DNA Aneuploidy in Malignant Salivary Gland
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Pan-Cancer Analysis of Homozygous Deletions in Primary Tumours Uncovers Rare Tumour Suppressors
Corrected: Author correction; Corrected: Author correction ARTICLE DOI: 10.1038/s41467-017-01355-0 OPEN Pan-cancer analysis of homozygous deletions in primary tumours uncovers rare tumour suppressors Jiqiu Cheng1,2, Jonas Demeulemeester 3,4, David C. Wedge5,6, Hans Kristian M. Vollan2,3, Jason J. Pitt7,8, Hege G. Russnes2,9, Bina P. Pandey1, Gro Nilsen10, Silje Nord2, Graham R. Bignell5, Kevin P. White7,11,12,13, Anne-Lise Børresen-Dale2, Peter J. Campbell5, Vessela N. Kristensen2, Michael R. Stratton5, Ole Christian Lingjærde 10, Yves Moreau1 & Peter Van Loo 3,4 1234567890 Homozygous deletions are rare in cancers and often target tumour suppressor genes. Here, we build a compendium of 2218 primary tumours across 12 human cancer types and sys- tematically screen for homozygous deletions, aiming to identify rare tumour suppressors. Our analysis defines 96 genomic regions recurrently targeted by homozygous deletions. These recurrent homozygous deletions occur either over tumour suppressors or over fragile sites, regions of increased genomic instability. We construct a statistical model that separates fragile sites from regions showing signatures of positive selection for homozygous deletions and identify candidate tumour suppressors within those regions. We find 16 established tumour suppressors and propose 27 candidate tumour suppressors. Several of these genes (including MGMT, RAD17, and USP44) show prior evidence of a tumour suppressive function. Other candidate tumour suppressors, such as MAFTRR, KIAA1551, and IGF2BP2, are novel. Our study demonstrates how rare tumour suppressors can be identified through copy number meta-analysis. 1 Department of Electrical Engineering (ESAT) and iMinds Future Health Department, University of Leuven, Kasteelpark Arenberg 10, B-3001 Leuven, Belgium. -
A Yeast Phenomic Model for the Influence of Warburg Metabolism on Genetic Buffering of Doxorubicin Sean M
Santos and Hartman Cancer & Metabolism (2019) 7:9 https://doi.org/10.1186/s40170-019-0201-3 RESEARCH Open Access A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin Sean M. Santos and John L. Hartman IV* Abstract Background: The influence of the Warburg phenomenon on chemotherapy response is unknown. Saccharomyces cerevisiae mimics the Warburg effect, repressing respiration in the presence of adequate glucose. Yeast phenomic experiments were conducted to assess potential influences of Warburg metabolism on gene-drug interaction underlying the cellular response to doxorubicin. Homologous genes from yeast phenomic and cancer pharmacogenomics data were analyzed to infer evolutionary conservation of gene-drug interaction and predict therapeutic relevance. Methods: Cell proliferation phenotypes (CPPs) of the yeast gene knockout/knockdown library were measured by quantitative high-throughput cell array phenotyping (Q-HTCP), treating with escalating doxorubicin concentrations under conditions of respiratory or glycolytic metabolism. Doxorubicin-gene interaction was quantified by departure of CPPs observed for the doxorubicin-treated mutant strain from that expected based on an interaction model. Recursive expectation-maximization clustering (REMc) and Gene Ontology (GO)-based analyses of interactions identified functional biological modules that differentially buffer or promote doxorubicin cytotoxicity with respect to Warburg metabolism. Yeast phenomic and cancer pharmacogenomics data were integrated to predict differential gene expression causally influencing doxorubicin anti-tumor efficacy. Results: Yeast compromised for genes functioning in chromatin organization, and several other cellular processes are more resistant to doxorubicin under glycolytic conditions. Thus, the Warburg transition appears to alleviate requirements for cellular functions that buffer doxorubicin cytotoxicity in a respiratory context. -
Novel Genetic Variants of Sporadic Atrial Septal Defect (ASD)
