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Abstract
ABSTRACT
Familial risk of tuberculosis (TB) has been recognized for centuries. Largely through studies of mono- and dizygotic twin concordance rates, studies of families with Mendelian susceptibility to mycobacterial disease, and candidate gene studies performed in the 20th century, it was recognized that susceptibility to TB disease has a substantial host genetic component. Limitations in candidate gene studies and early linkage studies made the robust identification of specific loci associated with disease challenging, and few loci have been convincingly associated across multiple populations. Genome-wide and transcriptome-wide association studies, based on microarray (commonly known as genechip) technologies, conducted in the past decade have helped shed some light on pathogenesis but only a handful of new pathways have been identified. This apparent paradox, of high heritability but few replicable associations, has spurred a new wave of collaborative global studies. This review aims to comprehensively review the heritability of TB, critically review the host genetic and transcriptomic correlates of disease, and highlight current studies and future prospects in the study of host genomics in TB. An implicit goal of elucidating host genetic correlates of susceptibility to
Mycobacterium tuberculosis
infection or TB disease is to identify pathophysiological features amenable to translation to new preventive, diagnostic, or therapeutic interventions. The translation of genomic insights into new clinical tools is therefore also discussed.
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Aldrich LN, Kuo SY, Castoreno AB, Goel G, Kuballa P, Rees MG, Seashore-Ludlow BA, Cheah JH, Latorre IJ, Schreiber SL, Shamji AF, Xavier RJ. Discovery of a Small-Molecule Probe for V-ATPase Function. J Am Chem Soc 2015; 137:5563-8. [PMID: 25860544 PMCID: PMC4416280 DOI: 10.1021/jacs.5b02150] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
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Lysosomes perform
a critical cellular function as a site of degradation
for diverse cargoes including proteins, organelles, and pathogens
delivered through distinct pathways, and defects in lysosomal function
have been implicated in a number of diseases. Recent studies have
elucidated roles for the lysosome in the regulation of protein synthesis,
metabolism, membrane integrity, and other processes involved in homeostasis.
Complex small-molecule natural products have greatly contributed to
the investigation of lysosomal function in cellular physiology. Here
we report the discovery of a novel, small-molecule modulator of lysosomal
acidification derived from diversity-oriented synthesis through high-content
screening.
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Affiliation(s)
- Leslie N Aldrich
- †Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States.,‡Center for the Science of Therapeutics, Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Szu-Yu Kuo
- ‡Center for the Science of Therapeutics, Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States.,§Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Adam B Castoreno
- ‡Center for the Science of Therapeutics, Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Gautam Goel
- ∥Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States.,⊥Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, 55 Fruit Street, Boston, Massachusetts 02114, United States.,#Program in Medical and Population Genetics, Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Petric Kuballa
- ∥Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States.,⊥Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, 55 Fruit Street, Boston, Massachusetts 02114, United States.,#Program in Medical and Population Genetics, Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Matthew G Rees
- ‡Center for the Science of Therapeutics, Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Brinton A Seashore-Ludlow
- ‡Center for the Science of Therapeutics, Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Jaime H Cheah
- ‡Center for the Science of Therapeutics, Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Isabel J Latorre
- ‡Center for the Science of Therapeutics, Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Stuart L Schreiber
- †Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States.,‡Center for the Science of Therapeutics, Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States.,∇Howard Hughes Medical Institute, Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Alykhan F Shamji
- ‡Center for the Science of Therapeutics, Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Ramnik J Xavier
- ∥Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States.,⊥Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, 55 Fruit Street, Boston, Massachusetts 02114, United States.,#Program in Medical and Population Genetics, Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
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3
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Zhan L, Ding H, Lin S, Tang J, Deng W, Xu Y, Xu Y, Qin C. Experimental Mycobacterium tuberculosis infection in the Chinese tree shrew. FEMS Microbiol Lett 2014; 360:23-32. [PMID: 25296288 DOI: 10.1111/1574-6968.12524] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 06/11/2014] [Accepted: 06/29/2014] [Indexed: 12/21/2022] Open
Abstract
In recent years, the Chinese tree shrew has been considered to be a promising experimental animal for numerous diseases. Yet the susceptibility of Mycobacterium tuberculosis (MTB) in Chinese tree shrew is still unknown. We infected Chinese tree shrews with a high dose (2.5 × 10(6) CFU) or a low dose (2.5 × 10(3) CFU) of the H37Rv strain via the femoral vein to cause severe or mild disease. Disease severity was determined by clinical signs, pathologic changes and bacteria distribution in organs. Furthermore, among lung samples of the uninfected, mildly and seriously ill Chinese tree shrews, differentially expressed protein profiles were analyzed through iTRAQ and validated by qPCR. Tuberculous nodules, skin ulceration, pleural effusion and cerebellum necrosis could be observed in seriously ill animals. Regulation of the actin cytoskeleton was newly defined as a possible MTB-related pathway correlated with disease progression. This comprehensive analysis of the experimental infection and the depiction of the proteomics profiles in the Chinese tree shrew provide a foundation for the establishment of a new animal model of tuberculosis and provide a better understanding of the mechanism of tuberculosis.
