bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 5732: p53 deficiency causes Myc dysregulation through a novel TGFβ-facilitated promoter switching mechanism to instigate osteosarcoma development
Authors: Date Yuki , Ueno Tomoya , Ito Kosei 
Published: June 2022

Abstract
p53 deficiency and Myc dysregulation, driven by genetic and epigenetic alterations, respectively, are frequently associated with cancer. Previously, we reported that the combination of p53 inactivation and Myc overexpression, mediated by Runx transcription factors (TFs), leads to osteosarcoma (OS), the most common primary bone cancer. However, the mechanisms leading to Myc upregulation by Runx in a p53-deficient microenvironment remain unclear.
TGFβ is a main driver of the epithelial-to-mesenchymal transition and its signal-dependent TFs, Smads, are known to associate with lineage-determining TFs including Runx. As TGFβ paracrine signalling is reportedly increased during human OS development, we immunodetected increased co-expression of TGFβ and phospho-Smad2 in the bone marrow of osteoprogenitor-specific p53 knockout mice, Osterix (Osx)/Sp7-Cre; p53fl/fl mice, which are widely used as an animal model of human OS. Heterozygous deletion of the type II TGFβ receptor in those mice weakened their susceptibility to OS, phenocopying the overall life-extending effect of Myc depletion in the same model.
p53 disruption caused TGFβ to aberrantly induce Myc in osteoprogenitors, rendering the cells tumorigenic upon transplantation into immunocompromised mice. Within the 3-Mb Myc regulatory region, we identified a TGFβ-responsive element dubbed m340, which contains binding sites for multiple TFs including Runx. The m340 enhancer caused Myc upregulation upon p53 disruption by switching its associated promoter from the lncRNA Pvt1 to Myc. In support of this promoter switching mechanism, a specific disruption of the evolutionarily conserved p53 site within the Pvt1 promoter recapitulated TGFβ-induced Myc overexpression. At m340, TGFβ promoted its occupancy by a transcriptional complex consisting of Runx, its cooperative factors Smads and AP1, and CBP, further activating the enhancer by increasing H3K27ac deposition. Runx inhibition not only repressed the aberrant upregulation of Myc by reducing Smad occupancy at m340, but also suppressed OS development in vivo.
These results suggest that p53 deficiency causes Myc dysregulation through a novel promoter switching programme that is facilitated by TGFβ signalling and reveals a novel epigenetic mechanism underlying the interaction between cancer-predisposing genetic alterations (p53 deficiency) and environmental cues (TGFβ) in tumorigenesis. Considering the mediating role Runx plays in m340 activation, our study may provide a clinical rationale for targeting Runx in p53-deficient malignancies.
Citation Format: Yuki Date, Tomoya Ueno, Kosei Ito. p53 deficiency causes Myc dysregulation through a novel TGFβ-facilitated promoter switching mechanism to instigate osteosarcoma development [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 5732.
Abstract 5784: Overcoming FFPE hurdles to enable high quality hybrid capture libraries and somatic mutation detection in matched tumor-normal patient samples
Authors: Heider Margaret R. , Sun Jian , Sexton Brittany S. , Langhorst Bradley W. , Gray Andrew , Higgins Lauren , Chen Lixin , Apone Lynne , Evans Thomas C. , Nichols Nicole M. , Dimalanta Eileen T. , Davis Theodore B. , Liu Pingfang 
Published: June 2022

Abstract
In cancer genomics, a common source of DNA is formalin-fixed, paraffin-embedded (FFPE) tissue from patient surgical samples, where in most cases high quality fresh or frozen tissue samples are not available. FFPE DNA poses many notable challenges for preparing NGS libraries, including low input amounts and highly variable damage from fixation, storage, and extraction methods. Due to the high cost of sequencing and variability of coverage, regions of interest are often specifically enriched using hybrid capture-based approaches, but these methods require a high input of diverse, uniform DNA library to achieve the coverage required for somatic mutation identification in tumor samples.We applied a multi-faceted approach to improving the yield, quality, and coverage from libraries generated from cancer patient sample sets. Using tumor-normal pairs, we evaluated the impact of our method on the sensitivity and accuracy of somatic variant detection. Matched frozen tissue provided a truth set of somatic variants for a particular tumor as well as a gold standard by which we could assess the quality of our FFPE hybrid capture libraries. Combining DNA damage repair and a novel enzymatic fragmentation mix upstream of library preparation not only reduced the false positive rate in somatic variant detection by repairing damage-derived mutations but also improved the library yield, complexity, coverage uniformity, and hybrid capture library quality metrics. The use of unique molecular identifier (UMI)-containing adaptors ensured accurate duplicate marking. Finally, a new PCR master mix boosts the library yield without compromising library quality in FFPE samples ranging from very poor quality to high quality. This combinatorial approach allows even the poorest quality FFPE samples to achieve high quality libraries with sufficient input for hybrid capture in our study.
