bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 2326: Differential lipid metabolism in mammary cancer cell progression
Authors: Andoline Chaylen , Pawar Parik , Teegarden Dorothy 
Published: July 2021

Abstract
There is an association between increased lipid accumulation and aggressive breast cancer phenotypes, and therefore poorer clinical outcomes. The mechanism by which dysregulated lipid metabolism may promote metastasis remains incompletely understood. Several potential mechanisms by which the neutral lipid storage organelles, cytoplasmic lipid droplets, may promote metastasis include utilization of fatty acids (FAs) for oxidation, protection against lipotoxcity, and production of lipid signaling mediators. We have previously demonstrated that metastatic MCF10CA1a mammary cancer cells rely on fatty acid oxidation (FAO) compared to non-metastatic MCF10A-ras cells, using etomoxir to inhibit the rate-limiting enzyme of FAO, carnitine palmitoyltransferase 1 (CPT1). Previous literature indicates that there is an increase in various lipid metabolism pathways, including FA uptake, de novo lipogenesis, and FA storage in neutral lipid. We found that there is no significant difference between palmitic acid uptake between the non-metastatic and metastatic cells. In the current study, we show that MCF10CA1a cells have significantly higher levels of carbon incorporation into palmitic and oleic FAs from 13C-acetate (25% and 20% greater), 13C-glucose (21% and 11% greater), and 13C-lactate (29% and 22% greater) respectively, compared to the MCF10A-ras cells, as detected by LC-MS/MS. In order to determine the source of FAs that contributes to the migration-dependent FAO, we assessed MCF10CA1a cell migration following inhibition of lipolysis (adipose triglyceride lipase—ATGL; ATGListatin) alone or in combination with the FAO inhibitor, etomoxir. We determined that inhibition of ATGL, the initial enzyme of triglyceride lipolysis pathway, significantly reduces MCF10CA1a cell migration (20% decrease compared to vehicle). Inhibition of FAO and lipolysis did not induce additional reduction in cell migration. We also showed that MCF10CA1a cells are more dependent on FA metabolism than the non-metastatic MCF10A-ras cells, demonstrated by MCF10CA1a cells having a greater decrease in cell viability compared to the MCF10A-ras cells given each FA metabolism inhibition (p&lt;0.05: 22% greater decrease for FAO inhibition and 16% greater decrease for dual FAO and lipolysis inhibition, p=0.05: 17% greater decrease for FA synthesis inhibition). These data suggest that metastatic MCF10CA1a cells rely on their increased FA metabolism to survive and migrate, and specifically that the catabolism of FAs from triglyceride supports the FAO-driven migration of metastatic cancer cells.
Citation Format: Chaylen Andoline, Parik Pawar, Dorothy Teegarden. Differential lipid metabolism in mammary cancer cell progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2326.
Abstract 2345: Development of a novel diagnostic system for bile duct cancer using urinary metabolites
Authors: Amano Hizuru , Hinoki Akinari , Uchida Hiroo , Yokota Kazuki , Ishigaki Takashi , Sakairi Minoru , Abe Mayumi , Terui Yasushi , Oda Hirohisa , Tainaka Takahisa , Shirota Chiyoe , Sumida Wataru , Makita satoshi , Takimoto Aitaro , Okamoto Masamune , Yasui Akihiro , Nakagawa Yoichi 
Published: July 2021

