1
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Deitermann AM, Lin SK, Nugent ST, Raj LK, Beer J, Perz A, Shin TM, Sobanko JF, Etzkorn JR, Miller CJ. Tunneled island pedicle flap reconstruction for upper lateral cutaneous lip defects. J Plast Reconstr Aesthet Surg 2023; 81:119-121. [PMID: 37141785 DOI: 10.1016/j.bjps.2023.04.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 03/23/2023] [Accepted: 04/18/2023] [Indexed: 05/06/2023]
Abstract
BACKGROUND Esthetic upper lateral cutaneous lip reconstruction preserves the apical triangle, nasolabial fold symmetry, and free margin position. The tunneled island pedicle flap (IPF) is a novel single-stage reconstruction to achieve these goals. OBJECTIVES Describe the technique and patient and surgeon-reported outcomes for the tunneled IPF reconstruction of upper lateral cutaneous lip defects. METHODS Retrospective chart review of consecutive tunneled IPF reconstruction following Mohs micrographic surgery (MMS) at a tertiary care center between 2014 and 2020. Patients rated their scars using the validated Patient Scar Assessment Scale (PSAS), and independent surgeons rated scars using the validated Observer Scar Assessment Scale (OSAS). Descriptive statistics were generated for patient demographics and tumor defect characteristics. RESULTS Twenty upper lateral cutaneous lip defects were repaired with the tunneled IPF. Surgeons rated scars with a composite OSAS score of 11.83 ± 4.29 (mean, SD) [scale of 5 (normal skin) to 50 (worst scar imaginable)] and an overall scar score of 2.81 ± 1.11 [scale of 1 (normal skin) to 10 (worst scar imaginable)]. Patients rated their scars with a composite PSAS score of 10 ± 5.39 [scale of 6 (best possible score) to 60 (worst)] and with an overall score of 2.2 ± 1.78 [scale of 1 (normal skin) and 10 (very different from normal skin)]. One flap was surgically revised for pincushioning, but none experienced necrosis, hematoma, or infection. CONCLUSIONS The tunneled IPF is a single-stage reconstruction for upper lateral cutaneous lip defects with favorable scar ratings by patients and observers.
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Affiliation(s)
- A M Deitermann
- University of Minnesota Medical School, Minneapolis, MN, United States
| | - S K Lin
- Donald & Barbara Zucker School of Medicine at Hofstra/Northwell, New Hyde Park, NY, United States
| | - S T Nugent
- Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, United States
| | - L K Raj
- Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, United States
| | - J Beer
- Department of Dermatology, Tulane University School of Medicine, New Orleans, LA, United States
| | - A Perz
- Department of Dermatology, Boston University School of Medicine, Boston, MA, United States
| | - T M Shin
- Department of Dermatology, Hospital of the University of Pennsylvania, Philadelphia, PA, United States
| | - J F Sobanko
- Department of Dermatology, Hospital of the University of Pennsylvania, Philadelphia, PA, United States
| | - J R Etzkorn
- Department of Dermatology, Hospital of the University of Pennsylvania, Philadelphia, PA, United States
| | - C J Miller
- Department of Dermatology, Hospital of the University of Pennsylvania, Philadelphia, PA, United States.
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2
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Foss L, Brown SA, Sutherland S, Miller CJ, Philliber S. A randomized controlled trial of the impact of the Teen Council peer education program on youth development. Health Educ Res 2022; 37:36-47. [PMID: 35134906 DOI: 10.1093/her/cyac001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 01/07/2022] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
This paper presents results of an impact evaluation of Teen Council, a program that trains youth as peer educators. Teen Council is designed to help peer educators make healthy sexual and reproductive decisions, increase their confidence and abilities to educate their peers and inspire them to advocate for just sexual policies. The program's impact on these educators was evaluated using a randomized controlled trial. Over 5 years, interested high school students in seven states were randomly assigned to a study condition. An intent-to-treat framework using ordinary least square (OLS) regression was employed to measure program effects. Relative to control, Teen Council youth showed enhanced comfort with their own sexuality, greater comfort with and more frequent communication with parents about sexuality and more positive sexual health behaviors, including accessing reproductive health care and adopting more effective means of contraception. Teen Council youth also reported greater confidence in talking with peers about sexuality and more confidence in their civic engagement skills.
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Affiliation(s)
- L Foss
- Philliber Research & Evaluation, 16 Main Street, Accord, NY 12404, USA
| | - S A Brown
- Philliber Research & Evaluation, 16 Main Street, Accord, NY 12404, USA
| | - S Sutherland
- Planned Parenthood of the Great Northwest and the Hawaiian Islands, 2001 E. Madison, Seattle, WA 98122, USA
| | - C J Miller
- Planned Parenthood of the Great Northwest and the Hawaiian Islands, 2001 E. Madison, Seattle, WA 98122, USA
| | - S Philliber
- Philliber Research & Evaluation, 16 Main Street, Accord, NY 12404, USA
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3
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Torres-Ayuso P, An E, Nyswaner KM, Bensen RC, Ritt DA, Specht SI, Das S, Andresson T, Cachau RE, Liang RJ, Ries AL, Robinson CM, Difilippantonio S, Gouker B, Bassel L, Karim BO, Miller CJ, Turk BE, Morrison DK, Brognard J. TNIK Is a Therapeutic Target in Lung Squamous Cell Carcinoma and Regulates FAK Activation through Merlin. Cancer Discov 2021; 11:1411-1423. [PMID: 33495197 DOI: 10.1158/2159-8290.cd-20-0797] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 11/21/2020] [Accepted: 01/20/2021] [Indexed: 12/14/2022]
Abstract
Lung squamous cell carcinoma (LSCC) is the second most prevalent type of lung cancer. Despite extensive genomic characterization, no targeted therapies are approved for the treatment of LSCC. Distal amplification of the 3q chromosome is the most frequent genomic alteration in LSCC, and there is an urgent need to identify efficacious druggable targets within this amplicon. We identify the protein kinase TNIK as a therapeutic target in LSCC. TNIK is amplified in approximately 50% of LSCC cases. TNIK genetic depletion or pharmacologic inhibition reduces the growth of LSCC cells in vitro and in vivo. In addition, TNIK inhibition showed antitumor activity and increased apoptosis in established LSCC patient-derived xenografts. Mechanistically, we identified the tumor suppressor Merlin/NF2 as a novel TNIK substrate and showed that TNIK and Merlin are required for the activation of focal adhesion kinase. In conclusion, our data identify targeting TNIK as a potential therapeutic strategy in LSCC. SIGNIFICANCE: Targeted therapies have not yet been approved for the treatment of LSCC, due to lack of identification of actionable cancer drivers. We define TNIK catalytic activity as essential for maintaining LSCC viability and validate the antitumor efficacy of TNIK inhibition in preclinical models of LSCC.This article is highlighted in the In This Issue feature, p. 1307.
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Affiliation(s)
- Pedro Torres-Ayuso
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, NCI, Frederick, Maryland.
| | - Elvira An
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, NCI, Frederick, Maryland
| | - Katherine M Nyswaner
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, NCI, Frederick, Maryland
| | - Ryan C Bensen
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, NCI, Frederick, Maryland
| | - Daniel A Ritt
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, NCI, Frederick, Maryland
| | - Suzanne I Specht
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, NCI, Frederick, Maryland
| | - Sudipto Das
- Protein Characterization Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Thorkell Andresson
- Protein Characterization Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Raul E Cachau
- Advanced Biomedical Computational Science, Biomedical Informatics and Data Science, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Roger J Liang
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, NCI, Frederick, Maryland
| | - Amy L Ries
- Laboratory Animal Sciences Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Christina M Robinson
- Laboratory Animal Sciences Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Simone Difilippantonio
- Laboratory Animal Sciences Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Brad Gouker
- Molecular Histopathology Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Laura Bassel
- Molecular Histopathology Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Baktiar O Karim
- Molecular Histopathology Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Chad J Miller
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut
| | - Benjamin E Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut
| | - Deborah K Morrison
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, NCI, Frederick, Maryland
| | - John Brognard
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, NCI, Frederick, Maryland.
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4
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van de Kooij B, Creixell P, van Vlimmeren A, Joughin BA, Miller CJ, Haider N, Simpson CD, Linding R, Stambolic V, Turk BE, Yaffe MB. Comprehensive substrate specificity profiling of the human Nek kinome reveals unexpected signaling outputs. eLife 2019; 8:44635. [PMID: 31124786 PMCID: PMC6570481 DOI: 10.7554/elife.44635] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 05/13/2019] [Indexed: 12/25/2022] Open
Abstract
Human NimA-related kinases (Neks) have multiple mitotic and non-mitotic functions, but few substrates are known. We systematically determined the phosphorylation-site motifs for the entire Nek kinase family, except for Nek11. While all Nek kinases strongly select for hydrophobic residues in the −3 position, the family separates into four distinct groups based on specificity for a serine versus threonine phospho-acceptor, and preference for basic or acidic residues in other positions. Unlike Nek1-Nek9, Nek10 is a dual-specificity kinase that efficiently phosphorylates itself and peptide substrates on serine and tyrosine, and its activity is enhanced by tyrosine auto-phosphorylation. Nek10 dual-specificity depends on residues in the HRD+2 and APE-4 positions that are uncommon in either serine/threonine or tyrosine kinases. Finally, we show that the phosphorylation-site motifs for the mitotic kinases Nek6, Nek7 and Nek9 are essentially identical to that of their upstream activator Plk1, suggesting that Nek6/7/9 function as phospho-motif amplifiers of Plk1 signaling.
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Affiliation(s)
- Bert van de Kooij
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States.,MIT Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, United States
| | - Pau Creixell
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States.,MIT Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, United States
| | - Anne van Vlimmeren
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States.,MIT Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, United States
| | - Brian A Joughin
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States.,MIT Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, United States
| | - Chad J Miller
- Department of Pharmacology, Yale School of Medicine, New Haven, United States
| | - Nasir Haider
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Craig D Simpson
- Biotech Research and Innovation Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rune Linding
- Biotech Research and Innovation Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Vuk Stambolic
- Department of Medical Biophysics, University of Toronto, Toronto, Canada.,Princess Margaret Cancer Center, University Health Network, Toronto, Canada
| | - Benjamin E Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, United States
| | - Michael B Yaffe
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States.,MIT Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, United States.,Department of Surgery, Beth Israel Deaconess Medical Center, Divisions of Acute Care Surgery, Trauma, and Critical Care and Surgical Oncology, Harvard Medical School, Boston, United States
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5
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Miller CJ, Lou HJ, Simpson C, van de Kooij B, Ha BH, Fisher OS, Pirman NL, Boggon TJ, Rinehart J, Yaffe MB, Linding R, Turk BE. Comprehensive profiling of the STE20 kinase family defines features essential for selective substrate targeting and signaling output. PLoS Biol 2019; 17:e2006540. [PMID: 30897078 PMCID: PMC6445471 DOI: 10.1371/journal.pbio.2006540] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 04/02/2019] [Accepted: 03/14/2019] [Indexed: 12/14/2022] Open
Abstract
Specificity within protein kinase signaling cascades is determined by direct and indirect interactions between kinases and their substrates. While the impact of localization and recruitment on kinase-substrate targeting can be readily assessed, evaluating the relative importance of direct phosphorylation site interactions remains challenging. In this study, we examine the STE20 family of protein serine-threonine kinases to investigate basic mechanisms of substrate targeting. We used peptide arrays to define the phosphorylation site specificity for the majority of STE20 kinases and categorized them into four distinct groups. Using structure-guided mutagenesis, we identified key specificity-determining residues within the kinase catalytic cleft, including an unappreciated role for the kinase β3-αC loop region in controlling specificity. Exchanging key residues between the STE20 kinases p21-activated kinase 4 (PAK4) and Mammalian sterile 20 kinase 4 (MST4) largely interconverted their phosphorylation site preferences. In cells, a reprogrammed PAK4 mutant, engineered to recognize MST substrates, failed to phosphorylate PAK4 substrates or to mediate remodeling of the actin cytoskeleton. In contrast, this mutant could rescue signaling through the Hippo pathway in cells lacking multiple MST kinases. These observations formally demonstrate the importance of catalytic site specificity for directing protein kinase signal transduction pathways. Our findings further suggest that phosphorylation site specificity is both necessary and sufficient to mediate distinct signaling outputs of STE20 kinases and imply broad applicability to other kinase signaling systems.
