The Transition from Gastric Intestinal Metaplasia to Gastric Cancer Involves POPDC1 and POPDC3 Downregulation
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The Popeye Domain Containing Protein Family E a Novel Class of Camp Effectors with Important Functions in Multiple Tissues
Progress in Biophysics and Molecular Biology xxx (2016) 1e9 Contents lists available at ScienceDirect Progress in Biophysics and Molecular Biology journal homepage: www.elsevier.com/locate/pbiomolbio The Popeye domain containing protein family e A novel class of cAMP effectors with important functions in multiple tissues * Roland F.R. Schindler, Thomas Brand Heart Science Centre, National Heart and Lung Institute (NHLI), Imperial College London, United Kingdom article info abstract Article history: Popeye domain containing (Popdc) proteins are a unique family, which combine several different Received 16 September 2015 properties and functions in a surprisingly complex fashion. They are expressed in multiple tissues and Received in revised form cell types, present in several subcellular compartments, interact with different classes of proteins, and 3 December 2015 are associated with a variety of physiological and pathophysiological processes. Moreover, Popdc proteins Accepted 4 January 2016 bind the second messenger cAMP with high affinity and it is thought that they act as a novel class of Available online xxx cAMP effector proteins. Here, we will review the most important findings about the Popdc family, which accumulated since its discovery about 15 years ago. We will be focussing on Popdc protein interaction Keywords: Popeye domain containing genes and function in striated muscle tissue. However, as a full picture only emerges if all aspects are taken into cAMP account, we will also describe what is currently known about the role of Popdc proteins in epithelial cells Proteineprotein interaction and in various types of cancer, and discuss these findings with regard to their relevance for cardiac and Ion channel skeletal muscle. -
Transcriptional Control of Tissue-Resident Memory T Cell Generation
Transcriptional control of tissue-resident memory T cell generation Filip Cvetkovski Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2019 © 2019 Filip Cvetkovski All rights reserved ABSTRACT Transcriptional control of tissue-resident memory T cell generation Filip Cvetkovski Tissue-resident memory T cells (TRM) are a non-circulating subset of memory that are maintained at sites of pathogen entry and mediate optimal protection against reinfection. Lung TRM can be generated in response to respiratory infection or vaccination, however, the molecular pathways involved in CD4+TRM establishment have not been defined. Here, we performed transcriptional profiling of influenza-specific lung CD4+TRM following influenza infection to identify pathways implicated in CD4+TRM generation and homeostasis. Lung CD4+TRM displayed a unique transcriptional profile distinct from spleen memory, including up-regulation of a gene network induced by the transcription factor IRF4, a known regulator of effector T cell differentiation. In addition, the gene expression profile of lung CD4+TRM was enriched in gene sets previously described in tissue-resident regulatory T cells. Up-regulation of immunomodulatory molecules such as CTLA-4, PD-1, and ICOS, suggested a potential regulatory role for CD4+TRM in tissues. Using loss-of-function genetic experiments in mice, we demonstrate that IRF4 is required for the generation of lung-localized pathogen-specific effector CD4+T cells during acute influenza infection. Influenza-specific IRF4−/− T cells failed to fully express CD44, and maintained high levels of CD62L compared to wild type, suggesting a defect in complete differentiation into lung-tropic effector T cells. -
Short Course 10 Metaplasia in The
