DOCSLIB.ORG

Mouse Sh3bp5 Knockout Project (CRISPR/Cas9)

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Mouse Sh3bp5 Knockout Project (CRISPR/Cas9) https://www.alphaknockout.com Mouse Sh3bp5 Knockout Project (CRISPR/Cas9) Objective: To create a Sh3bp5 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Sh3bp5 gene (NCBI Reference Sequence: NM_011894 ; Ensembl: ENSMUSG00000021892 ) is located on Mouse chromosome 14. 9 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 9 (Transcript: ENSMUST00000091903). Exon 4~5 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: Exon 4 starts from about 24.75% of the coding region. Exon 4~5 covers 21.54% of the coding region. The size of effective KO region: ~8495 bp. The KO region does not have any other known gene. Page 1 of 9 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele 5' gRNA region gRNA region 3' 1 4 5 9 Legends Exon of mouse Sh3bp5 Knockout region Page 2 of 9 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 4 is aligned with itself to determine if there are tandem repeats. No significant tandem repeat is found in the dot plot matrix. So this region is suitable for PCR screening or sequencing analysis. Overview of the Dot Plot (down) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 1068 bp section downstream of Exon 5 is aligned with itself to determine if there are tandem repeats. No significant tandem repeat is found in the dot plot matrix. So this region is suitable for PCR screening or sequencing analysis. Page 3 of 9 https://www.alphaknockout.com Overview of the GC Content Distribution (up) Window size: 300 bp Sequence 12 Summary: Full Length(2000bp) | A(20.25% 405) | C(24.45% 489) | T(26.9% 538) | G(28.4% 568) Note: The 2000 bp section upstream of Exon 4 is analyzed to determine the GC content. No significant high GC-content region is found. So this region is suitable for PCR screening or sequencing analysis. Overview of the GC Content Distribution (down) Window size: 300 bp Sequence 12 Summary: Full Length(1068bp) | A(21.54% 230) | C(25.66% 274) | T(30.15% 322) | G(22.66% 242) Note: The 1068 bp section downstream of Exon 5 is analyzed to determine the GC content. No significant high GC-content region is found. So this region is suitable for PCR screening or sequencing analysis. Page 4 of 9 https://www.alphaknockout.com BLAT Search Results (up) QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN ----------------------------------------------------------------------------------------------- browser details YourSeq 2000 1 2000 2000 100.0% chr14 - 31387884 31389883 2000 browser details YourSeq 59 148 526 2000 85.1% chr14 - 64082239 64082609 371 browser details YourSeq 52 725 1299 2000 92.1% chr12 + 4116851 4126362 9512 browser details YourSeq 48 727 1036 2000 74.1% chrX - 12535136 12535400 265 browser details YourSeq 46 763 874 2000 90.6% chr17 + 5556951 5557447 497 browser details YourSeq 40 436 521 2000 73.3% chr2 + 21466663 21466748 86 browser details YourSeq 38 437 494 2000 82.8% chr4 + 97519944 97520001 58 browser details YourSeq 36 799 874 2000 92.9% chr2 - 4396170 4396398 229 browser details YourSeq 36 856 939 2000 82.0% chr12 + 77352952 77353034 83 browser details YourSeq 34 452 524 2000 76.4% chr3 - 98233981 98234044 64 browser details YourSeq 34 445 521 2000 89.5% chr1 + 182152922 182152997 76 browser details YourSeq 33 366 499 2000 79.0% chr13 - 51279684 51279813 130 browser details YourSeq 33 294 368 2000 97.2% chr12 + 13595639 13595715 77 browser details YourSeq 31 482 526 2000 84.5% chr11 + 65692820 65692864 45 browser details YourSeq 30 732 783 2000 94.2% chr3 - 41408170 41408225 56 browser details YourSeq 29 961 1004 2000 87.2% chr12 + 100396082 100396126 45 browser details YourSeq 29 745 781 2000 94.0% chr12 + 85504708 85504842 135 browser details YourSeq 29 480 526 2000 80.9% chr10 + 24399817 24399863 47 browser details YourSeq 28 745 776 2000 93.8% chr6 + 9235741 9235772 32 browser details YourSeq 27 436 474 2000 93.6% chr13 + 102105581 102105621 41 Note: The 2000 bp section upstream of Exon 4 is BLAT searched against the genome. No significant similarity is found. BLAT Search Results (down) QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN ----------------------------------------------------------------------------------------------- browser details YourSeq 1068 1 1068 1068 100.0% chr14 - 31378321 31379388 1068 browser details YourSeq 28 613 641 1068 100.0% chr1 - 101367553 101367948 396 browser details YourSeq 24 613 640 1068 96.2% chr1 - 192767731 192767759 29 browser details YourSeq 24 848 875 1068 80.0% chr11 + 59011524 59011548 25 browser details YourSeq 23 1034 1060 1068 84.7% chr2 + 158128766 158128791 26 browser details YourSeq 22 128 152 1068 96.0% chr1 + 13135591 13135617 27 browser details YourSeq 21 271 293 1068 95.7% chr1 - 184772774 184772796 23 browser details YourSeq 20 1019 1038 1068 100.0% chr10 - 126462905 126462924 20 Note: The 1068 bp section downstream of Exon 5 is BLAT searched against the genome. No significant similarity is found. Page 5 of 9 https://www.alphaknockout.com Gene and protein information: Sh3bp5 SH3-domain binding protein 5 (BTK-associated) [ Mus musculus (house mouse) ] Gene ID: 24056, updated on 12-Aug-2019 Gene summary Official Symbol Sh3bp5 provided by MGI Official Full Name SH3-domain binding protein 5 (BTK-associated) provided by MGI Primary source MGI:MGI:1344391 See related Ensembl:ENSMUSG00000021892 Gene type protein coding RefSeq status VALIDATED Organism Mus musculus Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus Also known as Sab; SH3BP-5; AI606498 Expression Ubiquitous expression in CNS E18 (RPKM 46.1), CNS E14 (RPKM 37.5) and 25 other tissues See more Orthologs human all Genomic context Location: 14; 14 B See Sh3bp5 in Genome Data Viewer Exon count: 12 Annotation release Status Assembly Chr Location 108 current GRCm38.p6 (GCF_000001635.26) 14 NC_000080.6 (31372614..31436100, complement) Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 14 NC_000080.5 (32187141..32249219, complement) Chromosome 14 - NC_000080.6 Page 6 of 9 https://www.alphaknockout.com Transcript information: This gene has 4 transcripts Gene: Sh3bp5 ENSMUSG00000021892 Description SH3-domain binding protein 5 (BTK-associated) [Source:MGI Symbol;Acc:MGI:1344391] Gene Synonyms Sab Location Chromosome 14: 31,359,880-31,436,078 reverse strand. GRCm38:CM001007.2 About this gene This gene has 4 transcripts (splice variants), 263 orthologues, 1 paralogue, is a member of 1 Ensembl protein family and is associated with 2 phenotypes. Transcripts Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags Sh3bp5- ENSMUST00000091903.4 2684 458aa ENSMUSP00000089517.4 Protein coding CCDS36855 Q9Z131 TSL:1 201 GENCODE basic APPRIS P3 