tbuckley/cabot-search huggingface dataset:
Abstract 395: Transient Inactivation of Retinoblastoma Induces De-Novo Cardiomyogenesis From Human Myocardial Progenitors but Not Pre-Existing Cardiomyocyte Replication
Authors: Konstantinos E Hatzistergos, Julien Sage, Jamie F Conklin, Michael Bellio, Krystalenia Valasaki, Irene S Margitich, Courtney Premer, Wayne Balkan, Joshua M Hare
Journal: Circulation Research (2015)

Introduction: Activation of cardiac cell cycle re-entry is considered the primary therapeutic strategy for cardiomyocyte (CM) regeneration. However, the role of cardiac cell-cycle control in cardiomyogenesis remains elusive. Here, we combined RNA interference and stem cell modeling to investigate the role of Retinoblastoma (RB) in human cardiomyogenesis. Hypothesis: RB regulates proliferation and differentiation of cardiac progenitors (CPCs) but not CM replication. Methods: H9 human embryonic stem cells (hESCs) stably expressing tetracycline (tet)-inducible shRNAs against RB (hESCshRB) or hemagglutinin-tagged RB (hESCHA-RB) were tet-induced at selected time-points during or after CM differentiation. Results: Analysis of ser-608 illustrated stage-specific differences in the degree of RB inactivation during normal hESCs-cardiogenesis. Transient shRB knockdown in hESCshRB-derived embryoid bodies (EBs) during the CPC-stage (EB-days 5-8), significantly upregulated GATA4, ISL1, CTNNI, and cKit transcription (p&lt;0.05), while increasing the yield of beating EBs by 2.4-fold (n=6/group, p&lt;0.0001 vs. vehicle). Gene-expression arrays of 22 RB-related genes, illustrated that shRB-knockdown upregulated CCND1, CCND2, CCND3, and CDK4, CDK6 (p&lt;0.05), followed by a 3.6-fold increase in E2F3 (p&lt;0.05) expression. Moreover, expression of p107 and p130, p27, p57, ARF and CDKN3 were also significantly increased (p&lt;0.05), whereas TP53 and MDM2 remained unchanged. Ectopic HA-RB in CPCs did not significantly affect cardiogenesis (n=18). Conversely, shRB knockdown in EB-day 60-derived CMs (n=15) did not stimulate cell cycle re-entry, as assessed by analysis of EdU incorporation and Aurora-B kinase (AurB). Remarkably, co-culture of hESCHA-RB-derived CMs with adult cardiac (CSCs) and/or mesenchymal (MSCs) stem cells (n=15/group), increased cell-cycle re-entry ~2.8-fold, assessed by ser-10 Histone H3 (p=0.0002) and AurB (p&lt;0.0001). Conclusions: These findings suggest that RB regulates proliferation and differentiation of human CPCs in a cell-autonomous manner, via a CCND-CDK4/6-E2F3 mechanism. Conversely, CM replication may be enhanced via cell-cell interactions with MSCs and/or CSCs, but not cell-autonomously via RB inactivation.
Abstract P238: Snf1-Related Kinase Is a Novel Regulator of Cardiomyocyte Metabolism
Authors: Amy K Rines, Michael A Burke, Varun Nagpal, Hossein Ardehali
Journal: Circulation Research (2011)