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Affiliation(s)
- Chad J. Miller
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Hua Jane Lou
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Craig Simpson
- Biotech Research and Innovation Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bert van de Kooij
- Departments of Biological Engineering and Biology, MIT Center for Precision Cancer Medicine and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Byung Hak Ha
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Oriana S. Fisher
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Natasha L. Pirman
- Department of Cellular and Molecular Physiology and Systems Biology Institute, Yale University, New Haven, Connecticut, United States of America
| | - Titus J. Boggon
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Jesse Rinehart
- Department of Cellular and Molecular Physiology and Systems Biology Institute, Yale University, New Haven, Connecticut, United States of America
| | - Michael B. Yaffe
- Departments of Biological Engineering and Biology, MIT Center for Precision Cancer Medicine and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Rune Linding
- Biotech Research and Innovation Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Benjamin E. Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut, United States of America
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6
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Barber KW, Miller CJ, Jun JW, Lou HJ, Turk BE, Rinehart J. Kinase Substrate Profiling Using a Proteome-wide Serine-Oriented Human Peptide Library. Biochemistry 2018; 57:4717-4725. [PMID: 29920078 DOI: 10.1021/acs.biochem.8b00410] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The human proteome encodes >500 protein kinases and hundreds of thousands of potential phosphorylation sites. However, the identification of kinase-substrate pairs remains an active area of research because the relationships between individual kinases and these phosphorylation sites remain largely unknown. Many techniques have been established to discover kinase substrates but are often technically challenging to perform. Moreover, these methods frequently rely on substrate reagent pools that do not reflect human protein sequences or are biased by human cell line protein expression profiles. Here, we describe a new approach called SERIOHL-KILR (serine-oriented human library-kinase library reactions) to profile kinase substrate specificity and to identify candidate substrates for serine kinases. Using a purified library of >100000 serine-oriented human peptides expressed heterologously in Escherichia coli, we perform in vitro kinase reactions to identify phosphorylated human peptide sequences by liquid chromatography and tandem mass spectrometry. We compare our results for protein kinase A to those of a well-established positional scanning peptide library method, certifying that SERIOHL-KILR can identify the same predominant motif elements as traditional techniques. We then interrogate a small panel of cancer-associated PKCβ mutants using our profiling protocol and observe a shift in substrate specificity likely attributable to the loss of key polar contacts between the kinase and its substrates. Overall, we demonstrate that SERIOHL-KILR can rapidly identify candidate kinase substrates that can be directly mapped to human sequences for pathway analysis. Because this technique can be adapted for various kinase studies, we believe that SERIOHL-KILR will have many new victims in the future.
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Affiliation(s)
- Karl W Barber
- Department of Cellular & Molecular Physiology , Yale University , New Haven , Connecticut 06520 , United States.,Systems Biology Institute , Yale University , West Haven , Connecticut 06516 , United States
| | - Chad J Miller
- Department of Pharmacology , Yale University , New Haven , Connecticut 06520 , United States
| | - Jay W Jun
- Division of Nutritional Sciences , Cornell University , Ithaca , New York 14850 , United States.,The Cancer Systems Biology Consortium Research Center , Yale University , West Haven , Connecticut 06516 , United States
| | - Hua Jane Lou
- Department of Pharmacology , Yale University , New Haven , Connecticut 06520 , United States
| | - Benjamin E Turk
- Department of Pharmacology , Yale University , New Haven , Connecticut 06520 , United States
| | - Jesse Rinehart
- Department of Cellular & Molecular Physiology , Yale University , New Haven , Connecticut 06520 , United States.,Systems Biology Institute , Yale University , West Haven , Connecticut 06516 , United States.,The Cancer Systems Biology Consortium Research Center , Yale University , West Haven , Connecticut 06516 , United States
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7
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Miller CJ, Turk BE. Homing in: Mechanisms of Substrate Targeting by Protein Kinases. Trends Biochem Sci 2018; 43:380-394. [PMID: 29544874 DOI: 10.1016/j.tibs.2018.02.009] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 02/08/2018] [Accepted: 02/15/2018] [Indexed: 01/21/2023]
Abstract
Protein phosphorylation is the most common reversible post-translational modification in eukaryotes. Humans have over 500 protein kinases, of which more than a dozen are established targets for anticancer drugs. All kinases share a structurally similar catalytic domain, yet each one is uniquely positioned within signaling networks controlling essentially all aspects of cell behavior. Kinases are distinguished from one another based on their modes of regulation and their substrate repertoires. Coupling specific inputs to the proper signaling outputs requires that kinases phosphorylate a limited number of sites to the exclusion of hundreds of thousands of off-target phosphorylation sites. Here, we review recent progress in understanding mechanisms of kinase substrate specificity and how they function to shape cellular signaling networks.
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Affiliation(s)
- Chad J Miller
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520, USA.
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8
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Miller CJ, Lakhani DL. 16“WALK THIS WAY” - HOW WELL CAN A MULTIDISCIPLINARY TEAM RECOGNISE VARIOUS WALKING AIDS? Age Ageing 2017. [DOI: 10.1093/ageing/afx115.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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9
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Abstract
Extracellular signal-regulated kinases 1 and 2 (ERK1/2) phosphorylate a variety of substrates important for survival and proliferation, and their activity is frequently deregulated in tumors. ERK pathway inhibitors have shown clinical efficacy as anti-cancer drugs, but most patients eventually relapse due to reactivation of the pathway. One factor limiting the efficacy of current therapeutics is the difficulty in reaching clinically effective inhibition of the ERK pathway in the absence of on-target toxicities. Here, we describe an assay suitable for high throughput screening to discover substrate selective ERK1/2 inhibitors, which may have a larger therapeutic window than conventional inhibitors. Specifically, we aim to target a substrate-binding pocket within the ERK1/2 catalytic domain outside of the catalytic cleft. The assay uses an AlphaScreen format to detect phosphorylation of a high-efficiency substrate harboring an essential docking site motif. Pilot screening established that the assay is suitably robust for high-throughput screening. Importantly, the assay can be conducted at high ATP concentrations, which we show reduces the discovery of conventional ATP-competitive inhibitors. These studies provide the basis for high-throughput screens to discover new classes of non-conventional ERK1/2 inhibitors.
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Affiliation(s)
- Chad J Miller
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, United States
| | - Yagmur Muftuoglu
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, United States
| | - Benjamin E Turk
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, United States.
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10
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Abstract
![]()
Eukaryotic
protein kinases typically phosphorylate substrates in
the context of specific sequence motifs, contributing to specificity
essential for accurate signal transmission. Protein kinases recognize
their target sequences through complementary interactions within the
active site cleft. As a step toward the construction of orthogonal
kinase signaling systems, we have re-engineered the protein kinase
Pim1 to alter its phosphorylation consensus sequence. Residues in
the Pim1 catalytic domain interacting directly with a critical arginine
residue in the substrate were substituted to produce a kinase mutant
that instead accommodates a hydrophobic residue. We then introduced
a compensating mutation into a Pim1 substrate, the pro-apoptotic protein
BAD, to reconstitute phosphorylation both in vitro and in living cells. Coexpression of the redesigned kinase with
its substrate in cells protected them from apoptosis. Such orthogonal
kinase–substrate pairs provide tools to probe the functional
consequences of specific phosphorylation events in living cells and
to design synthetic signaling pathways.
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Affiliation(s)
- Catherine Chen
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520, United States
| | - Wutigri Nimlamool
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520, United States
| | - Chad J. Miller
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520, United States
| | - Hua Jane Lou
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520, United States
| | - Benjamin E. Turk
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520, United States
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11
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Goldberg AB, Cho E, Miller CJ, Lou HJ, Turk BE. Identification of a Substrate-selective Exosite within the Metalloproteinase Anthrax Lethal Factor. J Biol Chem 2016; 292:814-825. [PMID: 27909054 DOI: 10.1074/jbc.m116.761734] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 11/23/2016] [Indexed: 01/02/2023] Open
Abstract
The metalloproteinase anthrax lethal factor (LF) is secreted by Bacillus anthracis to promote disease virulence through disruption of host signaling pathways. LF is a highly specific protease, exclusively cleaving mitogen-activated protein kinase kinases (MKKs) and rodent NLRP1B (NACHT leucine-rich repeat and pyrin domain-containing protein 1B). How LF achieves such restricted substrate specificity is not understood. Previous studies have suggested the existence of an exosite interaction between LF and MKKs that promotes cleavage efficiency and specificity. Through a combination of in silico prediction and site-directed mutagenesis, we have mapped an exosite to a non-catalytic region of LF. Mutations within this site selectively impair proteolysis of full-length MKKs yet have no impact on cleavage of short peptide substrates. Although this region appears important for cleaving all LF protein substrates, we found that mutation of specific residues within the exosite differentially affects MKK and NLRP1B cleavage in vitro and in cultured cells. One residue in particular, Trp-271, is essential for cleavage of MKK3, MKK4, and MKK6 but dispensable for targeting of MEK1, MEK2, and NLRP1B. Analysis of chimeric substrates suggests that this residue interacts with the MKK catalytic domain. We found that LF-W271A blocked ERK phosphorylation and growth in a melanoma cell line, suggesting that it may provide a highly selective inhibitor of MEK1/2 for use as a cancer therapeutic. These findings provide insight into how a bacterial toxin functions to specifically impair host signaling pathways and suggest a general strategy for mapping protease exosite interactions.
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Affiliation(s)
- Allison B Goldberg
- From the Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Eunice Cho
- From the Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Chad J Miller
- From the Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Hua Jane Lou
- From the Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Benjamin E Turk
- From the Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520
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12
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Morrow CJ, Trapani F, Metcalf RL, Bertolini G, Hodgkinson CL, Khandelwal G, Kelly P, Galvin M, Carter L, Simpson KL, Williamson S, Wirth C, Simms N, Frankliln L, Frese KK, Rothwell DG, Nonaka D, Miller CJ, Brady G, Blackhall FH, Dive C. Tumourigenic non-small-cell lung cancer mesenchymal circulating tumour cells: a clinical case study. Ann Oncol 2016; 27:1155-1160. [PMID: 27013395 PMCID: PMC4880063 DOI: 10.1093/annonc/mdw122] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 02/24/2016] [Accepted: 02/25/2016] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Over the past decade, numerous reports describe the generation and increasing utility of non-small-cell lung cancer (NSCLC) patient-derived xenografts (PDX) from tissue biopsies. While PDX have proven useful for genetic profiling and preclinical drug testing, the requirement of a tissue biopsy limits the available patient population, particularly those with advanced oligometastatic disease. Conversely, 'liquid biopsies' such as circulating tumour cells (CTCs) are minimally invasive and easier to obtain. Here, we present a clinical case study of a NSCLC patient with advanced metastatic disease, a never smoker whose primary tumour was EGFR and ALK wild-type. We demonstrate for the first time, tumorigenicity of their CTCs to generate a patient CTC-derived eXplant (CDX). PATIENTS AND METHODS CTCs were enriched at diagnosis and again 2 months later during disease progression from 10 ml blood from a 48-year-old NSCLC patient and implanted into immunocompromised mice. Resultant tumours were morphologically, immunohistochemically, and genetically compared with the donor patient's diagnostic specimen. Mice were treated with cisplatin and pemetrexed to assess preclinical efficacy of the chemotherapy regimen given to the donor patient. RESULTS The NSCLC CDX expressed lung lineage markers TTF1 and CK7 and was unresponsive to cisplatin and pemetrexed. Examination of blood samples matched to that used for CDX generation revealed absence of CTCs using the CellSearch EpCAM-dependent platform, whereas size-based CTC enrichment revealed abundant heterogeneous CTCs of which ∼80% were mesenchymal marker vimentin positive. Molecular analysis of the CDX, mesenchymal and epithelial CTCs revealed a common somatic mutation confirming tumour origin and showed CDX RNA and protein profiles consistent with the predominantly mesenchymal phenotype. CONCLUSIONS This study shows that the absence of NSCLC CTCs detected by CellSearch (EpCAM(+)) does not preclude CDX generation, highlighting epithelial to mesenchymal transition and the functional importance of mesenchymal CTCs in dissemination of this disease.
