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Wo 2010/075007 A2
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date 1 July 2010 (01.07.2010) WO 2010/075007 A2 (51) International Patent Classification: (81) Designated States (unless otherwise indicated, for every C12Q 1/68 (2006.01) G06F 19/00 (2006.01) kind of national protection available): AE, AG, AL, AM, C12N 15/12 (2006.01) AO, AT, AU, AZ, BA, BB, BG, BH, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, (21) International Application Number: DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, PCT/US2009/067757 HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, (22) International Filing Date: KR, KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, 11 December 2009 ( 11.12.2009) ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PE, PG, PH, PL, PT, RO, RS, RU, SC, SD, (25) Filing Language: English SE, SG, SK, SL, SM, ST, SV, SY, TJ, TM, TN, TR, TT, (26) Publication Language: English TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (30) Priority Data: (84) Designated States (unless otherwise indicated, for every 12/3 16,877 16 December 2008 (16.12.2008) US kind of regional protection available): ARIPO (BW, GH, GM, KE, LS, MW, MZ, NA, SD, SL, SZ, TZ, UG, ZM, (71) Applicant (for all designated States except US): DODDS, ZW), Eurasian (AM, AZ, BY, KG, KZ, MD, RU, TJ, W., Jean [US/US]; 938 Stanford Street, Santa Monica, TM), European (AT, BE, BG, CH, CY, CZ, DE, DK, EE, CA 90403 (US). -
Immune Cells Lacking Y Chromosome Have Widespread Dysregulation of Autosomal Genes
Supplementary Information Immune cells lacking Y chromosome have widespread dysregulation of autosomal genes Dumanski, Halvardson, Davies, Rychlicka-Buniowska, Mattisson, Torabi Moghadam, Nagy, Węglarczyk, Bukowska-Strakova, Danielsson, Olszewski, Piotrowski, Oerton, Ambicka, Przewoźnik, Bełch, Grodzicki, Chłosta, Imreh, Giedraitis, Kilander, Nordlund, Ameur, Gyllensten, Johansson, Józkowicz, Siedlar, Klich-Rączka, Jaszczyński, Enroth, Baran, Ingelsson, Perry, Ryś, and Forsberg Item Page(s) Fig. S1…………………... 2 Fig. S2…………………... 3 Fig. S3…………………... 4 Fig. S4…………………... 5-6 Fig. S5……………...….... 7 Fig. S6…………………... 8-9 Fig. S7…………………... 10 Fig. S8……………...….... 11-12 Fig. S9……………...….... 13-15 Tables S1-S4 are available online. 1 Supplementary Fig. 1. Summary of genes from chromosome Y that are expressed in leukocytes. Normal functions of the 64 protein coding genes on chromosome Y, 19 located in the pseudo-autosomal regions (PAR, underlined) and 45 in the male specific region of chromosome Y (MSY). Red color indicates 20 genes expressed in leukocytes studied here using RNAseq, 13 in PARs and 7 in MSY regions. Gene ontology (GO) analyses were performed for each chromosome Y gene to identify known biological functions and the identified GO terms were annotated into four functional categories. The categories were: “Transcription, translation epigenetic and post-translational modifications (PTM) functions” (orange area), “Cell differentiation, migration proliferation and apoptosis” (grey area), “Sex determination, fertility and other functions” (blue area) and “Immune response and immune cell signaling. 2 Supplementary Fig. 2. Distribution and level of loss of chromosome Y (LOY) in leukocytes from aging men using two RNA-sequencing platforms. Panels a and b show results from single cell RNA sequencing of peripheral blood mononuclear cells (PBMCs) collected from 29 men, 26 diagnosed with Alzheimer’s disease. -
High-Density P300 Enhancers Control Cell State Transitions Steven Witte1,2, Allan Bradley2, Anton J