Citation Format: Margaret R. Heider, Jian Sun, Brittany S. Sexton, Bradley W. Langhorst, Andrew Gray, Lauren Higgins, Lixin Chen, Lynne Apone, Thomas C. Evans, Nicole M. Nichols, Eileen T. Dimalanta, Theodore B. Davis, Pingfang Liu. Overcoming FFPE hurdles to enable high quality hybrid capture libraries and somatic mutation detection in matched tumor-normal patient samples [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 5784.
Abstract 5791: Microfluidics-based library preparation strategies for targeted high-throughput sequencing and RNA sequencing in hematological malignancies in clinical samples
Authors: Pastoret Cédric , Aliouat Amyra , Boulland Marie-Laure , Denoual Florent , Desmares Anne , De Tayrac Marie , Fest Thierry , Letellier Celeste 
Published: June 2022

Abstract
Introduction We developed a unique panel of 54 target genes dedicated to hematological malignancies (HematoPanel) and screened 1,108 clinical samples. We also performed transcriptomic analysis and evaluated its relevance for patients with acute lymphoblastic leukemia (ALL).
Methods DNA and RNA were extracted from cell pellets with the Maxwell® RSC (Promega®). Libraries for targeted high-throughput DNA sequencing (HTS) were generated in duplicate from 100 ng with the Advanta™ NGS Library Prep Assay kit using the LP 48.48 IFC (integrated fluidic circuit) on a Juno™ and sequenced on the NextSeq™ 550 (Illumina®) to a median depth of coverage of approximately 1,200X per sample. Transcriptomic libraries were generated from 50 ng RNA with the Advanta RNA-Seq XT NGS Library Prep Kit using the LP 48.Atlas™ IFC on Juno and sequenced on the NextSeq 550. A bioinformatics pipeline was developed for fusion transcript detection. Differential gene expression was analyzed with the DESeq2 package after STAR alignment.
Results In 2020 we sequenced 1,108 consecutive samples in routine practice with HematoPanel. The main indications were the suspicion of myeloproliferative neoplasms (32%), the evaluation of chronic lymphocytic leukemia (23%), and the diagnostic workup of cytopenias (15%). We detected 1,306 mutations in 654 patients (59%) (1 to 8 mutations per sample). Eight genes (TET2, SF3B1, TP53, DNMT3A, ASXL1, JAK2, SRSF2 and MYD88) were reported as mutated for more than 50 patients. We sequenced 22 samples including the MOLT-4 cell line, healthy donor samples, and 16 ALL samples for transcriptomic evaluation. From ALL samples, we detected 5 fusion transcripts previously identified by specific PCR (1 BCR-ABL, 2 ETV6-RUNX1, 1 KMT2A-AFF1, 1 TCF3-PBX1). Moreover, we detected 4 other fusion transcripts for 3 patients (EBF1-PDGFRB, FGFR1-MYO18A, P2RY8-CRLF2, and PAX5-NOL4L). Interestingly, these patients clustered with the BCR-ABL positive sample based on their expression profile. It confirms the diagnosis of Phi-like ALL and thus offers a therapeutic target for these patients.