Sh3bp5- ENSMUST00000100730.9 2633 456aa ENSMUSP00000098296.3 Protein coding CCDS84108 Q9Z131 TSL:1 202 GENCODE basic APPRIS ALT2 Sh3bp5- ENSMUST00000140002.7 1686 463aa ENSMUSP00000117152.1 Nonsense mediated - Q9Z131 TSL:1 203 decay Sh3bp5- ENSMUST00000147586.1 382 No - lncRNA - - TSL:5 204 protein Page 7 of 9 https://www.alphaknockout.com 96.20 kb Forward strand 31.36Mb 31.38Mb 31.40Mb 31.42Mb 31.44Mb Genes Capn7-201 >protein coding (Comprehensive set... Capn7-202 >nonsense mediated decay Capn7-203 >nonsense mediated decay Capn7-204 >retained intron Contigs AC108416.5 > AC154616.2 > Genes (Comprehensive set... < Sh3bp5-203nonsense mediated decay < Sh3bp5-201protein coding < Sh3bp5-202protein coding < Sh3bp5-204lncRNA Regulatory Build 31.36Mb 31.38Mb 31.40Mb 31.42Mb 31.44Mb Reverse strand 96.20 kb Regulation Legend CTCF Open Chromatin Promoter Promoter Flank Transcription Factor Binding Site Gene Legend Protein Coding merged Ensembl/Havana Ensembl protein coding Non-Protein Coding processed transcript RNA gene Page 8 of 9 https://www.alphaknockout.com Transcript: ENSMUST00000091903 < Sh3bp5-201protein coding Reverse strand 62.28 kb ENSMUSP00000089... MobiDB lite Low complexity (Seg) Coiled-coils (Ncoils) Pfam SH3-binding 5 PANTHER PTHR19423:SF11 SH3-binding 5 All sequence SNPs/i... Sequence variants (dbSNP and all other sources) Variant Legend missense variant synonymous variant Scale bar 0 40 80 120 160 200 240 280 320 360 400 458 We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC. Page 9 of 9.
Load more

Recommended publications
  • S1 Supplemental Materials Supplemental Methods Supplemental Figure 1. Immune Phenotype of Mcd19 Targeted CAR T and Dose Titratio
    Supplemental Materials Supplemental Methods Supplemental Figure 1. Immune phenotype of mCD19 targeted CAR T and dose titration of in vivo efficacy. Supplemental Figure 2. Gene expression of fluorescent-protein tagged CAR T cells. Supplemental Figure 3. Fluorescent protein tagged CAR T cells function similarly to non-tagged counterparts. Supplemental Figure 4. Transduction efficiency and immune phenotype of mCD19 targeted CAR T cells for survival study (Figure 2D). Supplemental Figure 5. Transduction efficiency and immune phenotype of CAR T cells used in irradiated CAR T study (Fig. 3B-C). Supplemental Figure 6. Differential gene expression of CD4+ m19-humBBz CAR T cells. Supplemental Figure 7. CAR expression and CD4/CD8 subsets of human CD19 targeted CAR T cells for Figure 5E-G. Supplemental Figure 8. Transduction efficiency and immune phenotype of mCD19 targeted wild type (WT) and TRAF1-/- CAR T cells used for in vivo study (Figure 6D). Supplemental Figure 9. Mutated m19-musBBz CAR T cells have increased NF-κB signaling, improved cytokine production, anti-apoptosis, and in vivo function. Supplemental Figure 10. TRAF and CAR co-expression in human CD19-targeted CAR T cells. Supplemental Figure 11. TRAF2 over-expressed h19BBz CAR T cells show similar in vivo efficacy to h19BBz CAR T cells in an aggressive leukemia model. S1 Supplemental Table 1. Probesets increased in m19z and m1928z vs m19-musBBz CAR T cells. Supplemental Table 2. Probesets increased in m19-musBBz vs m19z and m1928z CAR T cells. Supplemental Table 3. Probesets differentially expressed in m19z vs m19-musBBz CAR T cells. Supplemental Table 4. Probesets differentially expressed in m1928z vs m19-musBBz CAR T cells.
