tbuckley/cabot-search huggingface dataset:
Abstract 4338: Introduction of CALR mutations to a human erythroleukemia cell line, HEL, by CRISPR/Cas9 systems
Authors: Shunichiro Yasuda, Satoru Aoyama, Daisuke Watanabe, Norihiko Kawamata
Journal: Cancer Research (2018)

Abstract [Introduction]Mutations of the calreticulin gene (CALR) are frequently found in patients with myeloproliferative neoplasms (MPN). Five-nucleotide insertion (Ins5) and 52-nucleotide deletion (Del52) in the last exon of the CALR gene are common mutations, generating an altered CALR protein with a mutated peptide sequence at the carboxy end due to the frame-shifts. Cell-lines with such CALR mutations have not been reported yet. CRISPR/Cas9 system is the novel technique commonly used in genetic engineering. CRISPR/Cas9 technology allows us to “edit” genome in mammalian cells. We introduced 46-nucleotide deletion (46Del) in the last exon of the CALR gene in a human erythroleukemia cell line, HEL. This 46Del abnormality lead to generation of an altered CALR protein with the abnormal peptide sequence at the carboxy end as seen in MPN cells with 52Del or Ins5. We compared the CALR-engineered HEL cells with the parental cells in the presence/absence of a Jak2 kinase inhibitor, ruxolitinib (RUX). [Methods and Results]To introduce 46Del abnormality, we have designed two guide RNAs. We co-transfected vectors encoding the Cas9 with a fluorescence protein as a marker as well as the two guide RNAs into HEL cells using nucleoporation. Fluorescence protein positive cells were isolated and the single cells were cultured in 96-well plates for 3 weeks. Genomic DNA of each the clone was extracted, and genomic status of CALR was examined by PCR/sequencing. We have isolated one clone with 46Del (HEL-46DEL), of which expression of abnormal transcripts was confirmed by RT-PCR/sequencing. We also confirmed expressions of abnormal CALR protein by western blot analysis. Since the JAK2-STAT5 pathway is known to be activated in MPN cells, phosphorylation status of STAT5 in HEL and HEL-DEL46 was examined, showing comparable levels in each the line. Proliferation of HEL and HEL-DEL46 was examined with XTT assay, showing that the two lines proliferated similarly. RUX inhibited proliferation of HEL cells as well as HEL-DEL46. HEL cells have a JAK2 mutation which causes constitutive activation of the JAK2-STAT5 pathway. Introduction of the Del46 mutation into HEL cells might not enhance activation of the pathway because the JAK2 mutation already activates the pathway at the maximum level. Citation Format: Shunichiro Yasuda, Satoru Aoyama, Daisuke Watanabe, Norihiko Kawamata. Introduction of CALR mutations to a human erythroleukemia cell line, HEL, by CRISPR/Cas9 systems [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4338.
Diastolic Fractional Flow Reserve to Assess the Functional Severity of Moderate Coronary Artery Stenoses
Authors: MasayukiAbe, HirofumiTomiyama, HideoYoshida, NobutakaDoba
Journal: Circulation (2000)

Background—Coronary blood flow occurs mainly during the diastolic phase of each cardiac cycle and is mainly dependent on diastolic driving pressure, especially in the left anterior descending coronary artery (LAD). We hypothesized that calculation of the ratio of the diastolic driving pressure of a stenotic LAD to its normal value, namely diastolic FFR (d-FFR), might provide precise insight into the mechanism of FFR for assessment of the functional severity of the stenosis. We compared d-FFR with FFR, coronary flow reserve (CFR), and exercise myocardial thallium scintigraphy in an lesion of intermediate severity. Methods and Results—The study population consisted of 46 consecutive patients with a moderate stenosis in the LAD in whom simultaneous measurements of aortic pressure, left ventricular pressure, and coronary pressure distal to the stenosis were obtained. Coronary flow velocity was successfully measured with a Doppler guidewire in 37 of the 46 patients. Values for FFR, d-FFR, and CFR in the noninv...
Erratum: Corrigendum: Themis is a member of a new metazoan gene family and is required for the completion of thymocyte positive selection
Authors: Andy L Johnson, L Aravind, Natalia Shulzhenko, Andre Morgun, See-Young Choi, Tanya L Crockford, Teresa Lambe, Heather Domaschenz, Edyta M Kucharska, Lixin Zheng, Carola G Vinuesa, Michael J Lenardo, Christopher C Goodnow, Richard J Cornall, Ronald H Schwartz
Journal: Nature Immunology (2009)
Abstract 18386: Using Social Media as a Method of Increasing Organ Donation
Authors: MartinCadeiras, MohammadSoroya, SagarPatel, CharlotteStarling, GeneLim, KevinDong, RonaldoMenezes, MarioDeng
Journal: Circulation (2014)