Background: Snf1-related Kinase (SNRK) is a serine/threonine kinase with sequence homology to AMP-activated kinase (AMPK). We have found that SNRK is upregulated in hearts from patients with ischemic cardiomyopathy, but the function of SNRK has not been studied in cardiomyocytes. Since previous gene array data show that SNRK alters expression of metabolic genes, we determined whether SNRK regulates cardiomyocyte metabolism. Results: SNRK downregulation reduced ATP levels by 23.34% in neonatal rat cardiomyocytes compared to nonsilencing siRNA, and SNRK overexpression increased ATP by 20.67% compared to GFP control. SNRK knockdown reduced baseline oxygen consumption rate (OCR) by 23.69%, and by 54.53% with the mitochondrial uncoupler carbonyl cyanide 3-chlorophenylhydrazone (CCCP). SNRK overexpression increased OCR by 9.57% with CCCP. Mitochondrial content was unchanged as measured by mitochondrial DNA and cardiolipin staining. However, tetramethylrhodamine ethyl ester (TMRE) staining was increased by SNRK, suggesting that SNRK maintains mitochondrial membrane potential. Furthermore, the extracellular acidification rate was reduced 19.47% with SNRK knockdown and increased 12.57% with overexpression, signifying enhanced glycolytic flux. SNRK also increased lactate levels and mRNA of the glycolytic proteins hexokinase I and II. Glucose uptake increased 29.61% with SNRK overexpression, and expression of glucose transporters GLUT1 and GLUT4 was also increased, demonstrating an increase in cellular glucose import. Glycogen was also decreased 40.69% with SNRK knockdown and increased 46.03% with overexpression, demonstrating that SNRK reduces storage of glucose into glycogen. Additionally, OCR with palmitate over baseline was reduced 43.56% with SNRK downregulation and increased 285.6% with overexpression, suggesting enhanced fatty acid oxidation. Phosphorylation of acetyl-coA carboxylase was also increased by SNRK. Fatty acid uptake, however, was unchanged. Conclusions: Our results demonstrate that SNRK increases ATP and oxygen consumption through augmented mitochondrial membrane potential, glucose utilization, and fatty acid oxidation. These findings reveal SNRK as a major modulator of cardiomyocyte metabolism.
Abstract P259: Functional Characterization of an ALOX15 Promoter Variant Associated with Coronary Artery Calcification: Regulation of ALOX15 by Vimentin
Authors: Susmita Samanta, Kurtis Anderson, Sean Moran, David Gorenstein, Myriam Fornage
Journal: Circulation Research (2011)

Human 12/15-lipoxygenase (ALOX15) catalyzes the oxidation of polyunsaturated fatty acids and has been implicated in the pathogenesis of atherosclerosis. We previously reported that a common haplotype of the ALOX15 gene is associated with higher prevalence of coronary artery calcification in a cohort of middle-aged African-Americans. This haplotype was uniquely tagged by a promoter variant (rs2255888). We carried out an in vitro characterization of this promoter variant to further investigate regulatory mechanisms of the ALOX15 gene. We evaluated the activity of ALOX15 variant A-carrying and wild type G-carrying promoter haplotypes using a luciferase assay. We demonstrated a 65% higher activity of the A-carrying promoter haplotype as compared to the G-carrying promoter haplotype. Using mass-spectrometry and electrophoretic mobility shift assay we showed that vimentin, a structural protein, specifically binds to both A-carrying and G-carrying promoter haplotypes in vitro. However, the A allele-carrying promoter haplotype had an 83% increased in vitro binding of vimentin compared to the G allele-carrying promoter haplotype. In vivo binding of vimentin to this particular promoter region has also been detected by chromatin immunoprecipitation. Using non-denaturing polyacrylamide gel electrophoresis and UV thermal melting we showed evidence of the formation of intramolecular G-quadruplex structure in the DNA sequence of the G-carrying promoter haplotype. However, for the A-carrying promoter haplotype, formation of intramolecular G-quadruplex structure was reduced and intermolecular G-quadruplex was increased. We also observed that vimentin increased ALOX15 gene expression. The current studies indicate that sequence variant of the rs2255888 polymorphism is associated with a structural change of ALOX15 promoter region. This change may be responsible for the increased binding of vimentin to the promoter region. Our study is the first to show that vimentin may act as a transcription regulator of ALOX15. It has been reported that vimentin is secreted by activated macrophages. Thus, the novel function identified here may be relevant to ALOX15 pathogenesis mechanisms in atherosclerosis.
Chromoendoscopy versus narrow band imaging in UC: a prospective randomised controlled trial
Authors: Raf Bisschops, Talat Bessissow, Joseph A Joseph, Filip Baert, Marc Ferrante, Vera Ballet, Hilde Willekens, Ingrid Demedts, Karel Geboes, Gert De Hertogh, Séverine Vermeire, Paul Rutgeerts, Gert Van Assche
Journal: Gut (2017)