Abstract
Background and Aim: Urine contains numerous small molecular metabolites that can be used as reliable, non-invasive cancer biomarkers. The aim of this study was to identify biomarkers for bile duct cancer by comprehensively analyzing urinary metabolites from patients with bile duct cancer.
Materials and Methods: This study was carried out on urine samples collected before and after tumor resection in 13 patients with bile duct cancer. Urine metabolites were extracted using liquid chromatography/mass spectrometry. Biomarker candidates were identified using the Wilcoxon rank-sum test, random forest method, and orthogonal partial least squares discriminant analysis.
Results: We developed an AI technology that efficiently searched for urine tumor markers based on the detailed medical information of each urine sample and used them to construct cancer test models. About 1500 metabolites, such as amino acids, nucleic acids, and lipids, were detected in one urine sample. Ten urine tumor marker candidates for bile duct cancer were identified.
Conclusions: We identified novel urine tumor marker candidates for bile duct cancer. We are currently investigating additional urine samples from 23 patients with bile duct cancer. The possibility of detecting and monitoring bile duct cancer using urine tumor markers has been examined.
Citation Format: Hizuru Amano, Akinari Hinoki, Hiroo Uchida, Kazuki Yokota, Takashi Ishigaki, Minoru Sakairi, Mayumi Abe, Yasushi Terui, Hirohisa Oda, Takahisa Tainaka, Chiyoe Shirota, Wataru Sumida, satoshi Makita, Aitaro Takimoto, Masamune Okamoto, Akihiro Yasui, Yoichi Nakagawa. Development of a novel diagnostic system for bile duct cancer using urinary metabolites [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2345.
Abstract 2359: MicroRNA 494-5p acts as tumor suppressor in colorectal cancer by targeting JAK1
Authors: Allgayer Heike , Patil Nitin , Abdelrahim Omar , Leupold Joerg H. 
Published: July 2021

Abstract
Recently, we have characterized the metastatically relevant microRNA landscape by comparing microRNA (miR) expression between human colorectal metastasis and matched primary tumors and normal tissues (Mudduluru et. al. Cancer Res. 2015; PMID: 26069251). One of these, miR-494-5p, was deregulated already in primary tumors. In vitro invasion and migration (Boyden chamber and Matrigel) assays of cultured colorectal cancer cells were significantly reduced after miR-494-5p overexpression (mimic). Conversely, this was abolished by anti-miR-494-5p as an inhibitor. Overexpression of miR-494-5p in cell lines showed a significant reduction in cellular proliferation, which was reversed upon inhibitor co-transfection in a time dependent manner. In silico analysis suggested an interaction of miR-494-5p with the 3´UTR of JAK1. Accordingly, an overexpression of miR-494-5p in cultured colon cancer significantly reduced luciferase activity of a reporter plasmid containing the wild type JAK1-3'UTR, which was abolished when the miR-494-5p seed sequence was mutated to prevent miR-494-5p binding, suggesting a physical interaction and translational repression of JAK1 by miR-494-5p. Furthermore, overexpression of miR-494-5p led to a significant reduction of JAK1 expression in colorectal cancer cell lines in a time dependent manner, which was abolished by co-transfecting a specific anti-miR-494-5p as an inhibitor. Taken together, our preliminary data suggests that miR-494-5p inhibits the expression of JAK1 as a direct molecular target via specific interaction at the JAK1-3'UTR. Additionally, miR-494-5p is capable of reducing proliferation, migration, and invasion, suggesting miR-494-5p as an early tumor suppressor molecule in colorectal cancer.
Citation Format: Heike Allgayer, Nitin Patil, Omar Abdelrahim, Joerg H. Leupold. MicroRNA 494-5p acts as tumor suppressor in colorectal cancer by targeting JAK1 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2359.
Abstract 2360: Identifying differentially expressed miRNAs in CRC stem cell subpopulations
Authors: Stark Victoria A. , Viswanathan Vignesh , Facey Caroline O. , Opdenaker Lynn M. , Boman Bruce M. 
Published: July 2021

Abstract
Our research goal is to discover the molecular mechanisms behind tumor heterogeneity in CRC. We previously showed that CRCs contain multiple subpopulations of cancer stem cells (CSCs) which may explain the occurrence tumor heterogeneity and resistance to treatment. To determine how CSC sub-populations might arise, we are studying miRNA expression in CRC SCs. MicroRNAs are known to regulate SC phenotype and are found to be dysregulated in many cancers.
Hypothesis: Tumor heterogeneity results from existence of multiple CSC subpopulations that are regulated by distinct miRNAs. Accordingly, we are using bioinformatics and miRNA profiling to identify miRNAs that target SC genes in CRCs.
Indeed, our miRNA expression profiling of normal and malignant ALDH+ human colonic SCs showed that miRNA92a targets the SC gene LRIG1 and upregulation of miRNA92a leads to decreased LRIG1 expression. We also discovered that miRNA23b targets the SC gene LGR5 and miRNA23b is upregulated in ALDH+ CSCs. We have identified several other candidate miRNAs that are predicted to target CD166, ALDH1A1, BMI1, LRG5, and LRIG1 SC genes. We are currently in the process of validating whether these miRNAs contribute to emergence of specific CSC sub-populations in CRCs. Thus, identifying miRNAs that regulate CSC subpopulations should provide new strategies to modulate CSC composition in order to sensitize tumors to treatments.
Citation Format: Victoria A. Stark, Vignesh Viswanathan, Caroline O. Facey, Lynn M. Opdenaker, Bruce M. Boman. Identifying differentially expressed miRNAs in CRC stem cell subpopulations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2360.
Abstract 2365: Intracellular interaction of downstream molecular mediators of miR-1207-3p in prostate cancer cells
Authors: Ghosh Priyanka , Ogunwobi Oloronseun 
Published: July 2021

