Identification of a Novel Cyclin Required for the Intrinsic Apoptosis Pathway in Lymphoid Cells
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												S41467-020-18249-3.Pdf
ARTICLE https://doi.org/10.1038/s41467-020-18249-3 OPEN Pharmacologically reversible zonation-dependent endothelial cell transcriptomic changes with neurodegenerative disease associations in the aged brain Lei Zhao1,2,17, Zhongqi Li 1,2,17, Joaquim S. L. Vong2,3,17, Xinyi Chen1,2, Hei-Ming Lai1,2,4,5,6, Leo Y. C. Yan1,2, Junzhe Huang1,2, Samuel K. H. Sy1,2,7, Xiaoyu Tian 8, Yu Huang 8, Ho Yin Edwin Chan5,9, Hon-Cheong So6,8, ✉ ✉ Wai-Lung Ng 10, Yamei Tang11, Wei-Jye Lin12,13, Vincent C. T. Mok1,5,6,14,15 &HoKo 1,2,4,5,6,8,14,16 1234567890():,; The molecular signatures of cells in the brain have been revealed in unprecedented detail, yet the ageing-associated genome-wide expression changes that may contribute to neurovas- cular dysfunction in neurodegenerative diseases remain elusive. Here, we report zonation- dependent transcriptomic changes in aged mouse brain endothelial cells (ECs), which pro- minently implicate altered immune/cytokine signaling in ECs of all vascular segments, and functional changes impacting the blood–brain barrier (BBB) and glucose/energy metabolism especially in capillary ECs (capECs). An overrepresentation of Alzheimer disease (AD) GWAS genes is evident among the human orthologs of the differentially expressed genes of aged capECs, while comparative analysis revealed a subset of concordantly downregulated, functionally important genes in human AD brains. Treatment with exenatide, a glucagon-like peptide-1 receptor agonist, strongly reverses aged mouse brain EC transcriptomic changes and BBB leakage, with associated attenuation of microglial priming. We thus revealed tran- scriptomic alterations underlying brain EC ageing that are complex yet pharmacologically reversible. - 
												
												Quantitative Proteomics Identify the Possible Tumor Suppressive Role of Protease-Activated Receptor-4 in Esophageal Squamous Cell Carcinoma Cells
Pathology & Oncology Research (2019) 25:937–943 https://doi.org/10.1007/s12253-018-0395-7 ORIGINAL ARTICLE Quantitative Proteomics Identify the Possible Tumor Suppressive Role of Protease-Activated Receptor-4 in Esophageal Squamous Cell Carcinoma Cells Ming Wang1 & Shuhong An1 & Diyi Wang2 & Haizhen Ji3 & Min Geng1 & Xingjing Guo 3 & Zhaojin Wang1 Received: 28 November 2017 /Accepted: 21 February 2018 /Published online: 4 March 2018 # Arányi Lajos Foundation 2018 Abstract Exposure to carcinogens of tobacco smoke may result in methylation of protease-activated receptors-4 (PAR4) gene and further induces the loss of PAR4 expression, which is considered to be involved in carcinogenesis of esophageal squamous cell carcinoma (ESCC). Here we employed a TMT-based quantitative proteomic approach to identify PAR4-regulated changes of proteomic profiles in ESCC cells and to identify potentially therapeutic value. A total of 33 proteins were found significantly changed with 15 up-regulated and 18 down-regulated in PAR4-activating peptide (PAR4-AP) treated ESCC cells compared with controls. Bioinformatics analysis showed that key higher expressed proteins included those associated with apoptosis and tumor suppressor (e.g. CASP9), and lower expressed proteins included those associated with anti-apoptosis, autophagy and promoting cell proliferation (e.g. CHMP1B, PURA, PARG and HIST1H2AH). Western blot verified changes in five representative proteins including CASP9, CHMP1B, PURA, PARG and HIST1H2AH. Immunohistochemistry analysis showed that CHMP1B, PURA, PARG and HIST1H2AH expression in ESCC tissues were significantly higher than those in adjacent nontumorous tissues. Our findings will be helpful in further investigations into the functions and molecular mechanisms of PAR4 in ESCC. - 
												