Witte et al. BMC Genomics (2015) 16:903 DOI 10.1186/s12864-015-1905-6 RESEARCH ARTICLE Open Access High-density P300 enhancers control cell state transitions Steven Witte1,2, Allan Bradley2, Anton J. Enright3* and Stefan A. Muljo1* Abstract Background: Transcriptional enhancers are frequently bound by a set of transcription factors that collaborate to activate lineage-specific gene expression. Recently, it was appreciated that a subset of enhancers comprise extended clusters dubbed stretch- or super-enhancers (SEs). These SEs are located near key cell identity genes, and enriched for non-coding genetic variations associated with disease. Previously, SEs have been defined as having the highest density of Med1, Brd4 or H3K27ac by ChIP-seq. The histone acetyltransferase P300 has been used as a marker of enhancers, but little is known about its binding to SEs. Results: We establish that P300 marks a similar SE repertoire in embryonic stem cells as previously reported using Med1 and H3K27ac. We also exemplify a role for SEs in mouse T helper cell fate decision. Similarly, upon activation of macrophages by bacterial endotoxin, we found that many SE-associated genes encode inflammatory proteins that are strongly up-regulated. These SEs arise from small, low-density enhancers in unstimulated macrophages. We also identified expression quantitative trait loci (eQTL) in human monocytes that lie within such SEs. In macrophages and Th17 cells, inflammatory SEs can be perturbed either genetically or pharmacologically thus revealing new avenues to target inflammation. Conclusions: Our findings support the notion that P300-marked SEs can help identify key nodes of transcriptional control during cell fate decisions. -
Discovery of Candidate Genes for Stallion Fertility from the Horse Y Chromosome
DISCOVERY OF CANDIDATE GENES FOR STALLION FERTILITY FROM THE HORSE Y CHROMOSOME A Dissertation by NANDINA PARIA Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY August 2009 Major Subject: Biomedical Sciences DISCOVERY OF CANDIDATE GENES FOR STALLION FERTILITY FROM THE HORSE Y CHROMOSOME A Dissertation by NANDINA PARIA Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Approved by: Chair of Committee, Terje Raudsepp Committee Members, Bhanu P. Chowdhary William J. Murphy Paul B. Samollow Dickson D. Varner Head of Department, Evelyn Tiffany-Castiglioni August 2009 Major Subject: Biomedical Sciences iii ABSTRACT Discovery of Candidate Genes for Stallion Fertility from the Horse Y Chromosome. (August 2009) Nandina Paria, B.S., University of Calcutta; M.S., University of Calcutta Chair of Advisory Committee: Dr. Terje Raudsepp The genetic component of mammalian male fertility is complex and involves thousands of genes. The majority of these genes are distributed on autosomes and the X chromosome, while a small number are located on the Y chromosome. Human and mouse studies demonstrate that the most critical Y-linked male fertility genes are present in multiple copies, show testis-specific expression and are different between species. In the equine industry, where stallions are selected according to pedigrees and athletic abilities but not for reproductive performance, reduced fertility of many breeding stallions is a recognized problem. Therefore, the aim of the present research was to acquire comprehensive information about the organization of the horse Y chromosome (ECAY), identify Y-linked genes and investigate potential candidate genes regulating stallion fertility. -
HERV-K(HML7) Integrations in the Human Genome: Comprehensive Characterization and Comparative Analysis in Non-Human Primates
biology Article HERV-K(HML7) Integrations in the Human Genome: Comprehensive Characterization and Comparative Analysis in Non-Human Primates Nicole Grandi 1,* , Maria Paola Pisano 1 , Eleonora Pessiu 1, Sante Scognamiglio 1 and Enzo Tramontano 1,2 1 Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, 09042 Monserrato, Cagliari, Italy; [email protected] (M.P.P.); [email protected] (E.P.); [email protected] (S.S.); [email protected] (E.T.) 2 Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), 09042 Monserrato, Cagliari, Italy * Correspondence: [email protected] Simple Summary: The human genome is not human at all, but it includes a multitude of sequences inherited from ancient viral infections that