Genetic Predictors of Response to Anti-Tumor Necrosis Factor Drugs In
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The Porcine Major Histocompatibility Complex and Related Paralogous Regions: a Review Patrick Chardon, Christine Renard, Claire Gaillard, Marcel Vaiman
The porcine Major Histocompatibility Complex and related paralogous regions: a review Patrick Chardon, Christine Renard, Claire Gaillard, Marcel Vaiman To cite this version: Patrick Chardon, Christine Renard, Claire Gaillard, Marcel Vaiman. The porcine Major Histocom- patibility Complex and related paralogous regions: a review. Genetics Selection Evolution, BioMed Central, 2000, 32 (2), pp.109-128. 10.1051/gse:2000101. hal-00894302 HAL Id: hal-00894302 https://hal.archives-ouvertes.fr/hal-00894302 Submitted on 1 Jan 2000 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Genet. Sel. Evol. 32 (2000) 109–128 109 c INRA, EDP Sciences Review The porcine Major Histocompatibility Complex and related paralogous regions: a review Patrick CHARDON, Christine RENARD, Claire ROGEL GAILLARD, Marcel VAIMAN Laboratoire de radiobiologie et d’etude du genome, Departement de genetique animale, Institut national de la recherche agronomique, Commissariat al’energie atomique, 78352, Jouy-en-Josas Cedex, France (Received 18 November 1999; accepted 17 January 2000) Abstract – The physical alignment of the entire region of the pig major histocompat- ibility complex (MHC) has been almost completed. In swine, the MHC is called the SLA (swine leukocyte antigen) and most of its class I region has been sequenced. -
Transcription Mediated Insulation and Interference Direct Gene Cluster
1 Transcription mediated insulation and interference direct gene 2 cluster expression switches 3 Tania Nguyen1, Harry Fischl1#, Françoise S. Howe1#, Ronja Woloszczuk1#, Ana Serra 4 Barros1*, Zhenyu Xu2*, David Brown1, Struan C. Murray1, Simon Haenni1, James M. 5 Halstead1, Leigh O’Connor1, Gergana Shipkovenska1, Lars M. Steinmetz2 and Jane Mellor1§ 6 1Department of Biochemistry, South Parks Road, Oxford, OX1 3QU, UK 7 2European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, 8 Germany 9 10 . 11 # , * Equal contribution 12 § Corresponding author: [email protected] 13 14 Competing interests statement: JM is an advisor to Oxford Biodynamics Ltd and Sibelius Ltd and sits 15 on the board of Chronos Therapeutics Ltd. OBD supported this work but have no commercial 16 interest in the study design, data collection and interpretation, or the decision to submit the work 17 for publication. 1 18 Abstract 19 In yeast, many tandemly arranged genes show peak expression in different phases of the 20 metabolic cycle (YMC) or in different carbon sources, indicative of regulation by a bi- 21 modal switch, but it is not clear how these switches are controlled. Using native 22 elongating transcript analysis (NET-seq), we show that transcription itself is a component 23 of bi-modal switches, facilitating reciprocal expression in gene clusters. HMS2, encoding a 24 growth-regulated transcription factor, switches between sense- or antisense-dominant 25 states that also coordinate up- and down-regulation of transcription at neighbouring 26 genes. Engineering HMS2 reveals alternative mono-, di- or tri-cistronic and antisense 27 transcription units (TUs), using different promoter and terminator combinations, that 28 underlie state-switching. -
Proteomic Shifts in Embryonic Stem Cells with Gene Dose Modifications Suggest the Presence of Balancer Proteins in Protein Regulatory Networks
Proteomic shifts in embryonic stem cells with gene dose modifications suggest the presence of balancer proteins in protein regulatory networks. Lei Mao, Claus Zabel, Marion Herrmann, Tobias Nolden, Florian Mertes, Laetitia Magnol, Caroline Chabert, Daniela Hartl, Yann Herault, Jean Maurice Delabar, et al. To cite this version: Lei Mao, Claus Zabel, Marion Herrmann, Tobias Nolden, Florian Mertes, et al.. Proteomic shifts in embryonic stem cells with gene dose modifications suggest the presence of balancer proteins in protein regulatory networks.. PLoS ONE, Public Library of Science, 2007, 2 (11), pp.e1218. 10.1371/jour- nal.pone.0001218. hal-00408296 HAL Id: hal-00408296 https://hal.archives-ouvertes.fr/hal-00408296 Submitted on 31 May 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Proteomic Shifts in Embryonic Stem Cells with Gene Dose Modifications Suggest the Presence of Balancer Proteins in Protein Regulatory Networks Lei Mao1,2*, Claus Zabel1, Marion Herrmann1, Tobias Nolden2, Florian Mertes2, Laetitia Magnol3, Caroline Chabert4, Daniela -
