bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 1759: Studying T-cell force activation and DNA repair dynamics at the single-molecule level with optical tweezers and correlated fluorescence microscopy
Authors: Raja Ali , Anderson Leif , Peutz Willem , Candelli Andrea , Sitters Gerrit 
Published: August 2019

Abstract
DNA repair, the collection of highly regulated mechanisms by which a cell identifies and repairs DNA damage, remains one of the most essential processes of human life. Without DNA repair mechanisms cells lose the ability to transcribe important regions of their genome, resulting in harmful mutations, which could eventually jeopardize cellular wellbeing.
Sources of DNA damage include double-stranded breaks and DNA intra- and interstrand crosslinks, which can ultimately become malignant tumors, leading to cancer. To study DNA repair, single-molecule studies have proven to greatly enhance understanding at the molecular level. However, it is often challenging to obtain adequate sensitivity and resolution, as well as biological conditions mimicking in vivo environments. The C-Trap™ system allows for realtime visualization of the interaction between DNA and DNA repair proteins, under biologically relevant conditions with high spatial and temporal resolution.
The C-Trap™ is the only instrument that integrates optical tweezers, confocal/STED microscopy, and an advanced microfluidics system in a truly correlated manner. It enables live, simultaneous and correlative visualization and manipulation of molecular interactions with sub-picoNewton (pN) force resolution and a kilo-Hz (to mega-Hz) temporal resolution. Previously we have presented applications in: protein (un)folding and conformational changes; DNA-protein interactions and genome modifications; effects of mechanical stress on DNA/RNA structure; motility of cytoskeletal molecular motors; and protein droplet and aggregation dynamics.
By culturing or adhering cells to the surface of the flow chamber, single-molecule cell-based studies can also be performed with the C-Trap. Cell-surface bound mechano-receptors can be activated by forming tethers with an optically trapped particle and then creating a controlled tension on the molecule. Correlated fluorescent imaging can elucidate internal protein cascades and other similar reactions to the applied force.
Here, we present our experiments visualizing and quantifying the mechanisms of DNA repair and the force activation of T-cells using the C-Trap system. These experiments show that the technological advances in hybrid single-molecule methods can be turned into an easy-to-use and stable instrument that opens up new venues in many research areas.
Citation Format: Ali Raja, Leif Anderson, Willem Peutz, Andrea Candelli, Gerrit Sitters. Studying T-cell force activation and DNA repair dynamics at the single-molecule level with optical tweezers and correlated fluorescence microscopy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1759.
Abstract 1773: The tyrosine phosphatase, SHP-2, is involved in regulating PD-L1 expression in non-small cell lung cancer
Authors: Toral Keller 
Published: August 2019

Abstract
Immune checkpoint inhibitors (ICIs), specifically those which target the T-cell surface receptor Programmed Cell Death-1 (PD-1) and its ligand, Programmed cell death ligand-1 (PD-L1), have demonstrated substantial clinical benefit in patients with non-small cell lung cancer (NSCLC). Tumoral PD-L1 expression may be important for response to therapy, but the precise mechanism of regulation has yet to be fully elucidated. It is known that PD-L1 expression is elevated in cancers harboring mutations in the RAS family of genes, specifically KRAS. Mutations in the KRAS gene are found in up to 30% of NSCLC tumors, and there are no targeted treatment options available for this subset of patients. The tyrosine phosphatase, SHP-2, has been shown to be a critical regulator of the KRAS signaling cascade. Therefore, genes regulated by the RAS/MAPK signaling cascade, including PD-L1, may be modulated by SHP-2 inhibition. Thus, this study aims to investigate the impact of SHP-2 activity on PD-L1 expression in NSCLC.
The allosteric inhibitor of SHP-2, SHP099, was used to ablate SHP-2 activity in KRAS-mutant NSCLC cell lines, H460, A549, H2122, and EGFR-mutant NSCLC cell line PC9. PD-L1 levels were quantified by western blot and flow cytometry analyses. PD-L1 mRNA was measured by quantitative real time PCR (qRT-PCR) analysis. SHP099 activity was confirmed by SHP-2, siRNA transfection in KRAS active cell lines. Inhibition of SHP-2 led to increased levels of PD-L1 expression in the KRAS-mutant cell lines, but not in the EGFR-mutant cells. Analysis of PD-L1 surface expression by flow cytometry confirmed that surface PD-L1 levels increased following exposure to SHP099. To determine whether SHP-2 controlled expression at the transcriptional level, mRNA quantification by qRT-PCR displayed increased levels of PD-L1 mRNA following SHP099 treatment. Together, these results suggest that SHP-2 regulates PD-L1 expression in KRAS-active NSCLC at the level of PD-L1 gene expression. It is presently unclear whether SHP-2 also has a role in controlling protein turnover. Using SHP-2 mutant constructs that mimic a constitutively active phosphatase, we hope to gain further insight into the roles of both SHP-2 catalytic and scaffolding functionality on PD-L1 expression.
Citation Format: Keller Toral. The tyrosine phosphatase, SHP-2, is involved in regulating PD-L1 expression in non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1773.
Abstract 1792: Exploring new therapeutic options for chemoresistant locally advanced lung cancer
Authors: Cuttano Roberto , Dama Elisa , Melocchi Valentina , Colangelo Tommaso , Carbonelli Cristiano , Maroni Giorgia , Levantini Elena , Bianchi Fabrizio 
Published: August 2019