CLINICAL RESEARCH e-ISSN 1643-3750 © Med Sci Monit, 2018; 24: 1340-1358 DOI: 10.12659/MSM.908923 Received: 2018.01.11 Accepted: 2018.02.08 Novel Genetic Variants of Sporadic Atrial Septal Published: 2018.03.05 Defect (ASD) in a Chinese Population Identified by Whole-Exome Sequencing (WES) Authors’ Contribution: ABCDEF 1,2,3 Yong Liu* 1 Department of Cardiovascular Surgery, Yan’an Affiliated Hospital of Kunming Study Design A A 1,2 Yu Cao* Medical University, Kunming, Yunnan, P.R. China Data Collection B 2 Department of Cardiovascular Surgery, The First Peoples’ Hospital of Yunnan Statistical Analysis C G 1,3 Yaxiong Li* Province, Kunming, Yunnan, P.R. China Data Interpretation D E 4 Dongyun Lei* 3 Key Laboratory of Cardiovascular Disease of Yunnan Province, Kunming, Yunnan, Manuscript Preparation E E 1,3 Lin Li P.R. China. Literature Search F 4 The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, Funds Collection G G 1,3 Zong Liu Hou P.R. China F 1,3 Shen Han G 1 Mingyao Meng C 1 Jianlin Shi G 1,3 Yayong Zhang B 1,3 Yi Wang B 1 Zhaoyi Niu G 1 Yanhua Xie B 1 Benshan Xiao B 1 Yuanfei Wang C 1 Xiao Li F 1 Lirong Yang ACDE 1,3 Wenju Wang AG 2 Lihong Jiang * Joint first authors; Yong Liu, Yu Cao, Yaxiong Li, Dongyun Lei Corresponding Authors: Lihong Jiang, e-mail: [email protected], Wenju Wang, e-mail: [email protected] Source of support: This study was supported by grants from National Natural Science Foundation of China (No. -
De Novo Mutations in Histone Modifying Genes in Congenital Heart Disease
De novo mutations in histone modifying genes in congenital heart disease The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Zaidi, S., M. Choi, H. Wakimoto, L. Ma, J. Jiang, J. D. Overton, A. Romano-Adesman, et al. 2013. “De novo mutations in histone modifying genes in congenital heart disease.” Nature 498 (7453): 220-223. doi:10.1038/nature12141. http://dx.doi.org/10.1038/ nature12141. Published Version doi:10.1038/nature12141 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:11879354 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA NIH Public Access Author Manuscript Nature. Author manuscript; available in PMC 2013 December 13. NIH-PA Author ManuscriptPublished NIH-PA Author Manuscript in final edited NIH-PA Author Manuscript form as: Nature. 2013 June 13; 498(7453): 220–223. doi:10.1038/nature12141. De novo mutations in histone modifying genes in congenital heart disease Samir Zaidi1,2,*, Murim Choi1,2,*, Hiroko Wakimoto3, Lijiang Ma4, Jianming Jiang3,5, John D. Overton1,6,7, Angela Romano-Adesman8, Robert D. Bjornson7,9, Roger E. Breitbart10, Kerry K. Brown3, Nicholas J. Carriero7,9, Yee Him Cheung11, John Deanfield12, Steve DePalma3, Khalid A. Fakhro1,2, Joseph Glessner13, Hakon Hakonarson13,14, Michael Italia15, Jonathan R. Kaltman16, Juan Kaski12, Richard Kim17, Jennie K. Kline18, Teresa Lee4, Jeremy Leipzig15, Alexander Lopez1,6,7, Shrikant M. -
DEFINING the FUNCTIONS of USP22 and USP44 in REGULATION of H2BUB1 LEVELS Xianjiang Lan
The Texas Medical Center Library DigitalCommons@TMC The University of Texas MD Anderson Cancer Center UTHealth Graduate School of The University of Texas MD Anderson Cancer Biomedical Sciences Dissertations and Theses Center UTHealth Graduate School of (Open Access) Biomedical Sciences 8-2016 DEFINING THE FUNCTIONS OF USP22 AND USP44 IN REGULATION OF H2BUB1 LEVELS xianjiang Lan Follow this and additional works at: https://digitalcommons.library.tmc.edu/utgsbs_dissertations Part of the Biochemistry Commons, Cancer Biology Commons, Cell Biology Commons, and the Molecular Biology Commons Recommended Citation Lan, xianjiang, "DEFINING THE FUNCTIONS OF USP22 AND USP44 IN REGULATION OF H2BUB1 LEVELS" (2016). The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access). 686. https://digitalcommons.library.tmc.edu/utgsbs_dissertations/686 This Dissertation (PhD) is brought to you for free and open access by the The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences at DigitalCommons@TMC. It has been accepted for inclusion in The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access) by an authorized administrator of DigitalCommons@TMC. For more information, please contact [email protected]. DEFINING THE FUNCTIONS OF USP22 AND USP44 IN REGULATION OF H2BUB1 LEVELS BY Xianjiang Lan, Ph.D. Candidate APPROVED: _____________________________________ -