Supplemental Material For
SUPPLEMENTAL MATERIAL FOR Coexpression network based on natural variation in human gene expression reveals gene interactions and functions Renuka Nayak, Michael Kearns, Richard S. Spielman, Vivian G. Cheung Supplementary Figure 1 Supplementary Table 1. Gene pairs whose correlations in gene expression levels differ significantly (Pc<0.05) among the 3 datasets. Supplementary Table 2. Gene pairs that are correlated in gene expression levels with |R|>0.5 and are found within 500 kb of each other. Supplementary Table 3. Predicted functions of poorly characterized genes based on the functions of neighboring genes. Supplementary Figure 1. Genes identified in genome-wide association studies (grey) and their neighbors in the network. Red and green connections refer to positive and negative correlations, respectively. MICB has been implicated in AIDS progression (PMID: 19115949) TNF has been implicated in AIDS progression (PMID: 19115949) LTB has been implicated in AIDS progression (PMID: 19115949) ZNF224 has been implicated in Alzheimer's disease (PMID: 19118814) NDUFAB1 has been implicated in bipolar disorder (PMID: 17554300) SFRS10 has been implicated in body mass index (PMID: 19079260) and weight (PMID: 19079260) CTNNBL1 has been implicated in bone mineral density (PMID: 17903296) TGFBR3 has been implicated in bone mineral density (PMID: 19249006) IGF2R has been implicated in brain lesion load (PMID: 19010793) LSP1 has been implicated in breast cancer (PMID: 17529967) FBN1 has been implicated in breast cancer (PMID: 17903305) GLG1 has been implicated in breast cancer (PMID: 18463975) SCHIP1 has been implicated in Celiac disease (PMID: 18311140) RGS1 has been implicated in Celiac disease (PMID: 18311140) FADS2 has been implicated in Cholesterol (total) (PMID: 19060911), HDL cholesterol (PMID: 19060911, 19060906), LDL cholesterol (PMID: 19060911, 19060910), and triglycerides (PMID: 19060906). -
Program in Human Neutrophils Fails To
Downloaded from http://www.jimmunol.org/ by guest on September 25, 2021 is online at: average * The Journal of Immunology Anaplasma phagocytophilum , 20 of which you can access for free at: 2005; 174:6364-6372; ; from submission to initial decision 4 weeks from acceptance to publication J Immunol doi: 10.4049/jimmunol.174.10.6364 http://www.jimmunol.org/content/174/10/6364 Insights into Pathogen Immune Evasion Mechanisms: Fails to Induce an Apoptosis Differentiation Program in Human Neutrophils Dori L. Borjesson, Scott D. Kobayashi, Adeline R. Whitney, Jovanka M. Voyich, Cynthia M. Argue and Frank R. DeLeo cites 28 articles Submit online. Every submission reviewed by practicing scientists ? is published twice each month by Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://jimmunol.org/subscription Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html http://www.jimmunol.org/content/suppl/2005/05/03/174.10.6364.DC1 This article http://www.jimmunol.org/content/174/10/6364.full#ref-list-1 Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* • Why • • Material References Permissions Email Alerts Subscription Supplementary The Journal of Immunology The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2005 by The American Association of Immunologists All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. This information is current as of September 25, 2021. The Journal of Immunology Insights into Pathogen Immune Evasion Mechanisms: Anaplasma phagocytophilum Fails to Induce an Apoptosis Differentiation Program in Human Neutrophils1 Dori L. -