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Affiliation(s)
- C J Morrow
- Clinical and Experimental Pharmacology Group, University of Manchester, Manchester, UK
| | - F Trapani
- Clinical and Experimental Pharmacology Group, University of Manchester, Manchester, UK
| | - R L Metcalf
- Clinical and Experimental Pharmacology Group, University of Manchester, Manchester, UK
| | - G Bertolini
- Tumour Genomics Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - C L Hodgkinson
- Clinical and Experimental Pharmacology Group, University of Manchester, Manchester, UK
| | - G Khandelwal
- RNA Biology Group, University of Manchester, Manchester
| | - P Kelly
- Clinical and Experimental Pharmacology Group, University of Manchester, Manchester, UK
| | - M Galvin
- Clinical and Experimental Pharmacology Group, University of Manchester, Manchester, UK
| | - L Carter
- Clinical and Experimental Pharmacology Group, University of Manchester, Manchester, UK
| | - K L Simpson
- Clinical and Experimental Pharmacology Group, University of Manchester, Manchester, UK
| | - S Williamson
- Clinical and Experimental Pharmacology Group, University of Manchester, Manchester, UK
| | - C Wirth
- Computational Biology Support Team, Cancer Research UK Manchester Institute, University of Manchester, Manchester
| | - N Simms
- Clinical and Experimental Pharmacology Group, University of Manchester, Manchester, UK
| | - L Frankliln
- Clinical and Experimental Pharmacology Group, University of Manchester, Manchester, UK
| | - K K Frese
- Clinical and Experimental Pharmacology Group, University of Manchester, Manchester, UK
| | - D G Rothwell
- Clinical and Experimental Pharmacology Group, University of Manchester, Manchester, UK
| | - D Nonaka
- The Christie NHS Foundation Trust, Manchester
| | - C J Miller
- RNA Biology Group, University of Manchester, Manchester
| | - G Brady
- Clinical and Experimental Pharmacology Group, University of Manchester, Manchester, UK
| | - F H Blackhall
- The Christie NHS Foundation Trust, Manchester; Institute of Cancer Sciences, University of Manchester, Manchester; Cancer Research UK Lung Cancer Centre of Excellence, Manchester, UK
| | - C Dive
- Clinical and Experimental Pharmacology Group, University of Manchester, Manchester, UK; Cancer Research UK Lung Cancer Centre of Excellence, Manchester, UK.
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13
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Abstract
Eukaryotic protein kinases phosphorylate substrates at serine, threonine, and tyrosine residues that fall within the context of short sequence motifs. Knowing the phosphorylation site motif for a protein kinase facilitates designing substrates for kinase assays and mapping phosphorylation sites in protein substrates. Here, we describe an arrayed peptide library protocol for rapidly determining kinase phosphorylation consensus sequences. This method uses a set of peptide mixtures in which each of the 20 amino acid residues is systematically substituted at nine positions surrounding a central site of phosphorylation. Peptide mixtures are arrayed in multiwell plates and analyzed by radiolabel assay with the kinase of interest. The preferred sequence is determined from the relative rate of phosphorylation of each peptide in the array. Consensus peptides based on these sequences typically serve as efficient and specific kinase substrates for high-throughput screening or incorporation into biosensors.
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Affiliation(s)
- Chad J Miller
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, 208066, New Haven, CT, 06520, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, 208066, New Haven, CT, 06520, USA.
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14
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Fernandes KA, Bloomsburg SJ, Miller CJ, Billingslea SA, Merrill MM, Burgess RW, Libby RT, Fuerst PG. Novel axon projection after stress and degeneration in the Dscam mutant retina. Mol Cell Neurosci 2015; 71:1-12. [PMID: 26691152 DOI: 10.1016/j.mcn.2015.12.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 11/30/2015] [Accepted: 12/07/2015] [Indexed: 11/17/2022] Open
Abstract
The Down syndrome cell adhesion molecule gene (Dscam) is required for normal dendrite patterning and promotes developmental cell death in the mouse retina. Loss-of-function studies indicate that Dscam is required for refinement of retinal ganglion cell (RGC) axons in the lateral geniculate nucleus, and in this study we report and describe a requirement for Dscam in the maintenance of RGC axon projections within the retina. Mouse Dscam loss of function phenotypes related to retinal ganglion cell axon outgrowth and targeting have not been previously reported, despite the abundance of axon phenotypes reported in Drosophila Dscam1 loss and gain of function models. Analysis of the Dscam deficient retina was performed by immunohistochemistry and Western blot analysis during postnatal development of the retina. Conditional targeting of Dscam and Jun was performed to identify factors underlying axon-remodeling phenotypes. A subset of RGC axons were observed to project and branch extensively within the Dscam mutant retina after eye opening. Axon remodeling was preceded by histological signs of RGC stress. These included neurofilament accumulation, axon swelling, axon blebbing and activation of JUN, JNK and AKT. Novel and extensive projection of RGC axons within the retina was observed after upregulation of these markers, and novel axon projections were maintained to at least one year of age. Further analysis of retinas in which Dscam was conditionally targeted with Brn3b or Pax6α Cre indicated that axon stress and remodeling could occur in the absence of hydrocephalus, which frequently occurs in Dscam mutant mice. Analysis of mice mutant for the cell death gene Bax, which executes much of Dscam dependent cell death, identified a similar axon misprojection phenotype. Deleting Jun and Dscam resulted in increased axon remodeling compared to Dscam or Bax mutants. Retinal ganglion cells have a very limited capacity to regenerate after damage in the adult retina, compared to the extensive projections made in the embryo. In this study we find that DSCAM and JUN limit ectopic growth of RGC axons, thereby identifying these proteins as targets for promoting axon regeneration and reconnection.
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Affiliation(s)
- K A Fernandes
- Flaum Eye Institute, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - S J Bloomsburg
- University of Idaho, Department of Biological Sciences, Moscow, ID 83844, USA
| | - C J Miller
- University of Idaho, Department of Biological Sciences, Moscow, ID 83844, USA
| | - S A Billingslea
- University of Idaho, Department of Biological Sciences, Moscow, ID 83844, USA
| | - M M Merrill
- University of Idaho, Department of Biological Sciences, Moscow, ID 83844, USA
| | - R W Burgess
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - R T Libby
- Flaum Eye Institute, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - P G Fuerst
- University of Idaho, Department of Biological Sciences, Moscow, ID 83844, USA; WWAMI Medical Education Program, Moscow, ID 83844, USA.
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15
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Creixell P, Palmeri A, Miller CJ, Lou HJ, Santini CC, Nielsen M, Turk BE, Linding R. Unmasking determinants of specificity in the human kinome. Cell 2015; 163:187-201. [PMID: 26388442 PMCID: PMC4644237 DOI: 10.1016/j.cell.2015.08.057] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Revised: 04/09/2015] [Accepted: 08/12/2015] [Indexed: 01/01/2023]
Abstract
Protein kinases control cellular responses to environmental cues by swift and accurate signal processing. Breakdowns in this high-fidelity capability are a driving force in cancer and other diseases. Thus, our limited understanding of which amino acids in the kinase domain encode substrate specificity, the so-called determinants of specificity (DoS), constitutes a major obstacle in cancer signaling. Here, we systematically discover several DoS and experimentally validate three of them, named the αC1, αC3, and APE-7 residues. We demonstrate that DoS form sparse networks of non-conserved residues spanning distant regions. Our results reveal a likely role for inter-residue allostery in specificity and an evolutionary decoupling of kinase activity and specificity, which appear loaded on independent groups of residues. Finally, we uncover similar properties driving SH2 domain specificity and demonstrate how the identification of DoS can be utilized to elucidate a greater understanding of the role of signaling networks in cancer (Creixell et al., 2015 [this issue of Cell]). Residues driving specificity in the kinase and SH2 domains are globally identified Three new such residues, termed αC1, αC3, and APE-7, are experimentally validated Specificity and catalytic activity appear to be encoded in distinct sets of residues The global identification of determinants allows the modeling of rewiring mutations
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Affiliation(s)
- Pau Creixell
- Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark.
| | - Antonio Palmeri
- Centre for Molecular Bioinformatics, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Chad J Miller
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Hua Jane Lou
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Cristina C Santini
- Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark; Biotech Research & Innovation Centre (BRIC), University of Copenhagen (UCPH), 2200 Copenhagen, Denmark
| | - Morten Nielsen
- Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Benjamin E Turk
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Rune Linding
- Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark; Biotech Research & Innovation Centre (BRIC), University of Copenhagen (UCPH), 2200 Copenhagen, Denmark.
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16
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Creixell P, Schoof EM, Simpson CD, Longden J, Miller CJ, Lou HJ, Perryman L, Cox TR, Zivanovic N, Palmeri A, Wesolowska-Andersen A, Helmer-Citterich M, Ferkinghoff-Borg J, Itamochi H, Bodenmiller B, Erler JT, Turk BE, Linding R. Kinome-wide decoding of network-attacking mutations rewiring cancer signaling. Cell 2015; 163:202-17. [PMID: 26388441 PMCID: PMC4644236 DOI: 10.1016/j.cell.2015.08.056] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 04/09/2015] [Accepted: 08/12/2015] [Indexed: 12/17/2022]
Abstract
Cancer cells acquire pathological phenotypes through accumulation of mutations that perturb signaling networks. However, global analysis of these events is currently limited. Here, we identify six types of network-attacking mutations (NAMs), including changes in kinase and SH2 modulation, network rewiring, and the genesis and extinction of phosphorylation sites. We developed a computational platform (ReKINect) to identify NAMs and systematically interpreted the exomes and quantitative (phospho-)proteomes of five ovarian cancer cell lines and the global cancer genome repository. We identified and experimentally validated several NAMs, including PKCγ M501I and PKD1 D665N, which encode specificity switches analogous to the appearance of kinases de novo within the kinome. We discover mutant molecular logic gates, a drift toward phospho-threonine signaling, weakening of phosphorylation motifs, and kinase-inactivating hotspots in cancer. Our method pinpoints functional NAMs, scales with the complexity of cancer genomes and cell signaling, and may enhance our capability to therapeutically target tumor-specific networks. Mutations perturbing signaling networks are systematically classified and interpreted Several such functional mutations are identified in cancer and experimentally validated The results suggest that a single point mutant can have profound signaling effects Systematic interpretation of genomic data may assist future precision-medicine efforts
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Affiliation(s)
- Pau Creixell
- Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Erwin M Schoof
- Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Craig D Simpson
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen (UCPH), 2200 Copenhagen, Denmark
| | - James Longden
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen (UCPH), 2200 Copenhagen, Denmark
| | - Chad J Miller
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Hua Jane Lou
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Lara Perryman
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen (UCPH), 2200 Copenhagen, Denmark
| | - Thomas R Cox
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen (UCPH), 2200 Copenhagen, Denmark
| | - Nevena Zivanovic
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Antonio Palmeri
- Centre for Molecular Bioinformatics, University of Rome Tor Vergata, 00133 Rome, Italy
| | | | | | - Jesper Ferkinghoff-Borg
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen (UCPH), 2200 Copenhagen, Denmark
| | | | - Bernd Bodenmiller
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Janine T Erler
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen (UCPH), 2200 Copenhagen, Denmark
| | - Benjamin E Turk
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Rune Linding
- Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark; Biotech Research and Innovation Centre (BRIC), University of Copenhagen (UCPH), 2200 Copenhagen, Denmark.