affected primates’ germ line. These elements can be seen as the fossils of now-extinct retroviruses, and are called Human Endogenous Retroviruses (HERVs). View as “junk DNA” for a long time, HERVs constitute 4 times the amount of DNA needed to produce all cellular proteins, and growing evidence indicates their crucial role in primate brain evolution, placenta development, and innate immunity shaping. HERVs are also intensively studied for a pathological role, even if the incomplete knowledge about their exact number and genomic position has thus far prevented any causal association. Among possible relevant HERVs, the HERV-K Citation: Grandi, N.; Pisano, M.P.; supergroup is of particular interest, including some of the oldest (HML5) as well as youngest (HML2) Pessiu, E.; Scognamiglio, S.; integrations. Among HERV-Ks, the HML7 group still lack a detailed description, and the present Tramontano, E. -
A Novel Foxp3-Related Immune Prognostic Signature for Glioblastoma Multiforme Based on Immunogenomic Profiling
www.aging-us.com AGING 2021, Vol. 13, No. 3 Research Paper A novel foxp3-related immune prognostic signature for glioblastoma multiforme based on immunogenomic profiling Xiao-Yu Guo1,*, Guan-Hua Zhang1,2,*, Zhen-Ning Wang1, Hao Duan1, Tian Xie1, Lun Liang1, Rui Cui1, Hong-Rong Hu1, Yi Wu3, Jia-jun Dong3, Zhen-Qiang He1, Yong-Gao Mou1 1Department of Neurosurgery AND Neuro-Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510000, China 2Department of Cerebrovascular Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510000, China 3Department of Neurosurgery, Jiangmen Central Hospital, Jiangmen 529030, China *Equal contribution Correspondence to: Yong-Gao Mou, Zhen-Qiang He; email: [email protected], [email protected] Keywords: glioblastoma multiforme, Foxp3, regulatory T cells, immune prognostic signature, nomogram Received: June 8, 2020 Accepted: October 31, 2020 Published: January 10, 2021 Copyright: © 2021 Guo et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ABSTRACT Foxp3+ regulatory T cells (Treg) play an important part in the glioma immunosuppressive microenvironment. This study analyzed the effect of Foxsp3 on the immune microenvironment and constructed a Foxp3-related immune prognostic signature (IPS)for predicting prognosis in glioblastoma multiforme (GBM). Immunohistochemistry (IHC) staining for Foxp3 was performed in 72 high-grade glioma specimens. RNA-seq data from 152 GBM samples were obtained from The Cancer Genome Atlas database (TCGA) and divided into two groups, Foxp3 High (Foxp3_H) and Foxp3 Low (Foxp3_L), based on Foxp3 expression. -
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 -
(P -Value<0.05, Fold Change≥1.4), 4 Vs. 0 Gy Irradiation
Table S1: Significant differentially expressed genes (P -Value<0.05, Fold Change≥1.4), 4 vs. 0 Gy irradiation Genbank Fold Change P -Value Gene Symbol Description Accession Q9F8M7_CARHY (Q9F8M7) DTDP-glucose 4,6-dehydratase (Fragment), partial (9%) 6.70 0.017399678 THC2699065 [THC2719287] 5.53 0.003379195 BC013657 BC013657 Homo sapiens cDNA clone IMAGE:4152983, partial cds. [BC013657] 5.10 0.024641735 THC2750781 Ciliary dynein heavy chain 5 (Axonemal beta dynein heavy chain 5) (HL1). 4.07 0.04353262 DNAH5 [Source:Uniprot/SWISSPROT;Acc:Q8TE73] [ENST00000382416] 3.81 0.002855909 NM_145263 SPATA18 Homo sapiens spermatogenesis associated 18 homolog (rat) (SPATA18), mRNA [NM_145263] AA418814 zw01a02.s1 Soares_NhHMPu_S1 Homo sapiens cDNA clone IMAGE:767978 3', 3.69 0.03203913 AA418814 AA418814 mRNA sequence [AA418814] AL356953 leucine-rich repeat-containing G protein-coupled receptor 6 {Homo sapiens} (exp=0; 3.63 0.0277936 THC2705989 wgp=1; cg=0), partial (4%) [THC2752981] AA484677 ne64a07.s1 NCI_CGAP_Alv1 Homo sapiens cDNA clone IMAGE:909012, mRNA 3.63 0.027098073 AA484677 AA484677 sequence [AA484677] oe06h09.s1 NCI_CGAP_Ov2 Homo sapiens cDNA clone IMAGE:1385153, mRNA sequence 3.48 0.04468495 AA837799 AA837799 [AA837799] Homo sapiens hypothetical