0 3: 436-446 Rev Esp Patot 1999; Vol. 32, N © Prous Science, SA. © Sociedad Espajiola de Anatomia Patot6gica Short Course 10 © Sociedad Espafiola de Citologia Metaplasia in the gut Chairperson: NA. Wright, UK. Co-chairpersons: G. Coggi, Italy and C. Cuvelier, Belgium. Overview of gastrointestinal metaplasias only in esophagus but also in the duodenum, intestine, gallbladder and even in the pancreas. Well established is columnar metaplasia J. Stachura of esophageal squamous epithelium. Its association with increased risk of esophageal cancer is widely recognized. Recent develop- Dept. of Pathomorphology, Jagiellonian University ments have suggested, however, that only the intestinal type of Faculty of Medicine, Krakdw, Poland. metaplastic epithelium (classic Barrett’s esophagus) predisposes to cancer. Another field of studies is metaplasia in the short seg- ment at the esophago-cardiac junction, its association with Metaplasia is a reversible change in which one aduit cell type is Helicobacter pylon infection and/or reflux disease and intestinal replaced by another. It is always associated with some abnormal metaplasia in the cardiac and fundic areas. stimulation of tissue growth, tissue regeneration or excessive hor- Studies on gastric mucosa metaplasia could be divided into monal stimulation. Heterotopia, on the other hand, takes place dur- those concerned with pathogenesis and detailed structural/func- ing embryogenesis and is usually supposed not to be associated tional features and those concerned with clinical significance. with tissue damage. Pancreatic acinar cell clusters in pediatric gas- We know now that gastric mucosa may show not only complete tric mucosa form another example of aberrant cell differentiation. and incomplete intestinal metaplasia but also others such as ciliary Metaplasia is usually divided into epithelial and connective tis- and pancreatic metaplasia. -
Tibbo, Amy J. (2020) Compartmentalized Camp Signaling Via the PDE4- Popeye Protein Complex
Tibbo, Amy J. (2020) Compartmentalized cAMP Signaling via the PDE4- Popeye Protein Complex. PhD thesis. http://theses.gla.ac.uk/81454/ Copyright and moral rights for this work are retained by the author A copy can be downloaded for personal non-commercial research or study, without prior permission or charge This work cannot be reproduced or quoted extensively from without first obtaining permission in writing from the author The content must not be changed in any way or sold commercially in any format or medium without the formal permission of the author When referring to this work, full bibliographic details including the author, title, awarding institution and date of the thesis must be given Enlighten: Theses https://theses.gla.ac.uk/ [email protected] 1 Compartmentalized cAMP Signaling via the PDE4-Popeye Protein Complex Amy Jane Tibbo (BSc Hons) Thesis submitted in fulfilment of the requirements for Degree of Doctor of Philosophy Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow April 2020 2 Abstract The Popeye domain containing (POPDC) protein family are a unique family of transmembrane proteins with several proposed functions that are not fully understood. POPDC proteins are abundantly expressed in cardiac and skeletal muscle. Within the heart, POPDC1 has been shown to be highly expressed in the pace making centres and at moderate to low levels in the atria and ventricles. Given this localisation, a role for POPDC1 was hypothesised to be in the maintenance of normal heartbeat rhythm. Studies involving POPDC1 mutant mice and zebrafish provided evidence for this proposed function as the genetically modified model animals displayed cardiac arrhythmias as the predominant phenotype. -
Análise Integrativa De Perfis Transcricionais De Pacientes Com
UNIVERSIDADE DE SÃO PAULO FACULDADE DE MEDICINA DE RIBEIRÃO PRETO PROGRAMA DE PÓS-GRADUAÇÃO EM GENÉTICA ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas Ribeirão Preto – 2012 ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas Tese apresentada à Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo para obtenção do título de Doutor em Ciências. Área de Concentração: Genética Orientador: Prof. Dr. Eduardo Antonio Donadi Co-orientador: Prof. Dr. Geraldo A. S. Passos Ribeirão Preto – 2012 AUTORIZO A REPRODUÇÃO E DIVULGAÇÃO TOTAL OU PARCIAL DESTE TRABALHO, POR QUALQUER MEIO CONVENCIONAL OU ELETRÔNICO, PARA FINS DE ESTUDO E PESQUISA, DESDE QUE CITADA A FONTE. FICHA CATALOGRÁFICA Evangelista, Adriane Feijó Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas. Ribeirão Preto, 2012 192p. Tese de Doutorado apresentada à Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo. Área de Concentração: Genética. Orientador: Donadi, Eduardo Antonio Co-orientador: Passos, Geraldo A. 1. Expressão gênica – microarrays 2. Análise bioinformática por module maps 3. Diabetes mellitus tipo 1 4. Diabetes mellitus tipo 2 5. Diabetes mellitus gestacional FOLHA DE APROVAÇÃO ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas. -