    [Show full text]
  • 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
    [Show full text]
  • Analysis of the Indacaterol-Regulated Transcriptome in Human Airway
    Supplemental material to this article can be found at: http://jpet.aspetjournals.org/content/suppl/2018/04/13/jpet.118.249292.DC1 1521-0103/366/1/220–236$35.00 https://doi.org/10.1124/jpet.118.249292 THE JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS J Pharmacol Exp Ther 366:220–236, July 2018 Copyright ª 2018 by The American Society for Pharmacology and Experimental Therapeutics Analysis of the Indacaterol-Regulated Transcriptome in Human Airway Epithelial Cells Implicates Gene Expression Changes in the s Adverse and Therapeutic Effects of b2-Adrenoceptor Agonists Dong Yan, Omar Hamed, Taruna Joshi,1 Mahmoud M. Mostafa, Kyla C. Jamieson, Radhika Joshi, Robert Newton, and Mark A. Giembycz Departments of Physiology and Pharmacology (D.Y., O.H., T.J., K.C.J., R.J., M.A.G.) and Cell Biology and Anatomy (M.M.M., R.N.), Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada Received March 22, 2018; accepted April 11, 2018 Downloaded from ABSTRACT The contribution of gene expression changes to the adverse and activity, and positive regulation of neutrophil chemotaxis. The therapeutic effects of b2-adrenoceptor agonists in asthma was general enriched GO term extracellular space was also associ- investigated using human airway epithelial cells as a therapeu- ated with indacaterol-induced genes, and many of those, in- tically relevant target. Operational model-fitting established that cluding CRISPLD2, DMBT1, GAS1, and SOCS3, have putative jpet.aspetjournals.org the long-acting b2-adrenoceptor agonists (LABA) indacaterol, anti-inflammatory, antibacterial, and/or antiviral activity. Numer- salmeterol, formoterol, and picumeterol were full agonists on ous indacaterol-regulated genes were also induced or repressed BEAS-2B cells transfected with a cAMP-response element in BEAS-2B cells and human primary bronchial epithelial cells by reporter but differed in efficacy (indacaterol $ formoterol .
    [Show full text]
  • Human Induced Pluripotent Stem Cell–Derived Podocytes Mature Into Vascularized Glomeruli Upon Experimental Transplantation
    BASIC RESEARCH www.jasn.org Human Induced Pluripotent Stem Cell–Derived Podocytes Mature into Vascularized Glomeruli upon Experimental Transplantation † Sazia Sharmin,* Atsuhiro Taguchi,* Yusuke Kaku,* Yasuhiro Yoshimura,* Tomoko Ohmori,* ‡ † ‡ Tetsushi Sakuma, Masashi Mukoyama, Takashi Yamamoto, Hidetake Kurihara,§ and | Ryuichi Nishinakamura* *Department of Kidney Development, Institute of Molecular Embryology and Genetics, and †Department of Nephrology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan; ‡Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, Japan; §Division of Anatomy, Juntendo University School of Medicine, Tokyo, Japan; and |Japan Science and Technology Agency, CREST, Kumamoto, Japan ABSTRACT Glomerular podocytes express proteins, such as nephrin, that constitute the slit diaphragm, thereby contributing to the filtration process in the kidney. Glomerular development has been analyzed mainly in mice, whereas analysis of human kidney development has been minimal because of limited access to embryonic kidneys. We previously reported the induction of three-dimensional primordial glomeruli from human induced pluripotent stem (iPS) cells. Here, using transcription activator–like effector nuclease-mediated homologous recombination, we generated human iPS cell lines that express green fluorescent protein (GFP) in the NPHS1 locus, which encodes nephrin, and we show that GFP expression facilitated accurate visualization of nephrin-positive podocyte formation in
    [Show full text]
  • Downloaded from the UCSC Genome Browser Prior to Use ( Et Al
    bioRxiv preprint doi: https://doi.org/10.1101/2019.12.16.877365; this version posted December 17, 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 4.0 International license. Pooled analysis of radiation hybrids identifies loci for growth and drug action in mammalian cells Arshad H. Khan1, Andy Lin2, Richard T. Wang3, Joshua S. Bloom3;4, Kenneth Lange3, Desmond J. Smith1;∗ 1 Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Box 951735, Los Angeles, CA 90095-1735, USA 2 Office of Information Technology, UCLA, Box 951557, 5308 MS, Los Angeles, CA 90095-1557, USA 3 Department of Human Genetics, David Geffen School of Medicine, UCLA, Box 957088, Los Angeles, CA 90095-7088, USA 4 Howard Hughes Medical Institute, David Geffen School of Medicine, UCLA, Box 957088, Los Angeles, CA 90095-7088, USA ∗ E-mail: [email protected] Running title: Pooled radiation hybrids Abstract Genetic screens in mammalian cells commonly focus on loss-of-function approaches. To evaluate the phenotypic consequences of extra gene copies, we used bulk segregant analysis (BSA) of radiation hybrid (RH) cells. We constructed six pools of RH cells, each consisting of ∼2500 independent clones, and placed the pools under selection in media with or without paclitaxel. Low pass sequencing identified 859 growth loci, 38 paclitaxel loci, 62 interaction loci and 3 loci for mitochondrial abundance at genome-wide significance. Resolution was measured as ∼30 kb, close to single-gene.
