DHX32 Expression Suggests a Role in Lymphocyte Differentiation
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Transcriptome Analyses of Rhesus Monkey Pre-Implantation Embryos Reveal A
Downloaded from genome.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press Transcriptome analyses of rhesus monkey pre-implantation embryos reveal a reduced capacity for DNA double strand break (DSB) repair in primate oocytes and early embryos Xinyi Wang 1,3,4,5*, Denghui Liu 2,4*, Dajian He 1,3,4,5, Shengbao Suo 2,4, Xian Xia 2,4, Xiechao He1,3,6, Jing-Dong J. Han2#, Ping Zheng1,3,6# Running title: reduced DNA DSB repair in monkey early embryos Affiliations: 1 State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China 2 Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China 3 Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China 4 University of Chinese Academy of Sciences, Beijing, China 5 Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China 6 Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China * Xinyi Wang and Denghui Liu contributed equally to this work 1 Downloaded from genome.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press # Correspondence: Jing-Dong J. Han, Email: [email protected]; Ping Zheng, Email: [email protected] Key words: rhesus monkey, pre-implantation embryo, DNA damage 2 Downloaded from genome.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press ABSTRACT Pre-implantation embryogenesis encompasses several critical events including genome reprogramming, zygotic genome activation (ZGA) and cell fate commitment. -
Genome-Wide DNA Methylation Map of Human Neutrophils Reveals Widespread Inter-Individual Epigenetic Variation
www.nature.com/scientificreports OPEN Genome-wide DNA methylation map of human neutrophils reveals widespread inter-individual Received: 15 June 2015 Accepted: 29 October 2015 epigenetic variation Published: 27 November 2015 Aniruddha Chatterjee1,2, Peter A. Stockwell3, Euan J. Rodger1, Elizabeth J. Duncan2,4, Matthew F. Parry5, Robert J. Weeks1 & Ian M. Morison1,2 The extent of variation in DNA methylation patterns in healthy individuals is not yet well documented. Identification of inter-individual epigenetic variation is important for understanding phenotypic variation and disease susceptibility. Using neutrophils from a cohort of healthy individuals, we generated base-resolution DNA methylation maps to document inter-individual epigenetic variation. We identified 12851 autosomal inter-individual variably methylated fragments (iVMFs). Gene promoters were the least variable, whereas gene body and upstream regions showed higher variation in DNA methylation. The iVMFs were relatively enriched in repetitive elements compared to non-iVMFs, and were associated with genome regulation and chromatin function elements. Further, variably methylated genes were disproportionately associated with regulation of transcription, responsive function and signal transduction pathways. Transcriptome analysis indicates that iVMF methylation at differentially expressed exons has a positive correlation and local effect on the inclusion of that exon in the mRNA transcript. Methylation of DNA is a mechanism for regulating gene function in all vertebrates. It has a role in gene silencing, tissue differentiation, genomic imprinting, chromosome X inactivation, phenotypic plasticity, and disease susceptibility1,2. Aberrant DNA methylation has been implicated in the pathogenesis of sev- eral human diseases, especially cancer3–5. Variation in DNA methylation patterns in healthy individuals has been hypothesised to alter human phenotypes including susceptibility to common diseases6 and response to drug treatments7. -
Aneuploidy: Using Genetic Instability to Preserve a Haploid Genome?