Subtypes of Intestinal Metaplasia and Helicobacter Pylorn Gut: First Published As 10.1136/Gut.33.5.597 on 1 May 1992
Gut, 1992, 33, 597-600 597 Subtypes of intestinal metaplasia and Helicobacter pylorn Gut: first published as 10.1136/gut.33.5.597 on 1 May 1992. Downloaded from M E Craanen, P Blok, W Dekker, J Ferwerda, G N J Tytgat Abstract ing lesion, intestinal metaplasia are widely To determine whether there is a relationship recognised as being the most prevalent pre- between the presence of H pylon and the cursors of intestinal type gastric carcinoma.7 various subtypes ofintestinal metaplasia in the Subtypes of intestinal metaplasia have been gastric antrum, 2274 antral gastroscopic biop- identified based upon histological, ultra- sies from 533 patients were examined. Hpylon structural, enzyme, and mucin histochemical was found in 289 patients. Intestinal meta- characteristics. Some of the latter studies have plasia in general was found in 135 patients. suggested that a sulphomucin secreting, incom- Type I intestinal metaplasia was found in 133 plete intestinal metaplasia subtype is particularly patients (98.5%), type II in 106 patients (78.5%) closely linked to intestinal type gastric carcinoma and type III in 21 patients (15.6%). Ninety eight and may therefore be a marker of increased of these 135 patients (72.6%) were H pylori gastric cancer risk.8'~3 In another study evidence positive and 37 patients (27.4%) were H pylon was found for a strong association between the negative. No statistically significant difference presence of intestinal metaplasia in general and was found in the prevalence of type I and II H pylorn in the gastric antral mucosa.'4 We intestinal metaplasia between the intestinal undertook this study in order to investigate metaplasia positive and H pylon positive and further the relationship between the presence of intestinal metaplasia negative and H pylon H pylorn and the various subtypes of intestinal negative patients. -
Probabilistic Models for Collecting, Analyzing, and Modeling Expression Data
Probabilistic Models for Collecting, Analyzing, and Modeling Expression Data Hai-Son Phuoc Le May 2013 CMU-ML-13-101 Probabilistic Models for Collecting, Analyzing, and Modeling Expression Data Hai-Son Phuoc Le May 2013 CMU-ML-13-101 Machine Learning Department School of Computer Science Carnegie Mellon University Thesis Committee Ziv Bar-Joseph, Chair Christopher Langmead Roni Rosenfeld Quaid Morris Submitted in partial fulfillment of the requirements for the Degree of Doctor of Philosophy. Copyright @ 2013 Hai-Son Le This research was sponsored by the National Institutes of Health under grant numbers 5U01HL108642 and 1R01GM085022, the National Science Foundation under grant num- bers DBI0448453 and DBI0965316, and the Pittsburgh Life Sciences Greenhouse. The views and conclusions contained in this document are those of the author and should not be interpreted as representing the official policies, either expressed or implied, of any sponsoring institution, the U.S. government or any other entity. Keywords: genomics, gene expression, gene regulation, microarray, RNA-Seq, transcriptomics, error correction, comparative genomics, regulatory networks, cross-species, expression database, Gene Expression Omnibus, GEO, orthologs, microRNA, target prediction, Dirichlet Process, Indian Buffet Process, hidden Markov model, immune response, cancer. To Mom and Dad. i Abstract Advances in genomics allow researchers to measure the complete set of transcripts in cells. These transcripts include messenger RNAs (which encode for proteins) and microRNAs, short RNAs that play an important regulatory role in cellular networks. While this data is a great resource for reconstructing the activity of networks in cells, it also presents several computational challenges. These challenges include the data collection stage which often results in incomplete and noisy measurement, developing methods to integrate several experiments within and across species, and designing methods that can use this data to map the interactions and networks that are activated in specific conditions. -
(Popdc2). Generation and Functional Characterization of a Null Mutant in Mice and Promoter Analysis
