bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 2478: Assessing regulatory network rewiring in cancer patients using chromatin accessibility profiles
Authors: Forbes Andre , Xu Duo , Khurana Ekta K. 
Published: September 2020

Abstract
The regulation of gene expression in humans is the result of a complex interplay between DNA, small RNA molecules and a multitude of proteins, particularly histones and transcription factors (TFs). To identify the key TFs regulating gene expression in cancer we are integrating ATAC-Seq data from 371 TCGA patients in conjunction with matching expression data and DNA-binding motifs for 780 TFs and TF families. We infer the regulatory networks in these patients by detecting true TF binding events in individual patients and the regulatory elements that said TFs are bound to using the Protein Interaction Quantification algorithm (PIQ). The inferred networks were then clustered by the similarity of inferred TF binding activity followed by identification of the TFs most likely driving the identity of each cluster. We observe robust clustering by site of origin of disease with canonical TFs such as FOXA1 and ESR1 being putative key TFs in ER+ breast cancer, PAX8 in renal cancer as well as TP63 and SOX2 in multiple squamous cell cancers. To validate these putative super-TFs, we used gene essentiality data from CRISPR-mediated knockout experiments of 18K genes in 625 well characterized cell lines performed by the Broad Institute. We observe statistically significant differences in the essentiality of putative super-TFs in cell lines matching the disease types of clusters.
Citation Format: Andre Forbes, Duo Xu, Ekta K. Khurana. Assessing regulatory network rewiring in cancer patients using chromatin accessibility profiles [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2478.
Abstract 2525: Identification of mRNA targets associated with PIWIL1 protein complex in lung cancer cells
Authors: Amaar Yousef G. , Reeves Mark E. 
Published: September 2020

Abstract
Introduction: In previous published work we have shown that RASSF1C promotes expression of PIWIL1 and PIWI interacting RNAs (piRNAs) in lung cancer cells, suggesting the hypothesis that that the RASSF1C-PIWI-piRNA pathway may promote lung cancer cell growth and progression. PIWIL1 protein-piRNA complexes have recently been shown to regulate mRNAs in mouse testes, suggesting that PIWIL1 plays an important role in mRNA cleavage to regulate specific targets involved in cellular growth. To investigate this hypothesis, we used a non-small cell lung cancer (NSCLC) cell model to identify candidate mRNAs targeted by the RASSF1C-PIWIL1-piRNA pathway through PIWIL1-protein complex co-immunoprecipitation and RNA sequencing.
Methods: Cell lysates were prepared under non-denaturing conditions from the lung cancer cell line H1299 over-expressing RASSF1C (experimental sample) and H1299 over-expressing the vector backbone (control sample) using a co-immunoprecipitation kit (Pierce). The PIWIL1 2C12 monoclonal antibody (Wako Chemicals Inc., Richmond, VA) was used to pull down PIWIL1 protein using 1 mg of cell lysates from experimental and control samples. The RNA associated with the precipitated PIWIL1 protein complex was isolated using a total RNA isolation kit (Qiagen) and the isolated RNA was subjected to RNA deep sequencing and bioinformatic analysis.
Results: Differential expression analysis based on read counts was carried out using a fold-change threshold of 2.0, maximum p-value of 0.05, and a minimum 1CPM, identified over 5505 genes that are differentially expressed when comparing read counts from H1299 cells over-expressing RASSF1C to H1299 cells over-expressing the vector back bone. Some of the genes identified with reduced mRNA levels correspond to tumor suppressors such as PTEN and p53 and apoptosis-inducing genes such as BAD and CASP3.
Conclusions: Our study was designed to show that PIWIL-protein complexes can be pulled down from lung cancer cell lysates, and that PIWIL-protein complexes are likely to bind and regulate mRNA targets in lung cancer cells. We have identified interesting mRNAs that are potentially silenced by the PIWIL1-piRNA protein complex. Ongoing work is focused on validating some of the potential mRNA targets identified. This paves the way for conducting RNA-sequencing studies to identify specific piRNAs that associate with PIWIL1-protein complexes in the nucleus and cytoplasm.
Citation Format: Yousef G. Amaar, Mark E. Reeves. Identification of mRNA targets associated with PIWIL1 protein complex in lung cancer cells [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2525.
Abstract 2575: Mechanoactivation of NOX2-generated ROS elicits persistent TRPM8 Ca2+ signals that are inhibited by oncogenic KRas
Authors: Pratt Stephen JP , Lee Rachel M. , Hernandez-Ochoa Erick O. , Ory Eleanor C. , Thompson Keyata N. , Bailey Patrick C. , Mathias Trevor J. , Ju Julia A. , Vitolo Michele I. , Schneider Martin F. , Stains Joseph P. , Ward Christopher W. , Martin Stuart S. 
Published: September 2020

