bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 2962: The oncogenic role of epigenetic factor, SNF2L in PCa
Authors: Brown LaKendria K. , Li Guoliang , Kanagasabai Thanigaivelan , Chen Zhenbang 
Published: June 2022

Abstract
Prostate cancer (PCa) is the second-leading cause of cancer mortality in the United States and is the most commonly diagnosed malignancy in African American men. Epigenetic regulation including chromatin remodeling plays a crucial role in the development and progression of many human diseases such as cancers. Epigenetic alterations contribute to the development and progression of PCa. These alterations may cause drug resistance to readily available treatment options for human cancers including PCa. Nucleosome-remodeling factor (NURF) consists of bromodomain-PHD finger transcription factor (BPTF), sucrose non-fermenting-2-like (SNF2L), and pRBAP46/48, controls the chromatin remodeling machinery. One of NURF’s major function is to regulate histone modifications and gene expression. Epigenetic factor, SNF2L, serves as the energy transducing subunit in NURF and is encoded by the SMARCA1 gene. SNF2L is a ubiquitously expressed transcription activator and its elevation is associated with cancer development. However, the role of SNF2L on PCa progression is still elusive. Therefore, there are unmet needs to understand the role of SNF2L in PCa in order to develop effective therapeutic approaches of controlling this malignancy. The objective of this project is to assess the impact of SNF2L loss on PCa progression. We hypothesized that SNF2L knockout (KO) will inhibit the proliferation of androgen-sensitive and castration-resistant PCa cells and targeting SNF2L or SMARCA-1 gene may be beneficial for controlling cancer progression. We have generated SNF2L KO PCa cells with CRISPR-Cas9 technology and inhibited SMARCA-1 gene via transient transfection application. Our results showed that SNF2L loss resulted in a reduced proliferation and altered morphology of PCa cells. SNF2L KO destabilizes the NURF complex and impairs chromatin remodeling and histone modifications for cell growth and survival. Thereby, targeting SNF2L may serve as a novel therapeutic regime in PCa control.
Citation Format: LaKendria K. Brown, Guoliang Li, Thanigaivelan Kanagasabai, Zhenbang Chen. The oncogenic role of epigenetic factor, SNF2L in PCa [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 2962.
Abstract 2968: Interrogating the function of histone methyltransferases in MYC-driven medulloblastoma
Authors: Mercier Audrey L. , Stripay Jennifer L. , Bilokapic Silvija , Williams Justin , Nance Stephanie , Liu Jingjing , Philips Steven , Kandikonda Suresh , Morfouace Marie , Bramoulle Aude , Advedissian Tamara , Yu Jiyang , Peng Junmin , Ansari Aseem , Halic Mario , Durbin Adam , Vakoc Christopher , Roussel Martine F. 
Published: June 2022

Abstract
Medulloblastoma (MB) is the most common malignant pediatric brain tumor of the cerebellum, with four distinct molecular subgroups, each carrying different clinical prognoses. Group 3 (G3) is the most aggressive subgroup and is associated with amplifications of the MYC gene. MYC expression and function are controlled in part by epigenetic regulation, and interestingly, the few mutations that are found in G3 medulloblastoma are mostly located in genes encoding epigenetic regulators. Surprisingly, many tumors had no mutations raising the question as to whether non-mutated or non-amplified epigenetic regulators may be drivers of G3MB tumorigenesis. We previously found that dysregulation of the H3K27 methyltransferase EZH2 cooperates with MYC in G3MB, indicating that epigenetic regulators may provide a source of potential therapeutic targets. Therefore, to identify novel epigenetic drivers in G3MB, we performed an unbiased shRNA screen of 243 known chromatin regulators. The most intriguing candidate was SMYD3, a multidomain-containing protein with histone H4-lysine 5 (H4K5) methyltransferase activity. Knockdown of SMYD3 suppressed G3MB proliferation in vitro and tumor progression in vivo. SMYD3 protein is nuclear and associated with the MYC promoter. Deletion of SMYD3 results in loss of MYC, G2/M and epithelial-to-mesenchymal target gene expression. Using a multi-omics approach including CUT&RUN sequencing, RNA-seq, DNA methylation, cryo-electron microscopy (cryo-EM) and proteomics we aim to elucidate how SMYD3 controls G3MB tumorigenesis. These results highlight the role of a potentially targetable new epigenetic regulator of tumorigenesis in G3MB.