Conclusion Microfluidics-based library prep using Juno offers a cost-effective strategy and straightforward workflows for both targeted HTS and RNA sequencing. We validated its use for hematological malignancy evaluation in routine practice.
Citation Format: Cédric Pastoret, Amyra Aliouat, Marie-Laure Boulland, Florent Denoual, Anne Desmares, Marie De Tayrac, Thierry Fest, Celeste Letellier. Microfluidics-based library preparation strategies for targeted high-throughput sequencing and RNA sequencing in hematological malignancies in clinical samples [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 5791.
Abstract 5806: Mieap forms membraneless organelles to compartmentalize and facilitate cardiolipin metabolism
Authors: Ikari Naoki , Nakamura Yasuyuki , Arakawa Hirofumi 
Published: June 2022

Abstract
Liquid droplets function as membraneless organelles that compartmentalize and facilitate efficient biological reactions. They are formed by proteins with intrinsically disordered regions (IDRs) via liquid-liquid phase separation. Mieap/SPATA18, a p53-inducible protein, participates in suppression of colorectal tumors by promoting mitochondrial quality control. However, the regulatory mechanism involved remains unclear. Here, we report that Mieap is an IDR-containing protein that drives formation of liquid droplets in mitochondria. Mieap liquid droplets specifically phase separate the mitochondrial phospholipid, cardiolipin. Lipidomic analysis of cardiolipin suggests that Mieap promotes enzymatic reactions involved in cardiolipin metabolism, including biosynthesis and remodeling. Accordingly, four cardiolipin biosynthetic enzymes, TAMM41, PGS1, PTPMT1, and CRLS1, and two remodeling enzymes, PLA2G6 and TAZ, are phase-separated by Mieap liquid droplets. Mieap-deficient mice exhibit altered crista structure in mitochondria of various tissues, including brown fat, and tend to become obese. These results suggest that Mieap drives formation of membraneless organelles to compartmentalize and promote cardiolipin metabolism at the inner mitochondrial membrane, thus potentially contributing to mitochondrial quality control.
Citation Format: Naoki Ikari, Yasuyuki Nakamura, Hirofumi Arakawa. Mieap forms membraneless organelles to compartmentalize and facilitate cardiolipin metabolism [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 5806.
Abstract 5812: Histone deacetylase 10 supports tumor growth under polyamine-limiting conditions
Authors: Stewart Tracy Murray , Steimbach Raphael R. , Foley Jackson R. , Miller Aubry K. , Casero Robert A. 
Published: June 2022

Abstract
Cytosolic histone deacetylase 10 (HDAC10) is specifically deacetylates the modified polyamine N8-acetylspermidine (N8-AcSpd). Although intracellular concentrations of N8-AcSpd are low, extracellular sources can be abundant, particularly in the colonic lumen. Extracellular polyamines, including those from the diet and microbiota, can support tumor growth both locally and at distant sites. However, the contribution of N8-AcSpd is unknown. We hypothesized that HDAC10, by converting N8-AcSpd to spermidine, may provide a source of this growth-supporting polyamine in circumstances of reduced polyamine biosynthesis, such as in polyamine-targeting, anticancer therapies. Inhibitors of polyamine biosynthesis, such as difluoromethylornithine (DFMO), inhibit tumor growth but with compensatory uptake of extracellular polyamines that have limited their clinical success. Combining DFMO with inhibitors of polyamine uptake have improved the antitumor response. However, acetylated polyamines may use different transport machinery than the parent molecules. The current study uses CRISPR/Cas9-mediated HDAC10-knockout cell lines and recently developed, selective HDAC10 inhibitors to investigate the contribution of HDAC10 in maintaining tumor cell proliferation. Inhibition of cell growth by DFMO-associated polyamine depletion is successfully rescued by the provision of physiological concentrations of exogenous N8-AcSpd, which is converted to spermidine and spermine, only in cell lines with HDAC10 activity. Loss of HDAC10 prevents both restoration of polyamine levels and growth rescue, implicating HDAC10 in supporting polyamine-associated tumor growth. These data suggest the utility of HDAC10-specific inhibitors as an antitumor strategy that may have particular value in improving the response to polyamine-blocking therapies.