Background Patients with long-standing UC have an increased risk for the development of colonic neoplastic lesions. Chromoendoscopy (CE) has been proven to enhance neoplasia detection while the role of virtual chromoendoscopy (VC) is still to be defined. Objective To compare the performance of CE to VC for the detection of neoplastic lesions in patients with long-standing UC. Design A multicentre prospective randomised controlled trial. 131 patients with long-standing UC were randomised between CE with methylene blue 0.1% (n=66) or VC with narrow band imaging (NBI) (n=65). Biopsies were taken from visible lesions and surrounding mucosa. No random biopsies were performed. The primary outcome was the difference in total number of neoplastic lesions detected in each group. Results There was no significant difference between NBI and CE for neoplasia detection. Mean number of neoplastic lesions per colonoscopy was 0.47 for CE and 0.32 for NBI (p=0.992). The neoplasia detection rate was not different between CE (21.2%) and NBI (21.5%) (OR 1.02 (95% CI 0.44 to 2.35, p=0.964). Biopsies from the surrounding mucosa yielded no diagnosis or dysplasia. The per lesion neoplasia detection was 17.4% for CE and 16.3% for NBI (OR 1.09 (95% CI 0.59 to 1.99, p=0.793). The total procedural time was on average 7 min shorter in the NBI group. Conclusion CE and NBI do not differ significantly for detection of colitis-associated neoplasia. Given the longer withdrawal time for CE and easier applicability, NBI may possibly replace classical CE. Trial registration number NCT01882205; Results.
Circulating tumor DNA (ctDNA) as a marker of recurrence risk in stage II colon cancer (CC).
Authors: Jeanne Tie, Isaac Kinde, Yuxuan Wang, Hui-li Wong, Iain Skinner, Rachel Wong, Malcolm Steel, Luis A. Diaz, Nickolas Papadopoulos, Suzanne Kosmider, Desmond Yip, Craig Underhill, Andrew Mark Haydon, Michael Christie, Robert Strausberg, Kenneth W. Kinzler, Bert Vogelstein, Peter Gibbs
Journal: Journal of Clinical Oncology (2014)

11015 Background: Markers that better define recurrence risk for patients (pts) with stage II CC are urgently required, potentially defining a subset that would most benefit from adjuvant chemotherapy (CTX) and intensive surveillance. An alternative strategy to standard analyses of the resected surgical specimen is to directly examine plasma for evidence of residual disease. Recently, ctDNA has shown promise as a blood biomarker in advanced colorectal cancer; here we explore the potential of this marker in stage II CC. Methods: In this prospective study, plasma samples are being collected at 4-10 weeks post-op in 250 stage II CC pts, with serial 3 monthly samples on a subset of 175 pts. Adjuvant CTX is at clinician discretion, blinded to ctDNA analysis. Surveillance includes 3 monthly CEA and 6 monthly CT imaging for 2 years. All samples were sent to Johns Hopkins Kimmel Cancer Center, where tumor tissue was analyzed for hotspot mutations in TP53, APC, KRAS, NRAS, BRAF, PIK3CA, CTNNB1, SMAD4, and FBXW7 using a massively parallel sequencing platform (Safe-SeqS). The identified mutation was queried and quantified in plasma using the same platform, blinded to clinical data. Results: Preliminary data is available on 78 of the 190 pts enrolled to date. Median age is 66 years, 25/78 (32%) received adjuvant CTX. At least 1 mutation was found in all tumors, with matching ctDNA detectable in 6/78 (7.7%) plasma samples. 10 (12.8%) recurrences have occurred at a median follow-up of 507 days, including 5 of 6 pts with detectable ctDNA and 5 of 72 with no detectable ctDNA (Table). Pts with detectable ctDNA had a shorter recurrence-free survival (median 234 days vs undefined, HR 23.09, log-rank p < 0.0001). In an exploratory analysis of the correlation between ctDNA and clinicopathologic features, detectable ctDNA maintained prognostic significance, including for T3 tumors (HR for time to recurrence 80.55, log-rank p < 0.0001). Conclusions: Early data suggests ctDNA is a promising marker of recurrence risk in stage II CC. Preliminary analyses suggests this may be independent of clinicopathologic features. Recurrence No recurrence Total Post-op ctDNA positive 5 1 6 Post-op ctDNA negative 5 67 72 Total 10 68 78 Fisher’s exact P < 0.0001. RR = 12 (95% CI 4.79 – 30.06).
Hypoxia-inducible factor-2α promotes tumor progression and has crosstalk with Wnt/β-catenin signaling in pancreatic cancer
Authors: Qi Zhang, Yu Lou, Jingying Zhang, Qihan Fu, Tao Wei, Xu Sun, Qi Chen, Jiaqi Yang, Xueli Bai, Tingbo Liang
Journal: Molecular Cancer (2017)