Abstract
Changes in the mechanical microenvironment and mechanical signals are observed during tumor progression, malignant transformation, and metastasis. In this context, understanding the molecular details of mechanotransduction signaling may provide unique therapeutic targets. Here we report that normal breast epithelial cells are mechanically sensitive, responding to mechanical stimuli through a two-part calcium signaling mechanism. We observed an immediate, robust rise in intracellular calcium (within seconds) followed by a persistent extracellular calcium influx (up to 30 minutes). This persistent calcium was sustained via microtubule-dependent mechano-activation of NADPH oxidase 2 (NOX2)-generated reactive oxygen species (ROS), which acted on TRPM8 channels to prolong calcium signaling. In contrast, the introduction of a constitutively-active oncogenic KRas mutation inhibited the magnitude of initial calcium signaling and severely blunted persistent calcium influx. The identification that oncogenic KRas suppresses mechanically-induced calcium at the level of ROS provides a novel mechanism for how KRas could alter cell responses to tumor microenvironment mechanics and may reveal new chemotherapeutic targets for cancer. Moreover, we find that expression changes in both NOX2 and TRPM8 mRNA predicts poor clinical outcome in estrogen receptor (ER) negative breast cancer patients, a population with limited available treatment options. The clinical and mechanistic data demonstrating disruption of this mechanically-activated calcium pathway in breast cancer patients and by KRas activation reveal novel signaling alterations that could influence cancer cell responses to the tumor mechanical microenvironment and impact patient survival.
Citation Format: Stephen JP Pratt, Rachel M. Lee, Erick O. Hernandez-Ochoa, Eleanor C. Ory, Keyata N. Thompson, Patrick C. Bailey, Trevor J. Mathias, Julia A. Ju, Michele I. Vitolo, Martin F. Schneider, Joseph P. Stains, Christopher W. Ward, Stuart S. Martin. Mechanoactivation of NOX2-generated ROS elicits persistent TRPM8 Ca2+ signals that are inhibited by oncogenic KRas [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2575.
Abstract 2605: Cytokeratin 5 promotes endocytosis to remodel cell adhesions in breast cancer
Authors: McGinn Olivia Frances , Ward Ashley V. , Finlay-Schultz Jessica , Paul Kiran Vinod , Kabos Peter , Sartorius Carol 
Published: September 2020