Abstract
Background: Non-small-cell lung cancer (NSCLC) is the leading cause of cancer-related mortality worldwide. About one third of NSCLC patients present at diagnosis with locally advanced disease (stage IIIA) which are characterized by lymph node metastases. For this group of patients, neoadjuvant chemotherapy (NACT) followed by surgery is the best therapeutic option. However, clinical response to NACT is heterogeneous including patients with a complete eradication of lymph node metastases (pN0), and patients with persistent disease (pN2). Of note, 'pN0' patients showed a favourable prognosis (~50-60% survival, at 5-year) when compared to 'pN2' patients (~20-30% survival, at 5-year).
Methods: To identify new molecular determinants involved in NACT response, we recently performed whole-microRNA expression profiling of metastatic lung tumor cells, which were collected from mediastinal lymph nodes before NACT either by endobronchial ultrasound transbronchial aspiration (EBUS-TBNA) (n=11) or mediastinoscopy (n=41). In addition, we performed a meta-analysis of a cohort (n=84) of NSCLC (i.e. The Cancer Genome Atlas LUAD and LUSC dataset) with complete follow-up.
Results: We found a set of 20 miRNAs significantly differentially expressed in pN2 vs. pN0 tumors. Hierarchical clustering analysis using this 20-miRNA set revealed a clear separation of pN0 patients from pN2 patients. However, when the 20-miRNA set was used in the primary NSCLCs from TCGA dataset, the chemoresponsive and chemoresistant tumors could not be stratified. This possibly suggests unique properties of this 20-miRNA set and their modulated target genes in metastatic cells, and in the acquisition of a chemoresistant phenotype. Furthermore, by coupling miRNA and mRNA expression profile in metastatic samples, we rewired i) cancer intrinsic gene networks with a role in chemotherapy resistance, and ii) an augmented infiltration of tumor promoting immune cell populations (TILs).
Conclusions: Lung cancer metastases are intrinsically distinct and there exist molecular subtypes with different NACT response, identifiable by miRNA expression profile. Future efforts will be directed to identify the landscape of molecular mechanisms mediated by miRNAs, including the modulation of TILs possibly involved in the acquired chemoresistance.
Citation Format: Roberto Cuttano, Elisa Dama, Valentina Melocchi, Tommaso Colangelo, Cristiano Carbonelli, Giorgia Maroni, Elena Levantini, Fabrizio Bianchi. Exploring new therapeutic options for chemoresistant locally advanced lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1792.
Abstract 1794: A comparative microRNA expression analysis in breast cancer and melanoma tissues
Authors: Zhang Yanping , Peng Guangyong , Hsueh Eddy C. 
Published: August 2019