Citation Format: Tracy Murray Stewart, Raphael R. Steimbach, Jackson R. Foley, Aubry K. Miller, Robert A. Casero. Histone deacetylase 10 supports tumor growth under polyamine-limiting conditions [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 5812.
Abstract 5815: Metabolomics in an Apc-mutant genetic background: Mechanistic insights from acute vs. chronic spinach intake
Authors: Neja Sultan , Dashwood Roderick H. 
Published: June 2022

Abstract
There is growing interest in the crosstalk between the gut microbiome, metabolomic features, and disease pathogenesis. Colorectal cancer is a major health burden worldwide, linked in part to modifiable risk factors associated with diet and lifestyle (1). The current investigation compared long-term (26 week) and acute (3 day) dietary spinach intake in a genetic model of colorectal cancer. Metabolomic analyses in the polyposis in rat colon (Pirc) model and in wildtype animals corroborated key contributions to anticancer outcomes by spinach-derived linoleate bioactives and a butanoate metabolite linked to increased α-diversity of the gut microbiome (2). Combining linoleate and butanoate metabolites in human colon cancer cells revealed enhanced apoptosis and reduced cell viability, paralleling the apoptosis induction observed in colon tumors from rats given long-term spinach treatment. Mechanistic studies indicated reactivation of immune-associated major histocompatibility complex genes in cell-based assays and in vivo, plus differential roles of the metabolites in targeting Wnt/β-catenin signaling (3). Clinical translation of the findings from this investigation to at-risk patients might provide valuable quality-of-life benefits by delaying surgical interventions and drug therapies with adverse side effects (4,5).
References1.Xi, Y., Xu, P. Global colorectal cancer burden in 2020 and projections to 2040. Transl Oncol 2021;14: 1011741.Chen, Y.-S. et al. Dietary spinach reshapes the gut microbiome in an Apc-mutant genetic background: mechanistic insights from integrated multi-omics. Gut Microbes 2021;13:1972756. 1.Liu, F. et al. Suppression of membranous LPR5 recycling, Wnt/β-catenin signaling, and colon carcinogenesis by 15-LOX-1 peroxidation of linoleic acid in PI3P. Cell Rep 2020;32:108049.1.Ulusan, A.M. et al. Optimization of erlotinib plus sulindac dosing regimens for intestinal cancer prevention in an Apc-mutant model of Familial Adenomatous Polyposis (FAP). Cancer Prev Res (Phila) 2021;14:325-336.1.Samadder, N.J. et al. Association of sulindac and erlotinib vs placebo with colorectal neoplasia in Familial Adenomatous Polyposis: secondary analysis of a randomized clinical trial. JAMA Oncol 2018:4:671-677.
Citation Format: Sultan Neja, Roderick H. Dashwood. Metabolomics in an Apc-mutant genetic background: Mechanistic insights from acute vs. chronic spinach intake [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 5815.