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Affiliation(s)
- Lingjun Zhan
- Key Laboratory of Human Diseases Comparative Medicine, Ministry of Health, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
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Muench SP, Rawson S, Eyraud V, Delmas AF, Da Silva P, Phillips C, Trinick J, Harrison MA, Gressent F, Huss M. PA1b inhibitor binding to subunits c and e of the vacuolar ATPase reveals its insecticidal mechanism. J Biol Chem 2014; 289:16399-408. [PMID: 24795045 PMCID: PMC4047407 DOI: 10.1074/jbc.m113.541250] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 04/14/2014] [Indexed: 12/03/2022] Open
Abstract
The vacuolar ATPase (V-ATPase) is a 1MDa transmembrane proton pump that operates via a rotary mechanism fuelled by ATP. Essential for eukaryotic cell homeostasis, it plays central roles in bone remodeling and tumor invasiveness, making it a key therapeutic target. Its importance in arthropod physiology also makes it a promising pesticide target. The major challenge in designing lead compounds against the V-ATPase is its ubiquitous nature, such that any therapeutic must be capable of targeting particular isoforms. Here, we have characterized the binding site on the V-ATPase of pea albumin 1b (PA1b), a small cystine knot protein that shows exquisitely selective inhibition of insect V-ATPases. Electron microscopy shows that PA1b binding occurs across a range of equivalent sites on the c ring of the membrane domain. In the presence of Mg·ATP, PA1b localizes to a single site, distant from subunit a, which is predicted to be the interface for other inhibitors. Photoaffinity labeling studies show radiolabeling of subunits c and e. In addition, weevil resistance to PA1b is correlated with bafilomycin resistance, caused by mutation of subunit c. The data indicate a binding site to which both subunits c and e contribute and inhibition that involves locking the c ring rotor to a static subunit e and not subunit a. This has implications for understanding the V-ATPase mechanism and that of inhibitors with therapeutic or pesticidal potential. It also provides the first evidence for the position of subunit e within the complex.
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Affiliation(s)
- Stephen P Muench
- From the School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT Leeds, West Yorkshire, United Kingdom,
| | - Shaun Rawson
- From the School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT Leeds, West Yorkshire, United Kingdom
| | - Vanessa Eyraud
- Institut National de la Recherche Agronomique, Institut National des Sciences Appliquées-Lyon, Université de Lyon, IFR 41, UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, Batiment Louis-Pasteur 20, avenue Albert Einstein, F-69621 Villeurbanne, France
| | - Agnès F Delmas
- the Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique Unité Propre de Recherche 4301, Rue Charles Sadron, 45071 Orléans cedex 2, France
| | - Pedro Da Silva
- Institut National de la Recherche Agronomique, Institut National des Sciences Appliquées-Lyon, Université de Lyon, IFR 41, UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, Batiment Louis-Pasteur 20, avenue Albert Einstein, F-69621 Villeurbanne, France
| | - Clair Phillips
- From the School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT Leeds, West Yorkshire, United Kingdom
| | - John Trinick
- the School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT Leeds, West Yorkshire, United Kingdom, and
| | - Michael A Harrison
- From the School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT Leeds, West Yorkshire, United Kingdom
| | - Frédéric Gressent
- Institut National de la Recherche Agronomique, Institut National des Sciences Appliquées-Lyon, Université de Lyon, IFR 41, UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, Batiment Louis-Pasteur 20, avenue Albert Einstein, F-69621 Villeurbanne, France
| | - Markus Huss
- Abteilung Tierphysiologie, Fachbereich Biologie/Chemie Universität Osnabrück, 49069 Osnabrück, Germany
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White MJ, Tacconelli A, Chen JS, Wejse C, Hill PC, Gomes VF, Velez-Edwards DR, Østergaard LJ, Hu T, Moore JH, Novelli G, Scott WK, Williams SM, Sirugo G. Epiregulin (EREG) and human V-ATPase (TCIRG1): genetic variation, ethnicity and pulmonary tuberculosis susceptibility in Guinea-Bissau and The Gambia. Genes Immun 2014; 15:370-7. [PMID: 24898387 DOI: 10.1038/gene.2014.28] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 04/23/2014] [Accepted: 04/24/2014] [Indexed: 02/07/2023]