Abstract
Prostate cancer (PCa) is the second most common cancer diagnosed among men in the United States. Human chromosome 8q24 is the most important PCa susceptibility locus. This region contains the MYC oncogene, which is involved in early PCa initiation. Downstream to MYC is the PVT1 gene, which is often amplified in PCa. PVT1 is a non-protein coding gene that encodes six annotated microRNAs (miRNAs), including miR-1207-3p. Our laboratory has previously demonstrated miR1207-3p to be a significant modulator in PCa and revealed that miR-1207-3p is significantly underexpressed in PCa cells and histologically confirmed PCa tissues compared to normal prostatic cells and tissues. We have also shown that miR-1207-3p has tumor suppressive activity in vivo. Moreover, we discovered that miR-1207-3p directly targets fibronectin type III domain containing 1 (FNDC1), which was found to be overexpressed in PCa cells and there is a concomitant overexpression of (FN1)/androgen receptor (AR)/c-MYC. In an effort to better understand the role of FNDC1/FN1/AR/c-MYC in PCa progression we examined the interaction between FNDC1/FN1/AR/c-MYC and found direct physical interaction through coimmunoprecipitation. We also examined the spatial localization of the FNDC1/FN1/AR/c-MYC pathway by performing immunofluorescence staining in PCa cells. Single staining analysis revealed that FNDC1 and c-MYC localize to the nucleus and cytoplasm while AR localizes to the nucleus and FN1 localizes to the cytoplasm in PCa cells. However, in normal prostate epithelial cells FNDC1, AR and c-MYC localize to the nucleus whereas FN1 localize to the cytoplasm. These results suggest that the underexpression of miR1207-3p may be affecting the localization of FNDC1 to cytoplasm and thus promoting interaction between FNDC1/FN1/AR/c-MYC. Future studies include examining the effect of miR-1207 on the spatial organization and interactions of the FNDC1/FN1/AR/c-MYC pathway through immunofluorescence and co-immunoprecipitation assays. Thus, understanding this molecular interaction could reveal interesting insight into the biology of microRNA-1207-3p regulation in PCa.
Citation Format: Priyanka Ghosh, Oloronseun Ogunwobi. Intracellular interaction of downstream molecular mediators of miR-1207-3p in prostate cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2365.
Abstract 2367: Role of miR-34a-MET axis in head and neck cancer squamous cell carcinoma
Authors: Wu Xun , Cheng Yi-Shing Lisa , Matthen Methew , Yoon Angela , Schwartz Gary , Bala Shashi , Taylor Alison M. , Momen-Heravi Fatemeh 
Published: July 2021