Abstract 5816: Serum metabolomic profile of exposure to hair dye
Authors: Lim Jungeun , Huang Jiaqi , Weinstein Stephanie J. , Albanes Demetrius 
Published: June 2022

Abstract
Hair dye products now represent one of the most rapidly growing beauty and personal care industries. The association between hair dye use and the development of cancer has been a research focus, including for breast, prostate, and bladder cancer, yet biological mechanisms have not been established. In this first examination of metabolomic response to hair dye exposure, we compared the serum metabolite profiles of male hair dye users and nonusers to identify differences related to biological mechanisms relevant to how exposure may influence cancer risk. The Alpha-Tocopherol, Beta-Carotene Cancer Prevention (ATBC) Study was a randomized, controlled cancer prevention trial of vitamin supplementation that enrolled 50–69-year-old Finnish male smokers of whom 75 hair dye users and 125 nonusers were studied. Ultrahigh performance liquid chromatography-tandem mass spectrometry was used to assay baseline serum samples, and the difference in log-transformed, batch-normalized metabolite signals between the exposed and unexposed men was estimated using linear regression, adjusting for age, body mass index, and smoking. We measured 1,401 metabolites, of which 11 compounds, including 4 amino acids and 3 xenobiotics, differed significantly between the two groups after correction for multiple comparisons (FDR&lt;0.1). Redox-related glutathione metabolism was heavily represented, including cysteineglutathione disulfide which showed the strongest association with hair dye use (effect size (β) = -0.685; p&lt;0.0001), along with oxidized cysteine-glycine (β = -0.325; p&lt;0.0001) and several compounds relevant to antioxidation/ROS pathways. Metabolites previously associated with prostate cancer risk also differed significantly between hair dye user and non-users. Our findings point to biological mechanisms through which exposure to hair dyes may impact risk of prostate and other cancers.
Citation Format: Jungeun Lim, Jiaqi Huang, Stephanie J. Weinstein, Demetrius Albanes. Serum metabolomic profile of exposure to hair dye [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 5816.
Abstract 5817: Exosomal miR-4466 from nicotine-activated neutrophils promotes tumor cell stemness & metabolism in brain metastasis
Authors: Tyagi Abhishek , Wu Shih-Ying , Sharma Sambad , Wu Kerui , Zhao Dan , Deshpande Ravindra , Watabe Kounosuke 
Published: June 2022

Abstract
Smoking is associated with lung cancer and has a profound impact on tumor immunity. Nicotine, the addictive and non-carcinogenic smoke component, influences various brain cells and the immune system. However, little is known how long-term use of nicotine affects clinical outcomes in patients with brain metastasis. To address this question, we conducted a retrospective analysis of 810 lung cancer patients with smoking history and assessed brain metastasis. We found that lung cancer patients of current smokers have significantly higher brain metastatic incidence compared to the never-smokers. Immune profiling of the brain metastatic lesions among smokers showed predominant infiltration of neutrophils compared to never-smokers. Notably, mice pre-exposed to nicotine showed a significantly increased number of neutrophils in the brains even before implantation of cancer cells (pre-metastatic niche), and their numbers progressively increased during the metastatic stage. Neutrophil depletion during metastatic colonization caused a remarkable decrease in brain metastasis. Furthermore, we found that chronic exposure of nicotine recruited STAT3-activated N2-neutrophils that secreted exosomal miR-4466 in the brain. This pre-metastatic niche promoted stemness and metabolic switching via SKI/SOX2/CPT1A axis in the tumor cells thereby enabling brain metastasis. Importantly, exosomal miR-4466 levels were found to be elevated in serum/urine of cancer-free subjects with a smoking history and promote tumor growth in vivo, suggesting that exosomal miR-4466 may serve as a promising prognostic biomarker for predicting increased risk of metastatic disease among smoker(s). Our findings suggest a novel pro-metastatic role of nicotine-induced N2-neutrophils in the progression of brain metastasis. We also demonstrated that inhibiting nicotine-induced STAT3-mediated neutrophil polarization effectively abrogated brain metastasis in vivo. Our finding for the first time provides compelling evidence related to the mechanism(s) of neutrophil-mediated brain metastasis that arises from nicotine use. Our results also identified a potential prognostic biomarker for the onset of metastasis as a risk-reduction measure in lung cancer patients and implicated the risk of using nicotine gateway for smoking cessation in cancer patients with a smoking history.
Citation Format: Abhishek Tyagi, Shih-Ying Wu, Sambad Sharma, Kerui Wu, Dan Zhao, Ravindra Deshpande, Kounosuke Watabe. Exosomal miR-4466 from nicotine-activated neutrophils promotes tumor cell stemness & metabolism in brain metastasis [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 5817.