Health Science Campus FINAL APPROVAL OF DISSERTATION Doctor of Philosophy in Biomedical Science (Cancer Biology) Aneuploidy: Using genetic instability to preserve a haploid genome? Submitted by: Ramona Ramdath In partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biomedical Science Examination Committee Signature/Date Major Advisor: David Allison, M.D., Ph.D. Academic James Trempe, Ph.D. Advisory Committee: David Giovanucci, Ph.D. Randall Ruch, Ph.D. Ronald Mellgren, Ph.D. Senior Associate Dean College of Graduate Studies Michael S. Bisesi, Ph.D. Date of Defense: April 10, 2009 Aneuploidy: Using genetic instability to preserve a haploid genome? Ramona Ramdath University of Toledo, Health Science Campus 2009 Dedication I dedicate this dissertation to my grandfather who died of lung cancer two years ago, but who always instilled in us the value and importance of education. And to my mom and sister, both of whom have been pillars of support and stimulating conversations. To my sister, Rehanna, especially- I hope this inspires you to achieve all that you want to in life, academically and otherwise. ii Acknowledgements As we go through these academic journeys, there are so many along the way that make an impact not only on our work, but on our lives as well, and I would like to say a heartfelt thank you to all of those people: My Committee members- Dr. James Trempe, Dr. David Giovanucchi, Dr. Ronald Mellgren and Dr. Randall Ruch for their guidance, suggestions, support and confidence in me. My major advisor- Dr. David Allison, for his constructive criticism and positive reinforcement. -
Supplementary Materials
Supplementary materials Supplementary Table S1: MGNC compound library Ingredien Molecule Caco- Mol ID MW AlogP OB (%) BBB DL FASA- HL t Name Name 2 shengdi MOL012254 campesterol 400.8 7.63 37.58 1.34 0.98 0.7 0.21 20.2 shengdi MOL000519 coniferin 314.4 3.16 31.11 0.42 -0.2 0.3 0.27 74.6 beta- shengdi MOL000359 414.8 8.08 36.91 1.32 0.99 0.8 0.23 20.2 sitosterol pachymic shengdi MOL000289 528.9 6.54 33.63 0.1 -0.6 0.8 0 9.27 acid Poricoic acid shengdi MOL000291 484.7 5.64 30.52 -0.08 -0.9 0.8 0 8.67 B Chrysanthem shengdi MOL004492 585 8.24 38.72 0.51 -1 0.6 0.3 17.5 axanthin 20- shengdi MOL011455 Hexadecano 418.6 1.91 32.7 -0.24 -0.4 0.7 0.29 104 ylingenol huanglian MOL001454 berberine 336.4 3.45 36.86 1.24 0.57 0.8 0.19 6.57 huanglian MOL013352 Obacunone 454.6 2.68 43.29 0.01 -0.4 0.8 0.31 -13 huanglian MOL002894 berberrubine 322.4 3.2 35.74 1.07 0.17 0.7 0.24 6.46 huanglian MOL002897 epiberberine 336.4 3.45 43.09 1.17 0.4 0.8 0.19 6.1 huanglian MOL002903 (R)-Canadine 339.4 3.4 55.37 1.04 0.57 0.8 0.2 6.41 huanglian MOL002904 Berlambine 351.4 2.49 36.68 0.97 0.17 0.8 0.28 7.33 Corchorosid huanglian MOL002907 404.6 1.34 105 -0.91 -1.3 0.8 0.29 6.68 e A_qt Magnogrand huanglian MOL000622 266.4 1.18 63.71 0.02 -0.2 0.2 0.3 3.17 iolide huanglian MOL000762 Palmidin A 510.5 4.52 35.36 -0.38 -1.5 0.7 0.39 33.2 huanglian MOL000785 palmatine 352.4 3.65 64.6 1.33 0.37 0.7 0.13 2.25 huanglian MOL000098 quercetin 302.3 1.5 46.43 0.05 -0.8 0.3 0.38 14.4 huanglian MOL001458 coptisine 320.3 3.25 30.67 1.21 0.32 0.9 0.26 9.33 huanglian MOL002668 Worenine -
REVIEW NUP98 Gene Fusions in Hematologic Malignancies
Leukemia (2001) 15, 1689–1695 2001 Nature Publishing Group All rights reserved 0887-6924/01 $15.00 www.nature.com/leu REVIEW NUP98 gene fusions in hematologic malignancies DH Lam1,2 and PD Aplan2 1Department of Immunology, Roswell Park Cancer Institute, Buffalo, NY; and 2Genetics Department, Medicine Branch, Division of Clinical Sciences, National Cancer Institute, Bethesda, MD, USA Acute leukemia is associated with a wide spectrum of recur- the malignant cells ofpatients with both myeloid and rent, non-random chromosomal translocations. Molecular lymphoid malignancies, including AML, CML, myelodysplas- analysis of the genes involved in these translocations has led to a better understanding of both the causes of chromosomal tic syndrome (MDS), and T cell acute lymphoblastic leukemia rearrangements as well as the mechanisms of leukemic trans- (T-ALL). This review will summarize the clinical and formation. Recently, a number of laboratories have cloned biological features of this emerging class of chromosomal translocations involving the NUP98 gene on chromosome rearrangements. 