Citation Format: Audrey L. Mercier, Jennifer L. Stripay, Silvija Bilokapic, Justin Williams, Stephanie Nance, Jingjing Liu, Steven Philips, Suresh Kandikonda, Marie Morfouace, Aude Bramoulle, Tamara Advedissian, Jiyang Yu, Junmin Peng, Aseem Ansari, Mario Halic, Adam Durbin, Christopher Vakoc, Martine F. Roussel. Interrogating the function of histone methyltransferases in MYC-driven medulloblastoma [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 2968.
Abstract 3026: Inhibition of glutaminolysis overcomes metabolic adaptation to devimistat treatment
Authors: Lang Liwei , Wang Fang , Shay Chloe , Ke Yonggang , Saba Nabil , Teng Yong 
Published: June 2022

Abstract
The identification and development of reagents that can limit preferential metabolic effectors in tumors as well as trigger unfavorable tumoral metabolic cues is of tremendous importance for suppressing malignancy. However, insufficient blocking of critical metabolic dependencies of cancer allows the development of metabolic bypasses, which significantly dampens therapeutic benefits of selective agents that target a single metabolic enzyme or pathway. We report here that head and neck squamous cell carcinoma (HNSCC) cells display strong addiction to glutamine. Devimistat, a novel lipoate analog, redirects cellular activity towards tumor-promoting glutaminolysis, leading to low anticancer efficacy in HNSCC cells. Mechanistically, devimistatinhibits the tricarboxylic acid cycle by blocking the enzyme activities of pyruvate dehydrogenase and alpha-ketoglutarate dehydrogenase, which upregulates GLS1 and eventually promotes the compensatory role of glutaminolysis in cancer cell survival. Most importantly, the addition of a GLS1 inhibitor CB-839 to devimistat treatment abrogates the metabolic dependency of HNSCC cells on glutamine, achieving a synergistic anticancer effect in glutamine-addicted HNSCC. These novel and significant findings could lay a scientific foundation for developing more effective treatments targeting the metabolic requirements of HNSCC.
Citation Format: Liwei Lang, Fang Wang, Chloe Shay, Yonggang Ke, Nabil Saba, Yong Teng. Inhibition of glutaminolysis overcomes metabolic adaptation to devimistat treatment [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 3026.
Abstract 3031: Impact of pyruvate kinase isoforms on cysteine metabolism in pancreatic cancer
Authors: Ensink Elliot , Lunt Sophia Y. 
Published: June 2022

Abstract
Pancreatic cancer cells undergo metabolic alterations to survive within a nutrient-depleted tumor microenvironment. Cysteine metabolism in particular is critical for supporting pancreatic cancer cell survival through its role in redox homeostasis. Targeting cysteine metabolism presents an underexplored opportunity for therapeutic exploitation, but much remains unknown about how cysteine metabolism is influenced by microenvironmental conditions and the overall metabolic state of the cell. One critical metabolic shift in pancreatic cancer cells occurs through altered isoform expression of the glycolytic enzyme, pyruvate kinase (PKM). Pancreatic cancer cells preferentially switch from the constitutively active M1 isoform to the allosterically regulated M2 isoform of PKM. Overexpression of PKM2 in pancreatic cancer cells produces a profound reprogramming of many metabolic pathways; however, the precise relationship between PKM isoform expression and cysteine metabolism is not well understood. We hypothesize that PKM isoform selection enables pancreatic cancer cell survival within a low cystine tumor microenvironment by reprogramming metabolic activity to increase cystine import and glutathione production and modulate glucose and glutamine metabolism to resist oxidative stress. We used lentiviral CRISPR-Cas9 vectors to genetically modify two human pancreatic ductal adenocarcinoma cell lines, AsPC-1 and Panc-1, to exclusively express either PKM1 or PKM2. We evaluated the effects of PKM isoform selection on tolerance of low cystine environments by assessing viability under a range of cystine concentrations (0 – 50 μM) reflective of physiologic and cystine starvation conditions. We observe altered viability and proliferation in PKM1 vs. PKM2 expressing cells under normoxic (21%) and hypoxic (1% O2) conditions. Targeted metabolomics using stable isotope labeling tracers further reveal impacts of PKM isoform expression in central carbon metabolism when cystine is limited. Additional experiments to elucidate the precise mechanism by which PKM isoform expression impacts pancreatic cancer cells are currently under investigation. This study provides valuable insight into the complexities of metabolic reprogramming within the tumor microenvironment and enhances our understanding of how cysteine metabolism could be targeted for the treatment of pancreatic cancer.