Autocrine IFN Signaling Inducing Profibrotic Fibroblast Responses By
Downloaded from http://www.jimmunol.org/ by guest on September 23, 2021 Inducing is online at: average * The Journal of Immunology , 11 of which you can access for free at: 2013; 191:2956-2966; Prepublished online 16 from submission to initial decision 4 weeks from acceptance to publication August 2013; doi: 10.4049/jimmunol.1300376 http://www.jimmunol.org/content/191/6/2956 A Synthetic TLR3 Ligand Mitigates Profibrotic Fibroblast Responses by Autocrine IFN Signaling Feng Fang, Kohtaro Ooka, Xiaoyong Sun, Ruchi Shah, Swati Bhattacharyya, Jun Wei and John Varga J Immunol cites 49 articles Submit online. Every submission reviewed by practicing scientists ? is published twice each month by Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://jimmunol.org/subscription Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html http://www.jimmunol.org/content/suppl/2013/08/20/jimmunol.130037 6.DC1 This article http://www.jimmunol.org/content/191/6/2956.full#ref-list-1 Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* Why • • • Material References Permissions Email Alerts Subscription Supplementary The Journal of Immunology The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2013 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. This information is current as of September 23, 2021. The Journal of Immunology A Synthetic TLR3 Ligand Mitigates Profibrotic Fibroblast Responses by Inducing Autocrine IFN Signaling Feng Fang,* Kohtaro Ooka,* Xiaoyong Sun,† Ruchi Shah,* Swati Bhattacharyya,* Jun Wei,* and John Varga* Activation of TLR3 by exogenous microbial ligands or endogenous injury-associated ligands leads to production of type I IFN. -
Haplotype-Specific Gene Expression Profiles in a Telomeric Major Histocompatibility Complex Gene Cluster and Susceptibility to Autoimmune Diseases
Genes and Immunity (2006) 7, 625–631 & 2006 Nature Publishing Group All rights reserved 1466-4879/06 $30.00 www.nature.com/gene ORIGINAL ARTICLE Haplotype-specific gene expression profiles in a telomeric major histocompatibility complex gene cluster and susceptibility to autoimmune diseases D Mewar, I Marinou, ME Lee, JM Timms, R Kilding, MD Teare, RC Read and AG Wilson School of Medicine and Biomedical Sciences, University of Sheffield, Sheffield, UK The telomeric class III region of the major histocompatibility complex is gene dense, but apart from the three tumour necrosis factor (TNF) superfamily members (TNF, lymphotoxin alpha and lymphotoxin beta) little is known of the expression and function of the majority of the genes. Recent genetic studies in autoimmune diseases, particularly rheumatoid arthritis (RA), have suggested a human leukocyte antigen (HLA)-DR-independent disease effect in this region. To gain further insights into these associations, we used lipopolysaccharide-stimulated human macrophages to examine inducible mRNA expression and genotype–phenotype relationships for genes in this region. Following stimulation in addition to the expected induction of TNF mRNA, a 14-fold increase of ATP6V1G2 at 18 h (Po0.001) was seen, whereas B-associated transcript (BAT)2 (Po0.001) and leucocyte-specific transcript (LST)1 (Po0.001) were both downregulated. By genotyping single-nucleotide polymorphisms spanning a 70 kb interval centred on the TNF locus, we constructed haplotypes and determined associated expression profiles for 10 genes in the cluster using quantitative real-time polymerase chain reaction. Overexpression of BAT1 mRNA was associated with carriers of a haplotype containing the LST1 marker transmitted to RA cases in a family study and also DRB1*15 associated with susceptibility to nephritis in systemic lupus erythematosus. -
Transposon Mutagenesis Identifies Genetic Drivers of Brafv600e Melanoma