Background: The lack of consent to organ donation is the main limiting factor for heart transplantation in the United States. Limited knowledge is available about using social media to change health behavior. Social and parasocial interactions are highly effective in increasing engagement with audiences by appropriate public influencers. We hypothesized that a Social Network (SN) intervention that engages members with short, specific content through public influencers is effective in improving attitudes about organ donation. Method: We disseminated public information related to organ donation to assess efficacy of engagement in social media sources through paid and organic campaigns. We used Facebook as a social media platform to engage audiences using three different methods of content delivery. The paid campaign ran for seven days without any other active intervention, followed by a one month organic phase where an audience was created and content delivered by engaging public influencers. Effectiveness ...
Abstract 12082: Cardiomyogenesis in Hypertrophic Cardiomyopathy
Authors: Christian A Arranto, Maria R Iascone, Chiara M Mangiaracina, Anna G Sanarico, Matteo Valle, Federico Quaini, Annarosa Leri, Jan Kajstura, Paolo Ferrazzi, Piero Anversa
Journal: Circulation (2012)

Hypertrophic cardiomyopathy (HCM) is the most prevalent heritable cardiovascular disease and the leading cause of sudden death in young adults. HCM is characterized by regional ventricular hypertrophy in the absence of cavitary dilation, myofibrillar disarray, mutations of sarcomeric proteins and collagen accumulation. Septal hypertrophy has been viewed as the result of an increase in size of preexisting myocytes, but whether myocyte formation contributes to septal thickening has never been determined. Thus, 50 patients with obstructive HCM undergoing septal myectomy were studied, and 14 sex- and age-matched septa, collected from patients who died from non-cardiovascular causes were used as controls. Mutations of genes coding for contractile proteins were present in 34 cases of HCM. The majority of patients, 67%, were in NYHA class III and mean LV outflow tract gradient was 81 mmHg. Arrhythmic events consisting of atrial fibrillation and ventricular tachycardia were seen in 15 patients. In 11 cases, HCM w...
Acute Inhibition of Myoglobin Impairs Contractility and Energy State of iNOS-Overexpressing Hearts
Authors: CarstenWunderlich, UlrichFlögel, AxelGödecke, JacquelineHeger, JürgenSchrader
Journal: Circulation Research (2003)

Elevated cardiac levels of nitric oxide (NO) generated by inducible nitric oxide synthase (iNOS) have been implicated in the development of heart failure. The surprisingly benign phenotype of recently generated mice with cardiac-specific iNOS overexpression (TGiNOS) provided the rationale to investigate whether NO scavenging by oxymyoglobin (MbO2) yielding nitrate and metmyoglobin (metMb) is involved in preservation of myocardial function in TGiNOS mice. 1H nuclear magnetic resonance (NMR) spectroscopy was used to monitor changes of cardiac myoglobin (Mb) metabolism in isolated hearts of wild-type (WT) and TGiNOS mice. NO formation by iNOS resulted in a significant decrease of the MbO2 signal and a concomitantly emerging metMb signal in spectra of TGiNOS hearts only (ΔMbO2: −46.3±38.4 μmol/kg, ΔmetMb: +41.4±17.6 μmol/kg, n=6; P<0.05) leaving contractility and energetics unaffected. Inhibition of the Mb-mediated NO degradation by carbon monoxide (20%) led to a deterioration of myocardial contractility in T...
Energetic Crosstalk Between Organelles
Authors: AllenKaasik, VladimirVeksler, ErnestBoehm, MartaNovotova, AveMinajeva, RenéeVentura-Clapier
Journal: Circulation Research (2001)