Title: a Yeast Phenomic Model for the Influence of Warburg Metabolism on Genetic
bioRxiv preprint doi: https://doi.org/10.1101/517490; this version posted January 15, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 1 Title Page: 2 3 Title: A yeast phenomic model for the influence of Warburg metabolism on genetic 4 buffering of doxorubicin 5 6 Authors: Sean M. Santos1 and John L. Hartman IV1 7 1. University of Alabama at Birmingham, Department of Genetics, Birmingham, AL 8 Email: [email protected], [email protected] 9 Corresponding author: [email protected] 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 1 bioRxiv preprint doi: https://doi.org/10.1101/517490; this version posted January 15, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 26 Abstract: 27 Background: 28 Saccharomyces cerevisiae represses respiration in the presence of adequate glucose, 29 mimicking the Warburg effect, termed aerobic glycolysis. We conducted yeast phenomic 30 experiments to characterize differential doxorubicin-gene interaction, in the context of 31 respiration vs. glycolysis. The resulting systems level biology about doxorubicin 32 cytotoxicity, including the influence of the Warburg effect, was integrated with cancer 33 pharmacogenomics data to identify potentially causal correlations between differential 34 gene expression and anti-cancer efficacy. -
Bioinformatic Gene Analysis for Potential Biomarkers And
Zou et al. J Transl Med (2019) 17:45 https://doi.org/10.1186/s12967-019-1790-x Journal of Translational Medicine RESEARCH Open Access Bioinformatic gene analysis for potential biomarkers and therapeutic targets of atrial fbrillation-related stroke Rongjun Zou1†, Dingwen Zhang1†, Lei Lv1†, Wanting Shi2, Zijiao Song3, Bin Yi1, Bingjia Lai4, Qian Chen5, Songran Yang6,7* and Ping Hua1* Abstract Background: Atrial fbrillation (AF) is one of the most prevalent sustained arrhythmias, however, epidemiological data may understate its actual prevalence. Meanwhile, AF is considered to be a major cause of ischemic strokes due to irregular heart-rhythm, coexisting chronic vascular infammation, and renal insufciency, and blood stasis. We studied co-expressed genes to understand relationships between atrial fbrillation (AF) and stroke and reveal potential biomarkers and therapeutic targets of AF-related stroke. Methods: AF-and stroke-related diferentially expressed genes (DEGs) were identifed via bioinformatic analysis Gene Expression Omnibus (GEO) datasets GSE79768 and GSE58294, respectively. Subsequently, extensive target prediction and network analyses methods were used to assess protein–protein interaction (PPI) networks, Gene Ontology (GO) terms and pathway enrichment for DEGs, and co-expressed DEGs coupled with corresponding predicted miRNAs involved in AF and stroke were assessed as well. Results: We identifed 489, 265, 518, and 592 DEGs in left atrial specimens and cardioembolic stroke blood samples at < 3, 5, and 24 h, respectively. LRRK2, CALM1, CXCR4, TLR4, CTNNB1, and CXCR2 may be implicated in AF and the hub- genes of CD19, FGF9, SOX9, GNGT1, and NOG may be associated with stroke. Finally, co-expressed DEGs of ZNF566, PDZK1IP1, ZFHX3, and PITX2 coupled with corresponding predicted miRNAs, especially miR-27a-3p, miR-27b-3p, and miR-494-3p may be signifcantly associated with AF-related stroke. -
W O 2019/067145 Al 04 April 2019 (04.04.2019) W IPO I PCT