Pancreatic cancer is a devastating disease that is characterized by persistent hypoxia. The roles of hypoxia-inducible factor-2α (hif-2α) are different to those of hif-1α, although both are critical for tumor cells to adapt to the hypoxic microenvironment. However, unlike the well-studied hif-1α, the role of hif-2α in tumors, including pancreatic cancer, is poorly understood.Herein, we used a mutated hif-2α (A530T) to figure out the problem that wild-type hif-2α is quickly degraded which limits the study of its function. Using several cell lines, mouse models, and human tissues, we obtained a general picture of hif-2α in pancreatic cancer progression.Functional assays revealed that hif-2α promotes epithelial-to-mesenchymal transition, enhances tumor proliferation and invasion, increases stemness, facilitates angiogenesis, and up-regulates aerobic glycolysis. We identified an interaction between hif-2α and β-catenin, and found that hif-2α/β-catenin complex formation increased the activity of β-catenin and the protein stability of hif-2α. In vivo study confirmed the pro-oncogenic role of hif-2α, whose expression correlated with those of E-cadherin, vimentin, Ki-67, and CD31, but not hif-1α. A human tissue study showed that hif-2α was associated with lymph node metastasis, pathological grade, stroma abundance, vascularization and patient survival. High expression of hif-2α was also identified as an independent indicator of poor prognosis in patients with pancreatic cancer.Our systematic study revealed the roles of hif-2α in pancreatic cancer, and may provide a novel target for this highly malignant disease.
Serological diagnostics in the detection of IgG autoantibodies against human collagen VII in epidermolysis bullosa acquisita: a multicentre analysis
Authors: T. Schmidt, M. Hoch, S.S. Lotfi Jad, F. Solimani, G. Di Zenzo, A.V. Marzano, M. Goebeler, E. Cozzani, J.S. Kern, C. Sitaru, I. Lakoš Jukić, M. Sárdy, S. Uzun, H. Jedlickova, R. Gläser, M. Kaneda, R. Eming, G. Göpel, N. Ishii, B. Greene, T. Hashimoto, M. Hertl
Journal: British Journal of Dermatology (2017)