    [Show full text]
  • Drosophila and Human Transcriptomic Data Mining Provides Evidence for Therapeutic
    Drosophila and human transcriptomic data mining provides evidence for therapeutic mechanism of pentylenetetrazole in Down syndrome Author Abhay Sharma Institute of Genomics and Integrative Biology Council of Scientific and Industrial Research Delhi University Campus, Mall Road Delhi 110007, India Tel: +91-11-27666156, Fax: +91-11-27662407 Email: [email protected] Nature Precedings : hdl:10101/npre.2010.4330.1 Posted 5 Apr 2010 Running head: Pentylenetetrazole mechanism in Down syndrome 1 Abstract Pentylenetetrazole (PTZ) has recently been found to ameliorate cognitive impairment in rodent models of Down syndrome (DS). The mechanism underlying PTZ’s therapeutic effect is however not clear. Microarray profiling has previously reported differential expression of genes in DS. No mammalian transcriptomic data on PTZ treatment however exists. Nevertheless, a Drosophila model inspired by rodent models of PTZ induced kindling plasticity has recently been described. Microarray profiling has shown PTZ’s downregulatory effect on gene expression in fly heads. In a comparative transcriptomics approach, I have analyzed the available microarray data in order to identify potential mechanism of PTZ action in DS. I find that transcriptomic correlates of chronic PTZ in Drosophila and DS counteract each other. A significant enrichment is observed between PTZ downregulated and DS upregulated genes, and a significant depletion between PTZ downregulated and DS dowwnregulated genes. Further, the common genes in PTZ Nature Precedings : hdl:10101/npre.2010.4330.1 Posted 5 Apr 2010 downregulated and DS upregulated sets show enrichment for MAP kinase pathway. My analysis suggests that downregulation of MAP kinase pathway may mediate therapeutic effect of PTZ in DS. Existing evidence implicating MAP kinase pathway in DS supports this observation.
    [Show full text]
  • A Graph-Theoretic Approach to Model Genomic Data and Identify Biological Modules Asscociated with Cancer Outcomes
    A Graph-Theoretic Approach to Model Genomic Data and Identify Biological Modules Asscociated with Cancer Outcomes Deanna Petrochilos A dissertation presented in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Washington 2013 Reading Committee: Neil Abernethy, Chair John Gennari, Ali Shojaie Program Authorized to Offer Degree: Biomedical Informatics and Health Education UMI Number: 3588836 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. UMI 3588836 Published by ProQuest LLC (2013). Copyright in the Dissertation held by the Author. Microform Edition © ProQuest LLC. All rights reserved. This work is protected against unauthorized copying under Title 17, United States Code ProQuest LLC. 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, MI 48106 - 1346 ©Copyright 2013 Deanna Petrochilos University of Washington Abstract Using Graph-Based Methods to Integrate and Analyze Cancer Genomic Data Deanna Petrochilos Chair of the Supervisory Committee: Assistant Professor Neil Abernethy Biomedical Informatics and Health Education Studies of the genetic basis of complex disease present statistical and methodological challenges in the discovery of reliable and high-confidence genes that reveal biological phenomena underlying the etiology of disease or gene signatures prognostic of disease outcomes. This dissertation examines the capacity of graph-theoretical methods to model and analyze genomic information and thus facilitate using prior knowledge to create a more discrete and functionally relevant feature space.