11p15.5, from patients with acute myelogenous leukemia (AML), myelodysplastic syndrome (MDS), chronic myelogen- ous leukemia (CML), and T cell acute lymphoblastic leukemia (T-ALL). To date, at least eight different chromosomal Structure and function of NUP98 rearrangements involving NUP98 have been identified. The resultant chimeric transcripts encode fusion proteins that The NUP98 protein is a component ofthe nuclear pore com- juxtapose the N-terminal GLFG repeats of NUP98 to the C-ter- plex (NPC), which regulates nucleocytoplasmic transport of minus of the partner gene. Of note, several of these protein and RNA (Figure 1a).17–22 The yeast NPC consists of translocations have been found in patients with therapy-related approximately 30 nucleoporins;23 the mammalian NPC has acute myelogenous leukemia (t-AML) or myelodysplastic syn- 20,22,24 drome (t-MDS), suggesting that genotoxic chemotherapeutic been estimated to contain 50–100 different proteins. -
Identification of Inherited Retinal Disease-Associated Genetic Variants in 11 Candidate Genes
G C A T T A C G G C A T genes Article Identification of Inherited Retinal Disease-Associated Genetic Variants in 11 Candidate Genes Galuh D. N. Astuti 1,2, L. Ingeborgh van den Born 3, M. Imran Khan 1,4, Christian P. Hamel 5,6,7,†, Béatrice Bocquet 5,6,7, Gaël Manes 5,6, Mathieu Quinodoz 8, Manir Ali 9 ID , Carmel Toomes 9, Martin McKibbin 10 ID , Mohammed E. El-Asrag 9,11, Lonneke Haer-Wigman 1, Chris F. Inglehearn 9 ID , Graeme C. M. Black 12, Carel B. Hoyng 13, Frans P. M. Cremers 1,4 and Susanne Roosing 1,4,* ID 1 Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; [email protected] (G.D.N.A.); [email protected] (M.I.K.); [email protected] (L.H.-W.); [email protected] (F.P.M.C.) 2 Radboud Institute for Molecular Life Sciences, Radboud University, 6525 GA Nijmegen, The Netherlands 3 The Rotterdam Eye Hospital, 3011 BH Rotterdam, The Netherlands; [email protected] 4 Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, 6525 EN Nijmegen, The Netherlands 5 Institut National de la Santé et de la Recherche Médicale, Institute for Neurosciences of Montpellier, 34080 Montpellier, France; [email protected] (B.B.); [email protected] (G.M.) 6 University of Montpellier, 34090 Montpellier, France 7 CHRU, Genetics of Sensory Diseases, 34295 Montpellier, France 8 Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, 1015 Lausanne, Switzerland; [email protected] 9 Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, St. -
Gene Ontology Functional Annotations and Pleiotropy
Network based analysis of genetic disease associations Sarah Gilman Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy under the Executive Committee of the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2014 © 2013 Sarah Gilman All Rights Reserved ABSTRACT Network based analysis of genetic disease associations Sarah Gilman Despite extensive efforts and many promising early findings, genome-wide association studies have explained only a small fraction of the genetic factors contributing to common human diseases. There are many theories about where this “missing heritability” might lie, but increasingly the prevailing view is that common variants, the target of GWAS, are not solely responsible for susceptibility to common diseases and a substantial portion of human disease risk will be found among rare variants. Relatively new, such variants have not been subject to purifying selection, and therefore may be particularly pertinent for neuropsychiatric disorders and other diseases with greatly reduced fecundity. Recently, several researchers have made great progress towards uncovering the genetics behind autism and schizophrenia. By sequencing families, they have found hundreds of de novo variants occurring only in affected individuals, both large structural copy number variants and single nucleotide variants. Despite studying large cohorts there has been little recurrence among the genes implicated suggesting that many hundreds of genes may underlie these complex phenotypes. The question -
Original Article Highly Expressed DDX10 Promotes Hepatocellular Carcinoma Cell Proliferation Through Wnt/Β-Catenin Signaling