Abstract
Breast cancer (BC) is clinically classified according to expression of estrogen receptor, progesterone receptor (ER+ BC), HER2 (HER2+), or absence of these markers (triple negative BC). While TNBC has the inferior prognosis in the short term, ER+ breast cancer has an extended risk of recurrence that lasts up to 20 years and accounts for the most deaths overall. Cytokeratin 5 (CK5) is an intermediate filament protein that is expressed in the majority of TNBC cases and 10-50% of ER+ BC. In CK5+/ER+ BC, there is widespread heterogeneity in the amount of CK5+ tumor cells (~1-50%). The mere presence of CK5+ cells is an indicator of poor prognosis across both subtypes of BC; the reasons for this are poorly understood. We have shown that CK5+ cells within ER+ and TNBC cell lines, and heterogeneous PDX tumor models lose membrane localization of adherens junction proteins β-catenin and E-cadherin. Loss of membrane β-catenin and E-cadherin is associated with poor prognosis in breast cancer and is a precursor to cell invasion. CK5+ cells have been reported to have increased invasive potential by us and others. Thus, identifying the mechanism of CK5-dependent loss of adherens proteins at the membrane could lead to development of therapies targeting this process. β-catenin and E-cadherin localization have been reported to be regulated through endocytosis which is mediated through the small GTPase family of Rab proteins. We performed a screen to identify potential CK5 interacting proteins in breast cancer cells and identified several Rab proteins. Thus, we hypothesize that CK5 acts as a scaffold for Rabs to promote endocytosis of β-catenin and E-cadherin to increase invasive potential.To investigate this, we treated CK5 overexpressing ER+ and TNBC cells with the endocytosis inhibitor Dyngo4a and found membrane β-catenin and E-cadherin localization were restored, suggesting that CK5 may be mediating endocytosis of β-catenin and E-cadherin. Rab5 is responsible for trafficking vesicles from the plasma membrane to the early endosomes. CK5 was confirmed to interact with Rab5 by co-IP in TNBC and CK5 overexpressing ER+ cell lines. In ongoing studies, we are testing whether Rab5 knockdown prevents loss of membrane β-catenin and E-cadherin and decreases cell invasiveness. These experiments will collectively determine whether CK5 regulated endocytosis is a targetable feature in breast cancer cells.
Citation Format: Olivia Frances McGinn, Ashley V. Ward, Jessica Finlay-Schultz, Kiran Vinod Paul, Peter Kabos, Carol Sartorius. Cytokeratin 5 promotes endocytosis to remodel cell adhesions in breast cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2605.
Abstract 2657: Sphingosine-1-phosphate receptor 1 signalling modulates macrophage recruitment to diffuse large B cell lymphomas and the phagocytosis of rituximab-opsonized tumor cells
Authors: Perry Tracey Adams , Lupino Lauren , Vrzalikova Katerina , Masand Navta , Kearns Pamela R. , Murray Paul G. 
Published: September 2020

Abstract
Diffuse large B cell lymphoma (DLBCL) is the most common form of non-Hodgkin lymphoma. Currently, approximately 40% of DLBCL patients treated with standard of care therapies, which include a combination of immunotherapy (rituximab; R) and chemotherapy (CHOP), will have disease that is refractory or will relapse. Tumor-associated macrophages can phagocytose opsonised DLBCL tumor cells and are therefore centrally important in determining therapeutic outcomes for patients treated with R-CHOP. Recent data from our lab and from others suggests that the modulation of sphingosine-1-phosphate (S1P) signalling may therapeutically benefit some patients with this tumor. Here, we have investigated the effects of S1P on macrophage functions relevant to DLBCL. We show that S1P signalling through the major receptor, S1P-receptor 1 (S1PR1), suppresses the phagocytosis of rituximab-opsonized DLBCL cells. However, we also show that chemotherapy potently induces monocyte recruitment to DLBCL tumors in vivo and that S1PR1 is a primary mediator of monocyte migration both in vitro and in vivo. According to our data, S1PR1 signalling inhibitors could improve the therapeutic efficacy of rituximab-based therapies for DLBCL patients. However, our data suggests that these drugs should be given only after chemotherapy and before rituximab administration so as to maximize the S1P-mediated recruitment of therapeutic macrophages to the tumor site.
Citation Format: Tracey Adams Perry, Lauren Lupino, Katerina Vrzalikova, Navta Masand, Pamela R. Kearns, Paul G. Murray. Sphingosine-1-phosphate receptor 1 signalling modulates macrophage recruitment to diffuse large B cell lymphomas and the phagocytosis of rituximab-opsonized tumor cells [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2657.
Abstract 2675: Single-CellRNA-Seq reveals the transcriptional landscape of the immune microenvironment in chemical induced liver cancer
Authors: He Jian 
Published: September 2020