Abstract
Recently studies have revealed that a subset of microRNAs (miRNAs) is aberrantly expressed in the development and progression of a variety of cancers including breast cancer and melanoma. Several miRNAs have been implicated in tumorigenesis and progression of human cancer. However, the underlying mechanisms in different types of cancers remain largely unknown. The aim of the study was to compare the expression profiled of miRNA between breast cancer and melanoma patient’s tissues. Methods: Expression levels of 7 miRNAs (miR-15b, miR-142-3p, miR-142-5p, miR-142a, miR-199a, miR-221, miR-424, ) were determine in 17 cases of breast cancer and 25 melanoma tissue samples. MiRNA isolation from tissue samples were performed using Trizol reagent ( Sigma, USA). RNA quality and quantity were assessed using a BioMate TM 3 Series Spectrophotometers (Thermo, Madison, WI). Synthesis of cDNA with reverse transcriptase was performed by TaqManTM microRNA Reversed Transcription Kits, For analysis of miRNA expression, real-time q-PCR analyses were using TaqMan MicroRNA Assays. All real-time q-RT-PCR were performed on a 7300 real-Time PCR system (Applied Biosystems, USA). MiR-24 was used as the internal control for normalization. The relative miRNA expression levels were calculated using the 2 DΔCt methods. Values were presented as means ± standard deviation (SD). The comparison of miRNA levels in breast cancer and melanoma tissues were performed using Student’s t-test. A p value less than 0.05 was considered statistically significant. The expression of miRNAs in different breast cancer subtypes (infiltrating and Invasive ductal cancer) and melanoma (primary and metastatic) was also performed. Results: Relative miRNA expression levels (miR-15b, miR-142-3p, miR-142-5p, miR-146a, miR-199a, miR-221 and miR-424) were found to be differentially expressed in breast cancer and melanoma tissues. Significantly higher relative miRNA expression levels were detected in melanoma tissues compared with breast cancer tissues in all miRNAs evaluated except for miR-424. Four miRNAs (miR-15b, miR-146a, miR-221, and miR-143-3p) had relative expressions over 1.5 compared with only 1 miRNA (miR-15b) in breast cancer tissue. DΔCt values are plotted following comparison with endogenous levels of miR-24 assessed in each sample. Conclusions: Our study demonstrated that miRNA is not only a potential biomarker, but also a valuable therapeutic target for breast cancer and melanoma.
Citation Format: Yanping Zhang, Guangyong Peng, Eddy C. Hsueh. A comparative microRNA expression analysis in breast cancer and melanoma tissues [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1794.
Abstract 1799: MicroRNA hsa-miR-26a expression in hepatocellular carcinoma correlates with patient survival
Authors: Nakajima Go , Hayashi Kazuhiko 
Published: August 2019

Abstract
Background: MicroRNAs (miRNAs) are small noncoding RNAs that act as important regulators of gene expression at a post-transcriptional level. Using a next-generation sequencer system, in a previous study, we have identified 49 miRNAs expressed differentially by comparing 26 pair samples of hepatocellular carcinoma (HCC) tumor tissue and nontumor liver tissue. For this validation study, we selected hsa-miR-26a, one of the candidate miRNAs. We measured hsa-miR-26a expression in the validation set HCC samples using real-time quantitative polymerase chain reaction (qPCR) and examined the correlation between miRNA expression and clinical data. Patients and Methods: Overall, 40 patients with HCC who underwent tumor resection from 1991 to 1997 at the Department of Surgery, Institute of Gastroenterology, Tokyo Women’s Medical University, Japan were enrolled. Formalin-fixed paraffin-embedded samples were prepared using the standard protocol. The paraffin blocks were cut into 10-μm sections; HCC tumor and adjacent nontumor liver tissues were collected using laser-captured microdissection, and total RNA, including miRNA fractions, were isolated. Following the synthesis of a complementary DNA (cDNA) using an miRNA-specific primer, real-time qPCR was performed using an miRNA-specific primer/probe. Results: The hsa-miR-26a expression tended to be downregulated in HCC tumor tissue compared to nontumor liver tissue (P = 0.0799). Patients in the higher hsa-miR-26a expression group showed a significantly longer overall survival time compared with those in the lower hsa-miR-26a expression group (P = 0.0409). Conclusion: Inhibition of hsa-miR-26a expression might play a role in tumorigenesis, and hsa-miR-26a expression could be a potential prognostic factor for patients with HCC.
Citation Format: Go Nakajima, Kazuhiko Hayashi. MicroRNA hsa-miR-26a expression in hepatocellular carcinoma correlates with patient survival [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1799.
Abstract 1804: Role of microRNAs in colorectal adenoma progression
Authors: Wallace LaShanale M. , Chaudhry Aneese F. , Aikhionbare Karen I. , Yao Xuebiao , Aikhionbare Felix O. 
Published: August 2019