Int J Clin Exp Pathol 2017;10(5):6047-6053 www.ijcep.com /ISSN:1936-2625/IJCEP0047545 Original Article Highly expressed DDX10 promotes hepatocellular carcinoma cell proliferation through Wnt/β-catenin signaling Ying Wang1,2, Wen-Ming Xiao2, Shu-Ming Wei3, Xiang-Ming Chen2, Lin Wei2, Rui-Hua Tian2, Li Meng2, Bao-Rong Xiao2, Ping-Xia Wu2, Yong-Hua Yu1 1Department of Radiation Oncology, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Uni- versity, Jinan, Shandong Province, China; Departments of 2Clinical Oncology, 3Anesthesiology, Taian City Central Hospital, Taian, Shandong Province, China Received December 18, 2016; Accepted March 17, 2017; Epub May 1, 2017; Published May 15, 2017 Abstract: DDX10, a putative DEAD-box RNA helicase gene, is poorly studied in cancer. Our previous study found that DDX10 was significantly up-regulated in hepatocellular carcinoma (HCC). However, the clinical significance of DDX10 and its biological roles and associated mechanisms in HCC tumorigenesis remain elusive. In current study, quantitative real-time PCR, Western bolt were applied to evaluate the expression of DDX10. The roles of DDX10 in cell viability and proliferation were analyzed by cell biological assays in vitro. Luciferase reporter assays was employed to investigate the mechanism. And we further confirmed that compared with adjacent tissues, DDX10 is remarkably increased in HCC tissues in fresh tissues. In addition, cellular function assays demonstrated that DDX10 promotes cell viability, proliferation. Furthermore, we validated that up-regulated DDX10 enhances the activity of Wnt/β-catenin signaling to promote cell proliferation. Keywords: DDX10, Wnt/β-catenin signaling, HCC Introduction human DEAD-box RNA helicase gene on chro- mosome 11q22-q23 [7], although its normal Hepatocellular carcinoma (HCC) ranks second function has not yet been identified, is suggest- among the most common cancer-related mor- ed to be involved in ribosome assembly. -
Newly Identified Gon4l/Udu-Interacting Proteins
www.nature.com/scientificreports OPEN Newly identifed Gon4l/ Udu‑interacting proteins implicate novel functions Su‑Mei Tsai1, Kuo‑Chang Chu1 & Yun‑Jin Jiang1,2,3,4,5* Mutations of the Gon4l/udu gene in diferent organisms give rise to diverse phenotypes. Although the efects of Gon4l/Udu in transcriptional regulation have been demonstrated, they cannot solely explain the observed characteristics among species. To further understand the function of Gon4l/Udu, we used yeast two‑hybrid (Y2H) screening to identify interacting proteins in zebrafsh and mouse systems, confrmed the interactions by co‑immunoprecipitation assay, and found four novel Gon4l‑interacting proteins: BRCA1 associated protein‑1 (Bap1), DNA methyltransferase 1 (Dnmt1), Tho complex 1 (Thoc1, also known as Tho1 or HPR1), and Cryptochrome circadian regulator 3a (Cry3a). Furthermore, all known Gon4l/Udu‑interacting proteins—as found in this study, in previous reports, and in online resources—were investigated by Phenotype Enrichment Analysis. The most enriched phenotypes identifed include increased embryonic tissue cell apoptosis, embryonic lethality, increased T cell derived lymphoma incidence, decreased cell proliferation, chromosome instability, and abnormal dopamine level, characteristics that largely resemble those observed in reported Gon4l/udu mutant animals. Similar to the expression pattern of udu, those of bap1, dnmt1, thoc1, and cry3a are also found in the brain region and other tissues. Thus, these fndings indicate novel mechanisms of Gon4l/ Udu in regulating CpG methylation, histone expression/modifcation, DNA repair/genomic stability, and RNA binding/processing/export. Gon4l is a nuclear protein conserved among species. Animal models from invertebrates to vertebrates have shown that the protein Gon4-like (Gon4l) is essential for regulating cell proliferation and diferentiation. -
Genome-Wide Linkage and Association Study Implicates the 10Q26 Region As a Major Genetic Contributor to Primary Nonsyndromic
www.nature.com/scientificreports OPEN Genome-wide linkage and association study implicates the 10q26 region as a major Received: 6 July 2017 Accepted: 6 October 2017 genetic contributor to primary Published: xx xx xxxx nonsyndromic vesicoureteric refux John M. Darlow1,2, Rebecca Darlay3, Mark G. Dobson1,2, Aisling Stewart3, Pimphen Charoen4,5, Jennifer Southgate 6, Simon C. Baker 6, Yaobo Xu3, Manuela Hunziker2,7, Heather J. Lambert8, Andrew J. Green1,9, Mauro Santibanez-Koref3, John A. Sayer 3, Timothy H. J. Goodship3, Prem Puri2,10, Adrian S. Woolf 11,12, Rajko B. Kenda13, David E. Barton1,9 & Heather J. Cordell3 Vesicoureteric refux (VUR) is the commonest urological anomaly in children. Despite treatment