tbuckley/cabot-search huggingface dataset:
Neighboring Genes Show Correlated Evolution in Gene Expression
Authors: Avazeh T. Ghanbarian, Laurence D. Hurst
Journal: Molecular Biology and Evolution (2015)

When considering the evolution of a gene's expression profile, we commonly assume that this is unaffected by its genomic neighborhood. This is, however, in contrast to what we know about the lack of autonomy between neighboring genes in gene expression profiles in extant taxa. Indeed, in all eukaryotic genomes genes of similar expression-profile tend to cluster, reflecting chromatin level dynamics. Does it follow that if a gene increases expression in a particular lineage then the genomic neighbors will also increase in their expression or is gene expression evolution autonomous? To address this here we consider evolution of human gene expression since the human-chimp common ancestor, allowing for both variation in estimation of current expression level and error in Bayesian estimation of the ancestral state. We find that in all tissues and both sexes, the change in gene expression of a focal gene on average predicts the change in gene expression of neighbors. The effect is highly pronounced in the immediate vicinity (<100 kb) but extends much further. Sex-specific expression change is also genomically clustered. As genes increasing their expression in humans tend to avoid nuclear lamina domains and be enriched for the gene activator 5-hydroxymethylcytosine, we conclude that, most probably owing to chromatin level control of gene expression, a change in gene expression of one gene likely affects the expression evolution of neighbors, what we term expression piggybacking, an analog of hitchhiking.
Regulation of Episodic Growth Hormone Secretion by the Central Epinephrine System
Authors: L. Cass Terry, W. R. Crowley, M. D. Johnson
Journal: Journal of Clinical Investigation (1982)

Catecholamines are postulated to regulate growth hormone (GH) secretion by their influence on the release of two hypothalamic substances, somatostatin, which inhibits GH release, and GH-releasing factor, as yet unidentified. Extensive pharmacologic studies in man and animals indicate a stimulatory effect of central norepinephrine and dopamine on GH, but the function of epiphephrine (EPI) is uncertain. Furthermore, many of the agents used to study the role of catecholamines in GH regulation are not selective in that they affect adrenergic as well as nor-adrenergic and/or dopaminergic neurotransmission. In the present investigation, central nervous system (CNS) EPI biosynthesis was selectively interrupted with the specific norepinephrine N-methyltransferase inhibitors, SK & F 64139 (Smith, Kline & French Laboratories) and LY 78335, (Eli Lilly & Co. Research Laboratories) and the effects of central EPI depletion on episodic GH secretion in the chronically cannulated rat model were determined. Inhibition of CNS EPI synthesis with SK & F 64139 caused complete suppression of episodic GH secretion and concomitantly reduced the EPI level in the hypothalamus without affecting dopamine or norepinephrine. Administration of LY 78335 produced similar effects on pulsatile GH. Morphine-induced, but not clonidine-induced, GH release also was blocked by SK & F 64139. These results indicate that (a) the central EPI system has a major stimulatory function in episodic GH release, (b) morphine-induced GH release is mediated by the central EPI system, and (c) clonidine stimulates GH release by activation of postsynaptic α-adrenergic receptors. Drugs that affect CNS adrenergic systems have a potential role in the diagnosis and treatment of disorders of GH secretion.
Tylophorine, a phenanthraindolizidine alkaloid isolated from Tylophora indica exerts antiangiogenic and antitumor activity by targeting vascular endothelial growth factor receptor 2–mediated angiogenesis
Authors: Sarita Saraswati, Pawan K Kanaujia, Shakti Kumar, Ranjeet Kumar, Abdulqader A Alhaider
Journal: Molecular Cancer (2013)