Abstract
Colorectal cancer (CRC) survival rates are stage related and majority of patients (75%) with CRC have sporadic of the disease which is in form of adenoma. Most of colorectal adenocarcinomas precursors are adenomatous polyps. Moreover, CRC appears to be an age related disease and studies have shown that mutations in mtDNA appear to accumulate with age because of inadequate repair. Also, oxidative stress has been shown to affect mitochondrial proteins resulting in a decrease of mitochondrial function associated with the precursor lesions of cancer. Recent findings suggest that the mitochondrion has sequences that code for certain miRNA which can regulate different pathways frequently dysregulated in cancer including colorectal cancer (CRC). Isolation of mitochondria RNA from colorectal precancerous polyps, cancer, and normal adjacent tissue samples was performed and assessed for gene expression differences using quantitative reverse transcription PCR. We demonstrate that mitochondria genome expression of miRNAs miR-24, miR 181, miR 210, and miR 21 in colorectal tissue samples varies during disease progression. Expression of microRNAs 24, 181, and 210 progressively increased from the earliest precancerous polyp to cancer. In addition, miR-210 and miR-181 expression increased 3 folds in villous adenomas when compared to tubular adenoma. Meanwhile, miR 21 increased progressively in adenoma tissues but decreased almost 4 folds in cancer tissues when compared to villous adenoma tissue. These results suggest miRNAs within the mitochondria genome may regulate important mitochondrial functional pathways leading to a more favorable environment for transformation or progression of adenomas to cancerous tumors.
Citation Format: LaShanale M. Wallace, Aneese F. Chaudhry, Karen I. Aikhionbare, Xuebiao Yao, Felix O. Aikhionbare. Role of microRNAs in colorectal adenoma progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1804.
Abstract 1809: LncRNA-SOX2-OT contributes to head and neck cancer cell proliferation by regulating DDIT4
Authors: Wang Ru , Yang Yifan , Tan Chen , Feng Ling , Fang Jugao 
Published: August 2019

Abstract
Background: Long non-coding RNAs (lncRNAs) have been shown to serve as an oncogenic role in human cancers. However, the role of lncRNAs in head and neck squamous cell carcinoma (HNSCC) is still unclear.
Methods and Results: Our previous microarray analysis showed that lncRNA SOX2-OT was upregulated in HNSCC tumor tissues and was correlated with DDIT4. To determine whether SOX2-OT served as a poor prognosis factor and targeted DDIT4 to facilitate cell proliferation and tumorigenesis in human HNSCC, qRT-PCR tested the relative expression of SOX2-OT and DDIT4 in 60 pairs of LSCC cancer tissues and the corresponding adjacent non-cancer tissues. Cell functional assay was conducted in vitro. We validated the up-regulation of SOX2-OT and DDIT4 in HNSCC tissues. Furthermore, we found that high SOX2-OT expression was significantly associated with advanced tumor differentiation, and worse prognosis. In vitro experiments demonstrated that SOX2-OT functioned as an oncogene by promoting cell proliferation and inhibiting cell apoptosis, and SOX2-OT targeted DDIT4 as its competing endogenous RNA in HNSCC cells.
Conclusions: Our findings for the first time identify the oncogenic role of SOX2-OT in HNSCC, demonstrating that SOX2-OT is a potential prognostic biomarker and promising therapeutic target in HNSCC.
Note: This abstract was not presented at the meeting.
Citation Format: Ru Wang, Yifan Yang, Chen Tan, Ling Feng, Jugao Fang. LncRNA-SOX2-OT contributes to head and neck cancer cell proliferation by regulating DDIT4 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1809.
Abstract 181: Prolyl-4-hydroxylase α subunit 3 promotes renal cancer progression and metastasis
Authors: Broome Larry E. , Wang Bingzhi , Zhao Menghuang , Yang Junhua , Bouamar Hakim , Cserhati Matyas , Sun Lu-Zhe 
Published: August 2019