Citation Format: Elliot Ensink, Sophia Y. Lunt. Impact of pyruvate kinase isoforms on cysteine metabolism in 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 3031.
Abstract 3054: Pan-cancer characterization of the tumor mycobiome and its clinical effects
Authors: Haziza Lian Narunsky , Sepich-Poore Gregory D. , Livyatan Ilana , Asraf Omer , Martino Cameron , Nejman Deborah , Gavert Nancy , Stajich Jason E. , Amit Guy , González Antonio , Wandro Stephen , Perry Gili , Ariel Ruthie , Meltser Arnon , Shaffer Justin P. , Zhu Qiyun , Balint-Lahat Nora , Barshack Iris , Dadian Maya , Gal-Yam Einav N. , Pate Sandip P. , Bashan Amir , Swafford Austin D. , Pilpel Yitzhak , Knight Rob , Straussman Ravid 
Published: June 2022

Abstract
While the study of the tumor microbiome and its effects on cancer biology has expanded considerably over the last few years, most of this research focused on bacteria and viruses, leaving behind the fungal kingdom. Recently, a few studies have demonstrated that specific fungi may promote tumor progression, stressing the importance of comprehensively studying the tumor mycobiome and its effects. To address this, we have characterized the mycobiome in 1,183 human tumors and their adjacent tissues, originating from eight major solid tumor types. Staining and imaging demonstrated the presence of fungi in both cancer and immune cells, with tumor-type specific distribution patterns. Quantitative PCR of the fungal 5.8s rDNA revealed the presence of fungal DNA in all tumor types. To characterize the tumor mycobiome and address potential contamination during tissue handling and processing, we subjected all samples, as well as 295 negative controls of different types, to sequencing of the ITS2 region that is situated between fungal rRNA genes. We found cancer-type specific mycobial signatures with relatively high similarity between tumors and their adjacent tissues. While the fungal mycobiome had a lower species richness as compared to the bacterial microbiome of the same tumors, fungi showed significant co-occurrences with specific bacteria, suggesting the existence of ecological niches within the tumors. We also found significant correlations with clinical parameters such as patient’s age, tumor stage, progression-free survival, overall survival, and response to immune checkpoint blockade therapy. Characterization of the tumor mycobiome may add a biologically relevant, previously overlooked, component to be considered in the study of cancer, including its effects on tumor initiation, progression, diagnosis, and response to therapy.
Citation Format: Lian Narunsky Haziza, Gregory D. Sepich-Poore, Ilana Livyatan, Omer Asraf, Cameron Martino, Deborah Nejman, Nancy Gavert, Jason E. Stajich, Guy Amit, Antonio González, Stephen Wandro, Gili Perry, Ruthie Ariel, Arnon Meltser, Justin P. Shaffer, Qiyun Zhu, Nora Balint-Lahat, Iris Barshack, Maya Dadian, Einav N. Gal-Yam, Sandip P. Pate, Amir Bashan, Austin D. Swafford, Yitzhak Pilpel, Rob Knight, Ravid Straussman. Pan-cancer characterization of the tumor mycobiome and its clinical effects [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 3054.