Abstract
We analyzed two West African samples (Guinea-Bissau: n=289 cases and 322 controls; The Gambia: n=240 cases and 248 controls) to evaluate single-nucleotide polymorphisms (SNPs) in Epiregulin (EREG) and V-ATPase (T-cell immune regulator 1 (TCIRG1)) using single and multilocus analyses to determine whether previously described associations with pulmonary tuberculosis (PTB) in Vietnamese and Italians would replicate in African populations. We did not detect any significant single locus or haplotype associations in either sample. We also performed exploratory pairwise interaction analyses using Visualization of Statistical Epistasis Networks (ViSEN), a novel method to detect only interactions among multiple variables, to elucidate possible interaction effects between SNPs and demographic factors. Although we found no strong evidence of marginal effects, there were several significant pairwise interactions that were identified in either the Guinea-Bissau or the Gambian samples, two of which replicated across populations. Our results indicate that the effects of EREG and TCIRG1 variants on PTB susceptibility, to the extent that they exist, are dependent on gene-gene interactions in West African populations as detected with ViSEN. In addition, epistatic effects are likely to be influenced by inter- and intra-population differences in genetic or environmental context and/or the mycobacterial lineages causing disease.
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Affiliation(s)
- M J White
- 1] Center for Human Genetics Research, Vanderbilt University, Nashville, TN, USA [2] Department of Genetics and Institute of Quantitative Biomedical Sciences, Dartmouth College, Hanover, NH, USA
| | - A Tacconelli
- Centro di Ricerca, Ospedale San Pietro Fatebenefratelli, Rome, Italy
| | - J S Chen
- Department of Genetics and Institute of Quantitative Biomedical Sciences, Dartmouth College, Hanover, NH, USA
| | - C Wejse
- 1] Bandim Health Project, Danish Epidemiology Science Centre and Statens Serum Institute, Bissau, Guinea-Bissau [2] Department of Infectious Diseases, Aarhus University Hospital, Skejby, Denmark [3] Center for Global Health, School of Public Health, Aarhus University, Skejby, Denmark
| | - P C Hill
- 1] Centre for International Health, University of Otago School of Medicine, Dunedin, New Zealand [2] MRC Laboratories, Fajara, The Gambia
| | - V F Gomes
- Bandim Health Project, Danish Epidemiology Science Centre and Statens Serum Institute, Bissau, Guinea-Bissau
| | - D R Velez-Edwards
- 1] Vanderbilt Epidemiology Center, Vanderbilt University, Nashville, TN, USA [2] Institute for Medicine and Public Health, Vanderbilt University, Nashville, TN, USA [3] Center for Human Genetics Research, Vanderbilt University, Nashville, TN, USA [4] Department of Obstetrics and Gynecology, Vanderbilt University, Nashville, TN, USA
| | - L J Østergaard
- Department of Infectious Diseases, Aarhus University Hospital, Skejby, Denmark
| | - T Hu
- Department of Genetics and Institute of Quantitative Biomedical Sciences, Dartmouth College, Hanover, NH, USA
| | - J H Moore
- Department of Genetics and Institute of Quantitative Biomedical Sciences, Dartmouth College, Hanover, NH, USA
| | - G Novelli
- 1] Centro di Ricerca, Ospedale San Pietro Fatebenefratelli, Rome, Italy [2] Dipartimento di Biomedicina e Prevenzione, Sezione di Genetica, Università di Roma 'Tor Vergata', Rome, Italy
| | - W K Scott
- Dr John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - S M Williams
- Department of Genetics and Institute of Quantitative Biomedical Sciences, Dartmouth College, Hanover, NH, USA
| | - G Sirugo
- Centro di Ricerca, Ospedale San Pietro Fatebenefratelli, Rome, Italy
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Qidwai T, Jamal F, Khan MY. DNA Sequence Variation and Regulation of Genes Involved in Pathogenesis of Pulmonary Tuberculosis. Scand J Immunol 2012; 75:568-87. [DOI: 10.1111/j.1365-3083.2012.02696.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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