The Popeye domain containing gene 2 (Popdc2). Generation and functional characterization of a null mutant in mice and promoter analysis. Dissertation For completion of the Doctorate degree in Natural Sciences at the Bayerische Julius-Maximilians-Universität Würzburg Alexander Froese from Dushanbe Würzburg 2007 Declaration: I hereby declare that the submitted dissertation was completed by myself and no other. I have not used any sources or materials other than those enclosed. Moreover I declare that the following dissertation has not been submitted further in this form or any other form, and has not been used to obtain any other equivalent qualifications at any other organisation/institution. Additionally, I have not applied for, nor will I attempt to apply for any other degree or qualification in relation to this work. Würzburg, den 21.12.2007 Alexander Froese The hereby submitted thesis was completed from January 2001 until April 2005 at the Cell and Molecular Biology Department, Technical University Braunschweig, Braunschweig and from May 2005 until December 2007 at the Department of Cell and Developmental Biology, University of Würzburg, under the supervision of Professor Dr. T. Brand. Members of the thesis committee: Chairman: Professor Dr. M. Müller Examiner: Professor Dr. T. Brand Examiner: PD Dr. S. Maier Submitted on: 21.12.2007 Date of oral exam: 20.02.2008 Wahrlich, wahrlich, ich sage euch: Wenn das Weizenkorn nicht in die Erde fällt und stirbt, bleibt es allein; wenn es aber stirbt, bringt es viel Frucht. Johannes 12;23-25 Истинно, истинно говорю вам: если пшеничное зерно, падши в землю, не умрёт, то останется одно; а если умрёт, то принесёт много плода. -
Role and Regulation of the P53-Homolog P73 in the Transformation of Normal Human Fibroblasts
Role and regulation of the p53-homolog p73 in the transformation of normal human fibroblasts Dissertation zur Erlangung des naturwissenschaftlichen Doktorgrades der Bayerischen Julius-Maximilians-Universität Würzburg vorgelegt von Lars Hofmann aus Aschaffenburg Würzburg 2007 Eingereicht am Mitglieder der Promotionskommission: Vorsitzender: Prof. Dr. Dr. Martin J. Müller Gutachter: Prof. Dr. Michael P. Schön Gutachter : Prof. Dr. Georg Krohne Tag des Promotionskolloquiums: Doktorurkunde ausgehändigt am Erklärung Hiermit erkläre ich, dass ich die vorliegende Arbeit selbständig angefertigt und keine anderen als die angegebenen Hilfsmittel und Quellen verwendet habe. Diese Arbeit wurde weder in gleicher noch in ähnlicher Form in einem anderen Prüfungsverfahren vorgelegt. Ich habe früher, außer den mit dem Zulassungsgesuch urkundlichen Graden, keine weiteren akademischen Grade erworben und zu erwerben gesucht. Würzburg, Lars Hofmann Content SUMMARY ................................................................................................................ IV ZUSAMMENFASSUNG ............................................................................................. V 1. INTRODUCTION ................................................................................................. 1 1.1. Molecular basics of cancer .......................................................................................... 1 1.2. Early research on tumorigenesis ................................................................................. 3 1.3. Developing -
The Genetics of Bipolar Disorder
Molecular Psychiatry (2008) 13, 742–771 & 2008 Nature Publishing Group All rights reserved 1359-4184/08 $30.00 www.nature.com/mp FEATURE REVIEW The genetics of bipolar disorder: genome ‘hot regions,’ genes, new potential candidates and future directions A Serretti and L Mandelli Institute of Psychiatry, University of Bologna, Bologna, Italy Bipolar disorder (BP) is a complex disorder caused by a number of liability genes interacting with the environment. In recent years, a large number of linkage and association studies have been conducted producing an extremely large number of findings often not replicated or partially replicated. Further, results from linkage and association studies are not always easily comparable. Unfortunately, at present a comprehensive coverage of available evidence is still lacking. In the present paper, we summarized results obtained from both linkage and association studies in BP. Further, we indicated new potential interesting genes, located in genome ‘hot regions’ for BP and being expressed in the brain. We reviewed published studies on the subject till December 2007. We precisely localized regions where positive linkage has been found, by the NCBI Map viewer (http://www.ncbi.nlm.nih.gov/mapview/); further, we identified genes located in interesting areas and expressed in the brain, by the Entrez gene, Unigene databases (http://www.ncbi.nlm.nih.gov/entrez/) and Human Protein Reference Database (http://www.hprd.org); these genes could be of interest in future investigations. The review of association studies gave interesting results, as a number of genes seem to be definitively involved in BP, such as SLC6A4, TPH2, DRD4, SLC6A3, DAOA, DTNBP1, NRG1, DISC1 and BDNF. -