												Cyclin-Dependent Kinases and Rare Developmental Disorders Pierre Colas
Colas Orphanet Journal of Rare Diseases (2020) 15:203 https://doi.org/10.1186/s13023-020-01472-y REVIEW Open Access Cyclin-dependent kinases and rare developmental disorders Pierre Colas Abstract Extensive studies in the past 30 years have established that cyclin-dependent kinases (CDKs) exert many diverse, important functions in a number of molecular and cellular processes that are at play during development. Not surprisingly, mutations affecting CDKs or their activating cyclin subunits have been involved in a variety of rare human developmental disorders. These recent findings are reviewed herein, giving a particular attention to the discovered mutations and their demonstrated or hypothesized functional consequences, which can account for pathological human phenotypes. The review highlights novel, important CDK or cyclin functions that were unveiled by their association with human disorders, and it discusses the shortcomings of mouse models to reveal some of these functions. It explains how human genetics can be used in combination with proteome-scale interaction databases to loom regulatory networks around CDKs and cyclins. Finally, it advocates the use of these networks to profile pathogenic CDK or cyclin variants, in order to gain knowledge on protein function and on pathogenic mechanisms. Keywords: CDKs , Cyclins , Developmental disorders , Regulatory networks , Interaction profiling Introduction Overexpression and/or dysfunction of CDKs or cyclins Cyclin-dependent kinases (CDKs) form a family of 20 have been reported in a very large number of human serine/threonine protein kinases that exert pivotal func- cancers and other diverse pathologies. These protein ki- tions in fundamental cellular and molecular processes, nases are thus considered as valuable therapeutic targets such as cell division, migration, senescence, death, gene for drug development. - 
												
												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 - 
												
												TET1 Contributes to Allergic Airway Inflammation and Regulates
www.nature.com/scientificreports OPEN TET1 contributes to allergic airway infammation and regulates interferon and aryl hydrocarbon Received: 6 July 2018 Accepted: 1 May 2019 receptor signaling pathways in Published: xx xx xxxx bronchial epithelial cells J. D. Burleson1, Dylan Siniard1,2, Veda K. Yadagiri1, Xiaoting Chen3, Matthew T. Weirauch 3,4,5, Brandy P. Ruf1, Eric B. Brandt1, Gurjit K. Khurana Hershey1,5 & Hong Ji1,2,5,6,7 Previous studies have suggested a role for Tet1 in the pathogenesis of childhood asthma. However, how Tet1 contributes to asthma remains unknown. Here we used mice defcient for Tet1 in a well-established model of allergic airway infammation and demonstrated that loss of Tet1 increased disease severity including airway hyperresponsiveness and lung eosinophilia. Increased expression of Muc5ac, Il13, Il33, Il17a, Egfr, and Tf2 were observed in HDM-challenged Tet1-defcient mice compared to Tet1+/+ littermates. Further, transcriptomic analysis of lung RNA followed by pathway and protein network analysis showed that the IFN signaling pathway was signifcantly upregulated and the aryl hydrocarbon receptor (AhR) pathway was signifcantly downregulated in HDM-challenged Tet1−/− mice. This transcriptional regulation of the IFN and AhR pathways by Tet1 was also present in human bronchial epithelial cells at base line and following HDM challenges. Genes in these pathways were further associated with changes in DNA methylation, predicted binding of transcriptional factors with relevant functions in their promoters, and the presence of histone marks generated by histone enzymes that are known to interact with Tet1. Collectively, our data suggest that Tet1 inhibits HDM-induced allergic airway infammation by direct regulation of the IFN and AhR pathways. - 
												