ARTICLES Transposon mutagenesis identifies genetic drivers of BrafV600E melanoma Michael B Mann1,2, Michael A Black3, Devin J Jones1, Jerrold M Ward2,12, Christopher Chin Kuan Yew2,12, Justin Y Newberg1, Adam J Dupuy4, Alistair G Rust5,12, Marcus W Bosenberg6,7, Martin McMahon8,9, Cristin G Print10,11, Neal G Copeland1,2,13 & Nancy A Jenkins1,2,13 Although nearly half of human melanomas harbor oncogenic BRAFV600E mutations, the genetic events that cooperate with these mutations to drive melanogenesis are still largely unknown. Here we show that Sleeping Beauty (SB) transposon-mediated mutagenesis drives melanoma progression in BrafV600E mutant mice and identify 1,232 recurrently mutated candidate cancer genes (CCGs) from 70 SB-driven melanomas. CCGs are enriched in Wnt, PI3K, MAPK and netrin signaling pathway components and are more highly connected to one another than predicted by chance, indicating that SB targets cooperative genetic networks in melanoma. Human orthologs of >500 CCGs are enriched for mutations in human melanoma or showed statistically significant clinical associations between RNA abundance and survival of patients with metastatic melanoma. We also functionally validate CEP350 as a new tumor-suppressor gene in human melanoma. SB mutagenesis has thus helped to catalog the cooperative molecular mechanisms driving BRAFV600E melanoma and discover new genes with potential clinical importance in human melanoma. Substantial sun exposure and numerous genetic factors, including including BrafV600E, recapitulate the genetic and histological hallmarks skin type and family history, are the most important melanoma risk of human melanoma. In these models, increased MEK-ERK signaling factors. Familial melanoma, which accounts for <10% of cases, is asso- initiates clonal expansion of melanocytes, which is limited by oncogene- ciated with mutations in CDKN2A1, MITF2 and POT1 (refs. -
Coexpression Networks Based on Natural Variation in Human Gene Expression at Baseline and Under Stress
University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations Fall 2010 Coexpression Networks Based on Natural Variation in Human Gene Expression at Baseline and Under Stress Renuka Nayak University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Computational Biology Commons, and the Genomics Commons Recommended Citation Nayak, Renuka, "Coexpression Networks Based on Natural Variation in Human Gene Expression at Baseline and Under Stress" (2010). Publicly Accessible Penn Dissertations. 1559. https://repository.upenn.edu/edissertations/1559 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/1559 For more information, please contact [email protected]. Coexpression Networks Based on Natural Variation in Human Gene Expression at Baseline and Under Stress Abstract Genes interact in networks to orchestrate cellular processes. Here, we used coexpression networks based on natural variation in gene expression to study the functions and interactions of human genes. We asked how these networks change in response to stress. First, we studied human coexpression networks at baseline. We constructed networks by identifying correlations in expression levels of 8.9 million gene pairs in immortalized B cells from 295 individuals comprising three independent samples. The resulting networks allowed us to infer interactions between biological processes. We used the network to predict the functions of poorly-characterized human genes, and provided some experimental support. Examining genes implicated in disease, we found that IFIH1, a diabetes susceptibility gene, interacts with YES1, which affects glucose transport. Genes predisposing to the same diseases are clustered non-randomly in the network, suggesting that the network may be used to identify candidate genes that influence disease susceptibility. -
Pathway Entry Into the T Lymphocyte Developmental Molecular