    [Show full text]
  • From Gene Expression to Functional Foods
    cancers Article Computational Approaches for Cancer-Fighting: From Gene Expression to Functional Foods Francesco Monticolo and Maria Luisa Chiusano * Department of Agricultural Sciences, Università degli Studi di Napoli Federico II, Via Università 100, 80055 Portici, Italy; [email protected] * Correspondence: [email protected] Simple Summary: It is today widely accepted that a healthy diet can be one of the fundamental approaches to prevent the risk of cancer. To this aim, nutrigenomics studies are indeed providing a precious source of information, favoring the search for compounds that could affect gene expression in a favorable way. Here we present a computational study to select candidate compounds that could play a role in cancer prevention and care. Starting from analyses of gene expression, we identified 7 genes that have opposite expression trends in apoptotic treatments when compared with 8 different cancer types. In addition, based on structure similarity with 6 compounds that affect the expression patterns of these genes in a favorable way against 8 cancer types, we selected 23 natural compounds as suitable candidates for further tests as possible novel drugs or for the design of functional food for cancer treatment and prevention. Abstract: It is today widely accepted that a healthy diet is very useful to prevent the risk for cancer or its deleterious effects. Nutrigenomics studies are therefore taking place with the aim to test the effects Citation: Monticolo, F.; Chiusano, of nutrients at molecular level and contribute to the search for anti-cancer treatments. These efforts M.L. Computational Approaches for are expanding the precious source of information necessary for the selection of natural compounds Cancer-Fighting: From Gene useful for the design of novel drugs or functional foods.
    [Show full text]
  • Substitution Scanning Identifies a Novel, Catalytically Active Ibrutinib
    OPEN Leukemia (2017) 31, 177–185 www.nature.com/leu ORIGINAL ARTICLE Substitution scanning identifies a novel, catalytically active ibrutinib-resistant BTK cysteine 481 to threonine (C481T) variant A Hamasy1,4, Q Wang1,4, KEM Blomberg1, DK Mohammad1,LYu2, M Vihinen3, A Berglöf1 and CIE Smith1 Irreversible Bruton tyrosine kinase (BTK) inhibitors, ibrutinib and acalabrutinib have demonstrated remarkable clinical responses in multiple B-cell malignancies. Acquired resistance has been identified in a sub-population of patients in which mutations affecting BTK predominantly substitute cysteine 481 in the kinase domain for catalytically active serine, thereby ablating covalent binding of inhibitors. Activating substitutions in the BTK substrate phospholipase Cγ2 (PLCγ2) instead confers resistance independent of BTK. Herein, we generated all six possible amino acid substitutions due to single nucleotide alterations for the cysteine 481 codon, in addition to threonine, requiring two nucleotide substitutions, and performed functional analysis. Replacement by arginine, phenylalanine, tryptophan or tyrosine completely inactivated the catalytic activity, whereas substitution with glycine caused severe impairment. BTK with threonine replacement was catalytically active, similar to substitution with serine. We identify three potential ibrutinib resistance scenarios for cysteine 481 replacement: (1) Serine, being catalytically active and therefore predominating among patients. (2) Threonine, also being catalytically active, but predicted to be scarce,
    [Show full text]
  • Jenkins Meredith Msc 2019.Pdf
    Structural and Biochemical Investigation of the Regulation of Rab11a by the Guanine Nucleotide Exchange Factors SH3BP5 and TRAPPII by Meredith L Jenkins B.Sc. (Hons) Microbiology, University of Victoria, 2015 A Thesis Submitted in Partial Fulfillment of the Requirements for the Degree of MASTER OF SCIENCE in the Department of Biochemistry and Microbiology © Meredith L Jenkins, 2019 University of Victoria All rights reserved. This thesis may not be reproduced in whole or in part, by photocopy or other means, without the permission of the author. ii Supervisory Committee Structural and Biochemical Investigation of the Regulation of Rab11a by the Guanine Nucleotide Exchange Factors SH3BP5 and TRAPPII by Meredith L Jenkins B.Sc. (Hons) Microbiology, University of Victoria, 2015 Supervisory Committee Dr. John E Burke, Supervisor Department of Biochemistry and Microbiology Dr. Alisdair Boraston, Departmental Member Department of Biochemistry and Microbiology Dr. Robert Chow, Outside Member Department of Biology iii Abstract Rab11 is a critical GTPase involved in the regulation of membrane trafficking in the endocytic pathway, and it’s misregulation is involved in a variety of human diseases including Huntington’s disease and Alzheimer’s disease. Additionally, de novo mutations (DNMs) of Rab11 have been identified in patients with developmental disorders, and interestingly several parasites, viruses, and bacteria can subvert membrane trafficking through Rab11 positive vesicles to allow for replication and evasion from the immune system. Although Rab11 is one of the best characterized Rab GTPases, hindering the capability to completely understand Rab11 regulation and its role in human disease is the lack of detail describing how Rab11 proteins are activated by their cognate guanine nucleotide exchange factors (GEFs).