												Clinical Characterization of Chromosome 5Q21.1–21.3 Microduplication: a Case Report
Open Medicine 2020; 15: 1123–1127 Case Report Shuang Chen, Yang Yu, Han Zhang, Leilei Li, Yuting Jiang, Ruizhi Liu, Hongguo Zhang* Clinical characterization of chromosome 5q21.1–21.3 microduplication: A case report https://doi.org/10.1515/med-2020-0199 Keywords: chromosome 5, prenatal diagnosis, microdu- received May 20, 2020; accepted September 28, 2020 plication, genetic counseling Abstract: Chromosomal microdeletions and microdupli- cations likely represent the main genetic etiologies for children with developmental delay or intellectual dis- ability. Through prenatal chromosomal microarray ana- 1 Introduction lysis, some microdeletions or microduplications can be detected before birth to avoid unnecessary abortions or Chromosomal microdeletions,microduplications,and birth defects. Although some microdeletions or microdu- unbalanced rearrangements represent the main genetic plications of chromosome 5 have been reported, nu- etiological factors for children with developmental delay [ ] - merous microduplications remain undescribed. We de- or intellectual disability 1 . Currently, chromosomal mi ( ) fi - - scribe herein a case of a 30-year-old woman carrying a croarray analysis CMA is considered a rst tier diag [ ] - fetus with a chromosome 5q21.1–q21.3 microduplication. nostic tool for these children 2 . Through prenatal diag Because noninvasive prenatal testing indicated a fetal nosis of CMA, some microdeletions or microduplications - chromosome 5 abnormality, the patient underwent am- can be detected before birth to avoid unnecessary abor [ ] niocentesis at 22 weeks 4 days of gestation. Karyotyping tions or birth defects 3 . The clinical features of some and chromosomal microarray analysis were performed on chromosome 5 microduplications have been described [ – ] [ ] amniotic fluid cells. Fetal behavioral and structural ab- previously 4 8 . - 
												
												Genetic Background of Ataxia in Children Younger Than 5 Years in Finland E444
Volume 6, Number 4, August 2020 Neurology.org/NG A peer-reviewed clinical and translational neurology open access journal ARTICLE Genetic background of ataxia in children younger than 5 years in Finland e444 ARTICLE Cerebral arteriopathy associated with heterozygous variants in the casitas B-lineage lymphoma gene e448 ARTICLE Somatic SLC35A2 mosaicism correlates with clinical fi ndings in epilepsy brain tissuee460 ARTICLE Synonymous variants associated with Alzheimer disease in multiplex families e450 Academy Officers Neurology® is a registered trademark of the American Academy of Neurology (registration valid in the United States). James C. Stevens, MD, FAAN, President Neurology® Genetics (eISSN 2376-7839) is an open access journal published Orly Avitzur, MD, MBA, FAAN, President Elect online for the American Academy of Neurology, 201 Chicago Avenue, Ann H. Tilton, MD, FAAN, Vice President Minneapolis, MN 55415, by Wolters Kluwer Health, Inc. at 14700 Citicorp Drive, Bldg. 3, Hagerstown, MD 21742. Business offices are located at Two Carlayne E. Jackson, MD, FAAN, Secretary Commerce Square, 2001 Market Street, Philadelphia, PA 19103. Production offices are located at 351 West Camden Street, Baltimore, MD 21201-2436. Janis M. Miyasaki, MD, MEd, FRCPC, FAAN, Treasurer © 2020 American Academy of Neurology. Ralph L. Sacco, MD, MS, FAAN, Past President Neurology® Genetics is an official journal of the American Academy of Neurology. Journal website: Neurology.org/ng, AAN website: AAN.com CEO, American Academy of Neurology Copyright and Permission Information: Please go to the journal website (www.neurology.org/ng) and click the Permissions tab for the relevant Mary E. Post, MBA, CAE article. Alternatively, send an email to [email protected]. - 
												