Anti-angiogenesis targeting VEGFR2 has been considered as an important strategy for cancer therapy. Tylophorine is known to possess anti-inflammatory and antitumor activity, but its roles in tumor angiogenesis, the key step involved in tumor growth and metastasis, and the involved molecular mechanism is still unknown. Therefore, we examined its anti-angiogenic effects and mechanisms in vitro and in vivo. We used tylophorine and analyzed its inhibitory effects on human umbilical vein endothelial cells (HUVEC) in vitro and Ehrlich ascites carcinoma (EAC) tumor in vivo. Tylophorine significantly inhibited a series of VEGF-induced angiogenesis processes including proliferation, migration, and tube formation of endothelial cells. Besides, it directly inhibited VEGFR2 tyrosine kinase activity and its downstream signaling pathways including Akt, Erk and ROS in endothelial cells. Using HUVECs we demonstrated that tylophorine inhibited VEGF-stimulated inflammatory responses including IL-6, IL-8, TNF-α, IFN-γ, MMP-2 and NO secretion. Tylophorine significantly inhibited neovascularization in sponge implant angiogenesis assay and also inhibited tumor angiogenesis and tumor growth in vivo. Molecular docking simulation indicated that tylophorine could form hydrogen bonds and aromatic interactions within the ATP-binding region of the VEGFR2 kinase unit. Tylophorine exerts anti-angiogenesis effects via VEGFR2 signaling pathway thus, may be a viable drug candidate in anti-angiogenesis and anti-cancer therapies.
Truncated RON Tyrosine Kinase Drives Tumor Cell Progression and Abrogates Cell-Cell Adhesion Through E-Cadherin Transcriptional Repression
Authors: Chiara Bardella, Barbara Costa, Piera Maggiora, Salvatore Patane’, Martina Olivero, Guglielmina N. Ranzani, Michele De Bortoli, Paolo M. Comoglio, Maria Flavia Di Renzo
Journal: Cancer Research (2004)

Abstract RON is a tyrosine kinase receptor that triggers scattering of normal cells and invasive growth of cancer cells on ligand binding. We identified a short RON mRNA, which is expressed in human lung, ovary, tissues of the gastrointestinal tract, and also in several human cancers, including ovarian carcinomas and cell lines from pancreatic carcinomas and leukemias. This transcript encodes a truncated protein (short-form RON; sf-RON), lacking most of the RON receptor extracellular domain but retaining the whole transmembrane and intracellular domains. Sf-RON shows strong intrinsic tyrosine kinase activity and is constitutively phosphorylated. Epithelial cells transduced with sf-RON display an aggressive phenotype; they shift to a nonepithelial morphology, are unable to form aggregates, grow faster in monolayer cultures, show anchorage-independent growth, and become motile. We show that in these cells, E-cadherin expression is lost through a dominant transcriptional repression pathway likely mediated by the transcriptional factor SLUG. Altogether, these data show that expression of a naturally occurring, constitutively active truncated RON kinase results in loss of epithelial phenotype and aggressive behavior and, thus, it might contribute to tumor progression.
Saw Palmetto for Benign Prostatic Hyperplasia
Authors: Stephen Bent, Christopher Kane, Katsuto Shinohara, John Neuhaus, Esther S. Hudes, Harley Goldberg, Andrew L. Avins
Journal: New England Journal of Medicine (2006)

Saw palmetto is used by over 2 million men in the United States for the treatment of benign prostatic hyperplasia and is commonly recommended as an alternative to drugs approved by the Food and Drug Administration.In this double-blind trial, we randomly assigned 225 men over the age of 49 years who had moderate-to-severe symptoms of benign prostatic hyperplasia to one year of treatment with saw palmetto extract (160 mg twice a day) or placebo. The primary outcome measures were changes in the scores on the American Urological Association Symptom Index (AUASI) and the maximal urinary flow rate. Secondary outcome measures included changes in prostate size, residual urinary volume after voiding, quality of life, laboratory values, and the rate of reported adverse effects.There was no significant difference between the saw palmetto and placebo groups in the change in AUASI scores (mean difference, 0.04 point; 95 percent confidence interval, -0.93 to 1.01), maximal urinary flow rate (mean difference, 0.43 ml per minute; 95 percent confidence interval, -0.52 to 1.38), prostate size, residual volume after voiding, quality of life, or serum prostate-specific antigen levels during the one-year study. The incidence of side effects was similar in the two groups.In this study, saw palmetto did not improve symptoms or objective measures of benign prostatic hyperplasia. (ClinicalTrials.gov number, NCT00037154.).
French Multicentric Survey of Outcome of Pregnancy in Women With Pregestational Diabetes
Journal: Diabetes Care (2003)