Cells with high and fluctuating energy demands such as cardiomyocytes need efficient systems to link energy production to energy utilization. This is achieved in part by compartmentalized energy transfer enzymes such as creatine kinase (CK). However, hearts from CK-deficient mice develop normal cardiac function under conditions of moderate workload. We have therefore investigated whether a direct functional interplay exists between mitochondria and sarcoplasmic reticulum or between mitochondria and myofilaments in cardiac cells that catalyzes direct energy and signal channeling between organelles. We used the selective permeabilization of sarcolemmal membranes with saponin to study the functional interactions between organelles within the cellular architecture. We measured contractile kinetics, oxygen consumption, and caffeine-induced tension transients. The results show that in hearts of normal mice, ATP produced by mitochondria (supplied with substrates, oxygen, and adenine nucleotides) was able to sust...
Abstract 964: Genome-wide CRISPR screen identifies potential therapeutic combination of EGFR and FGFR inhibitors in oral cancer
Authors: Megan Ludwig, Andrew Birkeland, Sai Nimmagadda, Sue Foltin, Aditi Kulkarni, Hui Jiang, Thomas Carey, John Chad Brenner
Journal: Cancer Research (2018)

Abstract Oral squamous cell carcinoma (OSCC) has remained a disease with poor survival for decades. Current treatment options such as targeting EGFR has had limited success. We hypothesize that inhibiting compensatory pathways in combination with EGFR signaling may result in greater efficacy. To identify synergistic combinations with EGFR-targeted therapy, we introduced Genome-scale CRISPR-Cas9 KnockOut (GeCKO) libraries into OSCC cell lines. CRISPR-Cas9 generates individual genetic knockouts through targeted gene editing. We used a pool of CRISPRs targeting over 18,000 genes to perform genome-scale screening for drivers of sensitivity to EGFR-targeted therapy. Upon selection of the OSCC GeCKO pool, we identified gene knockouts in the FGFR pathway that increased sensitivity to the EGFR inhibitor gefitinib. Using resazurin viability assays we tested combinations of EGFR and FGFR inhibitors in 14 OSCC cell lines. Six/14 (43%) of the cell lines were responsive to the combination, indicating that the FGFR pathway is an alternate mechanism of resistance to EGFR-targeted therapy in some tumors. We advanced an OSCC cell line to test in vivo by establishing subcutaneous cell line xenografts in mice. After treatment for 21 days, the mice receiving the combination of EGFR and FGFR inhibitors, gefitinib and BGJ398, had significantly smaller tumors than mice receiving vehicle or either monotherapy. These results suggest targeting EGFR in combination with its compensatory pathway such as FGFR signaling could be effective in vivo. While OSCC remains a common and frequently lethal cancer, there is great potential for the development of novel personalized targeted therapies. Here, we describe the use of genome-wide CRISPR-Cas9 library to discover the synergistic combination of EGFR and FGFR inhibition. Further investigation suggests the FGFR pathway is a common compensatory mechanism to EGFR inhibition, and that targeting EGFR and FGFR in combination has efficacy in an in vivo model. Overall, targeting compensatory mechanisms in combination with EGFR-targeted therapy could generate novel, beneficial treatment plans for patients with OSCC. Citation Format: Megan Ludwig, Andrew Birkeland, Sai Nimmagadda, Sue Foltin, Aditi Kulkarni, Hui Jiang, Thomas Carey, John Chad Brenner. Genome-wide CRISPR screen identifies potential therapeutic combination of EGFR and FGFR inhibitors in oral cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 964.
Localized Controlled Delivery of Gemcitabine via Microsol Electrospun Fibers to Prevent Pancreatic Cancer Recurrence
Authors: Guanggai Xia, Hongbo Zhang, Ruoyu Cheng, Hongcheng Wang, Ziliang Song, Lianfu Deng, Xinyu Huang, Hélder A. Santos, Wenguo Cui
Journal: Advanced Healthcare Materials (2018)

