely elusive. To identify new vulnerabilities in MM, a CRISPR/Cas9 screen targeting all human DUBs was performed. For validated candidates, phenotypical analysis regarding proliferation and cell cycle progression was performed, as well affinity and non-affinity mass spectrometry-based screens to identify substrates. We thereby identified OTUD6B as a novel oncogene that drives G1/S-transition. LIN28B, a suppressor of microRNA biogenesis, was delineated as both a cell cycle-specific deubiquitylation substrate and activator of OTUD6B. RNA-Seq and qPCR analyses of OTUD6B and LIN28B depleted MM cells revealed that the stabilization of LIN28B drives MYC expression and activity at the G1/S transition, which in turn allows for rapid S-phase entry. Thus, silencing of OTUD6B as well as LIN28B inhibited MM outgrowth in xenograft experiments. Analyses of large MM patient cohorts revealed a progressive increase of OTUD6B expression along the transition from normal plasma cells to MGUS to MM and that high expression of OTUD6B was associated with a significantly adverse overall survival. Furthermore, OTUD6B expression was found to strongly correlate with MYC expression and significantly reduced progression-free survival in patients treated with the PI bortezomib. Knockout of OTUD6B in MM cells significantly enhance the anti-myeloma activity of the drug when using sub-lethal doses. Together, these results validate OTUD6B as a new therapeutically targetable oncogene, dependency, and prognostic factor in MM, that eventually serves as a master regulator of MYC activity to drive cell cycle progression.
Citation Format: Ria Spallek, Carmen Paulmann, Oleksandra Karpiuk, Jana Zecha, Susan Klaeger, Isabell Schaeffer, Rupert Öllinger, Thomas Engleitner, Jan Krönke, Matthias Wirth, Ullrich Keller, Roland Rad, Bernahrd Kuster, Florian Bassermann. OTUD6B is a dependency in multiple myeloma that drives S-phase entry via MYC activation [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 2298.
Abstract 2302: The pan-cancer regulator of the mutant TERT promoter and a new model of the GABP-TERT axis
Authors: Stevers Nicholas O. , Barger Carter , Lenzo Olivia , Hong Chibo , Soczek Katarzyna , Wu Samuel H. , McKinney Andrew M. , Suwala Abigail , Doudna Jennifer A. , Costello Joseph F. 
Published: June 2022

Abstract
Ninety percent of human tumors reactivate telomerase reverse transcriptase (TERT) to achieve cellular immortality. The route to immortality found in over 50 cancer types is mutation of the TERT promoter (TERTp) mutations. Studies in glioblastoma have shown the two most common TERTp mutations, G228A and G250A, reactivate TERT expression through de novo E26 transformation specific (ETS) site generation that, in tandem with a native TERTp ETS site, recruits the tetrameric GA-binding protein (GABP) complex formed by two GABP alpha (GABPA) subunits and two tetramer specific GABPB1 (B1) subunits, GABPB1L (B1L). While ten additional TERTp mutations have been described across cancer types, functional studies have been limited to select mutations and cancer types. We found that each de novo ETS motif generating TERTp mutation increases TERTp transcriptional activity in a GABP-dependent manner. Furthermore, our pan-cancer analysis demonstrated selective enrichment of GABPA at the mutant TERTp across 14 cancer types and further determined that this recruitment is necessary for TERT expression. Prior investigations found that CRISPR-cas9 mediated mutagenesis of the B1 ninth exon, specific to B1L, reduces TERT transcriptional activity in a TERTp-mutation dependent manner. We explored B1L targeting in the reversal of tumor cell immortality in several cancers. We found that the B1 dimer restricted isoform, GABPB1S (B1S), is consistently and significantly increased following B1L reduction, which we determined to be the consequence of a disengagement of a GABP tetramer mediated negative feedback loop acting on the B1 promoter. Interestingly, this upregulated B1S expression enables GABP dimer binding and activation of the mutant TERTp thereby compensating for B1L loss. Indeed, knockout of B1L and B1S together resulted in a near complete elimination of GABPA TERTp recruitment and a striking reduction in TERT expression, leading to telomere shortening and ultimately resulting in tumor cell death and senescence. This data identifies GABP as the master regulator of the mutant TERTp across cancer type and de novo ETS mutation type and suggests a new model of the GABP-TERT axis involving both the GABP tetramer, and the GABP dimer.
Citation Format: Nicholas O. Stevers, Carter Barger, Olivia Lenzo, Chibo Hong, Katarzyna Soczek, Samuel H. Wu, Andrew M. McKinney, Abigail Suwala, Jennifer A. Doudna, Joseph F. Costello. The pan-cancer regulator of the mutant TERT promoter and a new model of the GABP-TERT 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 2302.
Abstract 2313: Fenbendazole induces cell cycle arrest in colorectal cancer cells and patient-derived colon cancer organoids
Authors: Kang Kyung-Sun , Kim Da-Hyun 
Published: June 2022