To evaluate perinatal outcome in pregnancies in women with type 1 and type 2 diabetes and the influence of preconception care 10 years after the St. Vincent's declaration.A cross-sectional study was conducted in 12 perinatal centers in France in 2000-2001. The main investigated outcomes were perinatal mortality, major congenital malformations, and preterm delivery.Among 435 single pregnancies, 289 (66.4%) were from women with type 1 and 146 (33.6%) from women with type 2 diabetes. Perinatal mortality rate was 4.4% (0.7% national rate), severe congenital malformations rate was 4.1% (2.2% national rate), and preterm delivery rate was 38.2% (4.7% national rate). Preconception care was provided in 48.5% women with type 1 diabetes and in 24.0% women with type 2 diabetes. Women whose first trimester HbA(1c) was >8% had higher rates of perinatal mortality (9.2 vs. 2.5%; odds ratio 3.9; 95% CI 1.5-9.7; P < 0.005), major congenital malformations (8.3 vs. 2.5%; 3.5; 1.3-8.9; P < 0.01), and preterm delivery (57.6 vs. 24.8%; 1.4; 1.1-1.7; P < 0.005) than those with first trimester HbA(1c) <8%. These results are similar to those reported in France in 1986-1988.Pregnancies in women with diabetes are still poorly planned and complicated by higher rates of perinatal mortality and major congenital malformations. Despite knowledge of the importance of intensified glycemic control before pregnancy, reaching the St. Vincent's target needs further implementation in France.
Role of breast regression protein 39 (BRP-39)/chitinase 3-like-1 in Th2 and IL-13–induced tissue responses and apoptosis
Authors: Chun Geun Lee, Dominik Hartl, Gap Ryol Lee, Barbara Koller, Hiroshi Matsuura, Carla A. Da Silva, Myung Hyun Sohn, Lauren Cohn, Robert J. Homer, Alexander A. Kozhich, Alison Humbles, Jennifer Kearley, Anthony Coyle, Geoffrey Chupp, Jennifer Reed, Richard A. Flavell, Jack A. Elias
Journal: The Journal of Experimental Medicine (2009)

Mouse breast regression protein 39 (BRP-39; Chi3l1) and its human homologue YKL-40 are chitinase-like proteins that lack chitinase activity. Although YKL-40 is expressed in exaggerated quantities and correlates with disease activity in asthma and many other disorders, the biological properties of BRP-39/YKL-40 have only been rudimentarily defined. We describe the generation and characterization of BRP-39−/− mice, YKL-40 transgenic mice, and mice that lack BRP-39 and produce YKL-40 only in their pulmonary epithelium. Studies of these mice demonstrated that BRP-39−/− animals have markedly diminished antigen-induced Th2 responses and that epithelial YKL-40 rescues the Th2 responses in these animals. The ability of interleukin13 to induce tissue inflammation and fibrosis was also markedly diminished in the absence of BRP-39. Mechanistic investigations demonstrated that BRP-39 and YKL-40 play an essential role in antigen sensitization and immunoglobulin E induction, stimulate dendritic cell accumulation and activation, and induce alternative macrophage activation. These proteins also inhibit inflammatory cell apoptosis/cell death while inhibiting Fas expression, activating protein kinase B/AKT, and inducing Faim 3. These studies establish novel regulatory roles for BRP-39/YKL-40 in the initiation and effector phases of Th2 inflammation and remodeling and suggest that these proteins are therapeutic targets in Th2- and macrophage-mediated disorders.
A3.20 The calcium sensor stromal interaction molecule 1 (STIM1) controls regulatory B cell functions and its activity is impaired in Systemic Lupus Erythematosus patients
Authors: T Fali, Y Renaudineau, M Burgos, E Bariller, S Jousse, A Saraux, C Hanrotel, D Cornec, C Jamin, O Mignen, J O Pers
Journal: Annals of the Rheumatic Diseases (2014)

<h3>Background and Objectives</h3> The immunosuppressive function of regulatory B cells (Breg) is defective in B cells from systemic lupus erythematosus (SLE) patients. Since the Ca<sup>2+</sup> pathway is also altered in SLE B cells, the aim of the study was to explore the contribution of the Ca<sup>2+</sup> channel Orai1 and its regulator, the stromal interaction molecule 1 (STIM1), on regulatory B cell functions. <h3>Materials and Methods</h3> Thirty SLE patients and healthy controls (HC) were included in the study. Orai1 and STIM1 expressions were explored in CD40/CpG activated B cells, and in the stimulated (anti-CD3, anti-CD28 plus CpG-ODN 2006) T- and B- cell autologous co-culture Breg model. Transfection were used using either siRNAs to down-modulate STIM1 in SLE B cells, or either the cDNA STIM1 vector in HC B cells. <h3>Results</h3> After 3 days, in CD40/CpG activated HC B cells, and in HC B cells stimulated during co-cultures, acquisition of the Breg phenotype (IgD/CD38/CD24/CD5<sup>high</sup>) was associated with an over-expression of the Ca<sup>2+</sup> regulator STIM1 (x10.8 and x7.1 fold increase respectively). At day 4 and even more at day 5, STIM1 expression declined in co-cultures and this down-regulation was accompanied with IL-10 and TGF-beta up-regulation in B cells, FoxP3<sup>+</sup> regulatory T cell expansion, and a reduction of T cell proliferation. Expression of the Ca<sup>2+</sup> channel Orai1 was stable. In SLE B cells, STIM1 expression was overexpressed at basal level when compared to HC B cells (x4.3 fold) and remains elevated in B cells during all the time of the autologous co-culture (x8.8 fold). Then we hypothesised that maintaining high levels of STIM1 was critic in the regulatory capacity of SLE B cells. Accordingly, we demonstrated that STIM1 downregulation in SLE B cells, using a specific siRNA, was effective to restore IL-10, but not TGF-beta, expression, FoxP3<sup>+</sup> regulatory SLE T cell expansion, and SLE T cell inhibition. In HC B cells, forcing STIM1 expression, with a STIM1 vector, was effective to reproduce the abnormalities observed in SLE B cells. No association was observed between STIM1 expression at basal level and organ involvement, disease activity (SLEDAI), or serological parameters thus suggesting that STIM1 over-expression and Ca<sup>2+</sup> dysregulations are primary events in SLE. <h3>Conclusions</h3> Altogether, this study reveals that acquisition of the Breg phenotype and Breg functions are tightly regulated by STIM1. Furthermore, this observation could provide innovative B-cell based treatment to convert B cells into immunosuppressive cells with applications in human autoimmunity and in SLE. <h3>Key words </h3> lupus, regulatory B cells, calcium, STIM1, IL-10
EAU Guidelines on Assessment and Nonsurgical Management of Urinary Incontinence
Authors: Malcolm G. Lucas, Ruud J.L. Bosch, Fiona C. Burkhard, Francisco Cruz, Thomas B. Madden, Arjun K. Nambiar, Andreas Neisius, Dirk J.M.K. de Ridder, Andrea Tubaro, William H. Turner, Robert S. Pickard
Journal: European Urology (2012)
Perilobar Nephrogenic Rests Are Nonobligate Molecular Genetic Precursor Lesions of Insulin-Like Growth Factor-II-Associated Wilms Tumors
Authors: Raisa Vuononvirta, Neil J. Sebire, Anthony R. Dallosso, Jorge S. Reis-Filho, Richard D. Williams, Alan Mackay, Kerry Fenwick, Anita Grigoriadis, Alan Ashworth, Kathy Pritchard-Jones, Keith W. Brown, Gordan M. Vujanic, Chris Jones
Journal: Clinical Cancer Research (2008)

Perilobar nephrogenic rests (PLNRs) are abnormally persistent foci of embryonal immature blastema that have been associated with dysregulation at the 11p15 locus by genetic/epigenetic means and are thought to be precursor lesions of Wilms tumor. The precise genomic events are, however, largely unknown.We used array comparative genomic hybridization to analyze a series of 50 PLNRs and 25 corresponding Wilms tumors characterized for 11p15 genetic/epigenetic alterations and insulin-like growth factor-II expression.The genomic profiles of PLNRs could be subdivided into three categories: those with no copy number changes (22 of 50, 44%); those with single, whole chromosome alterations (8 of 50, 16%); and those with multiple gains/losses (20 of 50, 40%). The most frequent aberrations included 1p- (7 of 50, 14%) +18 (6 of 50, 12%), +13 (5 of 50, 10%), and +12 (3 of 50, 6%). For the majority (19 of 25, 76%) of cases, the rest harbored a subset of the copy number changes in the associated Wilms tumor. We identified a temporal order of genomic changes, which occur during the insulin-like growth factor-II/PLNR pathway of Wilms tumorigenesis, with large-scale chromosomal alterations such as 1p-, +12, +13, and +18 regarded as "early" events. In some of the cases (24%), the PLNRs harbored large-scale copy number changes not observed in the concurrent Wilms tumor, including +10p, +14q, and +18.These data suggest that although the evidence for PLNRs as precursors is compelling, not all lesions must necessarily undergo malignant transformation.
Axillary Node Interventions in Breast Cancer
Authors: Roshni Rao, David Euhus, Helen G Mayo, Charles Balch
Journal: JAMA (2013)