Abstract
The immune cell types as well as their numbers and activities in the tumor microenvironment (TME) may contribute to tumor progression, metastasis, prognosis and clinical response to cancer immunotherapies. Hepatocellular Carcinoma (HCC) is a type of highly heterogeneous solid tumor, causing high morbidity and mortality in the world, especially in China, however, the immune microenvironment of HCC has not been well-defined so far. In the present work, we first employed single-cell RNA sequencing on diethylnitrosamine (DEN)-induced mouse HCC model to depict the changing landscape of the immune cell composition, lineages and functional activities in TME during tumorigenesis, showing the distinct immune features in precancerous and cancerous lesions. The data indicated that the tumor-associated immune changes appeared early in pathological progression and the specific subsets of T and B cells were preferentially enriched in TME of HCC. We identified the signature genes for these specific cell subsets, and then mapped them onto the HCC RNA-seq dataset of human The Cancer Genome Atlas (TCGA) database. We found a cluster of naïve B cells characterized by high expression of CD38 was associated with better prognosis of human HCC. In addition, the inter-cellular interaction map was established based on the receptor-ligand bonding at single cell resolution. Taken together, this study will be helpful to the comprehensive understanding of dynamic immune microenvironment and cellular networks, especial naïve B cells, during HCC pathogenesis, which could provide a novel insight into the therapeutics for the HCC.
Citation Format: Jian He. Single-CellRNA-Seq reveals the transcriptional landscape of the immune microenvironment in chemical induced liver cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2675.
Abstract 2677: Sequential same slide multiplex immunofluorescence and H&E staining for combined phenotypic and morphologic characterization of formalin-fixed paraffin-embedded tissue sections
Authors: Patel Katir K. , Bares Amanda , Manesse Mael , Burton Mark , Phillips Bonnie , Lillard Kate , Hellebust Anne , Duplessis Melinda , Teplitz Kyla , George Tad 
Published: September 2020

Abstract
Multiplex immunofluorescence (mIF) has become an established method for characterizing the tumor immune microenvironment. Currently, hematoxylin and eosin (H&E) staining is typically performed on a serial tissue section to provide morphologic context for the mIF data. Serial sections do not represent identical cell populations, however, and are not always possible to obtain when the amount of available tissue is limited. Consequently, a method to examine the same tissue section by both fluorescence and brightfield imaging would be advantageous. Here we present a streamlined method and system for serial mIF and H&E staining on a single tissue slide for a comprehensive analysis to support high-throughput tissue immunophenotyping. The UltiMapper I/O PD-L1 kit was used for multiplex immunofluorescence staining of CD8, CD68, PD-L1, and pan-Cytokeratin in formalin-fixed, paraffin-embedded (FFPE) samples from human tonsil and primary tumor biopsies using the Leica Biosystems BOND RX autostainer. Stained tissues were imaged in five spectrally distinct fluorescence channels (DAPI, FITC, TRITC, Cy5, Cy7) on the RareCyte CyteFinder II HT Instrument. Slides were de-coverslipped and stained with H&E, then imaged with brightfield using the CyteFinder II HT instrument. To segment the tumor and stroma tissue regions, a HALO AI classifier was created. Fluorescence images were analyzed using the HALO Highplex FL module to identify CD8+ cytotoxic T-cells, CD68+ macrophages, CD68+/PD-L1+ immuno-suppressive macrophages, pan-CK+ tumor cells, and pan-CK+/PD-L1+ immune-evading tumor cells within the tumor and stromal regions identified by the H&E stain. This novel combination of fluorescence and brightfield analysis enables deep phenotyping of immune cells as well as assessment of cellular morphology and tumor architecture in the same tissue section.
Citation Format: Katir K. Patel, Amanda Bares, Mael Manesse, Mark Burton, Bonnie Phillips, Kate Lillard, Anne Hellebust, Melinda Duplessis, Kyla Teplitz, Tad George. Sequential same slide multiplex immunofluorescence and H&E staining for combined phenotypic and morphologic characterization of formalin-fixed paraffin-embedded tissue sections [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2677.
Abstract 2766: Potassium channel expression in cervical cancer models
Authors: Ramírez Ana , Chávez-López María de Guadalupe , Vera Eunice , de la Garza Jaime , Gariglio Patricio , Camacho Javier 
Published: September 2020