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17
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Chang C, Vikram V, Jain B, Bacon D, Amara A, Becker MR, Bernstein G, Bonnett C, Bridle S, Brout D, Busha M, Frieman J, Gaztanaga E, Hartley W, Jarvis M, Kacprzak T, Kovács A, Lahav O, Lin H, Melchior P, Peiris H, Rozo E, Rykoff E, Sánchez C, Sheldon E, Troxel MA, Wechsler R, Zuntz J, Abbott T, Abdalla FB, Allam S, Annis J, Bauer AH, Benoit-Lévy A, Brooks D, Buckley-Geer E, Burke DL, Capozzi D, Carnero Rosell A, Carrasco Kind M, Castander FJ, Crocce M, D'Andrea CB, Desai S, Diehl HT, Dietrich JP, Doel P, Eifler TF, Evrard AE, Fausti Neto A, Flaugher B, Fosalba P, Gruen D, Gruendl RA, Gutierrez G, Honscheid K, James D, Kent S, Kuehn K, Kuropatkin N, Maia MAG, March M, Martini P, Merritt KW, Miller CJ, Miquel R, Neilsen E, Nichol RC, Ogando R, Plazas AA, Romer AK, Roodman A, Sako M, Sanchez E, Sevilla I, Smith RC, Soares-Santos M, Sobreira F, Suchyta E, Tarle G, Thaler J, Thomas D, Tucker D, Walker AR. Wide-Field Lensing Mass Maps from Dark Energy Survey Science Verification Data. Phys Rev Lett 2015; 115:051301. [PMID: 26274409 DOI: 10.1103/physrevlett.115.051301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Indexed: 06/04/2023]
Abstract
We present a mass map reconstructed from weak gravitational lensing shear measurements over 139 deg2 from the Dark Energy Survey science verification data. The mass map probes both luminous and dark matter, thus providing a tool for studying cosmology. We find good agreement between the mass map and the distribution of massive galaxy clusters identified using a red-sequence cluster finder. Potential candidates for superclusters and voids are identified using these maps. We measure the cross-correlation between the mass map and a magnitude-limited foreground galaxy sample and find a detection at the 6.8σ level with 20 arc min smoothing. These measurements are consistent with simulated galaxy catalogs based on N-body simulations from a cold dark matter model with a cosmological constant. This suggests low systematics uncertainties in the map. We summarize our key findings in this Letter; the detailed methodology and tests for systematics are presented in a companion paper.
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Affiliation(s)
- C Chang
- Department of Physics, ETH Zurich, Wolfgang-Pauli-Strasse 16, CH-8093 Zurich, Switzerland
| | - V Vikram
- Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, USA
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - B Jain
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - D Bacon
- Institute of Cosmology and Gravitation, University of Portsmouth, Portsmouth PO1 3FX, United Kingdom
| | - A Amara
- Department of Physics, ETH Zurich, Wolfgang-Pauli-Strasse 16, CH-8093 Zurich, Switzerland
| | - M R Becker
- Department of Physics, Stanford University, 382 Via Pueblo Mall, Stanford, California 94305, USA
- Kavli Institute for Particle Astrophysics and Cosmology, Stanford University, P. O. Box 2450, Stanford, California 94305, USA
| | - G Bernstein
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - C Bonnett
- Institut de Física d'Altes Energies, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Barcelona, Spain
| | - S Bridle
- Jodrell Bank Center for Astrophysics, School of Physics and Astronomy, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - D Brout
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - M Busha
- Department of Physics, Stanford University, 382 Via Pueblo Mall, Stanford, California 94305, USA
- Kavli Institute for Particle Astrophysics and Cosmology, Stanford University, P. O. Box 2450, Stanford, California 94305, USA
| | - J Frieman
- Kavli Institute for Cosmological Physics, University of Chicago, Chicago, Illinois 60637, USA
- Fermi National Accelerator Laboratory, P. O. Box 500, Batavia, Illinois 60510, USA
| | - E Gaztanaga
- Institut de Ciències de l'Espai, IEEC-CSIC, Campus UAB, Facultat de Ciències, Torre C5 par-2, 08193 Bellaterra, Barcelona, Spain
| | - W Hartley
- Department of Physics, ETH Zurich, Wolfgang-Pauli-Strasse 16, CH-8093 Zurich, Switzerland
| | - M Jarvis
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - T Kacprzak
- Department of Physics, ETH Zurich, Wolfgang-Pauli-Strasse 16, CH-8093 Zurich, Switzerland
| | - A Kovács
- Institut de Física d'Altes Energies, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Barcelona, Spain
| | - O Lahav
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - H Lin
- Fermi National Accelerator Laboratory, P. O. Box 500, Batavia, Illinois 60510, USA
| | - P Melchior
- Center for Cosmology and Astro-Particle Physics, The Ohio State University, Columbus, Ohio 43210, USA
- Department of Physics, The Ohio State University, Columbus, Ohio 43210, USA
| | - H Peiris
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - E Rozo
- Department of Physics, University of Arizona, 1118 East Fourth Street, Tucson, Arizona 85721, USA
| | - E Rykoff
- Kavli Institute for Particle Astrophysics and Cosmology, Stanford University, P. O. Box 2450, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - C Sánchez
- Institut de Física d'Altes Energies, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Barcelona, Spain
| | - E Sheldon
- Brookhaven National Laboratory, Building 510, Upton, New York 11973, USA
| | - M A Troxel
- Jodrell Bank Center for Astrophysics, School of Physics and Astronomy, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - R Wechsler
- Department of Physics, Stanford University, 382 Via Pueblo Mall, Stanford, California 94305, USA
- Kavli Institute for Particle Astrophysics and Cosmology, Stanford University, P. O. Box 2450, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - J Zuntz
- Jodrell Bank Center for Astrophysics, School of Physics and Astronomy, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - T Abbott
- Cerro Tololo Inter-American Observatory, National Optical Astronomy Observatory, Casilla 603, La Serena, Chile
| | - F B Abdalla
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - S Allam
- Fermi National Accelerator Laboratory, P. O. Box 500, Batavia, Illinois 60510, USA
| | - J Annis
- Fermi National Accelerator Laboratory, P. O. Box 500, Batavia, Illinois 60510, USA
| | - A H Bauer
- Institut de Ciències de l'Espai, IEEC-CSIC, Campus UAB, Facultat de Ciències, Torre C5 par-2, 08193 Bellaterra, Barcelona, Spain
| | - A Benoit-Lévy
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - D Brooks
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - E Buckley-Geer
- Fermi National Accelerator Laboratory, P. O. Box 500, Batavia, Illinois 60510, USA
| | - D L Burke
- Kavli Institute for Particle Astrophysics and Cosmology, Stanford University, P. O. Box 2450, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - D Capozzi
- Institute of Cosmology and Gravitation, University of Portsmouth, Portsmouth PO1 3FX, United Kingdom
| | - A Carnero Rosell
- Laboratório Interinstitucional de e-Astronomia-LIneA, Rua General Jos´e Cristino 77, Rio de Janeiro, RJ 20921-400, Brazil
- Observatório Nacional, Rua General Jos´e Cristino 77, Rio de Janeiro, RJ 20921-400, Brazil
| | - M Carrasco Kind
- Department of Physics, University of Illinois, 1110 West Green Street, Urbana, Illinois 61801, USA
- National Center for Supercomputing Applications, 1205 West Clark Street, Urbana, Illinois 61801, USA
| | - F J Castander
- Institut de Ciències de l'Espai, IEEC-CSIC, Campus UAB, Facultat de Ciències, Torre C5 par-2, 08193 Bellaterra, Barcelona, Spain
| | - M Crocce
- Institut de Ciències de l'Espai, IEEC-CSIC, Campus UAB, Facultat de Ciències, Torre C5 par-2, 08193 Bellaterra, Barcelona, Spain
| | - C B D'Andrea
- Institute of Cosmology and Gravitation, University of Portsmouth, Portsmouth PO1 3FX, United Kingdom
| | - S Desai
- Department of Physics, Ludwig-Maximilians-Universitaet, Scheinerstrasse 1, 81679 Munich, Germany
| | - H T Diehl
- Fermi National Accelerator Laboratory, P. O. Box 500, Batavia, Illinois 60510, USA
| | - J P Dietrich
- Department of Physics, Ludwig-Maximilians-Universitaet, Scheinerstrasse 1, 81679 Munich, Germany
- Excellence Cluster Universe, Boltzmannstrasse 2, 85748 Garching, Germany
| | - P Doel
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - T F Eifler
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, California 91109, USA
| | - A E Evrard
- Department of Physics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - A Fausti Neto
- Laboratório Interinstitucional de e-Astronomia-LIneA, Rua General Jos´e Cristino 77, Rio de Janeiro, RJ 20921-400, Brazil
| | - B Flaugher
- Fermi National Accelerator Laboratory, P. O. Box 500, Batavia, Illinois 60510, USA
| | - P Fosalba
- Institut de Ciències de l'Espai, IEEC-CSIC, Campus UAB, Facultat de Ciències, Torre C5 par-2, 08193 Bellaterra, Barcelona, Spain
| | - D Gruen
- Max Planck Institute for Extraterrestrial Physics, Giessenbachstrasse, 85748 Garching, Germany
- University Observatory Munich, Scheinerstrasse 1, 81679 Munich, Germany
| | - R A Gruendl
- Department of Physics, University of Illinois, 1110 West Green Street, Urbana, Illinois 61801, USA
- National Center for Supercomputing Applications, 1205 West Clark Street, Urbana, Illinois 61801, USA
| | - G Gutierrez
- Fermi National Accelerator Laboratory, P. O. Box 500, Batavia, Illinois 60510, USA
| | - K Honscheid
- Department of Physics, University of Illinois, 1110 West Green Street, Urbana, Illinois 61801, USA
- National Center for Supercomputing Applications, 1205 West Clark Street, Urbana, Illinois 61801, USA
| | - D James
- Cerro Tololo Inter-American Observatory, National Optical Astronomy Observatory, Casilla 603, La Serena, Chile
| | - S Kent
- Fermi National Accelerator Laboratory, P. O. Box 500, Batavia, Illinois 60510, USA
| | - K Kuehn
- Australian Astronomical Observatory, North Ryde, New South Wales 2113, Australia
| | - N Kuropatkin
- Fermi National Accelerator Laboratory, P. O. Box 500, Batavia, Illinois 60510, USA
| | - M A G Maia
- Laboratório Interinstitucional de e-Astronomia-LIneA, Rua General Jos´e Cristino 77, Rio de Janeiro, RJ 20921-400, Brazil
- Observatório Nacional, Rua General Jos´e Cristino 77, Rio de Janeiro, RJ 20921-400, Brazil
| | - M March
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - P Martini
- Center for Cosmology and Astro-Particle Physics, The Ohio State University, Columbus, Ohio 43210, USA
- Department of Physics, The Ohio State University, Columbus, Ohio 43210, USA
| | - K W Merritt
- Fermi National Accelerator Laboratory, P. O. Box 500, Batavia, Illinois 60510, USA
| | - C J Miller
- Department of Physics, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Astronomy, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - R Miquel
- Institut de Física d'Altes Energies, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, E-08010 Barcelona, Spain
| | - E Neilsen
- Fermi National Accelerator Laboratory, P. O. Box 500, Batavia, Illinois 60510, USA
| | - R C Nichol
- Institute of Cosmology and Gravitation, University of Portsmouth, Portsmouth PO1 3FX, United Kingdom
| | - R Ogando
- Laboratório Interinstitucional de e-Astronomia-LIneA, Rua General Jos´e Cristino 77, Rio de Janeiro, RJ 20921-400, Brazil
- Observatório Nacional, Rua General Jos´e Cristino 77, Rio de Janeiro, RJ 20921-400, Brazil
| | - A A Plazas
- Brookhaven National Laboratory, Building 510, Upton, New York 11973, USA
- Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, California 91109, USA
| | - A K Romer
- Department of Physics and Astronomy, Pevensey Building, University of Sussex, Brighton BN1 9QH, United Kingdom
| | - A Roodman
- Kavli Institute for Particle Astrophysics and Cosmology, Stanford University, P. O. Box 2450, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - M Sako
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - E Sanchez
- Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid 28040, Spain
| | - I Sevilla
- Department of Physics, University of Illinois, 1110 West Green Street, Urbana, Illinois 61801, USA
- Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid 28040, Spain
| | - R C Smith
- Cerro Tololo Inter-American Observatory, National Optical Astronomy Observatory, Casilla 603, La Serena, Chile
| | - M Soares-Santos
- Fermi National Accelerator Laboratory, P. O. Box 500, Batavia, Illinois 60510, USA
| | - F Sobreira
- Fermi National Accelerator Laboratory, P. O. Box 500, Batavia, Illinois 60510, USA
- Laboratório Interinstitucional de e-Astronomia-LIneA, Rua General Jos´e Cristino 77, Rio de Janeiro, RJ 20921-400, Brazil
| | - E Suchyta
- Center for Cosmology and Astro-Particle Physics, The Ohio State University, Columbus, Ohio 43210, USA
- Department of Physics, The Ohio State University, Columbus, Ohio 43210, USA
| | - G Tarle
- Department of Physics, Ludwig-Maximilians-Universitaet, Scheinerstrasse 1, 81679 Munich, Germany
| | - J Thaler
- Department of Physics, University of Illinois, 1110 West Green Street, Urbana, Illinois 61801, USA
| | - D Thomas
- Institute of Cosmology and Gravitation, University of Portsmouth, Portsmouth PO1 3FX, United Kingdom
- SEPnet, South East Physics Network, Southampton SO17 1BJ, United Kingdom
| | - D Tucker
- Fermi National Accelerator Laboratory, P. O. Box 500, Batavia, Illinois 60510, USA
| | - A R Walker
- Cerro Tololo Inter-American Observatory, National Optical Astronomy Observatory, Casilla 603, La Serena, Chile
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Metz MJ, Miller CJ, Lin WS, Abdel-Azim T, Zandinejad A, Crim GA. Dental student perception and assessment of their clinical knowledge in educating patients about preventive dentistry. Eur J Dent Educ 2015; 19:81-86. [PMID: 25040313 DOI: 10.1111/eje.12107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/29/2014] [Indexed: 06/03/2023]
Abstract
In today's dental school curricula, an increasing amount of time is dedicated to technological advances, and preventive dentistry topics may not be adequately addressed. Freshman (D1) students participated in a new Introduction to Preventive Dentistry course, which consisted of didactic lectures, active learning breakout sessions and case-based studies. The goal of this study was to determine if D1 dental students completing the course had a better knowledge and comfort level with basic preventive dentistry concepts and caries risk assessment than the upcoming graduating senior dental students. Following the completion of the course, D1 students were administered a survey that assessed their comfort level describing preventive dentistry topics to patients. This was immediately followed by an unannounced examination over the same topics. Senior (D4) students, who had not taken a formal course, reported statistically significant higher comfort levels than D1 students. However, the D4s scored significantly lower in all of the examination areas than the D1 students. Higher scores in D1s may have been due to recent exposure to the course material. However, the basic nature of the content-specific questions should be easily answered by novice practitioners educating their patients on oral disease prevention. As the current data shows lower content-specific scores of basic preventive dentistry knowledge amongst graduating D4 students, this may indicate a need for more guidance and education of students during the patient care. This study showed that implementation of a formalised course for D1 students can successfully ameliorate deficiencies in knowledge of preventive dentistry topics.