The low radical surgery rate of pancreatic cancer leads to increased local recurrence and poor prognosis. Gemcitabine (GEM) is the preferred chemotherapeutic for pancreatic cancer. However, systemic chemotherapy with GEM has reached a bottleneck due to its serious side effects after frequent injections. In this study, GEM is successfully enwrapped into electrospun fibers via microsol electrospinning technology to form a stable core-shell fibrous structure. The GEM release rate can be adjusted by altering the thickness of the hyaluronan-sol inner fiber and the quantity of loaded GEM, and the release can be sustained for as long as three weeks. In vitro assays show that these electrospun fibers effectively inhibit pancreatic cancer cells and promote apoptosis. In vivo studies show that the fibrous membranes are better for inhibiting the growth of residual tumors than that of integrated tumors. Furthermore, immunohistochemistry results show that GEM-loaded fibers promote a higher cell apoptosis rate than does systemically injected GEM in residual tumors. In addition, the local delivery of GEM with fibers significantly reduces liver toxicity. In summary, a core-shell electrospun fiber for the controlled and localized delivery of GEM, which greatly improves the treatment of residual tumors and prevents pancreatic tumor recurrence, is developed.
A Simple Method to Detect Candidate Overlapping Genes in Viruses Using Single Genome Sequences
Authors: Timothy E Schlub, Jan P Buchmann, Edward C Holmes
Journal: Molecular Biology and Evolution (2018)

Overlapping genes in viruses maximize the coding capacity of their genomes and allow the generation of new genes without major increases in genome size. Despite their importance, the evolution and function of overlapping genes are often not well understood, in part due to difficulties in their detection. In addition, most bioinformatic approaches for the detection of overlapping genes require the comparison of multiple genome sequences that may not be available in metagenomic surveys of virus biodiversity. We introduce a simple new method for identifying candidate functional overlapping genes using single virus genome sequences. Our method uses randomization tests to estimate the expected length of open reading frames and then identifies overlapping open reading frames that significantly exceed this length and are thus predicted to be functional. We applied this method to 2548 reference RNA virus genomes and find that it has both high sensitivity and low false discovery for genes that overlap by at least 50 nucleotides. Notably, this analysis provided evidence for 29 previously undiscovered functional overlapping genes, some of which are coded in the antisense direction suggesting there are limitations in our current understanding of RNA virus replication.
Abstract 4449: Synthetic lethality between CSTF2 and CSTF2T in lung adenocarcinoma and melanoma cell lines
Authors: Johannes Popow, Corinna Wieshofer, Andreas Schlattl, Simon Woehrle, Ralph Neumüller, Mark P. Petronczki, Jark Boettcher, Manfred Koegl, Mark Pearson
Journal: Cancer Research (2018)

Abstract Genomic instability is a hallmark of cancer and can result in the deletion of genes with no apparent or as yet unknown relevance to tumor survival and proliferation. Although the deletion of such genes may be tolerated due to functional compensation it, however, entails a cancer cell specific vulnerability as the tumor cell relies on the function of compensating redundant genes. Recurrent deletions of cleavage stimulation factor subunit 2 Tau (CSTF2T) have been observed in several tumor samples (TCGA). During meiosis CSTF2, a paralogue of CSTF2T, which resides on the X-chromosome, is transcriptionally silenced and the zygote depends on the activity of CSTF2T. As a result, CSTF2T knockout mice exhibit male sterility which corroborates that CSTF2 and CSTF2T form a functionally redundant pair of genes with an essential function (Dass et al. 2007). With the aim to apply these findings to tumor biology, we therefore tested whether tumor cells with homozygous CSTF2T deletions depend on CSTF2 using CRISPR-based growth competition assays and confirmed this concept in lung adenocarcinoma and melanoma cell line models. Our data establish synthetic lethality between CSTF2 and CSTF2T and suggest inhibition of CSTF2 in CSTF2T deficient tumors as a new therapeutic concept. Citation Format: Johannes Popow, Corinna Wieshofer, Andreas Schlattl, Simon Woehrle, Ralph Neumüller, Mark P. Petronczki, Jark Boettcher, Manfred Koegl, Mark Pearson. Synthetic lethality between CSTF2 and CSTF2T in lung adenocarcinoma and melanoma cell lines [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4449.
MicroRNA-101 Inhibited Postinfarct Cardiac Fibrosis and Improved Left Ventricular Compliance via the FBJ Osteosarcoma Oncogene/Transforming Growth Factor-β1 Pathway
Authors: ZhenweiPan, XuelinSun, HongliShan, NingWang, JinghaoWang, JinshuaiRen, ShuyaFeng, LiangjunXie, ChunyingLu, YeYuan, YangZhang, YingWang, YanjieLu, BaofengYang
Journal: Circulation (2012)