Abstract
Introduction. Cervical cancer is a public health problem in developing countries, and the fourth leading cause of cancer death in women worldwide. Most human cervical cancer cases are associated with high-risk human papillomavirus (HR-HPV) infection, but different cofactors including long-term use of oral contraceptives and multiple pregnancies increase the risk for cervical cancer in HPV-positive women. Ion channel expression and/or function differ between healthy and tumor cells. This alteration confers proliferation, progression, and survival advantages to tumor cells, making ion channels promising targets for cancer therapy and diagnosis. Here, we studied the mRNA expression of two potassium channels in human keratinocytes stably transfected with either E6 or both E6/E7 oncogenes of HPV16, and in a K14E7 transgenic mouse model of cervical cancer. These mice express the HPV16-E7 oncogene and develop cervical cancer after 6 months of treatment with 17β-estradiol (E2).
Methods. Human normal keratinocytes and keratinocytes transfected with either E6 or E6/E7 oncogenes of HPV16 were cultured. In addition, we used the K14E7-transgenic mice-cervical cancer model; some animals were treated with E2. Continuous-release pellets delivering daily 0.05 mg of E2 were implanted into 4–6-week old female mice for either 3 months to produce low-grade cervical dysplasia or 6 months to produce cervical cancer. Total RNA extraction and subsequent quantification by qPCR of Kv3.4 and KCa3.1 mRNA channel levels were performed both from cultured cells and the mice cervical tissue.
Results. Significantly higher KV3.4 and KCa3.1 channel mRNA expression was observed in keratinocytes transfected with either the E6 or E6/E7 HPV oncogenes in comparison with normal keratinocytes. In the cervical cancer mouse model, E2 treatment for 6 months increased the mRNA levels of KV3.4 and KCa3.1 channels both in the transgenic and the non-transgenic mice in comparison with the rest of the groups. The highest mRNA relative expression was observed for the KV3.4 channels in the transgenic mice displaying cervical cancer (K14E7+E2 group).
Conclusion. KV3.4 channel expression may serve as a cervical cancer biomarker.
This work was partially supported by Conacyt grant A1-S-9783.
Citation Format: Ana Ramírez, María de Guadalupe Chávez-López, Eunice Vera, Jaime de la Garza, Patricio Gariglio, Javier Camacho. Potassium channel expression in cervical cancer models [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2766.
Abstract 2838: Peritoneal immune evasion can be overcome with STING agonist treatment in peritoneal carcinomatosis of colon cancer
Authors: Yang Hannah , Lee Seung Jun , Lee Yu Seong , Lee Won Suk , Kong So Jung , Kang Beodeul , Chon Hong Jae , Kim Chan 
Published: September 2020

Abstract
Introduction: Peritoneal immune system plays an important role during the peritoneal dissemination of colon cancers. Therefore, tumor-induced T cell anergy in peritoneal cavity could lead to immune evasion and the progression of peritoneal carcinomatosis. Here, we aimed to reverse the immune evasion in peritoneal cavity and effectively suppress the peritoneal carcinomatosis of colon cancer by STING-based immunotherapy.
Methods: We established an animal model of peritoneal carcinomatosis by intraperitoneal injection of MC38 colon cancer cells to C57BL/6 mice. Temporal changes in peritoneal immune microenvironment during peritoneal tumor dissemination were first characterized by analyzing tumor nodules, malignant ascites, and peritoneum lavage by flow cytometry. Then, tumor-bearing mice were treated with either STING agonist (ADU-S100), and/or anti-PD-1 antibody. Tumor burden and the volume of ascites were assessed after the treatment. The tumors were analyzed with flow cytometric, histologic, and RNA sequencing analyses.
Results: The intraperitoneal inoculation of MC38 colon cancer cells led to dramatic immune cell changes in peritoneal cavity. While the number of myeloid-derived suppressor cells (MDSCs) were markedly increased, the number of CD8+ T cells and dendritic cells gradually decreased after initial influx in the peritoneal cavity. Treatment with STING agonist remarkably suppressed the growth of peritoneal seeding nodules (75%). Moreover, normalization and reduction of peritoneal tumor blood vessels resulted in an overt decrease in malignant ascites (85%) in the peritoneal cavity after STING agonist treatment. In addition, the number of dendritic cells and CD8+ T cells had markedly increased, but that of MDSCs was decreased in the peritoneal cavity. Moreover, the number of IFN-gamma-secreting cytotoxic T cells were increased in tumor nodules and peritoneal cavity after STING agonist treatment. Finally, the combination immunotherapy of STING agonist and anti-PD1 antibody induced stronger adaptive immunity against peritoneal carcinomatosis than monotherapy and showed potent anti-cancer activity with reduced ascites formation.
Conclusion: STING immunotherapy can normalize peritoneal tumor vasculature and immune system, and synergize with immune checkpoint blockade to control peritoneal carcinomatosis of colon cancer.
Citation Format: Hannah Yang, Seung Jun Lee, Yu Seong Lee, Won Suk Lee, So Jung Kong, Beodeul Kang, Hong Jae Chon, Chan Kim. Peritoneal immune evasion can be overcome with STING agonist treatment in peritoneal carcinomatosis of colon cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2838.