Abstract
Colorectal cancer is one of leading cause of cancer-related deaths. Therefore, there have been various attempts to cure the cancer by developing new efficient anti-cancer therapy in addition to surgical resection and chemotherapy. In this study, we investigated the effects of fenbendazole, an anti-helminthic drug, both colon cancer cells and patient-derived colon tumor organoids. Notably, we employed 3D tumor organoid models because 2D-cultured cell lines were not able to recapitulate the physiology of solid tumors. We first observed that treatment of fenbendazole to colon cancer cells induced apoptosis within 24 hours, which was extended for a long-term. We revealed that fenbendazole markedly suppressed proliferation rate via cell cycle arrest. Cell cycle progression is elaborately regulated by multiple genes, such as cyclins and cyclin-dependent kinases (CDKs). From a screening of cell cycle-related factors, we found that the protein levels of CDK1 phosphorylated at Tyr15 and cyclin B1 which was known to regulate M phase transition, were drastically downregulated when the tumor cells were exposed to fenbendazole. Next, colorectal tumor-bearing mouse model was established using AOM/DSS. Oral administration of fenbendazole into the mouse not only reduced the number of tumor cells but also lowered tumor grades. Overall, our study suggested a possibility that fenbendazole could be applied for anti-cancer therapy by targeting cell cycle arrest.
Citation Format: Kyung-Sun Kang, Da-Hyun Kim. Fenbendazole induces cell cycle arrest in colorectal cancer cells and patient-derived colon cancer organoids [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 2313.
Abstract 2324: Small-scale microwave-assisted acid hydrolysis method for glycogen determination and turnover in tumors using Stable Isotope Resolved Metabolomics
Authors: Lane Andrew N. , Scott Timothy L. , Zhu Juan , Cassel Teresa A. , Vicente-Munoz Sara , Lin Penghui , Higashi Richard M. , Fan Teresa W-M 
Published: June 2022

Abstract
Introduction: Glycogen is a readily deployed intracellular energy storage macromolecule composed of branched chains of glucose. Although glycogen primarily occurs in the liver and muscle, it can be found in most tissues throughout the body, and its metabolism has been shown to be important in cancers and immune cells. Robust analysis of glycogen turnover requires stable isotope tracing plus a reliable means of quantifying total and labeled glycogen derived from precursors such as 13C6-glucose. Current methods for analyzing glycogen are time- and sample-consuming, at best semi-quantitative, and unable to measure stable isotope enrichment.
Methods: We have developed a microscale method for quantifying both intact and acid-hydrolyzed glycogen by ultra-high-resolution Fourier transform mass spectrometric (UHR-FTMS) and/or NMR analysis in stable isotope resolved metabolomics (SIRM) studies. Polar metabolites, including intact glycogen and their 13C positional isotopomer distributions were first measured in crude biological extracts by high resolution NMR, followed by rapid and efficient acid hydrolysis to glucose in 1 N HCl for 10 minutes at 110 °C under a N2 atmosphere in a microwave-assisted synthesis reactor. The resulting glucose and its 13C isotopologues were then analyzed by UHR-FTMS and/or NMR.
Results: We optimized the microwave digestion time, temperature, and oxygen purging in terms of recovery versus degradation and found 10 minutes at 110-115 °C to give &gt; 90% recovery. The method was applied to track the fate of 13C6-glucose in primary human lung BEAS-2B cells, human macrophages, murine liver and patient-derived tumor xenograft (PDTX) in vivo, and the fate of 2H7-glucose in ex vivo lung organotypic tissue cultures of a lung cancer patient. We showed the incorporation of 13C6-glucose into glycogen and its metabolic intermediates, UDP-Glucose and glucose-1-phosphate, both in terms of the 13C levels and fractional enrichment, thereby demonstrating the utility of the method in tracing glycogen turnover in cells and tissues.
Conclusions: The method offers a quantitative, sensitive, and convenient means to analyze glycogen turnover in mg amounts of complex biological materials.
Keywords: glycogen turnover; 13C6-glucose, stable isotope resolved metabolomics (SIRM); microwave-assisted hydrolysis.
Citation Format: Andrew N. Lane, Timothy L. Scott, Juan Zhu, Teresa A. Cassel, Sara Vicente-Munoz, Penghui Lin, Richard M. Higashi, Teresa W-M Fan. Small-scale microwave-assisted acid hydrolysis method for glycogen determination and turnover in tumors using Stable Isotope Resolved Metabolomics [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 2324.