Background—Cardiac interstitial fibrosis is a major cause of the deteriorated performance of the heart in patients with chronic myocardial infarction. MicroRNAs (miRs) have recently been proven to be a novel class of regulators of cardiovascular diseases, including those associated with cardiac fibrosis. This study aimed to explore the role of miR-101 in cardiac fibrosis and the underlying mechanisms. Methods and Results—Four weeks after coronary artery ligation of rats, the expression of miR-101a and miR-101b (miR-101a/b) in the peri-infarct area was decreased. Treatment of cultured rat neonatal cardiac fibroblasts with angiotensin II also suppressed the expression of miR-101a/b. Forced expression of miR-101a/b suppressed the proliferation and collagen production in rat neonatal cardiac fibroblasts, as revealed by cell counting, MTT assay, and quantitative reverse transcription–polymerase chain reaction. The effect was abrogated by cotransfection with AMO-101a/b, the antisense inhibitors of miR-101a/b. c...
Chronic Atrial Fibrillation in Patients With Rheumatic Heart Disease
Authors: MohanNair, PrasadShah, RavinderBatra, ManojKumar, JagdishMohan, UpkarKaul, RameshArora
Journal: Circulation (2001)

Background There is little information concerning mapping and radiofrequency ablation (RFA) of arrhythmias seen during reinduction of atrial fibrillation (AF) after pharmacological and/or electrical cardioversion in patients with chronic AF and rheumatic heart disease. Methods and Results Seventeen patients with rheumatic heart disease and symptomatic chronic AF underwent multisite atrial mapping during reinduction of AF after cardioversion. An organized atrial arrhythmia of varying duration was seen to precede the AF in all patients. The earliest atrial activity during this organized rhythm was near the coronary sinus ostium (CS OS) in 14 patients and along the left side of the interatrial septum (IAS) in 3 patients. RFA was performed in 16 patients (14 near the CS OS and 2 along the IAS). Postablation AF was inducible in 1 patient in whom RFA was preformed near the CS OS and in both patients when it was performed along the IAS. At a follow-up of 6 to 56 weeks (mean, 32 weeks), 10 of the 13 patients who ...
Abstract 3293: Solid tumors have frequent mutation, copy number variation and differential mRNA expression of GPCRs: Are such GPCRs functional oncogenes
Authors: Krishna Sriram, Kevin Moyung, Ross Corriden, Paul Insel
Journal: Cancer Research (2018)

Abstract G protein-coupled receptors (GPCRs), the largest family of membrane receptors, regulate numerous cellular functions and are drug targets for many disorders but not generally in cancer. We analyzed The Cancer Genome Atlas (TCGA) for GPCR mutations, copy number variation (CNV) and mRNA expression in 20 categories of solid tumors. We found that numerous GPCRs are frequently mutated, in particular, certain adhesion GPCRs (e.g.,GPR98 and GPR112), which appear to have a higher density of mutation events than other genes of similar length. Tumors with high mutational burden show a high frequency of such GPCR mutations that may result from DNA damage. CNV (especially amplifications and single-copy deletions) of GPCRs is widespread. In certain tumor types, particular GPCRs (e. g., GPR160) show high-level amplification in &amp;gt;30% of tumors. However, CNV does not appear to be a major factor in determining differential expression (DE) of GPCRs in tumors. Compared to RNA expression in normal tissues (GTEX database), most solid tumor types (including those accounting for the most annual deaths) differentially express &amp;gt;50 GPCRs, including 77 GPCRs with increased expression in at least one tumor type that are targets for approved drugs, providing opportunities for drug repurposing. DE of GPCRs is largely independent of tumor stage/grade, largely insensitive to specific driver mutations, and similar in primary and metastatic tumors, which both have high expression of numerous GPCRs in nearly all members within tumor populations. Cancer cells highly express most GPCRs overexpressed in tumors, making such GPCRs (especially those that are druggable) attractive candidates for further validation and functional studies. Multiple published studies provide functional data for certain such GPCRs. These findings imply a previously unappreciated role for GPCRs in solid tumors. Overexpressed GPCRs in tumors may regulate tumor biology as “functional oncogenes” and are potentially novel biomarkers and therapeutic targets, including for approved drugs. Citation Format: Krishna Sriram, Kevin Moyung, Ross Corriden, Paul Insel. Solid tumors have frequent mutation, copy number variation and differential mRNA expression of GPCRs: Are such GPCRs functional oncogenes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3293.