												Analysis of the Mechanism of Zhichuanling Oral Liquid in Treating Bronchial Asthma Based on Network Pharmacology
Hindawi Evidence-Based Complementary and Alternative Medicine Volume 2020, Article ID 1875980, 10 pages https://doi.org/10.1155/2020/1875980 Research Article Analysis of the Mechanism of Zhichuanling Oral Liquid in Treating Bronchial Asthma Based on Network Pharmacology Ruiyin Wang1,2 and Jiangtao Lin 2 1Graduate School of Beijing University of Chinese Medicine, Beijing, China 2Respiratory and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China Correspondence should be addressed to Jiangtao Lin; [email protected] Received 17 September 2019; Revised 2 November 2019; Accepted 20 November 2019; Published 17 January 2020 Academic Editor: Hyunsu Bae Copyright © 2020 Ruiyin Wang and Jiangtao Lin. -is is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Zhichuanling oral liquid (ZOL) as a preparation of traditional Chinese medicine is widely used for the treatment of asthma in China; therefore, it is necessary to systematically clarify bioactive chemical ingredients and the mechanism of action of ZOL. Information on ZOL ingredients and asthma-related targets was collected, and we used the latest systematic pharmacological methods to construct protein-protein interaction network and compound-target network and then visualized them. Finally, GO and KEGG pathway enrichment analysis was conducted through the clusterProfiler package in the R software. -e results showed that 58 bioactive ingredients and 42 potential targets of ZOL related to asthma were identified, following six important components and nine hub genes screened. Further cluster and enrichment analysis suggested that NF-κB signaling pathway, PI3K/Akt signaling pathway, IL-17 signaling pathway, Toll-like receptor signaling pathway, and TNF signaling pathway might be core pathways of ZOL for asthma. - 
												
												PUR Promotes the Transcriptional Activation of PCK2 in Esophageal
G C A T T A C G G C A T genes Article PURα Promotes the Transcriptional Activation of PCK2 in Esophageal Squamous Cell Carcinoma Cells Yan Sun , Jiajia Gao , Zongpan Jing, Yan Zhao, Yulin Sun and Xiaohang Zhao * State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China; [email protected] (Y.S.); [email protected] (J.G.); [email protected] (Z.J.); [email protected] (Y.Z.); [email protected] (Y.S.) * Correspondence: [email protected]; Tel.: +86-106-7709-015 Received: 5 September 2020; Accepted: 30 October 2020; Published: 31 October 2020 Abstract: Esophageal squamous cell carcinoma (ESCC) is one of the most lethal gastrointestinal malignancies due to its characteristics of local invasion and distant metastasis. Purine element binding protein α (PURα) is a DNA and RNA binding protein, and recent studies have showed that abnormal expression of PURα is associated with the progression of some tumors, but its oncogenic function, especially in ESCC progression, has not been determined. Based on the bioinformatic analysis of RNA-seq and ChIP-seq data, we found that PURα affected metabolic pathways, including oxidative phosphorylation and fatty acid metabolism, and we observed that it has binding peaks in the promoter of mitochondrial phosphoenolpyruvate carboxykinase (PCK2). Meanwhile, PURα significantly increased the activity of the PCK2 gene promoter by binding to the GGGAGGCGGA motif, as determined though luciferase assay and ChIP-PCR/qPCR. The results of Western blotting and qRT-PCR analysis showed that PURα overexpression enhances the protein and mRNA levels of PCK2 in KYSE510 cells, whereas PURα knockdown inhibits the protein and mRNA levels of PCK2 in KYSE170 cells. - 
												
												PURA Gene Purine Rich Element Binding Protein A
PURA gene purine rich element binding protein A Normal Function The PURA gene provides instructions for making a protein called Pur-alpha (Pura ), which is able to attach (bind) to DNA and RNA (a molecular cousin of DNA). This protein has multiple roles in cells, including controlling the activity of genes (gene transcription) and aiding in the copying (replication) of DNA. The Pura protein is important for normal brain development. The protein helps direct the growth and division of nerve cells (neurons). It may also be involved in the formation or maturation of myelin, the protective substance that covers nerves and promotes the efficient transmission of nerve impulses. Health Conditions Related to Genetic Changes 5q31.3 microdeletion syndrome 5q31.3 microdeletion syndrome is caused by a chromosomal change in which a small piece of chromosome 5 is deleted in each cell. This rare condition is characterized by severely delayed or impaired development of speech and walking, weak muscle tone ( hypotonia), breathing problems, recurrent seizures (epilepsy) or seizure-like episodes, and distinctive facial features. The deletion that causes this condition occurs on the long (q) arm of the chromosome at a position designated q31.3. The size of the deletion can range from several thousand to several million DNA building blocks (base pairs). The deleted region typically contains at least three genes, one of which is PURA. A loss of one copy of the PURA gene is thought to alter normal brain development and impair the function of neurons, leading to developmental delay, hypotonia, and other neurological problems in people with 5q31.3 microdeletion syndrome. - 
												