Histopathology of Barrett's Esophagus and Early-Stage
Review Histopathology of Barrett’s Esophagus and Early-Stage Esophageal Adenocarcinoma: An Updated Review Feng Yin, David Hernandez Gonzalo, Jinping Lai and Xiuli Liu * Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA; fengyin@ufl.edu (F.Y.); hernand3@ufl.edu (D.H.G.); jinpinglai@ufl.edu (J.L.) * Correspondence: xiuliliu@ufl.edu; Tel.: +1-352-627-9257; Fax: +1-352-627-9142 Received: 24 October 2018; Accepted: 22 November 2018; Published: 27 November 2018 Abstract: Esophageal adenocarcinoma carries a very poor prognosis. For this reason, it is critical to have cost-effective surveillance and prevention strategies and early and accurate diagnosis, as well as evidence-based treatment guidelines. Barrett’s esophagus is the most important precursor lesion for esophageal adenocarcinoma, which follows a defined metaplasia–dysplasia–carcinoma sequence. Accurate recognition of dysplasia in Barrett’s esophagus is crucial due to its pivotal prognostic value. For early-stage esophageal adenocarcinoma, depth of submucosal invasion is a key prognostic factor. Our systematic review of all published data demonstrates a “rule of doubling” for the frequency of lymph node metastases: tumor invasion into each progressively deeper third of submucosal layer corresponds with a twofold increase in the risk of nodal metastases (9.9% in the superficial third of submucosa (sm1) group, 22.0% in the middle third of submucosa (sm2) group, and 40.7% in deep third of submucosa (sm3) group). Other important risk factors include lymphovascular invasion, tumor differentiation, and the recently reported tumor budding. In this review, we provide a concise update on the histopathological features, ancillary studies, molecular signatures, and surveillance/management guidelines along the natural history from Barrett’s esophagus to early stage invasive adenocarcinoma for practicing pathologists. -
Supplemental Figure and Table Legends
Supplemental figure and table legends Supplementary Figure 1: KIAA1841 is well conserved among vertebrates. NCBI HomoloGene pairwise alignment scores of human KIAA1841 sequence compared to other vertebrate orthologs. Supplementary Figure 2: µ-germline transcripts (GLT) and AID mRNA expression are not affected by overexpression of KIAA1841. Splenic B cells were isolated from wild-type mice, and transduced with retroviral vector control (pMIG) or a vector expressing KIAA1841. Levels of µ-GLT and AID mRNA were determined at 72h post-infection by RT-qPCR, and normalized to -actin mRNA and the pMIG control. The mean of three independent experiments +/- SD is shown. NS, p = not significant, p 0.05, two-tailed paired student’s t-test. Supplementary Figure 3: Overexpression of untagged and Xpress-tagged KIAA1841 does not affect cell proliferation. Splenic B cells were isolated from wild-type mice, stimulated with LPS+IL4, and transduced with retroviral vector control (pMIG) or a vector expressing KIAA1841 or Xpress (Xp)-tagged KIAA1841. Cells are labeled with seminaphthorhodafluor (SNARF) cell tracking dye and SNARF intensity was measured at 0h, 24h, and 48h after retroviral infection. Histograms of transduced cells (GFP+) for pMIG control, KIAA1841 and Xp-KIAA1841 were superimposed at each time point. Three independent retroviral infection experiments are shown. Supplementary Figure 4: Sequence alignment of the putative SANT domain of KIAA1841 with the SANT domain of SWI3. Alignment was performed using ClustalOmega; *, conserved residue, :, strongly similar residues, ., weakly similar residues. Numbers indicate amino acid residues in each sequence. Helix 3, which has been reported to be important for the chromatin remodeling function of SWI3 (Boyer et.