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Affiliation(s)
- M J Metz
- Department of General Dentistry and Oral Medicine, University of Louisville School of Dentistry, Louisville, KY, USA
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Miller CJ, Aiken SA, Metz MJ. Perceptions of D.M.D. student readiness for basic science courses in the United States: can online review modules help? Eur J Dent Educ 2015; 19:1-7. [PMID: 25756103 DOI: 10.1111/eje.12094] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
There can be a disconnect between the level of content covered in undergraduate coursework and the expectations of professional-level faculty of their incoming students. Some basic science faculty members may assume that students have a good knowledge base in the material and neglect to appropriately review, whilst others may spend too much class time reviewing basic material. It was hypothesised that the replacement of introductory didactic physiology lectures with interactive online modules could improve student preparedness prior to lectures. These modules would also allow faculty members to analyse incoming student abilities and save valuable face-to-face class time for alternative teaching strategies. Results indicated that the performance levels of incoming U.S. students were poor (57% average on a pre-test), and students often under-predicted their abilities (by 13% on average). Faculty expectations varied greatly between the different content areas and did not appear to correlate with the actual student performance. Three review modules were created which produced a statistically significant increase in post-test scores (46% increase, P < 0.0001, n = 114-115). The positive results of this study suggest a need to incorporate online review units in the basic science dental school courses and revise introductory material tailored to students' strengths and needs.
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Howard CJ, Hanson-Smith V, Kennedy KJ, Miller CJ, Lou HJ, Johnson AD, Turk BE, Holt LJ. Ancestral resurrection reveals evolutionary mechanisms of kinase plasticity. eLife 2014; 3. [PMID: 25310241 PMCID: PMC4228266 DOI: 10.7554/elife.04126] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 10/09/2014] [Indexed: 01/02/2023] Open
Abstract
Protein kinases have evolved diverse specificities to enable cellular information processing. To gain insight into the mechanisms underlying kinase diversification, we studied the CMGC protein kinases using ancestral reconstruction. Within this group, the cyclin dependent kinases (CDKs) and mitogen activated protein kinases (MAPKs) require proline at the +1 position of their substrates, while Ime2 prefers arginine. The resurrected common ancestor of CDKs, MAPKs, and Ime2 could phosphorylate substrates with +1 proline or arginine, with preference for proline. This specificity changed to a strong preference for +1 arginine in the lineage leading to Ime2 via an intermediate with equal specificity for proline and arginine. Mutant analysis revealed that a variable residue within the kinase catalytic cleft, DFGx, modulates +1 specificity. Expansion of Ime2 kinase specificity by mutation of this residue did not cause dominant deleterious effects in vivo. Tolerance of cells to new specificities likely enabled the evolutionary divergence of kinases. DOI:http://dx.doi.org/10.7554/eLife.04126.001 All living things have enzymes called protein kinases that transfer chemical tags called phosphates onto other proteins. Adding a phosphate to a protein can change the protein's activity—for example, by switching it on or off—and many biological processes involve large networks of kinases that phosphorylate hundreds of proteins. Humans have approximately 500 different protein kinases, which can each phosphorylate many proteins, and so human cells are regulated by tens of thousands of different phosphorylation sites. This raises a number of questions: how have these different kinases evolved over evolutionary history? And how have they come to recognize, and phosphorylate, so many different sites? Howard, Hanson-Smith et al. studied members of a large family of protein kinases called the CMGC group. These enzymes are found in all organisms that have a cell nucleus, including animals, plants, and fungi. All proteins, including kinases, are built up of a chain of smaller molecules called amino acids, and the ability of a kinase to phosphorylate a protein depends on the kinase recognizing a short string of amino acids known as a motif. The phosphate is added in the middle of this motif at the so-called ‘0’ position. Howard, Hanson-Smith et al. found that all of the CMGC protein kinases tested ‘preferred’ an arginine or proline amino acid at the ‘+1’ position of this motif. However, some kinases preferred motifs with an arginine amino acid at this position, and others preferred a proline instead. Howard, Hanson-Smith et al. predicted how the ancestors of a number of CMGC protein kinases might have looked and then ‘resurrected’ them by producing them in yeast cells. When the preference of these ancestral enzymes was tested, the oldest ancestor was found to slightly prefer motifs that had a proline amino acid at the +1 position. Testing six more recent ancestors showed that, over a billion years of evolution, this amino acid preference became broader to include both proline and arginine—and that some modern protein kinases subsequently evolved and specialized to prefer arginine at the +1 position, thus creating a new specificity. Kinases are sometimes likened to microchips in complex electronic networks. In this analogy, expanding the specificity of a kinase could be like creating many ‘loose wires’ and cause short-circuits. From their evolutionary analysis, Howard, Hanson-Smith et al. were able to identify a structural change in the enzyme that causes an expansion of kinase specificity, which allowed them to directly test this idea in cells. Expanding the specificity of a protein kinase that controls sexual cell division in yeast cells did not stop the yeast from dividing to produce spores, suggesting that these changes are more readily tolerated than was expected. Howard, Hanson-Smith et al. suggest that this unexpected robustness of cellular circuits enabled the evolution of the wide variety of protein kinases seen today. DOI:http://dx.doi.org/10.7554/eLife.04126.002
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Affiliation(s)
- Conor J Howard
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Victor Hanson-Smith
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, United States
| | - Kristopher J Kennedy
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Chad J Miller
- Department of Pharmacology, Yale University School of Medicine, New Haven, United States
| | - Hua Jane Lou
- Department of Pharmacology, Yale University School of Medicine, New Haven, United States
| | - Alexander D Johnson
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, United States
| | - Benjamin E Turk
- Department of Pharmacology, Yale University School of Medicine, New Haven, United States
| | - Liam J Holt
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
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Abstract
Three-component systems are often more complex than their two-component counterparts. Although the reversible association of three components in solution is critical for a vast array of chemical and biological processes, no general physical picture of such systems has emerged. Here we have developed a general, comprehensive framework for understanding ternary complex equilibria, which relates directly to familiar concepts such as EC50 and IC50 from simpler (binary complex) equilibria. Importantly, application of our model to data from the published literature has enabled us to achieve new insights into complex systems ranging from coagulation to therapeutic dosing regimens for monoclonal antibodies. We also provide an Excel spreadsheet to assist readers in both conceptualizing and applying our models. Overall, our analysis has the potential to render complex three-component systems--which have previously been characterized as "analytically intractable"--readily comprehensible to theoreticians and experimentalists alike.
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Affiliation(s)
- Eugene F Douglass
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
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Hall JS, Taylor J, Valentine HR, Irlam JJ, Eustace A, Hoskin PJ, Miller CJ, West CML. Enhanced stability of microRNA expression facilitates classification of FFPE tumour samples exhibiting near total mRNA degradation. Br J Cancer 2012; 107:684-94. [PMID: 22805332 PMCID: PMC3419950 DOI: 10.1038/bjc.2012.294] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Revised: 06/08/2012] [Accepted: 06/12/2012] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND As degradation of formalin-fixed paraffin-embedded (FFPE) samples limits the ability to profile mRNA expression, we explored factors predicting the success of mRNA expression profiling of FFPE material and investigated an approach to overcome the limitation. METHODS Bladder (n=140, stored 3-8 years) and cervix (n=160, stored 8-23 years) carcinoma FFPE samples were hybridised to Affymetrix Exon 1.0ST arrays. Percentage detection above background (%DABG) measured technical success. Biological signal was assessed by distinguishing cervix squamous cell carcinoma (SCC) and adenocarcinoma (AC) using a gene signature. As miR-205 had been identified as a marker of SCC, precursor mir-205 was measured by Exon array and mature miR-205 by qRT-PCR. Genome-wide microRNA (miRNA) expression (Affymetrix miRNA v2.0 arrays) was compared in eight newer FFPE samples with biological signal and eight older samples without. RESULTS RNA quality controls (QCs) (e.g., RNA integrity (RIN) number) failed to predict profiling success, but sample age correlated with %DABG in bladder (R=-0.30, P<0.01) and cervix (R=-0.69, P<0.01). Biological signal was lost in older samples and neither a signature nor precursor mir-205 separated samples by histology. miR-205 qRT-PCR discriminated SCC from AC, validated by miRNA profiling (26-fold higher in SCC; P=1.10 × 10(-5)). Genome-wide miRNA (R=0.95) and small nucleolar RNA (R=0.97) expression correlated well in the eight newer vs older FFPE samples and better than mRNA expression (R=0.72). CONCLUSION Sample age is the best predictor of successful mRNA profiling of FFPE material, and miRNA profiling overcomes the limitation of age and copes well with older samples.
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Affiliation(s)
- J S Hall
- Translational Radiobiology Group, School of Cancer and Enabling Sciences, Manchester Academic Health Science Centre, The University of Manchester, Christie Hospital NHS Trust, Wilmslow Road, Manchester M20 4BX, UK
| | - J Taylor
- Translational Radiobiology Group, School of Cancer and Enabling Sciences, Manchester Academic Health Science Centre, The University of Manchester, Christie Hospital NHS Trust, Wilmslow Road, Manchester M20 4BX, UK
- Applied Computational Biology and Bioinformatics Group, Paterson Institute for Cancer Research, Wilmslow Road, Manchester M20 4BX, UK
| | - H R Valentine
- Translational Radiobiology Group, School of Cancer and Enabling Sciences, Manchester Academic Health Science Centre, The University of Manchester, Christie Hospital NHS Trust, Wilmslow Road, Manchester M20 4BX, UK
| | - J J Irlam
- Translational Radiobiology Group, School of Cancer and Enabling Sciences, Manchester Academic Health Science Centre, The University of Manchester, Christie Hospital NHS Trust, Wilmslow Road, Manchester M20 4BX, UK
| | - A Eustace
- Translational Radiobiology Group, School of Cancer and Enabling Sciences, Manchester Academic Health Science Centre, The University of Manchester, Christie Hospital NHS Trust, Wilmslow Road, Manchester M20 4BX, UK
| | - P J Hoskin
- Cancer Centre, Mount Vernon Hospital, Rickmansworth Road, Northwood HA6 2RN, UK
| | - C J Miller
- Applied Computational Biology and Bioinformatics Group, Paterson Institute for Cancer Research, Wilmslow Road, Manchester M20 4BX, UK
| | - C M L West
- Translational Radiobiology Group, School of Cancer and Enabling Sciences, Manchester Academic Health Science Centre, The University of Manchester, Christie Hospital NHS Trust, Wilmslow Road, Manchester M20 4BX, UK
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Hutchison AT, Schmitz JE, Miller CJ, Sastry KJ, Nehete PN, Major AM, Ansari AA, Tatevian N, Lewis DE. Increased inherent intestinal granzyme B expression may be associated with SIV pathogenesis in Asian non-human primates. J Med Primatol 2011; 40:414-26. [PMID: 21732950 PMCID: PMC3193863 DOI: 10.1111/j.1600-0684.2011.00482.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
BACKGROUND Unlike Asian non-human primates, chronically SIV-infected African non-human primates (NHP) display a non-pathogenic disease course. The different outcomes may be related to the development of an SIV-mediated breach of the intestinal mucosa in the Asian species that is absent in the African animals. METHODS To examine possible mechanisms that could lead to the gut breach, we determined whether the colonic lamina propria (LP) of SIV-naïve Asian monkeys contained more granzyme B (GrB) producing CD4 T cells than did that of the African species. GrB is a serine protease that may disrupt mucosal integrity by damaging tight junction proteins. RESULTS We found that the colonic LP of Asian NHP contain more CD4(+) /GrB(+) cells than African NHP. We also observed reduced CD4 expression on LP T cells in African green monkeys. CONCLUSION Both phenotypic differences could protect against SIV-mediated damage to the intestinal mucosa and could lead to future therapies in HIV(+) humans.
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Affiliation(s)
- A T Hutchison
- University of Texas Health Science Center-Medical School at Houston, Division of Infectious Diseases, Department of Internal Medicine, Houston, 77030, USA.
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Hall JS, Leong HS, Armenoult LSC, Newton GE, Valentine HR, Irlam JJ, Möller-Levet C, Sikand KA, Pepper SD, Miller CJ, West CML. Exon-array profiling unlocks clinically and biologically relevant gene signatures from formalin-fixed paraffin-embedded tumour samples. Br J Cancer 2011; 104:971-81. [PMID: 21407225 PMCID: PMC3065290 DOI: 10.1038/bjc.2011.66] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Background: Degradation and chemical modification of RNA in formalin-fixed paraffin-embedded (FFPE) samples hamper their use in expression profiling studies. This study aimed to show that useful information can be obtained by Exon-array profiling archival FFPE tumour samples. Methods: Nineteen cervical squamous cell carcinoma (SCC) and 9 adenocarcinoma (AC) FFPE samples (10–16-year-old) were profiled using Affymetrix Exon arrays. The gene signature derived was tested on a fresh-frozen non-small cell lung cancer (NSCLC) series. Exploration of biological networks involved gene set enrichment analysis (GSEA). Differential gene expression was confirmed using Quantigene, a multiplex bead-based alternative to qRT–PCR. Results: In all, 1062 genes were higher in SCC vs AC, and 155 genes higher in AC. The 1217-gene signature correctly separated 58 NSCLC into SCC and AC. A gene network centered on hepatic nuclear factor and GATA6 was identified in AC, suggesting a role in glandular cell differentiation of the cervix. Quantigene analysis of the top 26 differentially expressed genes correctly partitioned cervix samples as SCC or AC. Conclusion: FFPE samples can be profiled using Exon arrays to derive gene expression signatures that are sufficiently robust to be applied to independent data sets, identify novel biology and design assays for independent platform validation.
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Affiliation(s)
- J S Hall
- Translational Radiobiology Group, School of Cancer and Enabling Sciences, Manchester Academic Health Science Centre, The University of Manchester, Wilmslow Road, Manchester M20 4BX, UK
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Buffa FM, Harris AL, West CM, Miller CJ. Erratum: Large meta-analysis of multiple cancers reveals a common, compact and highly prognostic hypoxia metagene. Br J Cancer 2010. [PMCID: PMC2965883 DOI: 10.1038/sj.bjc.6605933] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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26
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Buffa FM, Harris AL, West CM, Miller CJ. Erratum: Large meta-analysis of multiple cancers reveals a common, compact and highly prognostic hypoxia metagene. Br J Cancer 2010. [PMCID: PMC2966636 DOI: 10.1038/sj.bjc.6605893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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27
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Abstract
Background: There is a need to develop robust and clinically applicable gene expression signatures. Hypoxia is a key factor promoting solid tumour progression and resistance to therapy; a hypoxia signature has the potential to be not only prognostic but also to predict benefit from particular interventions. Methods: An approach for deriving signatures that combine knowledge of gene function and analysis of in vivo co-expression patterns was used to define a common hypoxia signature from three head and neck and five breast cancer studies. Previously validated hypoxia-regulated genes (seeds) were used to generate hypoxia co-expression cancer networks. Results: A common hypoxia signature, or metagene, was derived by selecting genes that were consistently co-expressed with the hypoxia seeds in multiple cancers. This was highly enriched for hypoxia-regulated pathways, and prognostic in multivariate analyses. Genes with the highest connectivity were also the most prognostic, and a reduced metagene consisting of a small number of top-ranked genes, including VEGFA, SLC2A1 and PGAM1, outperformed both a larger signature and reported signatures in independent data sets of head and neck, breast and lung cancers. Conclusion: Combined knowledge of multiple genes' function from in vitro experiments together with meta-analysis of multiple cancers can deliver compact and robust signatures suitable for clinical application.
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Affiliation(s)
- F M Buffa
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK.
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Ferrer MG, Ma M, Li J, Fritts L, McChesney MB, Miller CJ. P01-02. Anti-inflammatory and regulatory mechanisms provide the context for an effective CD8+ T cell response in live-attenuated immunized animals. Retrovirology 2009. [PMCID: PMC2767692 DOI: 10.1186/1742-4690-6-s3-p2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Stone M, Keele BF, Ma Z, Bailes E, Dutra J, Hahn BH, Shaw GM, Miller CJ. P20-13. Identification and characterization of early founder populations in Rhesus macaques vaginally infected with SIVmac251. Retrovirology 2009. [PMCID: PMC2767896 DOI: 10.1186/1742-4690-6-s3-p383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Schweighardt B, Ma Z, Petropoulos CJ, Miller CJ, Wrin T. P04-47. High-titer autologous and heterologous neutralizing antibody activity in acute SIV-infection. Retrovirology 2009. [PMCID: PMC2767979 DOI: 10.1186/1742-4690-6-s3-p75] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Genescà M, McChesney MB, Miller CJ. Antiviral CD8+ T cells in the genital tract control viral replication and delay progression to AIDS after vaginal SIV challenge in rhesus macaques immunized with virulence attenuated SHIV 89.6. J Intern Med 2009; 265:67-77. [PMID: 19093961 PMCID: PMC3401014 DOI: 10.1111/j.1365-2796.2008.02051.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The recently failed clinical efficacy trial of an acquired immunodeficiency syndrome (AIDS) vaccine that elicits antiviral CD8(+) T-cell responses has emphasized the challenge of producing an effective vaccine against human immunodeficiency virus (HIV). In the simian immunodeficiency virus (SIV)/ rhesus monkey model of AIDS, live-attenuated lentivirus 'vaccines' provide the best protection from uncontrolled viral replication and clinical disease after pathogenic SIV challenge. This review summarizes a recent series of studies in which we show that after vaginal SIV challenge of rhesus macaques immunized with an attenuated lentivirus protection from uncontrolled viral replication is primarily mediated by CD8(+) T cells in the vaginal mucosa. Immunization with a chimeric simian/human immunodeficiency virus (SHIV) results in a systemic infection that induces a moderate population of SIV-specific CD8(+) and CD4(+) T cells with cytolytic potential in the vaginal mucosa. Depletion of CD8(+) T cells at the time of SIV challenge completely abrogates the protection mediated by prior infection with attenuated SHIV. Further after vaginal SIV challenge, the only significant expansion of SIV-specific T cells occurs in the vagina in these animals. No significant expansion of T-cell responses was observed in systemic lymphoid tissues. Thus, the presence of SIV-specific CD8(+) T cells in the vagina on the day of vaginal SIV challenge and a modest expansion of local effector T cells is sufficient to stop uncontrolled SIV replication. It seems that T-cell based vaccine strategies that can elicit mucosal effector CD8(+) T-cell populations and avoid inducing systemic T-cell proliferation upon exposure to HIV have the greatest potential for mimicking the success of live-attenuated lentiviral vaccines.
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Affiliation(s)
- M Genescà
- Center for Comparative Medicine, California National Primate Research Center, University of California, Davis, CA 95616, USA
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Barenco M, Papouli E, Shah S, Brewer D, Miller CJ, Hubank M. rHVDM: an R package to predict the activity and targets of a transcription factor. ACTA ACUST UNITED AC 2008; 25:419-20. [PMID: 19074958 DOI: 10.1093/bioinformatics/btn639] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
SUMMARY Highly parallel genomic platforms like microarrays often present researchers with long lists of differentially expressed genes but contain little or no information on how these genes are regulated. rHVDM is a novel R package which uses gene expression time course data to predict the activity and targets of a transcription factor. In the first step, rHVDM uses a small number of known targets to derive the activity profile of a given transcription factor. Then, in a subsequent step, this activity profile is used to predict other putative targets of that transcription factor. A dynamic and mechanistic model of gene expression is at the heart of the technique. Measurement error is taken into account during the process, which allows an objective assessment of the robustness of fit and, therefore, the quality of the predictions. The package relies on efficient algorithms and vectorization to accomplish potentially time consuming tasks including optimization and differential equation integration. We demonstrate the efficiency and accuracy of rHVDM by examining the activity of the tumour-suppressing transcription factor, p53. AVAILABILITY The version of the package presented here (1.8.1) is freely available from the Bioconductor Web site (http://bioconductor.org/packages/2.3/bioc/html/rHVDM.html).
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Affiliation(s)
- M Barenco
- Institute of Child Health, University College London, 30 Guilford street, London WC1N 1EH, UK.
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Linton KM, Hey Y, Saunders E, Jeziorska M, Denton J, Wilson CL, Swindell R, Dibben S, Miller CJ, Pepper SD, Radford JA, Freemont AJ. Erratum: Acquisition of biologically relevant gene expression data by Affymetrix microarray analysis of archival formalin-fixed paraffin-embedded tumours. Br J Cancer 2008. [PMCID: PMC2480966 DOI: 10.1038/sj.bjc.6604506] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Phelps TJ, Palumbo AV, Bischoff BL, Miller CJ, Fagan LA, McNeilly MS, Judkins RR. Micron-pore-sized metallic filter tube membranes for filtration of particulates and water purification. J Microbiol Methods 2008; 74:10-6. [PMID: 17884208 DOI: 10.1016/j.mimet.2007.08.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2007] [Revised: 08/01/2007] [Accepted: 08/01/2007] [Indexed: 11/22/2022]
Abstract
Robust filtering techniques capable of efficiently removing particulates and biological agents from water or air suffer from plugging, poor rejuvenation, low permeance, and high backpressure. Operational characteristics of pressure-driven separations are in part controlled by the membrane pore size, charge of particulates, transmembrane pressure and the requirement for sufficient water flux to overcome fouling. With long term use filters decline in permeance due to filter-cake plugging of pores, fouling, or filter deterioration. Though metallic filter tube development at ORNL has focused almost exclusively on gas separations, a small study examined the applicability of these membranes for tangential filtering of aqueous suspensions of bacterial-sized particles. A mixture of fluorescent polystyrene microspheres ranging in size from 0.5 to 6 microm in diameter simulated microorganisms in filtration studies. Compared to a commercial filter, the ORNL 0.6 microm filter averaged approximately 10-fold greater filtration efficiency of the small particles, several-fold greater permeance after considerable use and it returned to approximately 85% of the initial flow upon backflushing versus 30% for the commercial filter. After filtering several liters of the particle-containing suspension, the ORNL composite filter still exhibited greater than 50% of its initial permeance while the commercial filter had decreased to less than 20%. When considering a greater filtration efficiency, greater permeance per unit mass, greater percentage of rejuvenation upon backflushing (up to 3-fold), and likely greater performance with extended use, the ORNL 0.6 microm filters can potentially outperform the commercial filter by factors of 100-1,000 fold.
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Affiliation(s)
- T J Phelps
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6036, United States.
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Abstract
BACKGROUND In vitro and clinical observations in HIV-infected patients receiving interferon alpha therapy have shown a reduction in HIV loads. Limited investigations have explored the innate or adaptive immune responses of IFN-alpha on SIV replication in vivo. METHODS Seven chronically infected rhesus macaques were given pegylated IFN-alpha 2a (n = four) or saline (n = three) injections once weekly for 14 weeks. Weekly peripheral blood samples were taken for safety parameters, viral load determinations, and measurements of innate and adaptive immune responses. RESULTS Pharmacokinetic measurements demonstrated therapeutic peg-IFN-alpha levels for the initial period of therapy and IFN-alpha inducible antiviral molecules were increased sporadically in the PBMC mRNA of the treatment group. Despite the demonstrable effect of the IFN-alpha injections, the treatment had no effect on plasma viral RNA levels. CONCLUSIONS This work demonstrates that while short term IFN-alpha therapy induces innate antiviral immunity, it does not dramatically enhance or suppress viral replication. However, studies in the SIV model to determine therapeutic potential of chronic IFN-alpha therapy for the treatment of HIV will require macaque specific cytokines.
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Affiliation(s)
- D M Asmuth
- Division of Infectious Diseases, Department of Internal Medicine, University of California-Davis Medical Center, 4150 V Street, Sacramento, CA 95817, USA.
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Genescà M, Skinner PJ, Bost KM, Lu D, Wang Y, Rourke TL, Haase AT, McChesney MB, Miller CJ. Protective attenuated lentivirus immunization induces SIV-specific T cells in the genital tract of rhesus monkeys. Mucosal Immunol 2008; 1:219-28. [PMID: 19079181 PMCID: PMC3401012 DOI: 10.1038/mi.2008.6] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Live attenuated lentivirus immunization is the only vaccine strategy that elicits consistent protection against intravaginal challenge with pathogenic simian immunodeficiency virus (SIV). To determine the mechanism of protection in rhesus monkeys infected with attenuated simian-human immunodeficiency virus (SHIV)89.6, a detailed analysis of SIV Gag-specific T-cell responses in several tissues including the genital tract was performed. Six months after SHIV infection, antiviral T-cell responses were rare in the cervix; however, polyfunctional, cytokine-secreting, and degranulating SIV Gag-specific CD4(+) T cells were consistently found in the vagina of the immunized macaques. SIV-specific CD8(+) T cells were also detected in the vagina, blood, and genital lymph nodes of most of the animals. Thus, an attenuated SHIV vaccine induces persistent antiviral T cells in tissues, including the vagina, where these effector T-cell responses may mediate the consistent protection from vaginal SIV challenge observed in this model.
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Affiliation(s)
- M Genescà
- Center for Comparative Medicine, University of California, Davis, California, USA, California National Primate Research Center, University of California, Davis, California, USA
| | - PJ Skinner
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St Paul, Minnesota, USA
| | - KM Bost
- Center for Comparative Medicine, University of California, Davis, California, USA, California National Primate Research Center, University of California, Davis, California, USA
| | - D Lu
- California National Primate Research Center, University of California, Davis, California, USA
| | - Y Wang
- California National Primate Research Center, University of California, Davis, California, USA
| | - TL Rourke
- Center for Comparative Medicine, University of California, Davis, California, USA, California National Primate Research Center, University of California, Davis, California, USA
| | - AT Haase
- Department of Microbiology, University of Minnesota, St Paul, Minnesota, USA
| | - MB McChesney
- California National Primate Research Center, University of California, Davis, California, USA
| | - CJ Miller
- Center for Comparative Medicine, University of California, Davis, California, USA, California National Primate Research Center, University of California, Davis, California, USA, Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, California, USA, Division of Infectious Diseases, School of Medicine, University of California, Davis, California, USA
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Linton KM, Hey Y, Saunders E, Jeziorska M, Denton J, Wilson CL, Swindell R, Dibben S, Miller CJ, Pepper SD, Radford JA, Freemont AJ. Acquisition of biologically relevant gene expression data by Affymetrix microarray analysis of archival formalin-fixed paraffin-embedded tumours. Br J Cancer 2008; 98:1403-14. [PMID: 18382428 PMCID: PMC2361698 DOI: 10.1038/sj.bjc.6604316] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Robust protocols for microarray gene expression profiling of archival formalin-fixed paraffin-embedded tissue (FFPET) are needed to facilitate research when availability of fresh-frozen tissue is limited. Recent reports attest to the feasibility of this approach, but the clinical value of these data is poorly understood. We employed state-of-the-art RNA extraction and Affymetrix microarray technology to examine 34 archival FFPET primary extremity soft tissue sarcomas. Nineteen arrays met stringent QC criteria and were used to model prognostic signatures for metastatic recurrence. Arrays from two paired frozen and FFPET samples were compared: although FFPET sensitivity was low ( approximately 50%), high specificity (95%) and positive predictive value (92%) suggest that transcript detection is reliable. Good agreement between arrays and real time (RT)-PCR was confirmed, especially for abundant transcripts, and RT-PCR validated the regulation pattern for 19 of 24 candidate genes (overall R(2)=0.4662). RT-PCR and immunohistochemistry on independent cases validated prognostic significance for several genes including RECQL4, FRRS1, CFH and MET - whose combined expression carried greater prognostic value than tumour grade - and cmet and TRKB proteins. These molecules warrant further evaluation in larger series. Reliable clinically relevant data can be obtained from archival FFPET, but protocol amendments are needed to improve the sensitivity and broad application of this approach.
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Affiliation(s)
- K M Linton
- Cancer Research UK, Department of Medical Oncology, Christie Hospital NHS Foundation Trust, Wilmslow Road, Withington, Manchester, M20 4BX, UK.
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Sims AH, Finnon P, Miller CJ, Bouffler SD, Howell A, Scott D, Clarke RB. TPD52 and NFKB1 gene expression levels correlate with G2 chromosomal radiosensitivity in lymphocytes of women with and at risk of hereditary breast cancer. Int J Radiat Biol 2007; 83:409-20. [PMID: 17487680 DOI: 10.1080/09553000701317366] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
PURPOSE To evaluate a transcriptomic approach to identify healthy women at increased risk of breast cancer due to G2-radiosensitivity and look at transcripts that are differentially expressed between individuals. MATERIALS AND METHODS We perform the first study to assess the association of G2 radiosensitivity with basal gene expression in cultured T-lymphocytes from 11 women with breast cancer and 12 healthy female relatives using Affymetrix GeneChips. RESULTS Transcripts associated with radiosensitivity and breast cancer risk were predominantly involved in innate immunity and inflammation, such as interleukins and chemokines. Genes differentially expressed in radiosensitive individuals were more similarly expressed in close family members than in un-related individuals, suggesting heritability of the trait. The expression of tumour protein D52 (TPD52), a gene implicated in cell proliferation, apoptosis, and vesicle trafficking was the most strongly correlated with G2 score while nuclear factor (kappa)-B (NFKB1) was highly inversely correlated with G2 score. NFKB1 is known to be activated by irradiation and its inhibition has been previously shown to increase radiosensitivity. CONCLUSIONS Gene expression analysis of lymphocytes may provide a quantitative measure of radiation response potential and is a promising marker of breast cancer susceptibility.
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Affiliation(s)
- A H Sims
- Breast Biology Group, Paterson Institute for Cancer Research, University of Manchester, UK.
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Miller CJ, Joseph J, Safa W, Flood PE, Dunn EV, Shaheen HM. Accuracy of Arabic versions of three asthma symptoms questionnaires against the clinical diagnosis of asthma. J Asthma 2007; 44:29-34. [PMID: 17365201 DOI: 10.1080/02770900601034361] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Validation studies of asthma symptom questionnaires against provocation tests of bronchial hyperresponsiveness have shown comparable performances of written and video taped questionnaires. This study aimed to determine the test characteristics of Arabic versions of two written and one video taped questionnaires when compared to the clinical diagnosis of asthma made by two respiratory physicians. The written International Study of Asthma and Allergies in Childhood (ISAAC) questionnaire had higher sensitivities and greater accuracy than the other two questionnaires. Comparisons between corresponding questions and scenes in the ISAAC questionnaires in general revealed no significant differences in performance. The ISAAC written questionnaire had test characteristics consistent with its potential use as a screening instrument for asthma in this population of children.
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Affiliation(s)
- C J Miller
- Ngaanyatjarra Health Service, Alice Springs, Northern Territory, Australia.
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Modise CM, Bendick JA, Miller CJ, Neufeld RD, Vidic RD. Use of hydrophilic and hydrophobic microfiltration membranes to remove microorganisms and organic pollutants from primary effluents. Water Environ Res 2006; 78:557-64. [PMID: 16894981 DOI: 10.2175/106143006x99777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Primary-effluent wastewater from the Allegheny County Sanitary Authority (Pennsylvania) was used as a surrogate for combined-sewer-overflow waters contained in the sewershed. Pathogens contained in combined-primary-effluent wastewaters or combined-sewer overflows (CSOs) may pose a human-health threat to those coming in contact with such receiving waters. Polymeric ultra- and nano-membranes can be used to capture these microorganisms from CSOs. This research investigates the ability of polymeric hydrophobic and hydrophilic membranes, ranging in pore size from 0.2 to 0.8 microm, to remove pathogen-indicator organisms (Escherichia coli, enterococcus, and fecal coliforms). Membranes, with pore size 0.45 microm and smaller, were able to reduce the bacteria levels to nondetectable levels, with the sole exception of one membrane with pore size 0.3 microm.
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Affiliation(s)
- Claude M Modise
- Department of Civil and Environmental Engineering, University of Pittsburgh, Pennsylvania 15261, USA
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Abstract
Oestrogen (E) is essential for normal and cancer development in the breast, while anti-oestrogens have been shown to reduce the risk of the disease. However, little is known about the effect of E on gene expression in the normal human breast, particularly when the epithelium and stroma are intact. Previous expression profiles of the response to E have been performed on tumour cell lines, in the absence of stroma. We investigated gene expression in normal human breast tissue transplanted into 9-10-week-old female athymic nude (Balb/c nu/nu) mice. After 2 weeks, when epithelial proliferation is minimal, one-third of the mice were treated with 17beta-oestradiol (E2) to give human luteal-phase levels in the mouse, which we have previously shown to induce maximal epithelial cell proliferation. RNA was isolated from treated and untreated mice, labelled and hybridized to Affymetrix HG-U133A (human) GeneChips. Gene expression levels were generated using BioConductor implementations of the RMA and MAS5 algorithms. E2 treatment was found to represent the largest source of variation in gene expression and cross-species hybridization of mouse RNA from xenograft samples was demonstrated to be negligible. Known E2-responsive genes (such as TFF1 and AREG), and genes thought to be involved in breast cancer metastasis (including mammoglobin, KRT19 and AGR2), were upregulated in response to E treatment. Genes known to be co-expressed with E receptor alpha in breast cancer cell lines and tumours were both upregulated (XBP-1 and GREB1) and downregulated (RARRES1 and GATA3). In addition, genes that are normally expressed in the myoepithelium and extracellular matrix that maintain the tissue microenvironment were also differentially expressed. This suggests that the response to oestrogen in normal breast is highly dependent upon epithelial-stromal/myoepithelial interactions which maintain the tissue microenvironment during epithelial cell proliferation.