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property (1) Organization11111111111111111111111I1111111111111ii111liiili International Bureau (10) International Publication Number (43) International Publication Date W O 2019/067145 Al 04 April 2019 (04.04.2019) W IPO I PCT (51) International Patent Classification: TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, A61K47/40 (2017.01) A61K 9/08 (2006.01) KM, ML, MR, NE, SN, TD, TG). A61K9/00(2006.01) Rule 4.17: (21) International Application Number: Declarations under be granted a PCT/US2018/048414 - as to applicant's entitlement to applyfor and patent (Rule 4.17(i)) (22) International Filing Date: - as to the applicant'sentitlement to claim the priority ofthe 28 August 2018 (28.08.2018) earlier application (Rule 4.17(iii)) (25) Filing Language: English Published: (26) Publication Language: English with internationalsearch report (Art. 21(3)) (30) Priority Data: 62/565,053 28 September 2017 (28.09.2017) US 62/573,658 17 October 2017 (17.10.2017) US 62/586,826 15 November 2017 (15.11.2017) US 62/551,193 04 December 2017 (04.12.2017) US 62/643,694 15 March 2018 (15.03.2018) US 62/679,912 03 June 2018 (03.06.2018) US (71) Applicant: ASDERA LLC [US/US]; 220 E. 70th Street, #5C, New York, NY 10021 (US). (72) Inventor: WITTKOWSKI, Knut, M.; 220 E. 70th Street, #5C, New York, NY 10021 (US). (74) Agent: ZURAWSKI, John, A. et al.; BALLARD SPAHR LLP, 1735 Market Street, 51st Floor, Philadelphia, PA 19103 (US). (81) Designated States (unless -
Mouse Usp44 Knockout Project (CRISPR/Cas9)
https://www.alphaknockout.com Mouse Usp44 Knockout Project (CRISPR/Cas9) Objective: To create a Usp44 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Usp44 gene (NCBI Reference Sequence: NM_001206851 ; Ensembl: ENSMUSG00000020020 ) is located on Mouse chromosome 10. 6 exons are identified, with the ATG start codon in exon 2 and the TGA stop codon in exon 6 (Transcript: ENSMUST00000216224). Exon 2~3 will be selected as target site. Cas9 and gRNA will be co-injected into fertilized eggs for KO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Mice homozygous for a knock-out allele exhibit chromosomal instability, aneuploidy and increased tumor incidence. Exon 2 starts from the coding region. Exon 2~3 covers 76.0% of the coding region. The size of effective KO region: ~3259 bp. The KO region does not have any other known gene. Page 1 of 8 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele 5' gRNA region gRNA region 3' 1 2 3 6 Legends Exon of mouse Usp44 Knockout region Page 2 of 8 https://www.alphaknockout.com Overview of the Dot Plot (up) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 2000 bp section upstream of Exon 2 is aligned with itself to determine if there are tandem repeats. Tandem repeats are found in the dot plot matrix. The gRNA site is selected outside of these tandem repeats. Overview of the Dot Plot (down) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 2000 bp section downstream of Exon 3 is aligned with itself to determine if there are tandem repeats. -
Homo Sapiens, Homo Neanderthalensis and the Denisova Specimen: New Insights on Their Evolutionary Histories Using Whole-Genome Comparisons
Genetics and Molecular Biology, 35, 4 (suppl), 904-911 (2012) Copyright © 2012, Sociedade Brasileira de Genética. Printed in Brazil www.sbg.org.br Research Article Homo sapiens, Homo neanderthalensis and the Denisova specimen: New insights on their evolutionary histories using whole-genome comparisons Vanessa Rodrigues Paixão-Côrtes, Lucas Henrique Viscardi, Francisco Mauro Salzano, Tábita Hünemeier and Maria Cátira Bortolini Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil. Abstract After a brief review of the most recent findings in the study of human evolution, an extensive comparison of the com- plete genomes of our nearest relative, the chimpanzee (Pan troglodytes), of extant Homo sapiens, archaic Homo neanderthalensis and the Denisova specimen were made. The focus was on non-synonymous mutations, which consequently had an impact on protein levels and these changes were classified according to degree of effect. A to- tal of 10,447 non-synonymous substitutions were found in which the derived allele is fixed or nearly fixed in humans as compared to chimpanzee. Their most frequent location was on chromosome 21. Their presence was then searched in the two archaic genomes. Mutations in 381 genes would imply radical amino acid changes, with a frac- tion of these related to olfaction and other important physiological processes. Eight new alleles were identified in the Neanderthal and/or Denisova genetic pools. Four others, possibly affecting cognition, occured both in the sapiens and two other archaic genomes. The selective sweep that gave rise to Homo sapiens could, therefore, have initiated before the modern/archaic human divergence. -