Abstract
MicroRNAs (miR) are evolutionarily highly conserved non-coding RNAs that play roles in fundamental cellular functions by post-translational gene regulation. In cancer pathogenesis, miRs exert both anti-tumorigenic and pro-tumorigenic effects by virtue of miR-specific and context-dependent mechanisms. The role of chromosomal changes and mutation status on miR expression in cancer remains unknown. Here we provide evidence that chromosome arm 1p loss and P53 mutations are associated with lower levels of miR-34a, particularly in squamous cancers such as head and neck squamous cell carcinoma (HNSCC). miR-34a acts as a tumor suppressor and physically interacts with and functionally targets the proto-oncogene MET, and modulates cell proliferation. miR-34a expression is inversely correlated with MET in tumor tissue. We found that miR-34a suppresses HNSCC carcinogenesis, at least in part, by downregulating MET, consequently inhibiting HNSCC proliferation. Moreover, ectopic expression of miR-34a reduces HNSCC cell proliferation and tumor burden in vitro and in vivo, represses expression of genes and proteins involved in epithelial-mesenchymal transition, and negates the oncogenic effect of MET in mouse tumors. Our work demonstrates a role of miR-34a in maintaining tumor immunity, as overexpression of miR-34a resulted in a decease in percentage of anti-inflammatory (M2-like) TAMs and PDL1+TAMs, which are reported to have pro-tumorigenic activity. In HNSCC patient samples, higher levels of miR-34a are significantly associated with a higher frequency of Th1 cells, myeloid cells, and regulatory T cells. Our results demonstrate that miR-34a directly targets MET and maintains anti-tumor immune activity, and could potentially represent a new therapeutic approach for HNSCC.
Citation Format: Xun Wu, Yi-Shing Lisa Cheng, Methew Matthen, Angela Yoon, Gary Schwartz, Shashi Bala, Alison M. Taylor, Fatemeh Momen-Heravi. Role of miR-34a-MET axis in head and neck cancer squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2367.
Abstract 238: Exhaustive tumor specific antigen detection with RNAseq
Authors: Sharpnack Michael , Johnson Travis , Chalkley Robert , Han Zhi , Carbone David , Huang Kun , He Kai 
Published: July 2021

Abstract
Background: Tumor specific antigen (TSA) identification in human cancer predicts response to immunotherapy and provides vaccine targets for precision medicine. In addition to neoantigens from somatic coding mutations, numerous non-mutated TSAs can elicit T-cell responses but are often overlooked by current methods. We present a method that accurately and comprehensively predict TSAs from RNAseq data regardless of mutation status.
Methods: HLA-I genotypes were predicted with seq2HLA. RNAseq fastq files were translated into all possible peptides of length 8-11, and peptides with high expression in the tumor and comparatively low expression in normal were tested for their MHC-I binding potential with netMHCpan-4.0. We defined our predicted TSA by i) high expression in tumor samples, ii) low expression in normal samples, and iii) high predicted patient-specific MHC-I binding affinity.
Results: We developed a novel pipeline for TSA prediction from RNAseq that is not limited to mutation-derived TSAs. This pipeline was used to predict all possible unique peptides size 8-11 on previously published murine and human lung and lymphoma tumors then validated on matched tumor and control lung adenocarcinoma (LUAD) samples. This pipeline is able to predict TSAs in MHC-I ligand-purified proteomics data with favorable performance to existing methods. Furthermore, neoantigens predicted by exomeSeq are typically poorly expressed at the RNA level, (28% of predicted neoantigens with &gt;0 expression, mean of 15.6 reads/sample) and a fraction of them (47/6,928, 0.68%) are expressed in matched normal samples. Finally, a set of 6 TSAs are expressed in 22/39 (56%) of LUAD tumors and represent attractive vaccine targets.
Conclusion: Direct quantification of RNAseq evidence of the potential peptidome in matched tumor and control RNAseq samples, via our novel pipeline, allows for exhaustive detection of TSAs.
Citation Format: Michael Sharpnack, Travis Johnson, Robert Chalkley, Zhi Han, David Carbone, Kun Huang, Kai He. Exhaustive tumor specific antigen detection with RNAseq [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 238.
Abstract 2387: Targeting PVT1 exon 9 transcript is not pro-apoptotic but induces claudin 4 expression and inhibits migration in triple negative breast cancer cells
Authors: Levine Fayola A. , Ogunwobi Olorunseun O. 
Published: July 2021

