bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 2278: Expanding cancer therapy options by leveraging synthetic lethal interactions between druggable paralogs
Authors: Parrish Phoebe C. , Thomas James D. , Gabel Austin M. , Kamlapurkar Shriya , Bradley Robert K. , Berger Alice H. 
Published: June 2022

Abstract
Synthetic lethal therapies are a promising approach to expand therapeutic options for cancer patients. Since synthetic lethal therapies target tumor cells specifically, they have fewer off-target effects than oncogene targeted approaches. To identify new cancer drug targets, we focused on paralogs, ancestrally-duplicated genes that frequently retain redundant or overlapping functions.
To find synthetic lethal human paralogs, we developed paired guide RNAs for Paralog gENetic interaction mapping (pgPEN), a pooled CRISPR-Cas9 single and double knockout approach targeting over 2,000 paralogs. We applied pgPEN to two cancer cell lines and found that 12% of human paralogs exhibit synthetic lethality in at least one context. To our knowledge, pgPEN represents the largest experimental assessment of human paralog synthetic lethality to date.
We next identified paralog pairs to prioritize for follow-up study. A key drawback to synthetic lethal therapies is that many genetic interactions are context-dependent. To identify likely penetrant interactions, we compared our data to other published paralog screens and computational predictions of paralog synthetic lethality. We found that over 75% (n=96) of pgPEN hits were predicted to be broadly synthetic lethal, and nearly 10% (n=10) of pairs were synthetic lethal in multiple paralog screens.
Finally, we prioritized paralogs targeted by existing small molecule therapies. Of the 122 synthetic lethal pairs identified by pgPEN, 16% (n=20) are currently druggable. We mined drug repurposing data from DepMap to find pairs where a paralog-targeting drug showed a stronger effect in cell lines with low target gene copy number or expression relative to cell lines with normal target gene copy number or expression. These drugs could selectively target cancer cells in cases where one or both paralogs is lost in tumors but retained in normal tissue. We also leveraged The Cancer Genome Atlas tumor sequencing data to find paralog pairs where one member is recurrently lost in cancer.
Taken together, these studies identify druggable, highly penetrant synthetic lethal paralog interactions. In combination with tumor sequencing data, we identify high-priority paralog drug targets that can be further tested and translated to the clinic. Paralog synthetic lethal therapies could provide a relatively low-toxicity therapeutic approach to improve the efficacy of cancer treatments and prevent the emergence of acquired resistance.
Citation Format: Phoebe C. Parrish, James D. Thomas, Austin M. Gabel, Shriya Kamlapurkar, Robert K. Bradley, Alice H. Berger. Expanding cancer therapy options by leveraging synthetic lethal interactions between druggable paralogs [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 2278.
Abstract 2287: Dissecting the heterogeneity of central nervous system hemangioblastomas by single-cell and single-nuclei RNA sequencing
Authors: Konstantakou Eumorphia , Perez Elizabeth , Barbera Alex , Haradhvala Nicholas , Stanzione Marcello , Barker Fred , Nahed Brian , Stemmer-Rachamimov Anat , Dyson Nick , Getz Gad , Suva Mario , Iliopoulos Othon 
Published: June 2022

Abstract
Hemangioblastomas (HBs) are highly vascular tumors of the Central Nervous System that are commonly associated with the familial von Hippel-Lindau (VHL) disease and contribute significantly to the morbidity and mortality of VHL patients. They are characterized by high heterogeneity but the cell origin of HB tumors is still unclear, and the genomic landscape and signaling pathways underlying the tumor formation are unknown. We performed single-cell and single-nuclei RNA sequencing of cerebellar and spinal HBs surgically removed from VHL patients, in order to identify the lineage of the tumor cells and to profile the tumor microenvironment (TME). The percentage of VHL-/- tumor cells ranges from 8-80% of the cell population; the TME is reactive, contributing to a high percentage of the total tumor volume and playing a critical role in HB development. Single-cell and single-nuclei HB analysis provided significant insights into the cell of origin as well as the oncogenic pathways that drive the growth of HB. Whole exome sequencing (WES) in a cohort of HB patients revealed that biallelic VHL inactivation is necessary for the tumor formation of VHL disease-related HBs.
Citation Format: Eumorphia Konstantakou, Elizabeth Perez, Alex Barbera, Nicholas Haradhvala, Marcello Stanzione, Fred Barker, Brian Nahed, Anat Stemmer-Rachamimov, Nick Dyson, Gad Getz, Mario Suva, Othon Iliopoulos. Dissecting the heterogeneity of central nervous system hemangioblastomas by single-cell and single-nuclei RNA sequencing [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 2287.
Abstract 2310: Histone methyltransferase-independent function of EZH2 in the cell cycle regulation
Authors: Colon Tania Marlyn , Choi Byeong Hyeok , Dai Wei 
Published: June 2022

Abstract
Enhancer of zeste homologue 2 (EZH2) is an evolutionarily conserved histone methyltransferase that mediates the methylation of lysine 27 of histone H3 (H3K27me3). EZH2 is frequently mutated or overexpressed in many types of cancer. Extensive research in the past has revealed that EZH2 forms part of the polycomb repressive complex 2 (PRC2), an essential multi-protein complex required for gene silencing and chromatin compaction. EZH2 also displays additional cellular functions that include transcriptional activation of certain gene expression and methylation of non-histone substrates, the latter modulating protein stability or actin polymerization. Moreover, EZH2 is known to play a role in regulating cell cycle progression. However, it remains unclear whether EZH2 has an enzyme-independent function in the cell cycle. Here we show that EZH2 knockdown by small interfering RNAs (siRNAs) results in an increased expression of cyclin-dependent kinase inhibitors including p21, p27, and p57, which is associated with G1/S arrest. We have also observed that HeLa cells treated with Tazemestostat, a specific EZH2 inhibitor, display a significant reduction in H3K27me3. However, Tazemestostat treatment neither increases expression of p21, p27, and p57 nor induces cell cycle arrest. Taken together, our findings suggest a novel mechanism by which EZH2 regulates cell cycle progression through its enzyme-independent function.
Citation Format: Tania Marlyn Colon, Byeong Hyeok Choi, Wei Dai. Histone methyltransferase-independent function of EZH2 in the cell cycle regulation [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 2310.
Abstract 2348: Contribution of the GR/LEDGFp75 axis to prostate cancer chemoresistance
Authors: Hernandez Evelyn S. Sanchez , Hernandez Greisha L. Ortiz , Ochoa Pedro T. , Gomez Christian R. , Casiano Carlos A. 
Published: June 2022

Abstract
Prostate cancer (PCa) is the second leading cause of cancer deaths in the U.S., disproportionally affecting African American (AA) men. Glucocorticoids (GCs) are administered to PCa patients and have been implicated in therapy resistance. This may be critical to AA men with PCa since they have elevated endogenous GCs levels compared to Caucasian American (CA) men. GCs bind to the glucocorticoid receptor (GR) to exert their actions. The mechanisms of GR-mediated chemoresistance, and its possible contribution to PCa mortality disparities are unknown. We demonstrated that GCs upregulate the chemoresistance-associated protein and transcription co-activator LEDGF/p75 in PCa cells and identified consensus GR binding sites in the promoter region of this protein. Given that both GR and LEDGF/p75 are components of the RNA polymerase II transcription complex, we hypothesized that GR transcriptionally upregulates LEDGF/p75 and then interacts with it to enhance taxane resistance in PCa cells. Pharmacological and genetic inhibition of GR in a panel of docetaxel (DTX)-sensitive and -resistant PCa cells decreased the expression of LEDGF/p75, confirming its status as a candidate GR target gene. However, silencing of LEDGF/p75 had no effects on GR expression. Immunoprecipitation studies revealed that GR and LEDGF/p75 interact in DTX-resistant PCa cells. This interaction was confirmed by confocal microscopy. Immunohistochemical analysis of GR and LEDGF/p75 expression in normal and tumor prostate tissues was performed, and the results are currently being analyzed. Our studies use a mechanistic approach to evaluate the potential contribution of the GR-LEDGF/p75 axis to PCa chemoresistance. Evaluating the co-expression of these proteins in racially diverse PCa tissues may also reveal race-related differential expression, providing insights into the potential contribution of this axis to PCa chemoresistance and mortality disparities.
Citation Format: Evelyn S. Sanchez Hernandez, Greisha L. Ortiz Hernandez, Pedro T. Ochoa, Christian R. Gomez, Carlos A. Casiano. Contribution of the GR/LEDGFp75 axis to prostate cancer chemoresistance [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 2348.
Abstract 2364: ABI1 regulates transcriptional activity of STAT3
Authors: Li Xiang , Porter Baylee , Kemraj Allysa , Bah Alaji , Kortylewski Marcin , Kotula Leszek 
Published: June 2022

Abstract
Background: Prostate cancer (PCa) is characterized by the complexity of oncogenic signaling and heterogeneity of transcriptional landscapes. Adaptor protein ABI1 is a tumor suppressor in PCa as evidenced by its loss or downregulation in high grade and metastatic tumors. STAT3 activation is a hallmark of high-risk prostate tumors. ABI1 loss is associated with STAT3 activation leading to transcriptional reprogramming and epithelial-mesenchymal-transition (EMT) of prostate cancer cells (Nath, Li et al. 2019 Cell Commun Signal). EMT changes involve several homeobox transcription factors. The fact that ABI1 contains a homeobox homology region (HHR) suggested the possibility that it plays a role in EMT through directly regulating transcriptional activity by DNA binding.
Methods: To examine this hypothesis we set out to analyze ABI1-DNA binding. We purified ABI1 HHR and demonstrated its in vitro interactions with different homeobox DNA-binding consensus of double-stranded DNA sequences. We created DU145 ABI1 CRISPR KO cell line and rescue ABI1 expression using retroviral transfection with either ABI1 wild type or Abi1 HHR mutants. DU145 cell lines STAT3 cellular localization was studied by Immunofluorescence staining and the STAT3 transcription activities was studied by Firefly Luciferase Assays with STAT3 specific luciferase reporter plasmid.
Results: We found that the presence of alternatively spliced Exon 4-encoded sequence, located in the C-terminus of HHR, regulates binding of ABI1 to DNA. Structural NMR studies confirmed ABI1 binding to DNA. Subsequent functional studies using DU145 CRISPR KO cell lines expressing wild type or HHR mutants of ABI1 demonstrated that HHR regulates the nuclear localization and transcriptional activity of STAT3.
Conclusion: We propose that ABI1 is a critical regulator of STAT3 activity during prostate cancer progression by the ABI1 HHR mediated DNA binding mechanism.
Funding resources: NCI R01 CA161018; R21 CA260381
Conflicts of Interest Disclosure Statement: The authors declare no conflicts of interest.
Citation Format: Xiang Li, Baylee Porter, Allysa Kemraj, Alaji Bah, Marcin Kortylewski, Leszek Kotula. ABI1 regulates transcriptional activity of STAT3 [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 2364.
Abstract 2384: Investigating Fis1 upregulation as a stress response in glioblastoma cells
Authors: Buckley Yuli , Brett-Morris Adina , Stoll Maria , Mears Jason 
Published: June 2022

Abstract
Dysfunctional mitochondrial dynamics contribute to many pathologies, and elevated levels of mitochondrial fission have been observed in glioblastoma (GBM). Mitochondrial fission 1 protein (Fis1) plays a minor role in basal fission, but has been shown to be more critical for pathological fission. Further, it has been shown to facilitate peripheral fission events, generally occurring after cellular exposure to stress, as a means to prepare damaged mitochondria for degradation through mitophagy. Therefore, my goal is to elucidate the role of Fis1, an integral outer membrane partner protein, in mitochondrial fission within GBM cells. I propose that Fis1 plays a protective role against therapeutic treatment in GBM. This is demonstrated through experiments showing that ionizing radiation (IR) leads to upregulation of Fis1 protein levels, while GBM cell viability is simultaneously unaffected. Further, this increase in Fis1 results in an increase in mitochondrial fission, which likely reflects an increase in mitophagy as a response to IR stress. Thus, I anticipate that GBM cells upregulate Fis1 as a protective measure and that targeting Fis1 function could have therapeutic benefit. In this regard, I have found that depletion of Fis1 alters mitochondrial morphology, and I am studying changes in mitochondrial bioenergetics to correlate ultrastructural changes with mitochondrial function. Preliminary data suggests that Fis1 knockdown in Gli36 cells leads to decreased oxidative phosphorylation and ATP production, with deficits observed specifically in Complex I and III. Concurrently, I am assessing potential synergistic effects of combined radiation and Fis1 inhibition on GBM cell viability and proliferation. To do this, I will use genetic and small molecule approaches to inhibit Fis1-dependent mitochondrial fission. Overall, these studies will demonstrate whether Fis1 drives pathological fission to promote cancer cell growth and proliferation. Additionally, the selective inhibition will evaluate Fis1 as a novel therapeutic target in GBM.
Citation Format: Yuli Buckley, Adina Brett-Morris, Maria Stoll, Jason Mears. Investigating Fis1 upregulation as a stress response in glioblastoma cells [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 2384.
Abstract 2392: Adapted tumor suspension cells rewire metabolic pathways for anchorage independent survival
Authors: Yang Young , Ju Hyun Jeong 
Published: June 2022

Abstract
Metastatic spread of cancer cells is the main cause of cancer-related death. As cancer cells adapt themselves in a suspended state in the blood stream before penetration and regrowth at distal tissues, understanding their survival strategy in an anchorage-independent condition is important to develop appropriate therapeutics. We have previously generated adapted suspension cells (ASCs) from parental adherent cancer cells to study the characteristics of circulating tumor cells. In this study, we explored metabolic rewiring in MDA-MB-468 ASCs to adapt to suspension growth conditions through extracellular flux analyses and various metabolic assays. We also determined the relationship between protein kinase B (AKT) activation and metabolic rewiring in ASCs using the AKT inhibitor, MK2206. ASCs reprogramed metabolism to enhance glycolysis and basal oxygen consumption rate. RNA-sequencing analysis revealed the upregulation in the genes related to glycolysis, tricarboxylic acid cycle, and oxidative phosphorylation. The changes in the metabolic program led to a remarkable dependency of ASCs on carbohydrates as an energy source for proliferation as compared to parental adherent cells (ADs). AKT activation was observed in ASCs and those generated from pancreatic and other breast cancer cells, and AKT activation inhibition in ASCs decreased glycolysis and oxygen consumption. AKT activation is an important strategy for obtaining energy through the enhancement of glycolysis in ASCs. The regulation of AKT activity and/or glycolysis may provide a new therapeutic strategy to prevent the metastatic spread of cancer cells.
Citation Format: Young Yang, Hyun Jeong Ju. Adapted tumor suspension cells rewire metabolic pathways for anchorage independent survival [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 2392.
Abstract 2408: Elevated phosphate promotes a pro-migration phenotype in lung cancer
Authors: Arnst Jamie , Beck George 
Published: June 2022

Abstract
Despite advances in treatment, metastasis remains a major cause of cancer-associated death in the US. Thus, identification of intrinsic and extrinsic factors that promote or inhibit tumor migration and invasion are critical. Increasingly, the dysregulation of cellular metabolism is being linked not only to tumor growth but tumor cell migration. Phosphorus (Pi) is an essential micronutrient necessary for energy metabolism, cell signaling via ATP, formation of nucleic acids and the cell membrane, and mineralization of the skeleton. Unsurprisingly, high levels of Pi are observed in tumor tissue compared to normal tissue, consistent with a demand for this metabolite in rapidly growing cells. Further, our lab has reported that high extracellular Pi increases cell growth, alters gene expression and protein translation, and promotes angiogenesis. High dietary Pi levels has also been shown to increase tumorigenesis in both lung and skin cancer models. However, it remains unknown how phosphate metabolism affects tumor migration and invasion. Here we report that high levels of Pi increases gene expression of EMT-related genes such as Twist, Vimentin, CD44, and OPN in the lung cancer cell line, A549. Further, increased Pi promotes tumor cell migration in a transwell assay and decreased Pi levels or inhibition of phosphate transport by phosphonoformic acid (PFA) impaired migration. Suggesting that high Pi can promote a pro-migration phenotype by upregulating EMT in cancer cells and by increasing directed cell migration. Ongoing research will focus on how intracellular Pi flux changes during cell invasion using a novel FRET-based phosphate sensor in vitro and the effect of Pi inhibition on metastasis in vivo. These findings provide further evidence for the role dysregulated Pi metabolism in promoting cancer progression and the potential for therapeutic intervention with broad impacts on patient outcomes.
Citation Format: Jamie Arnst, George Beck. Elevated phosphate promotes a pro-migration phenotype in lung 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 2408.
Abstract 2419: Understanding the role of DCLK1 mediated invadopodia regulation in HNSCC
Authors: Arnold Levi K. , Standing David , Ramamoorthy Prabhu , Saunders Harmony , Ly Thuc , Anant Shrikant , Thomas Sufi 
Published: June 2022

Abstract
Despite therapeutic advances, head and neck squamous cell carcinoma (HNSCC) is marked by high mortality, particularly with increasing stage. Locoregional invasion, an early step in metastasis, is driven by the development of finger-like processes on the tumor cell known as invadopodia. Mature, active invadopodia secrete matrix metalloproteases (MMP) that enable extension of the cell into the extracellular matrix (ECM). Kinesins haul RAB-bound vesicles containing MMPs along microtubules the length of invadopodia for secretion to the most distal aspect of the invadopodia. It is unclear how these kinesins are modulated within invadopodia. In preliminary studies on patient samples, we identified high levels of doublecortin like kinase (DCLK1) at the invasive front of HNSCC. We hypothesize DCLK1 supports the function of kinesins as a mechanism of invasion. DCKL1 was knocked down in HNSCC lines with a short hairpin RNA (shDCLK1). Invasion and migration assays were performed in shDCLK1 and shcontrol tumor cells by utilizing a transwell assay. Confocal microscopy using Leica LAS X, was performed to assess colocalization of DCLK1 and markers of mature invadopodia (cortactin, TKS5, MT1-MMP) in HNSCC lines for. . To validate the association of DCLK1 with Kif16B and RAB40b, we carried out a co-immunoprecipitation analysis. Finally, conditioned media from shDCLK1 and shControl HNSCC cells was used to assess MMP activity using gelatin zymography and MMP profiler arrays. Transwell assay demonstrates reduced movement in shDCLK1 compared to shcontrol tumor cells (p &lt;0.0001 invasion, p &lt;0.001 migration). Confocal microscopy shows colocalization of MMP 9 and DCLK1 to invadopodia. DCLK1 immunoprecipitation show RAB40b and Kif16b complex together. Additionally, DCLK1, RAB40b, and Kif16b colocalize to invadopodia in confocal studies. We found that DCLK1 colocalizes with markers of mature invadopodia, and that DCLK1 colocalizes to Rab40b, Kif16b, and MMP9 within invadopodia. DCLK1 and MMP9 co-localize to invadopodia as well. Cells expressing DCLK1 had increased MMP 1, and 9 (p &lt;0.041, p &lt;0.001) expression compared to shDCLK1 cells. Further, shDCLK1 cells have significantly attenuated MMP 1 and 9 activity as measured by gelatin zymography. These studies reveal a novel role of DCLK1 in the molecular mechanism driving invadopodia, MMP trafficking and signaling. These early studies indicate that targeting DCLK1 in HNSCC may reduce locoregional invasion and help prevent early metastatic spread.
Citation Format: Levi K. Arnold, David Standing, Prabhu Ramamoorthy, Harmony Saunders, Thuc Ly, Shrikant Anant, Sufi Thomas. Understanding the role of DCLK1 mediated invadopodia regulation in HNSCC [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 2419.