    [Show full text]
  • 1P31, 7Q21 and 18Q21 Chromosomal Aberrations and Candidate Genes in Acquired Vinblastine Resistance of Human Cervical Carcinoma KB Cells
    1155-1164 4/4/08 16:56 Page 1155 ONCOLOGY REPORTS 19: 1155-1164, 2008 1p31, 7q21 and 18q21 chromosomal aberrations and candidate genes in acquired vinblastine resistance of human cervical carcinoma KB cells JIN WANG1,3, LAI-SHAN TAI2, CHI-HUNG TZANG1, WAN FONG FONG1, XIN-YUAN GUAN2 and MENGSU YANG1 1Department of Biology and Chemistry, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon; 2Department of Clinical Oncology, Queen Mary Hospital, The University of Hong Kong, Hong Kong, P.R. China Received January 25, 2008; Accepted March 3, 2008 Abstract. Vinblastine (VBL) is used to treat certain kinds of resistance. This study also demonstrates that the combination cancer including Hodgkin's lymphoma, lung cancer, breast of CGH and cDNA microarray is a very useful tool to detect cancer, testicular cancer and cervical carcinoma. However, drug resistant targets in cancer treatment. the rapid development of resistance during therapy remains a major clinical challenge. In order to reverse cancer cell Introduction resistance, the goal of this study was to find differentially expressed genes and chromosomal alterations in multidrug Drug resistance is the major obstacle to be overcome during resistant (MDR) KB-v1 cells, further to probe the relation- the systemic therapy of cancer. The terms of drug resistance ship between drug resistance and differential genes, and and sensitivity are relative conditions that must be defined chromosomal changes in MDR cancer cells. Comparative with respect to some standard reference frames. Once a drug genomic hybridization (CGH) analysis of MDR KB-v1 and has achieved a critical threshold, it will interact with a range their parental KB-3-1 cells revealed chromosomal changes; of cellular macromolecules.
    [Show full text]
  • Profiling Cell Development by Gene Expression Characterization Of
    Characterization of Early Stages of Human B Cell Development by Gene Expression Profiling This information is current as Marit E. Hystad, June H. Myklebust, Trond H. Bø, Einar A. of September 28, 2021. Sivertsen, Edith Rian, Lise Forfang, Else Munthe, Andreas Rosenwald, Michael Chiorazzi, Inge Jonassen, Louis M. Staudt and Erlend B. Smeland J Immunol 2007; 179:3662-3671; ; doi: 10.4049/jimmunol.179.6.3662 Downloaded from http://www.jimmunol.org/content/179/6/3662 Supplementary http://www.jimmunol.org/content/suppl/2008/03/12/179.6.3662.DC1 Material http://www.jimmunol.org/ References This article cites 59 articles, 28 of which you can access for free at: http://www.jimmunol.org/content/179/6/3662.full#ref-list-1 Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision by guest on September 28, 2021 • No Triage! Every submission reviewed by practicing scientists • 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 Characterization of Early Stages of Human B Cell Development by Gene Expression Profiling1 Marit E.
    [Show full text]