protein LOC340109, mRNA (cDNA clone IMAGE:5578073), partial 3.27 0.031178378 BC039509 LOC643401 cds. [BC039509] Homo sapiens Fas (TNF receptor superfamily, member 6) (FAS), transcript variant 1, mRNA 3.24 0.022156298 NM_000043 FAS [NM_000043] 3.20 0.021043295 A_32_P125056 BF803942 CM2-CI0135-021100-477-g08 CI0135 Homo sapiens cDNA, mRNA sequence 3.04 0.043389246 BF803942 BF803942 [BF803942] 3.03 0.002430239 NM_015920 RPS27L Homo sapiens ribosomal protein S27-like (RPS27L), mRNA [NM_015920] Homo sapiens tumor necrosis factor receptor superfamily, member 10c, decoy without an 2.98 0.021202829 NM_003841 TNFRSF10C intracellular domain (TNFRSF10C), mRNA [NM_003841] 2.97 0.03243901 AB002384 C6orf32 Homo sapiens mRNA for KIAA0386 gene, partial cds. -
Concurrent Mutations Associated with Trastuzumab-Resistance Revealed by Single Cell Sequencing
Concurrent Mutations Associated With Trastuzumab-resistance Revealed by Single Cell Sequencing Yan Gao Tianjin Medical University Cancer Institute and Hospital: Tianjin Tumor Hospital Ning Wu Tianjin Medical University Cancer Institute and Hospital: Tianjin Tumor Hospital Shuai Wang Tianjin Medical University Cancer Institute and Hospital: Tianjin Tumor Hospital Xue Yang Tianjin Medical University Cancer Institute and Hospital: Tianjin Tumor Hospital Xin Wang Tianjin Medical University Cancer Institute and Hospital: Tianjin Tumor Hospital Bo Xu ( [email protected] ) Tianjin Medical University Cancer Institute and Hospital: Tianjin Tumor Hospital https://orcid.org/0000-0001-8693-3060 Research Article Keywords: HER2-positive breast cancer, trastuzumab-resistance, single cell sequencing, concurrent mutations Posted Date: February 25th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-253665/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/17 Abstract Purpose: HER2-positive breast cancer patients benet from HER2 targeted therapies, among which the most commonly used is trastuzumab. However, acquired resistance typically happens within one year. The cellular heterogeneity of it is less clear. Methods: Here we generated trastuzumab-resistant cells in two HER2-positive breast cancer cell lines, SK- BR-3 and BT-474. Cells at different time points during the resistance induction were examined by exome sequencing to study changes of genomic alterations over time. Single cell targeted sequencing was also used to identify resistance associated concurrent mutations. Results: We found a rapid increase of copy number variation (CNV) regions and gradual accumulation of single nucleotide variations (SNVs). On the pathway level, nonsynonymous SNVs for SK-BR-3 cells were enriched in the MAPK signaling pathway, while for BT-474 cells were enriched in mTOR and PI3K-Akt signaling pathways. -
Open Data for Differential Network Analysis in Glioma
International Journal of Molecular Sciences Article Open Data for Differential Network Analysis in Glioma , Claire Jean-Quartier * y , Fleur Jeanquartier y and Andreas Holzinger Holzinger Group HCI-KDD, Institute for Medical Informatics, Statistics and Documentation, Medical University Graz, Auenbruggerplatz 2/V, 8036 Graz, Austria; [email protected] (F.J.); [email protected] (A.H.) * Correspondence: [email protected] These authors contributed equally to this work. y Received: 27 October 2019; Accepted: 3 January 2020; Published: 15 January 2020 Abstract: The complexity of cancer diseases demands bioinformatic techniques and translational research based on big data and personalized medicine. Open data enables researchers to accelerate cancer studies, save resources and foster collaboration. Several tools and programming approaches are available for analyzing data, including annotation, clustering, comparison and extrapolation, merging, enrichment, functional association and statistics. We exploit openly available data via cancer gene expression analysis, we apply refinement as well as enrichment analysis via gene ontology and conclude with graph-based