Abstract
Triple negative breast cancer (TNBC) is a lethal molecular subtype of invasive breast cancer (BC) that is ER-, PR- and HER2-. Claudin low (CL) TNBC, a distinct molecular subtype of TNBC, has the worst prognosis compared to other BC subtypes. Aberrant expression of claudin proteins disrupts the function of tight junctions. Consequently, inducing epithelial-to-mesenchymal transition (EMT) in cancers, an important factor for enhanced motility and metastasis. Therefore, understanding the molecular mechanisms that modulate claudin expression in TNBC is crucial. The 8q24 genomic locus is an important cancer susceptibility locus that is associated with poor clinical outcomes in cancer due to common amplification events that occur in many malignant diseases. This locus contains the PVT1 gene, which encodes a long noncoding RNA (lncRNA) that has been implicated in multiple cancers including BC. PVT1 consists of 12 exons that are alternatively spliced to generate lncRNAs. Although previous research has implicated PVT1 as an important player in BC, the underlying molecular mechanisms of PVT1 in CL TNBC is unknown. To examine the role of PVT1 in CL TNBC, we assessed PVT1 expression in T47D (ER+), MDA MB 231 (CL) and MDA MB 468 (claudin high (CH)) BC cells. We observed that PVT1 exons 4A, 4B, and 9 are significantly overexpressed in CL MDA MB 231 and significantly underexpressed in CH MDA MB 468 in comparison to T47D cells, suggesting a protumorigenic role of PVT1 in CL TNBC. We analyzed the functional consequences of siRNA targeting of PVT1 exon 9 expression in CL TNBC cells. siRNA targeting of PVT1 exon 9 expression in the MDA MB 231 CL TNBC cells led to a significant reduction in migration and the re-expression of claudin 4. To determine the role of PVT1 on EMT, we assessed the expression of EMT markers (vimentin, fibronectin, and E-cadherin) in MDA MB 231 cells. We observed no changes in the expression of EMT markers when PVT1 exon 9 is knocked down. However, our data show that mesenchymal markers are more highly expressed in MDA MB 231 cells in comparison to MDA MB 468 cells. Further, knockdown of PVT1 exon 9 did not induce apoptosis in MDA MB 231 cells as assessed by caspase 3 and caspase 9 expression. Taken together, our data indicate that PVT1 exon 9 regulates claudin expression and migration in CL TNBC, and may have implications for clinical outcomes in TNBC.
Citation Format: Fayola A. Levine, Olorunseun O. Ogunwobi. Targeting PVT1 exon 9 transcript is not pro-apoptotic but induces claudin 4 expression and inhibits migration in triple negative breast cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2387.
Abstract 2389: LINC00901 regulates glucose metabolism in pancreatic cancer
Authors: Peng Wan-Xin , Yang Liu , Mo Yin-Yuan 
Published: July 2021

Abstract
Dysregulation of metabolism is one of the cancer hallmarks. However, little is known whether long coding RNAs (lncRNAs) play a role in the regulation of metabolism in pancreatic ductal adenocarcinoma (PDAC). In the present study, we focused on lncRNA LINC00901 because a high level of LINC00901 is associated with the poor outcome of PDAC patients. Functional studies showed that LINC00901 promotes PDAC cell proliferation and invasion, whereas knockout (KO) of LINC00901 impairs these abilities of PDAC cells. Furthermore, the xenograft animal model suggested that LINC00901 promotes tumorigenesis. To determine the underlying mechanism of LINC00901-mediated tumorigenesis, we performed RNA-seq analysis in LINC00901 overexpression or KO cells. Gene Set Enrichment Analysis (GSEA) analysis showed that gene sets involved in glucose biological processes such as ‘‘MYC targets”, “Glycolysis” and “Gluconeogenesis” are significantly enriched in the LINC00901 overexpression group, whereas these genes are down-regulated in the LINC00901 KO group. The top-scoring genes recurring in the three gene sets include key glycolysis-related genes, lactate dehydrogenase A (LDHA), hexokinase 2 (HK2), and enolase 1 (ENO1), all of which were validated by qRT-PCR and western blot. Moreover, we found that LINC00901 upregulates c-Myc by stabilizing c-Myc RNA. Together, these results suggest that LINC00901 is an oncogenic lncRNA capable of regulating glucose metabolism, leading to PDAC development. Experiments are underway to determine how LINC00901 regulates c-Myc RNA stability in pancreatic cancer cells.
Citation Format: Wan-Xin Peng, Liu Yang, Yin-Yuan Mo. LINC00901 regulates glucose metabolism in pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2389.