												Deletions of PURA, at 5Q31, and PURB, at 7P13, in Myelodysplastic Syndrome and Progression to Acute Myelogenous Leukemia K Lezon-Geyda1,2, V Najfeld2 and EM Johnson1
Leukemia (2001) 15, 954–962 2001 Nature Publishing Group All rights reserved 0887-6924/01 $15.00 www.nature.com/leu Deletions of PURA, at 5q31, and PURB, at 7p13, in myelodysplastic syndrome and progression to acute myelogenous leukemia K Lezon-Geyda1,2, V Najfeld2 and EM Johnson1 1Departments of Pathology, Biochemistry and Molecular Biology, the Derald H Ruttenberg Cancer Center; and 2Tumor Cytogenetics Laboratory, Polly Annenberg Levee Hematology Center, Mount Sinai School of Medicine, New York, NY, USA Deletions or monosomy of chromosomes 5 and 7 are frequently gle gene product, the levels of which are critical, may be con- observed in myelodysplastic syndromes (MDS) and acute myel- ferred by haploinsufficiency.16 Similarly, no tumor suppressor ogenous leukemia (AML). In this study two genes, PURA and PURB, encoding functionally cooperative proteins in the Pur genes have yet been identified at deleted loci on chromosome family, are localized to chromosome bands 5q31.1 and 7p13, 7. The possibility has been noted that tumor suppressor genes respectively. One or both of these loci are shown to be hemiz- are present at more than one site on the long arms of chromo- ygously deleted in 60 MDS or AML patients using fluorescence some 7,17 as deletions of 7q are more frequently seen in MDS in situ hybridization (FISH). High-resolution mapping of PURA patients than deletions in 7p.1 On the other hand, deletions localizes it approximately 1.1 Mb telomeric to the EGR-1 gene. of 7p are seen in a significant number of cases,1,18 and thus Frequency of PURA deletion and segregation with EGR-1 indi- cate that PURA is within the most commonly deleted segment it is conceivable that the high prevalence of monosomy 7 in myeloid disorders characterized by del(5)(q31). - 
												
												Setd1 Histone 3 Lysine 4 Methyltransferase Complex Components in Epigenetic Regulation
SETD1 HISTONE 3 LYSINE 4 METHYLTRANSFERASE COMPLEX COMPONENTS IN EPIGENETIC REGULATION Patricia A. Pick-Franke Submitted to the faculty of the University Graduate School in partial fulfillment of the requirements for the degree Master of Science in the Department of Biochemistry and Molecular Biology Indiana University December 2010 Accepted by the Faculty of Indiana University, in partial fulfillment of the requirements for the degree of Master of Science. _____________________________________ David Skalnik, Ph.D., Chair _____________________________________ Kristin Chun, Ph.D. Master’s Thesis Committee _____________________________________ Simon Rhodes, Ph.D. ii DEDICATION This thesis is dedicated to my sons, Zachary and Zephaniah who give me great joy, hope and continuous inspiration. I can only hope that I successfully set a good example demonstrating that one can truly accomplish anything, if you never give up and reach for your dreams. iii ACKNOWLEDGEMENTS I would like to thank my committee members Dr. Skalnik, Dr. Chun and Dr. Rhodes for allowing me to complete this dissertation. They have been incredibly generous with their flexibility. I must make a special thank you to Jeanette McClintock, who willingly gave her expertise in statistical analysis with the Cfp1 microarray data along with encouragement, support and guidance to complete this work. I would like to thank Courtney Tate for her ceaseless willingness to share ideas, and her methods and materials, and Erika Dolbrota for her generous instruction as well as the name of a good doctor. I would also like to acknowledge the superb mentorship of Dr. Jeon Heong Lee, PhD and the contagious passion and excitement for the life of science of Dr.