improvements, associated renal lesions – congenital dysplasia, acquired scarring or both – are a common cause of childhood hypertension and renal failure. Primary VUR is familial, with transmission rate and sibling risk both approaching 50%, and appears highly genetically heterogeneous. It is often associated with other developmental anomalies of the urinary tract, emphasising its etiology as a disorder of urogenital tract development. We conducted a genome-wide linkage and association study in three European populations to search for loci predisposing to VUR. Family-based association analysis of 1098 parent-afected-child trios and case/control association analysis of 1147 cases and 3789 controls did not reveal any compelling associations, but parametric linkage analysis of 460 families (1062 afected individuals) under a dominant model identifed a single region, on 10q26, that showed strong linkage (HLOD = 4.90; ZLRLOD = 4.39) to VUR. The ~9Mb region contains 69 genes, including some good biological candidates. -
DEAH-Box Polypeptide 32 Promotes Hepatocellular Carcinoma Progression Via Activating the Β-Catenin Pathway
DEAH-box polypeptide 32 promotes hepatocellular carcinoma progression via activating the β-catenin pathway Xiaoyun Hu Southern Medical University Nanfang Hospital Guosheng Yuan Southern Medical University Nanfang Hospital Qi Li Southern Medical University Nanfang Hospital Jing Huang Southern Medical University Nanfang Hospital Xiao Cheng Southern Medical University Nanfang Hospital Jinzhang Chen ( [email protected] ) Southern Medical University Nanfang Hospital https://orcid.org/0000-0003-4881-4663 Primary research Keywords: hepatocellular carcinoma, DHX32, EMT, proliferation, β-catenin Posted Date: May 15th, 2020 DOI: https://doi.org/10.21203/rs.3.rs-27420/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/18 Abstract Background Hepatocellular carcinoma (HCC) is a refractory cancer with high morbidity and high mortality. It has been reported that DEAH-box polypeptide 32 (DHX32) was upregulated in several types of malignancies and predicted poor prognosis, which was associated with tumor growth and metastasis. However, the expression of DHX32 in HCC and its role in HCC progression remain largely unknown. Methods Western blot and RT-PCR assays were used to detect the expression of DHX32 and epithelial mesenchymal transition (EMT)-related genes in HCC cells. Wound-healing and Transwell invasion assays were performed to determine the effect of DHX32 and β-catenin on the migration and invasion of HCC cells. Cell proliferation was examined by EdU cell proliferation assay. Results In our study, we found that high level of DHX32 expression was associated with reduced overall survival in HCC patients. DHX32 expression was upregulated in human HCC cells and ectopic expression of DHX32 induced EMT, promoted the migration, invasion, and proliferation of HCC cells, and enhanced tumor growth. -
Primepcr™Assay Validation Report
PrimePCR™Assay Validation Report Gene Information Gene Name DEAD (Asp-Glu-Ala-Asp) box polypeptide 10 Gene Symbol DDX10 Organism Human Gene Summary DEAD box proteins characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD) are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation nuclear and mitochondrial splicing and ribosome and spliceosome assembly. Based on their distribution patterns some members of this family are believed to be involved in embryogenesis spermatogenesis and cellular growth and division. This gene encodes a DEAD box protein and it may be involved in ribosome assembly. Fusion of this gene and the nucleoporin gene NUP98 by inversion 11 (p15q22) chromosome translocation is found in the patients with de novo or therapy-related myeloid malignancies. Gene Aliases HRH-J8 RefSeq Accession No. NC_000011.9, NT_033899.8 UniGene ID Hs.591931 Ensembl Gene ID ENSG00000178105 Entrez Gene ID 1662 Assay Information Unique Assay ID qHsaCED0047288 Assay Type SYBR® Green Detected Coding Transcript(s) ENST00000322536 Amplicon Context Sequence GGATGAAGAGCTGGTGTTACATCTGCTAAGAAGTCAAAGCTAAATACTTCCTGCG CCTGCCTTCTCCTTGAAACCTTGGTTATGACTGCGTAGGCAAGAAGTTGAAAAAC AGTTGATTTGGGGGCACT Amplicon Length (bp) 98 Chromosome Location 11:108811108-108811235 Assay Design Exonic Purification Desalted Validation Results Efficiency (%) 95 R2 0.9995 cDNA Cq 21.43 Page 1/5 PrimePCR™Assay Validation Report cDNA Tm (Celsius) 81.5 gDNA Cq 24.2 Specificity (%)