Epidermolysis bullosa acquisita (EBA) is a rare, potentially devastating autoimmune disease of the skin. IgG autoantibodies directed against type VII collagen (Col7), the major component of anchoring fibrils, induce skin fragility leading to cutaneous and mucocutaneous blister formation, which is mostly of a scarring phenotype. Thus, powerful and reproducible diagnostic assays are critical to establish the diagnosis of EBA early to avoid irreversible sequelae.The present international, retrospective multicentre study included a large cohort of patients with EBA and evaluated the diagnostic power of four different diagnostic assays for the detection of anti-Col7 IgG autoantibodies.Overall, 95 EBA sera and 200 control sera consisting of 100 bullous pemphigoid sera, 50 pemphigus vulgaris sera and 50 sera of healthy controls were tested for anti-Col7 IgG autoantibodies using indirect immunofluorescence (IIF), two commercial enzyme-linked immunosorbent assay (ELISA) systems and Western blot (WB) analysis. EBA sera were taken from patients with positive direct immunofluorescence and IgG reactivity in at least one of the immunoserological assays (IIF, ELISA, WB).A Col7-NC1/NC2 ELISA (MBL, Nagoya, Japan) showed the highest sensitivity (97·9%), followed by a Col7-NC1 ELISA (Euroimmun, Lübeck, Germany) (89·5%), WB with Col7-NC1 (85·3%), and IIF on saline-split human skin (74·7%). The specificities of both ELISA systems were comparable (NC1 98·7%, NC1/NC2 99·3%). Furthermore, WB was more sensitive than IIF, which was more specific.The two commercially available ELISA systems allow for a highly sensitive and specific diagnosis of EBA. The sensitivity of the Col7-NC1/NC2 ELISA is significantly higher compared with the ELISA based on the Col7-NC1 domain only.
Choose and Use Your Chemical Probe Wisely to Explore Cancer Biology
Authors: Julian Blagg, Paul Workman
Journal: Cancer Cell (2017)

Small-molecule chemical probes or tools have become progressively more important in recent years as valuable reagents to investigate fundamental biological mechanisms and processes causing disease, including cancer. Chemical probes have also achieved greater prominence alongside complementary biological reagents for target validation in drug discovery. However, there is evidence of widespread continuing misuse and promulgation of poor-quality and insufficiently selective chemical probes, perpetuating a worrisome and misleading pollution of the scientific literature. We discuss current challenges with the selection and use of chemical probes, and suggest how biologists can and should be more discriminating in the probes they employ.
Blimp-1–dependent and –independent natural antibody production by B-1 and B-1–derived plasma cells
Authors: Hannah P. Savage, Vanessa M. Yenson, Sanjam S. Sawhney, Betty J. Mousseau, Frances E. Lund, Nicole Baumgarth
Journal: The Journal of Experimental Medicine (2017)

Natural antibodies contribute to tissue homeostasis and protect against infections. They are secreted constitutively without external antigenic stimulation. The differentiation state and regulatory pathways that enable continuous natural antibody production by B-1 cells, the main cellular source in mice, remain incompletely understood. Here we demonstrate that natural IgM-secreting B-1 cells in the spleen and bone marrow are heterogeneous, consisting of (a) terminally differentiated B-1–derived plasma cells expressing the transcriptional regulator of differentiation, Blimp-1, (b) Blimp-1+, and (c) Blimp-1neg phenotypic B-1 cells. Blimp-1neg IgM-secreting B-1 cells are not simply intermediates of cellular differentiation. Instead, they secrete similar amounts of IgM in wild-type and Blimp-1–deficient (PRDM-1ΔEx1A) mice. Blimp-1neg B-1 cells are also a major source of IgG3. Consequently, deletion of Blimp-1 changes neither serum IgG3 levels nor the amount of IgG3 secreted per cell. Thus, the pool of natural antibody-secreting B-1 cells is heterogeneous and contains a distinct subset of cells that do not use Blimp-1 for initiation or maximal antibody secretion.
Abstract 359: Tripartite Motif Protein 58 (trim58) is a Novel Regulator of Membrane Repair With Increased Expression in Failing Cardiac Muscle
Authors: Karthikeyan Krishnamurthy, Jenna Alloush, Zhaobin Xu, Eric X Beck, Peter J Mohler, Paul Janssen, Noah Weisleder
Journal: Circulation Research (2015)