Overexpression of Ubiquitin Specific Protease 44 (USP44) Induces Chromosomal Instability and Is Frequently Observed in Human T-Cell Leukemia
Overexpression of Ubiquitin Specific Protease 44 (USP44) Induces Chromosomal Instability and Is Frequently Observed in Human T-Cell Leukemia Ying Zhang1,2, Jan van Deursen1,2, Paul J. Galardy1,2* 1 Department of Pediatrics and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota, United States of America, 2 Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, United States of America Abstract Cdc20-anaphase promoting complex/cyclosome (Cdc20-APC/C) E3 ubiquitin ligase activity is essential for orderly mitotic progression. The deubiqituinase USP44 was identified as a key regulator of APC/C and has been proposed to suppress Cdc20-APC/C activity by maintaining its association with the inhibitory protein Mad2 until all chromosomes are properly attached to the mitotic spindle. However, this notion has been challenged by data in which a lysine-less mutant of Cdc20 leads to premature anaphase, suggesting that it’s ubiquitination is not required for APC/C activation. To further evaluate its role in checkpoint function and chromosome instability, we studied the consequences of over-expression of mouse Usp44 in non-transformed murine embryonic fibroblasts. Here we show that cells with high Usp44 are prone to chromosome segregation errors and aneuploidization. We find that high Usp44 promotes association of Mad2 with Cdc20 and reinforces the mitotic checkpoint. Surprisingly, the APC/C-Cdc20 substrate cyclin B1 is stabilized in G2 when Usp44 is over-expressed, but is degraded with normal kinetics once cells enter mitosis. Furthermore, we show that USP44 expression is elevated in subset of T-cell leukemias. These data are consistent with an important role for USP44 in regulating Cdc20-APC/C activity and suggest that high levels of this enzyme may contribute to the pathogenesis of T-ALL. -
(12) Patent Application Publication (10) Pub. No.: US 2015/0050728A1 Benvenisty Et Al
US 2015.0050728A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2015/0050728A1 Benvenisty et al. (43) Pub. Date: Feb. 19, 2015 (54) IDENTIFICATION OF NOVEL CELL (60) Provisional application No. 61/536,099, filed on Sep. SURFACE MARKERS FOR PANCREATC 19, 2011, provisional application No. 61/417.364, PROGENITOR CELLS AND DEFINITE filed on Nov. 26, 2010. ENDODERMAL CELLS Publication Classification (71) Applicants: Nissim Benvenisty, Jerusalem (IL); Joseph Itskovitz-Eldor, Haifa (IL); (51) Int. Cl. Bettina Fishman, Haifa (IL); Hanna CI2N5/071 (2006.01) Segev, Doar-Na Emek Hefer (IL); (52) U.S. Cl. Danny Kitsberg, Jerusalem (IL) CPC .................................... CI2N5/0678 (2013.01) USPC .......................................................... 435/325 (72) Inventors: Nissim Benvenisty, Jerusalem (IL); Joseph Itskovitz-Eldor, Haifa (IL); (57) ABSTRACT Bettina Fishman, Haifa (IL); Hanna Segev, Doar-Na Emek Hefer (IL); Methods of identifying, isolating and qualifying pancreatic Danny Kitsberg, Jerusalem (IL) progenitor cells and definite endodermal cells. An isolated population of pancreatic progenitor cells, including at least (21) Appl. No.: 14/528,837 75% of cells having a TROP-2+ and/or TROP-2+/GPR50+ expression pattern and an isolated population of definite (22) Filed: Oct. 30, 2014 endodermal cells, including at least 50% of cells having a SOX17+/SOX7+/GSC+/CER+/FOXA2+/CXCR4+f Related U.S. Application Data NANOG expression pattern. Nucleic acid constructs includ (63) Continuation of application No. 13/903,815, filed on ing a reporter protein under the transcriptional regulation of May 28, 2013, which is a continuation of application SOX17 regulatory sequence or of PDX1 regulatory sequence, No. PCT/IB2011/055283, filed on Nov.