Abstract 3060: Changes in mouse gut microbiome upon exposure to N-butyl-N-(4-hydroxybutyl) nitrosamine
Authors: Ginwala Rashida , Bukavina Laura , Franklin Jodie , Sindhani Mohit , Abbosh Philip 
Published: June 2022

Abstract
Background: BBN (N-butyl-N-(4-hydroxybuytl) nitrosamine), a closely related compound to the carcinogens found in tobacco smoke is an attractive and most commonly used agent to model bladder cancer in mice. BBN closely recapitulates the morphological characteristics of human bladder cancer and conceptually simulates tobacco exposure as the leading risk factor for bladder cancer. We employ the BBN model in mice to decipher the microbial changes that occur in the gut of the mice during the chemical carcinogenesis induced by BBN exposure.
Methods: Starting at 8-12 weeks of age, male (N=30) and female (N=21) C57BL/6 mice were administered 0.05% BBN in drinking water for 12 weeks then switched to regular water. Control mice drank regular water. Stool was collected pre-exposure, after 6 and 12 weeks of exposure, and at the time of tumor identification (tumors typically detectable between 14-22 weeks from start of treatment using this model). DNA extracted from stool was subjected to PCR amplification using primers for the V3-V4 regions of the bacterial 16S rRNA.
Results: Gender-based differences in the microbial composition were noted in response to BBN treatment. While gut microbial diversity in the female mice was markedly reduced (Shannon, Simpson, Inverse Simpson, and Richness) upon BBN treatment, that of male mice remained unchanged from baseline. Additionally, there was a distinct clustering of microbes based on sex (p=0.024) but not BBN exposure (p=0.86) as evidenced by principal coordinate analysis. Differences in the microbial composition were seen upon BBN exposure, with BBN mice showing an increase in Bacteroidales (53%), Lactobacillales (17.5%), Coriobacteriales (19.87%) in females and male mice exhibited an increase in Erysipelotrichales (14.76%) at the order level. On the other hand while male mice showed no significant decreases, female mice exhibited reduction in abundance of Clostridiales (log change -7.79, padj &lt;0.004), Veeruccomicrobiales (log change -2.21, padj&lt;0.005), and Bacillales (log -17.60, padj =0.005).
Conclusions: Pronounced gut microbial changes are induced by BBN in the murine model, with microbiome of the female mice exhibiting more significant variations compared to baseline, suggesting gender-based disparities in the effect of BBN exposure.
Citation Format: Rashida Ginwala, Laura Bukavina, Jodie Franklin, Mohit Sindhani, Philip Abbosh. Changes in mouse gut microbiome upon exposure to N-butyl-N-(4-hydroxybutyl) nitrosamine [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 3060.
Abstract 3062: Modifiable factors and gut microbiome alteration among colorectal cancer patients
Authors: Hoang Tung , Kim Min Jung , Park Ji Won , Jeong Seung-Yong , Lee Jeeyoo , Shin Aesun 
Published: June 2022

Abstract
Background: Previous study have indicated an association of microbial dysbiosis with stages of colorectal cancer (CRC). Meanwhile, higher microbial stochasticity has been introduced as the Anna Karenina principle (AKP) effect, which originates from the opening line of Leo Tolstoy and is translated in the microbiome as “all healthy microbiomes are similar; each dysbiotic microbiome is dysbiotic in its own way”. Here, we aim to elucidate the effect of modifiable factors on microbiome stochasticity related to dysbiosis in CRC.
Methods: Fecal samples from 331 CRC patients, were collected prior to their surgery at Seoul National University Hospital. Bacteria that were enriched in early- and late-stage CRC groups were identified by linear discrimination analysis effect size (LEfSE) method, which was then used to calculate microbial dysbiosis index (MDI). The association of dietary choices with microbiome variability was addressed using the LEfSE analysis. The difference of intra-sample similarity index among lifestyle factors and metabolic diseases was tested to examine the AKP effect. A tree-based analysis of food choices was constructed. We then applied Procrustes framework to analyze the shape of dietary diversity and microbiome.