In recent years, members of the tripartite motif-containing (TRIM) family of E3 ubiquitin ligases have been shown to be both positively and negatively regulated in various disease pathologies. TRIM72 (MG53) has been directly linked with regulation of sarcolemmal membrane repair in striated muscle cells, including cardiomyocytes. Recently, we were first to identify that a novel tripartite motif family member, TRIM58, is a negative regulator of the cell membrane repair process in striated muscle cells. Overexpression of TRIM58 decreases the membrane repair capacity of cultured myoblasts as measured by dye occlusion following laser-mediated disruption of the sarcolemmal membrane. We also find that TRIM58 can directly interact with TRIM72/MG53 and alter signaling through phosphatidylinositol-4,5-bisphosphate 3-kinase (PI3K). Protein profiling experiments show that TRIM58 expression increases during the development of heart failure suggesting that TRIM58 may be relevant in the development of cardiac failure. Western blot and histological examination in both human (Fig.1) and mouse transverse aortic constriction (TAC) heart failure samples clearly show an increased expression of TRIM58 in cardiac tissue. Our results suggest that TRIM58 levels might serve as a potential prognostic marker and that TRIM58 may be a therapeutic target for the management of cardiovascular disease.
Erratum: Prefontal cortex in long-term memory: an “interference” approach using magnetic stimulation
Authors: Simone Rossi, Stefano F. Cappa, Claudio Babiloni, Patrizio Pasqualetti, Carlo Miniussi, Filippo Carducci, Fabio Babiloni, Paolo M. Rossini
Journal: Nature Neuroscience (2002)
Effect of a novel agent, SL-401, targeting interleukin-3 (IL-3)-receptor on plasmacytoid dendritic cell (pDC)-induced myeloma cell growth and drug resistance.
Authors: Dharminder Chauhan, Arghya Ray, Christopher Brooks, Eric K. Rowinsky, Kenneth Carl Anderson
Journal: Journal of Clinical Oncology (2013)

8582 Background: Multiple myeloma (MM) remains incurable despite novel therapies, highlighting the need for further identification of factors mediating disease progression and drug resistance. The bone marrow (BM) microenvironment confers growth, survival, and drug resistance in MM cells. Our recent study utilized in vitro and in vivo MM xenograft models to show that plasmacytoid dendritic cells (pDCs) were significantly increased in MM BM and promote MM growth (Chauhan et al., Cancer Cell 2009, 16:309). Importantly, we found increased IL-3 levels upon pDC-MM interaction, which in turn, trigger MM cell growth and pDCs survival. IL-3R is highly expressed on pDCs. We utilized SL-401, a novel biologic conjugate that targets IL-3R, to examine whether abrogation of IL-3–IL-3R signaling axis affects pDC-MM interaction and its tumor promoting sequelae. Methods: MM cell lines, patient MM cells, and pDCs from healthy donors or MM patients were utilized to study the anti-MM activity of SL-401. MM cells and pDCs were cultured alone or together in the presence or absence of SL-401, followed by analysis of cell growth or viability. Results: SL-401 significantly decreased the viability of pDCs at low concentrations (IC 50 : 0.83 ng/ml; P &lt; 0.005, n = 3). SL-401 also decreased the viability of MM cells at clinically achievable doses. Co-culture of pDCs with MM cells induced growth of MM cell lines; and importantly, low doses (0.8 ng/ml) of SL-401 blocked MM cell growth-promoting activity of pDCs. MM patient-derived pDCs induced growth of MM cell lines and primary MM cells as well; conversely, SL-401 inhibited pDC-triggered MM cell growth (P &lt; 0.005, n= 5). Tumor cells from 3 of the 5 patients were from patients whose disease was progressing while on bortezomib, dexamethasone, and lenalidomide therapies. In agreement with these results, SL-401 blocked pDC-induced growth of dexamethasone-resistant MM cell lines. Conclusions: Our study therefore provides the basis for directly targeting pDCs or blocking the pDC-MM interaction, as well as targeting MM, in novel therapeutic strategies with SL-401 to enhance MM cytotoxicity, overcome drug-resistance, and improve patient outcome.