Abstract
Collagen is the major component of the extracellular matrix, its overexpression has been shown to facilitate tumor development and progression. Prolyl-4-hydroxylase α subunit 3 (P4HA3) plays a crucial role in the synthesis of collagen, as it is involved in the catalysis to convert proline residues to 4 hydroxyproline residues, which are essential for the conformational stability of mature collagen. It has been reported that P4HA3 functions as a tumor promoter in gastric cancer. However, the role of P4HA3 in renal cell carcinoma (RCC) has not been established. To identify the role of P4HA3 in RCC, we analyzed the expression of P4HA3 in RCC patients and knocked down the expression of P4HA3 in two renal cancer cell lines with different P4HA3 siRNAs and P4HA3 shRNAs. We performed cell proliferation, migration and invasion assays in vitro and in vivo. Our results demonstrated that expression of P4HA3 was upregulated in RCC patients and knockdown of P4HA3 significantly inhibited renal cancer cell proliferation, migration and invasion. Mouse xenograft studies demonstrated the tumor promoting role of P4HA3 in renal cancer. Therefore, P4HA3 appears to be a potential therapeutic target for the treatment of RCC.
Citation Format: Larry E. Broome, Bingzhi Wang, Menghuang Zhao, Junhua Yang, Hakim Bouamar, Matyas Cserhati, Lu-Zhe Sun. Prolyl-4-hydroxylase α subunit 3 promotes renal cancer progression and metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 181.
Abstract 1833: KLF4 regulates metabolic homeostasis in response to energy stress
Authors: Rosencrans William M. , Walsh Zachary H. , Blum Andrew C. , Hagos Engda G. 
Published: August 2019

Abstract
Krüppel-like factor 4 (KLF4) is a zinc finger-containing transcription factor with diverse regulatory functions in cellular growth, proliferation, differentiation, autophagy and genomic stability. Furthermore, KLF4 exerts a cell-cycle checkpoint effect in part by acting as a transcriptional activator of the cyclin-dependent kinase inhibitor, p21. Our lab has found that KLF4 regulates autophagy, mitophagy, and mitochondrial dynamics. Given the close relationship these processes have with cellular metabolism, we aimed to determine how KLF4 regulates glycolytic and oxidative metabolism. Using various assays, we find that cells lacking KLF4 have both oxidative and glycolytic impairments. Using western blotting, we find that when KLF4 is overexpressed in RKO human colorectal cancer cells, Hexokinase 2 (HK2), a rate determining enzyme in glycolysis, PKM2, a facilitator of lactate production, and MCT4, a lactic acid export protein and marker of glycolysis, are all significantly upregulated. In MEFs, we find that GLUT1, a glucose transport protein, has greater expression in WT than Klf4-null cells. Furthermore, we determined that KLF4 regulates aspects of the basal cell metabolism in a p21-dependent manner. Given that KLF4 has been found to act as an immediate early gene in response to certain stresses, and given the importance of fast metabolic shifts, we also look at how KLF4 influences short term metabolic stress responses. Since metabolic stress tests showed that WT MEFs have an increased glycolytic capacity, we investigate whether the cells have an increased ability to quickly intake glucose in response to particular stresses. Accordingly, we looked at GLUT1 expression and membrane localization with respect to KLF4. Immunostaining in RKO and MEFs suggests that KLF4 plays a role in localizing GLUT1 to the outer membrane, allowing for increased glucose intake. Taken together, our findings provide a rationale for the impaired metabolism of KLF4-null MEFs, where KLF4 plays a role responding to energy stress by modifying the localization of GLUT1, and regulating various metabolic enzymes both directly, and in a p21-dependent manner.
Citation Format: William M. Rosencrans, Zachary H. Walsh, Andrew C. Blum, Engda G. Hagos. KLF4 regulates metabolic homeostasis in response to energy stress [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1833.