Recent data from clinical trials have challenged traditional thinking about axillary surgery in patients with breast cancer.To summarize evidence regarding the role of axillary interventions (surgical and nonsurgical) in breast cancer treatment and to review the association of these axillary interventions with recurrence of axillary node metastases, mortality, and morbidity outcomes in patients with breast cancer.Ovid MEDLINE (1946-July 2013), Cochrane Database of Systematic Reviews (2005-July 2013), Cochrane Database of Abstracts of Reviews of Effects (1994-July 2013), and Cochrane Central Register of Controlled Trials (1989-July 2013) were searched for publications on axillary interventions in breast cancer. Clinical trials, observational studies, and meta-analyses with at least 2-year follow-up were included. A total of 1070 publications were reviewed, 17 of which met final inclusion criteria.Partial mastectomy followed by whole breast radiation is breast-conserving therapy. For women with no suspicious, palpable axillary nodes who undergo breast-conserving therapy, there is little evidence of benefit from surgical complete axillary node dissection compared with sentinel node biopsy alone. Complete axillary node dissection in patients with no palpable lymph nodes, compared with sentinel node biopsy, provides no survival benefit and is associated with a 1% to 3% reduction in recurrence of axillary lymph node metastases, but is associated with a 14% risk of lymphedema. Surgical axillary staging via sentinel node biopsy in patients with benign axillary nodes on radiological and clinical examination helps to inform decisions regarding adjuvant systemic and radiation therapy. Patients and physicians should tailor axillary lymph node interventions to maximize regional disease control and minimize morbidity. Complete axillary lymph node dissection is indicated in patients who present with palpable or needle biopsy-proven axillary metastases, patients with positive sentinel nodes undergoing mastectomy (who do not, as a standard, receive adjuvant radiation), patients with more than 3 positive sentinel nodes undergoing breast-conserving therapy, and patients not meeting eligibility criteria for recent trials establishing the safety of sentinel node biopsy alone in patients with breast cancer and metastases in their sentinel nodes.Available evidence suggests that axillary node dissection is associated with more harm than benefit in women undergoing breast-conserving therapy who do not have palpable, suspicious lymph nodes, who have tumors 3.0 cm or smaller, and who have 3 or fewer positive nodes on sentinel node biopsy.
Prognostic Implications of the Seventh Edition of the International Union Against Cancer Classification for Patients With Gastric Cancer: The Western Experience of Patients Treated in a Single-Center European Institution
Authors: Daniel Reim, Martin Loos, Fabian Vogl, Alexander Novotny, Tibor Schuster, Rupert Langer, Karen Becker, Heinz Höfler, Jens Siveke, Florian Bassermann, Helmut Friess, Christoph Schuhmacher
Journal: Journal of Clinical Oncology (2012)

Validity of the seventh edition of the American Joint Committee on Cancer/International Union Against Cancer (AJCC/UICC) staging systems for gastric cancer has been evaluated in several studies, mostly in Asian patient populations. Only few data are available on the prognostic implications of the new classification system on a Western population. Therefore, we investigated its prognostic ability based on a German patient cohort.Data from a single-center cohort of 1,767 consecutive patients surgically treated for gastric cancer were classified according to the seventh edition and were compared using the previous TNM/UICC classification. Kaplan-Meier analyses were performed for all TNM stages and UICC stages in a comparative manner. Additional survival receiver operating characteristic analyses and bootstrap-based goodness-of-fit comparisons via Bayesian information criterion (BIC) were performed to assess and compare prognostic performance of the competing classification systems.We identified the UICC pT/pN stages according to the seventh edition of the AJCC/UICC guidelines as well as resection status, age, Lauren histotype, lymph-node ratio, and tumor grade as independent prognostic factors in gastric cancer, which is consistent with data from previous Asian studies. Overall survival rates according to the new edition were significantly different for each individual's pT, pN, and UICC stage. However, BIC analysis revealed that, owing to higher complexity, the new staging system might not significantly alter predictability for overall survival compared with the old system within the analyzed cohort from a statistical point of view.The seventh edition of the AJCC/UICC classification was found to be valid with distinctive prognosis for each stage. However, the AJCC/UICC classification has become more complex without improving predictability for overall survival in a Western population. Therefore, simplification with better predictability of overall survival of patients with gastric cancer should be considered when revising the seventh edition.
Low dose alpha interferon treatment in chronic hepatitis B virus infection.
Authors: R Muller, R Baumgarten, R Markus, M Schulz, H Wittenberg, B Hintsche-Kilger, J D Fengler, P von Wussow, H Meisel, H Klein
Journal: Gut (1993)

Fifty eight patients with chronic viral hepatitis B (HBV) were randomised in a prospectively controlled trial. Thirty patients were treated with 3 million units (MU) of interferon alfa-2b subcutaneously thrice weekly for four months. Twenty eight controls received no treatment. The follow up period after treatment was six months. Twenty eight treated patients and 27 controls completed the protocol. One woman in the treatment group showed a complete response, and eight other treated patients (32%) showed a partial response. Three patients in the control group (11%) lost hepatitis B e antigen and HBV-DNA spontaneously. This finding is statistically significant (p &lt; 0.05). The elimination of HBV markers from the serum was associated with a return to normal of serum aminotransferase activities. Reactivation of hepatitis was not observed after seroconversion.