Molecular Dissection of Prethymic Progenitor Entry into the T Lymphocyte Developmental Pathway This information is current as C. Chace Tydell, Elizabeth-Sharon David-Fung, Jonathan E. of October 1, 2021. Moore, Lee Rowen, Tom Taghon and Ellen V. Rothenberg J Immunol 2007; 179:421-438; ; doi: 10.4049/jimmunol.179.1.421 http://www.jimmunol.org/content/179/1/421 Downloaded from Supplementary http://www.jimmunol.org/content/suppl/2008/03/13/179.1.421.DC1 Material References This article cites 76 articles, 38 of which you can access for free at: http://www.jimmunol.org/ http://www.jimmunol.org/content/179/1/421.full#ref-list-1 Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists by guest on October 1, 2021 • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2007 by The American Association of Immunologists All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology Molecular Dissection of Prethymic Progenitor Entry into the T Lymphocyte Developmental Pathway1 C. Chace Tydell,2 Elizabeth-Sharon David-Fung,2,3 Jonathan E. -
Application of Gene Network Analysis Techniques Identifies AXIN1/PDIA2 and Endoglin Haplotypes Associated with Bicuspid Aortic Valve
Application of Gene Network Analysis Techniques Identifies AXIN1/PDIA2 and Endoglin Haplotypes Associated with Bicuspid Aortic Valve The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Wooten EC, Iyer LK, Montefusco MC, Hedgepeth AK, Payne DD, et al. (2010) Application of Gene Network Analysis Techniques Identifies AXIN1/PDIA2 and Endoglin Haplotypes Associated with Bicuspid Aortic Valve. PLoS ONE 5(1): e8830. doi:10.1371/ journal.pone.0008830 As Published http://dx.doi.org/10.1371/journal.pone.0008830 Publisher Public Library of Science Version Final published version Citable link http://hdl.handle.net/1721.1/54784 Terms of Use Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. Application of Gene Network Analysis Techniques Identifies AXIN1/PDIA2 and Endoglin Haplotypes Associated with Bicuspid Aortic Valve Eric C. Wooten1, Lakshmanan K. Iyer1, Maria Claudia Montefusco1, Alyson Kelley Hedgepeth1, Douglas D. Payne2, Navin K. Kapur1, David E. Housman3, Michael E. Mendelsohn1, Gordon S. Huggins1* 1 MCRI Center for Translational Genomics, Molecular Cardiology Research Institute, Boston, Massachusetts, United States of America, 2 Cardiothoracic Surgery Division, Tufts Medical Center, Boston, Massachusetts, United States of America, 3 Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America Abstract Bicuspid Aortic Valve (BAV) is a highly heritable congenital heart defect. The low frequency of BAV (1% of general population) limits our ability to perform genome-wide association studies. We present the application of four a priori SNP selection techniques, reducing the multiple-testing penalty by restricting analysis to SNPs relevant to BAV in a genome-wide SNP dataset from a cohort of 68 BAV probands and 830 control subjects. -
Affymetrix Probe ID Gene Symbol 1007 S at DDR1 1494 F At
Affymetrix Probe ID Gene Symbol 1007_s_at DDR1 1494_f_at CYP2A6 1552312_a_at MFAP3 1552368_at CTCFL 1552396_at SPINLW1 /// WFDC6 1552474_a_at GAMT 1552486_s_at LACTB 1552586_at TRPV3 1552619_a_at ANLN 1552628_a_at HERPUD2 1552680_a_at CASC5 1552928_s_at MAP3K7IP3 1552978_a_at SCAMP1 1553099_at TIGD1 1553106_at C5orf24 1553530_a_at ITGB1 1553997_a_at ASPHD1 1554127_s_at MSRB3 1554152_a_at OGDH 1554168_a_at SH3KBP1 1554217_a_at CCDC132 1554279_a_at TRMT2B 1554334_a_at DNAJA4 1554480_a_at ARMC10 1554510_s_at GHITM 1554524_a_at OLFM3 1554600_s_at LMNA 1555021_a_at SCARF1 1555058_a_at LPGAT1 1555197_a_at C21orf58 1555282_a_at PPARGC1B 1555460_a_at SLC39A6 1555559_s_at USP25 1555564_a_at CFI 1555594_a_at MBNL1 1555729_a_at CD209 1555733_s_at AP1S3 1555906_s_at C3orf23 1555945_s_at FAM120A 1555947_at FAM120A 1555950_a_at CD55 1557137_at TMEM17 1557910_at HSP90AB1 1558027_s_at PRKAB2 1558680_s_at PDE1A 1559136_s_at FLJ44451 /// IDS 1559490_at LRCH3 1562378_s_at PROM2 1562443_at RLBP1L2 1563522_at DDX10 /// LOC401533 1563834_a_at C1orf62 1566509_s_at FBXO9 1567214_a_at PNN 1568678_s_at FGFR1OP 1569629_x_atLOC389906 /// LOC441528 /// LOC728687 /// LOC729162 1598_g_at GAS6 /// LOC100133684 200064_at HSP90AB1 200596_s_at EIF3A 200597_at EIF3A 200604_s_at PRKAR1A 200621_at CSRP1 200638_s_at YWHAZ 200640_at YWHAZ 200641_s_at YWHAZ 200702_s_at DDX24 200742_s_at TPP1 200747_s_at NUMA1 200762_at DPYSL2 200872_at S100A10 200878_at EPAS1 200931_s_at VCL 200965_s_at ABLIM1 200998_s_at CKAP4 201019_s_at EIF1AP1 /// EIF1AX 201028_s_at CD99 201036_s_at HADH