Results: The LEfSE identified Leuconostoc, Oxalobacter, Acidaminococcus, and Methanobrevibacter were enriched in early-stage CRC, whereas Bacteroides, Fusobacterium, Lachnoanaerobaculum, Clostridium, and Granulicatella were enriched in late-stage CRC patients. The MDI derived from these bacteria had 64.2% predictive ability for CRC stages, with sensitivity and specificity of 61% and 69%, respectively. The AKP effect was found for history of smoking, alcohol consumption, and diabetes, whereas obesity and hypertension showed anti-AKP effect. For dietary choices, the hierarchical tree of foods and nutrients did not shape the microbial between-sample diversity. Additionally, high MDI was related with a high intake of pizza/hamburger, poultry, and light-vegetable combination.
Conclusion: Our study contributed to current evidence of the microbiome structure and dysbiosis at different stages of CRC. Furthermore, history of smoking, alcohol consumption, and diabetes showed AKP effect in CRC patients. Non-significant association between dietary choices and microbiome diversity supported a small variation of microbiome profiles explained by dietary intake at the population level.
Citation Format: Tung Hoang, Min Jung Kim, Ji Won Park, Seung-Yong Jeong, Jeeyoo Lee, Aesun Shin. Modifiable factors and gut microbiome alteration among colorectal cancer patients [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 3062.
Abstract 3078: A pipeline for functional precision medicine in bone and soft tissue sarcoma organoids
Authors: Al Shihabi Ahmad , Tebon Peyton J. , Chantharasamee Jomjit , Nguyen Huyen T. , Sartini Sara , Davarifar Ardalan , Tavanaie Nasrin , Nelson Scott D. , Federman Noah , Yanagawa Jane , Soragni Alice 
Published: June 2022

Abstract
Bone and soft tissue sarcomas span a spectrum of over one hundred histologic subtypes. Developing clinical trials and identifying effective therapies remains a challenge given the rarity of these tumors and scarcity of available tumor models. Patient-derived tumor organoids (PDTOs) are representative of the native physiology of tumors across an array of malignancies (Phan et al, 2019; Al Shihabi et al, 2021). For rare tumors such as bone and soft tissue sarcomas, PDTOs could constitute an important tool to better understand the biology of the disease and identify treatment options. Here, we present the pipeline we have established at UCLA to systematically procure tissue, develop and characterize individualized sarcoma PDTOs, and identify tumor sensitivities using high-throughput drug screening. We have collected tumor specimens from 114 patients diagnosed with sarcomas, representing more than 30 distinct subtypes of soft tissue and bone tumors. We have established suitable conditions to generate organoids from over 100 samples collected from needle biopsies, tumor resections, and metastasectomies, including soft tissue sarcomas (liposarcoma, undifferentiated pleomorphic sarcoma, leiomyosarcoma, etc.) and bone sarcomas (chondrosarcoma, osteosarcoma, Ewing sarcoma, etc.). We take advantage of our mini-ring technology to generate PDTOs in a format compatible with high-throughput drug screening (Phan et al, 2019; Nguyen et al, 2020). Our results highlight tumor-specific drug susceptibilities to chemotherapeutics, targeted agents, and combination therapies, generating results within a week from surgery. We will show how several of the organoid response patterns we identified transcend cancer subtype and patient characteristics. Our findings support the feasibility of rapidly generating individualized organoid models from bone and soft tissue sarcomas to facilitate biological interrogations and investigate response to treatment. Direct testing of PDTOs derived from clinical specimens can provide timely, actionable information for functional precision medicine approaches with the potential to improve patient outcomes.
Citation Format: Ahmad Al Shihabi, Peyton J. Tebon, Jomjit Chantharasamee, Huyen T. Nguyen, Sara Sartini, Ardalan Davarifar, Nasrin Tavanaie, Scott D. Nelson, Noah Federman, Jane Yanagawa, Alice Soragni. A pipeline for functional precision medicine in bone and soft tissue sarcoma 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 3078.