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Affiliation(s)
- C L Wilson
- Cancer Research UK Bioinformatics Group, Paterson Institute for Cancer Research, Wilmslow Road, Withington, Manchester M20 4BX, UK
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Mabey JE, Anderson MJ, Giles PF, Miller CJ, Attwood TK, Paton NW, Bornberg-Bauer E, Robson GD, Oliver SG, Denning DW. CADRE: the Central Aspergillus Data REpository. Nucleic Acids Res 2004; 32:D401-5. [PMID: 14681443 PMCID: PMC308744 DOI: 10.1093/nar/gkh009] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
CADRE is a public resource for housing and analysing genomic data extracted from species of Aspergillus. It arose to enable maintenance of the complete annotated genomic sequence of Aspergillus fumigatus and to provide tools for searching, analysing and visualizing features of fungal genomes. By implementing CADRE using Ensembl, a framework is in place for storing and comparing several genomes: the resource will thus expand by including other Aspergillus genomes (such as Aspergillus nidulans) as they become available. CADRE is accessible at http://www.cadre. man.ac.uk.
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Affiliation(s)
- J E Mabey
- School of Medicine, University of Manchester, Manchester M13 9PT, UK.
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Miller CJ, Dunn EV, Thomas EJ, Sankarankutty M. Urinary free deoxypyridinoline excretion in lactating and non-lactating Arabic women of the United Arab Emirates. Ann Clin Biochem 2003; 40:394-7. [PMID: 12880541 DOI: 10.1258/000456303766477048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
BACKGROUND This study aimed to measure urinary free deoxypyridinoline (Dpd) excretion in non-lactating and lactating Arabic women of the United Arab Emirates. METHODS Morning urine specimens were obtained from 679 non-pregnant, non-lactating women and 268 lactating women. Commercial enzyme-linked immunoassay kits were used for urinary free Dpd determinations. RESULTS For the non-lactating women, the mean urinary free Dpd excretion was 9.20 nmol/mmol creatinine (95% confidence interval: 8.82-9.59). This result was significantly higher than those reported elsewhere. There was a trend towards lower Dpd excretion with increasing age (ANOVA test of linearity P<0.05). Urinary free Dpd in lactating women was 9.92 (9.33-10.5); this was not significantly different from that of non-lactating women (P=0.052). Dpd excretion was higher in the first month post-partum, with a significant trend towards diminishing levels thereafter, returning to non-lactating levels by 9 months post-partum (ANOVA test for linearity P<0.005). CONCLUSION Dpd excretion in UAE Arabic women aged 20-44 years was higher than in other groups. This could be due to ethnicity or vitamin D status.
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Affiliation(s)
- C J Miller
- Department of Family Medicine, Faculty of Medicine and Health Sciences, UAE University, Al Ain, United Arab Emirates.
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Abstract
In silico biology has gathered momentum as, worldwide, scientists have united in a common quest to sequence, store and analyse complete genomes. This year, a pivotal achievement of this cooperative endeavour was realised in the release of a public draft of the human genome, and with it the promises to improve our understanding of diverse aspects of biology and to yield a healthier future with safe personalized medicines. Key to these goals will be the need to elucidate and characterise the genes and gene products encoded not just in the human genome, but in many genomes. These tasks are underpinned by the concepts and processes of genome and gene/protein evolution, regulation of gene expression, mechanisms of protein folding, the manifestation of protein function, and so on, all of which must be understood in the context of complex, dynamic biological systems. Our use of computers to model such concepts and systems must be placed in the context of the current limits of our understanding of them:- it is important to recognise, for example, that we don't have a common understanding either of what constitutes a gene or a protein function; we can't invariably say that a particular sequence or fold has arisen via divergent or convergent evolution; and we don't fully understand the rules of protein folding. Accepting what we can't do in silico is essential in appreciating what we can do. Without this understanding, it is easy to be misled, as notions of what particular computational approaches can achieve are sometimes rather optimistic. There are valuable lessons to be learned here from the field of Artificial Intelligence, principal among which is the realisation that capturing and representing complex knowledge is time consuming, expensive and hard. Thus, we argue here that if bioinformatics is to tackle biological complexity in earnest, it would be wise to absorb the experience distilled from decades of artificial intelligence research, and to approach the road ahead with caution, rigour and pragmatism.
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Affiliation(s)
- T K Attwood
- School of Biological Sciences, Department of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PT, UK.
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Miller CJ, Dunn EV, Hashim IB. The glycaemic index of dates and date/yoghurt mixed meals. Are dates 'the candy that grows on trees'? Eur J Clin Nutr 2003; 57:427-30. [PMID: 12627179 DOI: 10.1038/sj.ejcn.1601565] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2002] [Revised: 05/06/2002] [Accepted: 06/17/2002] [Indexed: 11/08/2022]
Abstract
OBJECTIVE To determine the glycaemic index of one variety of date, alone and in mixed meals with plain full-milk yoghurt. DESIGN An experimental study involving the measurement of the glycaemic responses of participants to the ingestion of dates, alone and with yoghurt. SETTING Within the Department of Family Medicine, Faculty of Medicine and Health Sciences, UAE University. SUBJECTS Healthy male and female volunteers aged 32-67 y. INTERVENTION Glycaemic responses to date and date/yoghurt meal ingestion were plotted for each subject. Glycaemic indexes were calculated as the ratios of the incremental areas under these response curves to those for glucose ingestion. Results are presented using means and standard deviations. Glycaemic indexes were compared using paired t-tests. RESULTS Mean glycaemic indexes of the dates were 47.2, 45.3, 35.5, 37.3, 28.9 for rutab, traditionally stored, commercial, rutab/yoghurt and commercial tamer/yoghurt preparations, respectively. There was a significant difference between the results for rutab vs commercial tamer dates (P<0.05), but other comparisons failed to reach statistical significance. CONCLUSIONS Khalas dates, when eaten alone or in mixed meals with plain yoghurt have low glycaemic indexes. The consumption of dates may be of benefit in glycaemic and lipid control of diabetic patients. The consumption of dates in mixed meals with yoghurt appears to have, at most, a minimal effect on the glycaemic index.
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Affiliation(s)
- C J Miller
- Department of Family Medicine, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates.
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Lena P, Villinger F, Giavedoni L, Miller CJ, Rhodes G, Luciw P. Co-immunization of rhesus macaques with plasmid vectors expressing IFN-gamma, GM-CSF, and SIV antigens enhances anti-viral humoral immunity but does not affect viremia after challenge with highly pathogenic virus. Vaccine 2002; 20 Suppl 4:A69-79. [PMID: 12477432 DOI: 10.1016/s0264-410x(02)00391-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To investigate the adjuvant capacity of granulocyte-macrophage colony-stimulating factor (GM-CSF) and interferon (IFN-gamma), we cloned these rhesus cytokines into a mammalian expression vector. Two groups of six rhesus macaques (Macaca mulatta) received intradermal immunizations of plasmid DNA coding for SIV Eng and Gag, and influenza virus nucleoprotein (Flu-NP), with or without the co-administration of plasmid DNA coding for these cytokines. Humoral immune responses to antigens of both of these viruses and SIV specific T cell proliferative responses were significantly enhanced by co-immunization with the cytokines. These twelve monkeys, and a group of six naive controls, were challenged by the oral mucosal route with the uncloned and highly pathogenic SIVmac251. All monkeys became infected. The early CD4 decline was reduced in the group co-immunized with cytokine and viral plasmids. Unexpectedly, plasma viremia set points were not different in this co-immunized group and the non-immunized control group. On the other hand, monkeys vaccinated with equivalent amounts of empty vector plasmid (i.e. no cytokine inserts) along with plasmids expressing viral antigens demonstrated a slight but significant decrease in acute viremia compared to non-immunized controls (P<0.02). However, viral loads at set points were not significantly different between both the immunized and the non-immunized control group. Thus, although the cytokine vectors demonstrated detectable enhancement of the immune response to different viral antigens, such enhanced response did not translate into better anti-viral control in our experiment. These results underscore the need for further testing of cytokines as vaccine adjuvants in relevant animal models.
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Affiliation(s)
- P Lena
- Center for Comparative Medicine, University of California, Davis, CA 95616, USA.
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Lü FX, Abel K, Ma Z, Rourke T, Lu D, Torten J, McChesney M, Miller CJ. The strength of B cell immunity in female rhesus macaques is controlled by CD8+ T cells under the influence of ovarian steroid hormones. Clin Exp Immunol 2002; 128:10-20. [PMID: 11982585 PMCID: PMC1906365 DOI: 10.1046/j.1365-2249.2002.01780.x] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
To understand more clearly how mucosal and systemic immunity is regulated by ovarian steroid hormones during the menstrual cycle, we evaluated the frequency of immunoglobulin- and antibody-secreting cells (ISC, AbSC) in genital tract and systemic lymphoid tissues of normal cycling female rhesus macaques. The frequency of ISC and AbSC was significantly higher in tissues collected from animals in the periovulatory period of the menstrual cycle than in tissues collected from animals at other stages of the cycle. The observed changes were not due to changes in the relative frequency of lymphocyte subsets and B cells in tissues, as these did not change during the menstrual cycle. In vitro, progesterone had a dose-dependent inhibitory effect, and oestrogen had a dose-dependent stimulatory effect on the frequency of ISC in peripheral blood mononuclear cell (PBMC) cultures. The in vitro effect of progesterone and oestrogen on ISC frequency could not be produced by incubating enriched B cells alone with hormone, but required the presence of CD8+ T cells. Following oestrogen stimulation, a CD8+ enriched cell population expressed high levels of IFN-gamma and IL-12. The changes in B cell Ig secretory activity that we document in the tissues of female rhesus macaques during the menstrual cycle is due apparently to the action of ovarian steroid hormones on CD8+ T cells. Thus, CD8+ T cells control B cell secretory activity in both mucosal and systemic immune compartments. Understanding, and eventually manipulating, the CD8+ regulatory cell-B cell interactions in females may produce novel therapeutic approaches for autoimmune diseases and new vaccine strategies to prevent sexually transmitted diseases.
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Affiliation(s)
- F X Lü
- California Regional Primate Research Center, School of Veterinary Medicine, University of California-Davis, CA 95616, USA
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Miller CJ, Townsend AH, Dunn EV. The introduction of a ten-week general practice clerkship in the United Arab Emirates. Med Teach 2002; 24:205-207. [PMID: 12098443 DOI: 10.1080/01421590220125349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Clerkships in general practice have become established in medical curricula around the world. The reorganization of the clinical course at the United Arab Emirates University Faculty of Medicine and Health Sciences was an opportunity to design and introduce a new 10-week clerkship in general practice. This article reports the aims, structure and educational processes of the clerkship including the student assessment methods adopted. Early student feedback on the clerkship is positive.
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Affiliation(s)
- C J Miller
- Department of Family Medicine, Faculty of Medicine and Health Sciences, UAE University, PO Box 17-666, Al-Ain, United Arab Emirates.
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Shah S, Miller CJ, Pethick N, O'dowd L. Patients with allergic rhinitis prefer budesonide aqueous nasal spray to fluticasone propionate nasal spray based on sensory attributes. J Allergy Clin Immunol 2002. [DOI: 10.1016/s0091-6749(02)81418-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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