visualization of involved protein interaction networks as a basis for signaling. The different databases allowed for the construction of huge networks or specified ones consisting of high-confidence interactions only. Several genes associated to glioma were isolated via a network analysis from top hub nodes as well as from an outlier analysis. The latter approach highlights a mitogen-activated protein kinase next to a member of histondeacetylases and a protein phosphatase as genes uncommonly associated with glioma. Cluster analysis from top hub nodes lists several identified glioma-associated gene products to function within protein complexes, including epidermal growth factors as well as cell cycle proteins or RAS proto-oncogenes. -
L1TD1 Sirna (H): Sc-88192
SANTA CRUZ BIOTECHNOLOGY, INC. L1TD1 siRNA (h): sc-88192 BACKGROUND STORAGE AND RESUSPENSION L1TD1 (LINE-1 type transposase domain containing 1), also known as ECAT11 Store lyophilized siRNA duplex at -20° C with desiccant. Stable for at least (ES cell-associated protein 11), is an 865 amino acid protein that belongs to one year from the date of shipment. Once resuspended, store at -20° C, the transposase 22 family and is encoded by a gene that maps to human avoid contact with RNAses and repeated freeze thaw cycles. chromosome 1p31.3. Chromosome 1 spans 260 million base pairs, contains Resuspend lyophilized siRNA duplex in 330 µl of the RNAse-free water over 3,000 genes and comprises nearly 8% of the human genome. Chromo- provided. Resuspension of the siRNA duplex in 330 µl of RNAse-free water some 1 houses a large number of disease-associated genes, including those makes a 10 µM solution in a 10 µM Tris-HCl, pH 8.0, 20 mM NaCl, 1 mM that are involved in familial adenomatous polyposis, Stickler syndrome, EDTA buffered solution. Parkinson’s disease, Gaucher disease, schizophrenia and Usher syndrome. Aberrations in chromosome 1 are found in a variety of cancers, including APPLICATIONS head and neck cancer, malignant melanoma and multiple myeloma. L1TD1 siRNA (h) is recommended for the inhibition of L1TD1 expression in REFERENCES human cells. 1. Eudy, J.D., et al. 1998. Mutation of a gene encoding a protein with extra- SUPPORT REAGENTS cellular matrix motifs in Usher syndrome type IIa. Science 280: 1753-1757. For optimal siRNA transfection efficiency, Santa Cruz Biotechnology’s 2. -
A Systems-Genetics Analyses of Complex Phenotypes
A systems-genetics analyses of complex phenotypes A thesis submitted to the University of Manchester for the degree of Doctor of Philosophy in the Faculty of Life Sciences 2015 David Ashbrook Table of contents Table of contents Table of contents ............................................................................................... 1 Tables and figures ........................................................................................... 10 General abstract ............................................................................................... 14 Declaration ....................................................................................................... 15 Copyright statement ........................................................................................ 15 Acknowledgements.......................................................................................... 16 Chapter 1: General introduction ...................................................................... 17 1.1 Overview................................................................................................... 18 1.2 Linkage, association and gene annotations .............................................. 20 1.3 ‘Big data’ and ‘omics’ ................................................................................ 22 1.4 Systems-genetics ..................................................................................... 24 1.5 Recombinant inbred (RI) lines and the BXD .............................................. 25 Figure 1.1: