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Boehler JF, Brown KJ, Ricotti V, Morris CA. N-terminal titin fragment: a non-invasive, pharmacodynamic biomarker for microdystrophin efficacy. Skelet Muscle 2024; 14:2. [PMID: 38229112 PMCID: PMC10790446 DOI: 10.1186/s13395-023-00334-y] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 12/29/2023] [Indexed: 01/18/2024] Open
Abstract
BACKGROUND Multiple clinical trials to assess the efficacy of AAV-directed gene transfer in participants with Duchenne muscular dystrophy (DMD) are ongoing. The success of these trials currently relies on standard functional outcome measures that may exhibit variability within and between participants, rendering their use as sole measures of drug efficacy challenging. Given this, supportive objective biomarkers may be useful in enhancing observed clinical results. Creatine kinase (CK) is traditionally used as a diagnostic biomarker of DMD, but its potential as a robust pharmacodynamic (PD) biomarker is difficult due to the wide variability seen within the same participant over time. Thus, there is a need for the discovery and validation of novel PD biomarkers to further support and bolster traditional outcome measures of efficacy in DMD. METHOD Potential PD biomarkers in DMD participant urine were examined using a proteomic approach on the Somalogic platform. Findings were confirmed in both mdx mice and Golden Retriever muscular dystrophy (GRMD) dog plasma samples. RESULTS Changes in the N-terminal fragment of titin, a well-known, previously characterized biomarker of DMD, were correlated with the expression of microdystrophin protein in mice, dogs, and humans. Further, titin levels were sensitive to lower levels of expressed microdystrophin when compared to CK. CONCLUSION The measurement of objective PD biomarkers such as titin may provide additional confidence in the assessment of the mechanism of action and efficacy in gene therapy clinical trials of DMD. TRIAL REGISTRATION ClinicalTrials.gov NCT03368742.
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Affiliation(s)
- Jessica F Boehler
- Solid Biosciences, 500 Rutherford Avenue 3rd Floor, Boston, MA, 02129, USA.
| | - Kristy J Brown
- Rejuvenate Bio, 11425 Sorrento Valley Road, San Diego, CA, 92121, USA
| | - Valeria Ricotti
- National Institute for Health and Care Research Great Ormond Street Hospital Biomedical Research Centre/University College London Great Ormond Street Institute of Child Health, London, UK
| | - Carl A Morris
- PHDL Consulting LLC, 43 Sylvanus Wood Lane, Woburn, MA, 01801, USA
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Chamberlain JS, Robb M, Braun S, Brown KJ, Danos O, Ganot A, Gonzalez-Alegre P, Hunter N, McDonald C, Morris C, Tobolowsky M, Wagner KR, Ziolkowski O, Duan D. Microdystrophin Expression as a Surrogate Endpoint for Duchenne Muscular Dystrophy Clinical Trials. Hum Gene Ther 2023; 34:404-415. [PMID: 36694468 PMCID: PMC10210223 DOI: 10.1089/hum.2022.190] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 12/12/2022] [Indexed: 01/26/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is a serious, rare genetic disease, affecting primarily boys. It is caused by mutations in the DMD gene and is characterized by progressive muscle degeneration that results in loss of function and early death due to respiratory and/or cardiac failure. Although limited treatment options are available, some for only small subsets of the patient population, DMD remains a disease with large unmet medical needs. The adeno-associated virus (AAV) vector is the leading gene delivery system for addressing genetic neuromuscular diseases. Since the gene encoding the full-length dystrophin protein exceeds the packaging capacity of a single AAV vector, gene replacement therapy based on AAV-delivery of shortened, yet, functional microdystrophin genes has emerged as a promising treatment. This article seeks to explain the rationale for use of the accelerated approval pathway to advance AAV microdystrophin gene therapy for DMD. Specifically, we provide support for the use of microdystrophin expression as a surrogate endpoint that could be used in clinical trials to support accelerated approval.
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Affiliation(s)
- Jeffrey S. Chamberlain
- Department of Neurology, Sen. Paul D. Wellstone Muscular Dystrophy Specialized Research Center, University of Washington, Seattle, Washington, USA
| | - Melissa Robb
- Robb Consulting (contractor of REGENXBIO, Inc.), Columbia, Maryland, USA
| | | | | | | | - Annie Ganot
- Solid Biosciences, Inc., Charlestown, Massachusetts, USA
| | | | | | - Craig McDonald
- University of California Davis Medical Center, Sacramento, California, USA
| | - Carl Morris
- Solid Biosciences, Inc., Charlestown, Massachusetts, USA
| | - Mark Tobolowsky
- Hyman, Phelps & McNamara, P.C. (former contractor of REGENXBIO, Inc.), Washington, District of Columbia, USA
| | | | | | - Dongsheng Duan
- Department of Molecular Microbiology and Immunology, Neurology, Biomedical Sciences, and Biomedical, Biological & Chemical Engineering, University of Missouri, Columbia, Missouri, USA
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Birch SM, Lawlor MW, Conlon TJ, Guo LJ, Crudele JM, Hawkins EC, Nghiem PP, Ahn M, Meng H, Beatka MJ, Fickau BA, Prieto JC, Styner MA, Struharik MJ, Shanks C, Brown KJ, Golebiowski D, Bettis AK, Balog-Alvarez CJ, Clement N, Coleman KE, Corti M, Pan X, Hauschka SD, Gonzalez JP, Morris CA, Schneider JS, Duan D, Chamberlain JS, Byrne BJ, Kornegay JN. Assessment of systemic AAV-microdystrophin gene therapy in the GRMD model of Duchenne muscular dystrophy. Sci Transl Med 2023; 15:eabo1815. [PMID: 36599002 PMCID: PMC11107748 DOI: 10.1126/scitranslmed.abo1815] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [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] [Received: 01/18/2022] [Accepted: 12/09/2022] [Indexed: 01/06/2023]
Abstract
Duchenne muscular dystrophy (DMD) is a progressive muscle wasting disease caused by the absence of dystrophin, a membrane-stabilizing protein encoded by the DMD gene. Although mouse models of DMD provide insight into the potential of a corrective therapy, data from genetically homologous large animals, such as the dystrophin-deficient golden retriever muscular dystrophy (GRMD) model, may more readily translate to humans. To evaluate the clinical translatability of an adeno-associated virus serotype 9 vector (AAV9)-microdystrophin (μDys5) construct, we performed a blinded, placebo-controlled study in which 12 GRMD dogs were divided among four dose groups [control, 1 × 1013 vector genomes per kilogram (vg/kg), 1 × 1014 vg/kg, and 2 × 1014 vg/kg; n = 3 each], treated intravenously at 3 months of age with a canine codon-optimized microdystrophin construct, rAAV9-CK8e-c-μDys5, and followed for 90 days after dosing. All dogs received prednisone (1 milligram/kilogram) for a total of 5 weeks from day -7 through day 28. We observed dose-dependent increases in tissue vector genome copy numbers; μDys5 protein in multiple appendicular muscles, the diaphragm, and heart; limb and respiratory muscle functional improvement; and reduction of histopathologic lesions. As expected, given that a truncated dystrophin protein was generated, phenotypic test results and histopathologic lesions did not fully normalize. All administrations were well tolerated, and adverse events were not seen. These data suggest that systemically administered AAV-microdystrophin may be dosed safely and could provide therapeutic benefit for patients with DMD.
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Affiliation(s)
- Sharla M. Birch
- Texas A&M University, College of Veterinary Medicine and Biomedical Sciences, College Station, TX; 77843
| | | | - Thomas J. Conlon
- University of Florida, Powell Gene Therapy Center, Gainesville, FL; 32610
| | - Lee-Jae Guo
- Texas A&M University, College of Veterinary Medicine and Biomedical Sciences, College Station, TX; 77843
| | | | - Eleanor C. Hawkins
- North Carolina State University, College of Veterinary Medicine, Raleigh, NC; 27606
| | - Peter P. Nghiem
- Texas A&M University, College of Veterinary Medicine and Biomedical Sciences, College Station, TX; 77843
| | - Mihye Ahn
- University of Nevada-Reno, Reno, NV; 89557
| | - Hui Meng
- Medical College of Wisconsin, Milwaukee, WI; 53226
| | | | | | | | | | | | | | | | | | - Amanda K. Bettis
- Texas A&M University, College of Veterinary Medicine and Biomedical Sciences, College Station, TX; 77843
| | - Cynthia J. Balog-Alvarez
- Texas A&M University, College of Veterinary Medicine and Biomedical Sciences, College Station, TX; 77843
| | - Nathalie Clement
- University of Florida, Powell Gene Therapy Center, Gainesville, FL; 32610
| | - Kirsten E. Coleman
- University of Florida, Powell Gene Therapy Center, Gainesville, FL; 32610
| | - Manuela Corti
- University of Florida, Powell Gene Therapy Center, Gainesville, FL; 32610
| | - Xiufang Pan
- University of Missouri, School of Medicine, Columbia, MO 65212
| | | | | | | | | | - Dongsheng Duan
- University of Missouri, School of Medicine, Columbia, MO 65212
| | | | - Barry J. Byrne
- University of Florida, Powell Gene Therapy Center, Gainesville, FL; 32610
| | - Joe. N. Kornegay
- Texas A&M University, College of Veterinary Medicine and Biomedical Sciences, College Station, TX; 77843
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Boehler JF, Brown KJ, Beatka M, Gonzalez JP, Donisa Dreghici R, Soustek-Kramer M, McGonigle S, Ganot A, Palmer T, Lowie C, Chamberlain JS, Lawlor MW, Morris CA. Clinical potential of microdystrophin as a surrogate endpoint. Neuromuscul Disord 2023; 33:40-49. [PMID: 36575103 DOI: 10.1016/j.nmd.2022.12.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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] [Received: 09/09/2022] [Revised: 11/28/2022] [Accepted: 12/13/2022] [Indexed: 12/15/2022]
Abstract
Accelerated approval based on a likely surrogate endpoint can be life-changing for patients suffering from a rare progressive disease with unmet medical need, as it substantially hastens access to potentially lifesaving therapies. In one such example, antisense morpholinos were approved to treat Duchenne muscular dystrophy (DMD) based on measurement of shortened dystrophin in skeletal muscle biopsies as a surrogate biomarker. New, promising therapeutics for DMD include AAV gene therapy to restore another form of dystrophin termed mini- or microdystrophin. AAV-microdystrophins are currently in clinical trials but have yet to be accepted by regulatory agencies as reasonably likely surrogate endpoints. To evaluate microdystrophin expression as a reasonably likely surrogate endpoint for DMD, this review highlights dystrophin biology in the context of functional and clinical benefit to support the argument that microdystrophin proteins have a high probability of providing clinical benefit based on their rational design. Unlike exon-skipping based strategies, the approach of rational design allows for functional capabilities (i.e. quality) of the protein to be maximized with every patient receiving the same optimized microdystrophin. Therefore, the presence of rationally designed microdystrophin in a muscle biopsy is likely to predict clinical benefit and is consequently a strong candidate for a surrogate endpoint analysis to support accelerated approval.
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Affiliation(s)
- Jessica F Boehler
- Solid Biosciences, 500 Rutherford Avenue 3rd Floor, Boston, MA 02129, United States
| | - Kristy J Brown
- Solid Biosciences, 500 Rutherford Avenue 3rd Floor, Boston, MA 02129, United States
| | - Margaret Beatka
- Diverge TSL, 247 Freshwater Way Suite 610, Milwaukee, WI 53204, United States
| | - J Patrick Gonzalez
- Solid Biosciences, 500 Rutherford Avenue 3rd Floor, Boston, MA 02129, United States
| | | | | | - Sharon McGonigle
- Solid Biosciences, 500 Rutherford Avenue 3rd Floor, Boston, MA 02129, United States
| | - Annie Ganot
- Solid Biosciences, 500 Rutherford Avenue 3rd Floor, Boston, MA 02129, United States
| | - Timothy Palmer
- Solid Biosciences, 500 Rutherford Avenue 3rd Floor, Boston, MA 02129, United States
| | - Caitlin Lowie
- Solid Biosciences, 500 Rutherford Avenue 3rd Floor, Boston, MA 02129, United States
| | - Jeffrey S Chamberlain
- Department of Neurology, University of Washington School of Medicine, Seattle, United States
| | - Michael W Lawlor
- Diverge TSL, 247 Freshwater Way Suite 610, Milwaukee, WI 53204, United States
| | - Carl A Morris
- Solid Biosciences, 500 Rutherford Avenue 3rd Floor, Boston, MA 02129, United States.
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Li N, Parkes JE, Spathis R, Morales M, Mcdonald J, Kendra RM, Ott EM, Brown KJ, Lawlor M, Nagaraju K. The Effect of Immunomodulatory Treatments on Anti-Dystrophin Immune Response After AAV Gene Therapy in Dystrophin Deficient mdx Mice. J Neuromuscul Dis 2021; 8:S325-S340. [PMID: 34569971 DOI: 10.3233/jnd-210706] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND AAV-based gene therapy is an attractive approach to treat Duchenne muscular dystrophy (DMD) patients. Although the long-term consequences of a gene therapy approach for DMD are unknown, there is evidence in both DMD patients and animal models that dystrophin replacement by gene therapy leads to an anti-dystrophin immune response that is likely to limit the long-term use of these therapeutic strategies. OBJECTIVE Our objective is to test whether the anti-dystrophin immune response is affected by immunomodulatory drugs in mdx mice after rAAV gene therapy. METHODS mdx mice were treated with rAAV microdystrophin alone or in combination with immunomodulatory drugs. Dystrophin expression in skeletal muscle was assessed by mass spectrometry. Immune responses were assessed by immunophenotyping, western blot for anti-dystrophin antibodies and flow cytometry assays for antigen-specific T-cell cytokine expression. The impact on muscle was measured by grip strength assessment, in vivo torque, optical imaging for inflammation and H&E staining of sections to assess muscle damage. RESULTS We found that AAV-9-microdystrophin gene therapy induced expression of microdystrophin, anti-dystrophin antibodies, and T-cell cytokine responses. Immunomodulatory treatments, rituximab and VBP-6 completely abrogated the anti-dystrophin antibody response. Prednisolone, CTLA4-Ig, and Eplerenone showed variable efficacy in blocking the anti-dystrophin immune response. In contrast, none of the drugs completely abrogated the antigen specific IFN-γ response. AAV-microdystrophin treatment significantly reduced inflammation in both forelimbs and hindlimbs, and the addition of prednisolone and VBP6 further reduced muscle inflammation. Treatment with immunomodulatory drugs, except eplerenone, enhanced the beneficial effects of AAV-microdystrophin therapy in terms of force generation. CONCLUSIONS Our data suggest that AAV-microdystrophin treatment results in anti-dystrophin antibody and T-cell responses, and immunomodulatory treatments have variable efficacy on these responses.
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Affiliation(s)
- Ning Li
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University, Binghamton, NY, USA
| | - Joanna E Parkes
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University, Binghamton, NY, USA
| | - Rita Spathis
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University, Binghamton, NY, USA
| | - Melissa Morales
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University, Binghamton, NY, USA
| | - John Mcdonald
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University, Binghamton, NY, USA
| | - Ryan M Kendra
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University, Binghamton, NY, USA
| | | | | | | | - Kanneboyina Nagaraju
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University, Binghamton, NY, USA
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Novak JS, Spathis R, Dang UJ, Fiorillo AA, Hindupur R, Tully CB, Mázala DA, Canessa E, Brown KJ, Partridge TA, Hathout Y, Nagaraju K. Interrogation of Dystrophin and Dystroglycan Complex Protein Turnover After Exon Skipping Therapy. J Neuromuscul Dis 2021; 8:S383-S402. [PMID: 34569969 PMCID: PMC8673539 DOI: 10.3233/jnd-210696] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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] [Indexed: 01/02/2023]
Abstract
Recently, the Food and Drug Administration granted accelerated approvals for four exon skipping therapies -Eteplirsen, Golodirsen, Viltolarsen, and Casimersen -for Duchenne Muscular Dystrophy (DMD). However, these treatments have only demonstrated variable and largely sub-therapeutic levels of restored dystrophin protein in DMD patients, limiting their clinical impact. To better understand variable protein expression and the behavior of truncated dystrophin protein in vivo, we assessed turnover dynamics of restored dystrophin and dystrophin glycoprotein complex (DGC) proteins in mdx mice after exon skipping therapy, compared to those dynamics in wild type mice, using a targeted, highly-reproducible and sensitive, in vivo stable isotope labeling mass spectrometry approach in multiple muscle tissues. Through statistical modeling, we found that restored dystrophin protein exhibited altered stability and slower turnover in treated mdx muscle compared with that in wild type muscle (∼44 d vs. ∼24 d, respectively). Assessment of mRNA transcript stability (quantitative real-time PCR, droplet digital PCR) and dystrophin protein expression (capillary gel electrophoresis, immunofluorescence) support our dystrophin protein turnover measurements and modeling. Further, we assessed pathology-induced muscle fiber turnover through bromodeoxyuridine (BrdU) labeling to model dystrophin and DGC protein turnover in the context of persistent fiber degeneration. Our findings reveal sequestration of restored dystrophin protein after exon skipping therapy in mdx muscle leading to a significant extension of its half-life compared to the dynamics of full-length dystrophin in normal muscle. In contrast, DGC proteins show constant turnover attributable to myofiber degeneration and dysregulation of the extracellular matrix (ECM) in dystrophic muscle. Based on our results, we demonstrate the use of targeted mass spectrometry to evaluate the suitability and functionality of restored dystrophin isoforms in the context of disease and propose its use to optimize alternative gene correction strategies in development for DMD.
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Affiliation(s)
- James S. Novak
- Center for Genetic Medicine Research, Children’sResearch Institute, Children’s National Hospital, Washington, DC, USA
- Department of Genomics and PrecisionMedicine, The George Washington University School of Medicine and Health Sciences, Washington DC, USA
- Department of Pediatrics, The George Washington University School of Medicine and Health Sciences, Washington DC, USA
- Correspondence to: James Novak, 111 Michigan Avenue NW, Washington, DC, 20010-2916 USA. Tel.: +1 202 476 6135; E-mail: . and Kanneboyina Nagaraju, PO Box 6000, Binghamton, NY, 13902-6000 USA. Tel.: +1 607 777 5814; E-mail:
| | - Rita Spathis
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University, Binghamton, NY USA
| | - Utkarsh J. Dang
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University, Binghamton, NY USA
- Department of Health Sciences, Carleton University, Ottawa, Ontario, Canada
| | - Alyson A. Fiorillo
- Center for Genetic Medicine Research, Children’sResearch Institute, Children’s National Hospital, Washington, DC, USA
- Department of Genomics and PrecisionMedicine, The George Washington University School of Medicine and Health Sciences, Washington DC, USA
- Department of Pediatrics, The George Washington University School of Medicine and Health Sciences, Washington DC, USA
| | - Ravi Hindupur
- Center for Genetic Medicine Research, Children’sResearch Institute, Children’s National Hospital, Washington, DC, USA
| | - Christopher B. Tully
- Center for Genetic Medicine Research, Children’sResearch Institute, Children’s National Hospital, Washington, DC, USA
| | - Davi A.G. Mázala
- Center for Genetic Medicine Research, Children’sResearch Institute, Children’s National Hospital, Washington, DC, USA
- Department of Kinesiology, College of Health Professionals, Towson University, Towson, MD, USA
| | - Emily Canessa
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University, Binghamton, NY USA
| | | | - Terence A. Partridge
- Center for Genetic Medicine Research, Children’sResearch Institute, Children’s National Hospital, Washington, DC, USA
| | - Yetrib Hathout
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University, Binghamton, NY USA
| | - Kanneboyina Nagaraju
- Department of Genomics and PrecisionMedicine, The George Washington University School of Medicine and Health Sciences, Washington DC, USA
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University, Binghamton, NY USA
- Correspondence to: James Novak, 111 Michigan Avenue NW, Washington, DC, 20010-2916 USA. Tel.: +1 202 476 6135; E-mail: . and Kanneboyina Nagaraju, PO Box 6000, Binghamton, NY, 13902-6000 USA. Tel.: +1 607 777 5814; E-mail:
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Boehler JF, Ricotti V, Gonzalez JP, Soustek-Kramer M, Such L, Brown KJ, Schneider JS, Morris CA. Membrane recruitment of nNOSµ in microdystrophin gene transfer to enhance durability. Neuromuscul Disord 2019; 29:735-741. [PMID: 31521486 DOI: 10.1016/j.nmd.2019.08.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/23/2019] [Accepted: 07/31/2019] [Indexed: 12/25/2022]
Abstract
Several gene transfer clinical trials are currently ongoing with the common aim of delivering a shortened version of dystrophin, termed a microdystrophin, for the treatment of Duchenne muscular dystrophy (DMD). However, one of the main differences between these trials is the microdystrophin protein produced following treatment. Each gene transfer product is based on different selections of dystrophin domain combinations to assemble microdystrophin transgenes that maintain functional dystrophin domains and fit within the packaging limits of an adeno-associated virus (AAV) vector. While domains involved in mechanical function, such as the actin-binding domain and β-dystroglycan binding domain, have been identified for many years and included in microdystrophin constructs, more recently the neuronal nitric oxide synthase (nNOS) domain has also been identified due to its role in enhancing nNOS membrane localization. As nNOS membrane localization has been established as an important requirement for prevention of functional ischemia in skeletal muscle, inclusion of the nNOS domain into a microdystrophin construct represents an important consideration. The aim of this mini review is to highlight what is currently known about the nNOS domain of dystrophin and to describe potential implications of this domain in a microdystrophin gene transfer clinical trial.
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Affiliation(s)
- Jessica F Boehler
- Solid Biosciences, 141 Portland Street, Cambridge, MA 02139, United States
| | - Valeria Ricotti
- Solid Biosciences, 141 Portland Street, Cambridge, MA 02139, United States
| | - J Patrick Gonzalez
- Solid Biosciences, 141 Portland Street, Cambridge, MA 02139, United States
| | | | - Lauren Such
- Solid Biosciences, 141 Portland Street, Cambridge, MA 02139, United States
| | - Kristy J Brown
- Solid Biosciences, 141 Portland Street, Cambridge, MA 02139, United States
| | - Joel S Schneider
- Solid Biosciences, 141 Portland Street, Cambridge, MA 02139, United States
| | - Carl A Morris
- Solid Biosciences, 141 Portland Street, Cambridge, MA 02139, United States.
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Shahnoor N, Siebers EM, Brown KJ, Lawlor MW. Pathological Issues in Dystrophinopathy in the Age of Genetic Therapies. Annu Rev Pathol 2018; 14:105-126. [PMID: 30148687 DOI: 10.1146/annurev-pathmechdis-012418-012945] [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] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Dystrophinopathy is a class of genetic skeletal muscle disease characterized by myofiber degeneration and regeneration due to insufficient levels or functioning of dystrophin. Pathological evaluation for dystrophinopathy includes the identification of dystrophic skeletal muscle pathology and the immunohistochemical evaluation of dystrophin epitopes, but biopsies have become rare in recent years. However, the evaluation of dystrophin expression in the research setting has become critically important due to recent advances in genetic therapies, including exon skipping and gene therapy. Given the number of these therapies under evaluation in patients, it is likely that the traditional methods of evaluating dystrophinopathy will need to evolve in the near future. This review discusses current muscle biopsy diagnostic practices in dystrophinopathy and further focuses on how these practices have evolved in the context of therapeutic interventions for dystrophinopathy.
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Affiliation(s)
- Nazima Shahnoor
- Department of Pathology and Laboratory Medicine, and Neuroscience Research Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA; , ,
| | - Emily M Siebers
- Department of Pathology and Laboratory Medicine, and Neuroscience Research Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA; , ,
| | - Kristy J Brown
- Solid Biosciences, Inc., Cambridge, Massachusetts 02139, USA;
| | - Michael W Lawlor
- Department of Pathology and Laboratory Medicine, and Neuroscience Research Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA; , ,
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Rivero-Hinojosa S, Lau LS, Stampar M, Staal J, Zhang H, Gordish-Dressman H, Northcott PA, Pfister SM, Taylor MD, Brown KJ, Rood BR. Proteomic analysis of Medulloblastoma reveals functional biology with translational potential. Acta Neuropathol Commun 2018; 6:48. [PMID: 29880060 PMCID: PMC5992829 DOI: 10.1186/s40478-018-0548-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 05/17/2018] [Indexed: 12/14/2022] Open
Abstract
Genomic characterization has begun to redefine diagnostic classifications of cancers. However, it remains a challenge to infer disease phenotypes from genomic alterations alone. To help realize the promise of genomics, we have performed a quantitative proteomics investigation using Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) and 41 tissue samples spanning the 4 genomically based subgroups of medulloblastoma and control cerebellum. We have identified and quantitated thousands of proteins across these groups and find that we are able to recapitulate the genomic subgroups based upon subgroup restricted and differentially abundant proteins while also identifying subgroup specific protein isoforms. Integrating our proteomic measurements with genomic data, we calculate a poor correlation between mRNA and protein abundance. Using EPIC 850 k methylation array data on the same tissues, we also investigate the influence of copy number alterations and DNA methylation on the proteome in an attempt to characterize the impact of these genetic features on the proteome. Reciprocally, we are able to use the proteome to identify which genomic alterations result in altered protein abundance and thus are most likely to impact biology. Finally, we are able to assemble protein-based pathways yielding potential avenues for clinical intervention. From these, we validate the EIF4F cap-dependent translation pathway as a novel druggable pathway in medulloblastoma. Thus, quantitative proteomics complements genomic platforms to yield a more complete understanding of functional tumor biology and identify novel therapeutic targets for medulloblastoma.
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Raaymakers BW, Jürgenliemk-Schulz IM, Bol GH, Glitzner M, Kotte ANTJ, van Asselen B, de Boer JCJ, Bluemink JJ, Hackett SL, Moerland MA, Woodings SJ, Wolthaus JWH, van Zijp HM, Philippens MEP, Tijssen R, Kok JGM, de Groot-van Breugel EN, Kiekebosch I, Meijers LTC, Nomden CN, Sikkes GG, Doornaert PAH, Eppinga WSC, Kasperts N, Kerkmeijer LGW, Tersteeg JHA, Brown KJ, Pais B, Woodhead P, Lagendijk JJW. First patients treated with a 1.5 T MRI-Linac: clinical proof of concept of a high-precision, high-field MRI guided radiotherapy treatment. ACTA ACUST UNITED AC 2017; 62:L41-L50. [PMID: 29135471 DOI: 10.1088/1361-6560/aa9517] [Citation(s) in RCA: 346] [Impact Index Per Article: 49.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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11
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Hathout Y, Conklin LS, Seol H, Gordish-Dressman H, Brown KJ, Morgenroth LP, Nagaraju K, Heier CR, Damsker JM, van den Anker JN, Henricson E, Clemens PR, Mah JK, McDonald C, Hoffman EP. Serum pharmacodynamic biomarkers for chronic corticosteroid treatment of children. Sci Rep 2016; 6:31727. [PMID: 27530235 PMCID: PMC4987691 DOI: 10.1038/srep31727] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [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] [Received: 04/14/2016] [Accepted: 07/25/2016] [Indexed: 12/13/2022] Open
Abstract
Corticosteroids are extensively used in pediatrics, yet the burden of side effects is significant. Availability of a simple, fast, and reliable biochemical read out of steroidal drug pharmacodynamics could enable a rapid and objective assessment of safety and efficacy of corticosteroids and aid development of corticosteroid replacement drugs. To identify potential corticosteroid responsive biomarkers we performed proteome profiling of serum samples from DMD and IBD patients with and without corticosteroid treatment using SOMAscan aptamer panel testing 1,129 proteins in <0.1 cc of sera. Ten pro-inflammatory proteins were elevated in untreated patients and suppressed by corticosteroids (MMP12, IL22RA2, CCL22, IGFBP2, FCER2, LY9, ITGa1/b1, LTa1/b2, ANGPT2 and FGG). These are candidate biomarkers for anti-inflammatory efficacy of corticosteroids. Known safety concerns were validated, including elevated non-fasting insulin (insulin resistance), and elevated angiotensinogen (salt retention). These were extended by new candidates for metabolism disturbances (leptin, afamin), stunting of growth (growth hormone binding protein), and connective tissue remodeling (MMP3). Significant suppression of multiple adrenal steroid hormones was also seen in treated children (reductions of 17-hydroxyprogesterone, corticosterone, 11-deoxycortisol and testosterone). A panel of new pharmacodynamic biomarkers for corticosteroids in children was defined. Future studies will need to bridge specific biomarkers to mechanism of drug action, and specific clinical outcomes.
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Affiliation(s)
- Yetrib Hathout
- Research Center for Genetic Medicine, Children's National Health Systems, Washington, DC 20010, USA
| | - Laurie S Conklin
- Research Center for Genetic Medicine, Children's National Health Systems, Washington, DC 20010, USA
| | - Haeri Seol
- Research Center for Genetic Medicine, Children's National Health Systems, Washington, DC 20010, USA
| | - Heather Gordish-Dressman
- Research Center for Genetic Medicine, Children's National Health Systems, Washington, DC 20010, USA
| | - Kristy J Brown
- Research Center for Genetic Medicine, Children's National Health Systems, Washington, DC 20010, USA
| | - Lauren P Morgenroth
- Research Center for Genetic Medicine, Children's National Health Systems, Washington, DC 20010, USA
| | - Kanneboyina Nagaraju
- Research Center for Genetic Medicine, Children's National Health Systems, Washington, DC 20010, USA
| | - Christopher R Heier
- Research Center for Genetic Medicine, Children's National Health Systems, Washington, DC 20010, USA
| | - Jesse M Damsker
- Research Center for Genetic Medicine, Children's National Health Systems, Washington, DC 20010, USA
| | - John N van den Anker
- Research Center for Genetic Medicine, Children's National Health Systems, Washington, DC 20010, USA
| | - Erik Henricson
- Department of Physical Medicine &Rehabilitation, University of California, Davis School of Medicine, Davis, CA 95618, USA
| | - Paula R Clemens
- Neurology Service, Department of Veterans Affairs Medical Center, Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jean K Mah
- Department of Pediatrics, Alberta Children's Hospital, Calgary, AB, T3B 6A8 Canada
| | - Craig McDonald
- Department of Physical Medicine &Rehabilitation, University of California, Davis School of Medicine, Davis, CA 95618, USA
| | - Eric P Hoffman
- Research Center for Genetic Medicine, Children's National Health Systems, Washington, DC 20010, USA
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12
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Abstract
OBJECTIVE The goal of the study is to identity proteins, which interact with the promoter region of double homeobox protein 4 (DUX4) gene known to be causative for the autosomal dominant disorder Facioscapulohumeral Muscular Dystrophy (FSHD). METHODS We performed a DNA pull down assay coupled with mass spectrometry analysis to identify proteins that interact with a DUX4 promoter probe in Rhabdomyosarcomca (RD) cells. We selected the top ranked protein poly (ADP-ribose) polymerase 1 (PARP1) from our mass spectrometry data for further ChIP-qPCR validation using patients' myoblasts. We then treated FSHD myoblasts with PARP1 inhibitors to investigate the role of PARP1 in the FSHD myoblasts. RESULTS In our mass spectrometry analysis, PARP1 was found to be the top ranked protein interacting preferentially with the DUX4 promoter probe in RD cells. We further validated this interaction by immunoblotting in RD cells (2-fold enrichment compared to proteins pulled down by a control probe, p<0.05) and ChIP-qPCR in patients' myoblasts (65-fold enrichment, p<0.01). Interestingly, the interaction was only observed in FSHD myoblasts but not in the control myoblasts. Upon further treatment of FSHD myoblasts with PARP1 inhibitors, we showed that treatment with a PARP1 inhibitor, 3-aminobenzamide (0.5 mM), for 24 h had a suppression of DUX4 (2.6 fold, p<0.05) and ZSCAN4, a gene previously shown to be upregulated by DUX4, (1.6 fold, p<0.01) in FSHD myoblasts. Treatment with fisetin (0.5 mM), a polyphenol compound with PARP1 inhibitory property, for 24 h also suppressed the expression of DUX4 (44.8 fold, p<0.01) and ZSCAN4 (2.2 fold, p<0.05) in the FSHD myoblasts. We further showed that DNA methyltransferase 1 (DNMT1), a gene regulated by PARP1 was also enriched at the DUX4 promoter in RD cells through immunoblotting (2-fold, p<0.01) and immortalized FSHD myoblasts (42-fold, p<0.01) but not control myoblasts through ChIP qPCR. CONCLUSION Our results showed that PARP1 and DNMT1 interacted with DUX4 promoter and may be involved in modulating DUX4 expression in FSHD.
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Affiliation(s)
- Vishakha Sharma
- Department of Molecular Medicine, George Washington University, Washington DC, USA
| | - Sachchida Nand Pandey
- Center for Genetic Medicine Research, Children's National Health System, Washington DC, USA
| | - Hunain Khawaja
- Center for Genetic Medicine Research, Children's National Health System, Washington DC, USA
| | - Kristy J Brown
- Center for Genetic Medicine Research, Children's National Health System, Washington DC, USA
| | - Yetrib Hathout
- Center for Genetic Medicine Research, Children's National Health System, Washington DC, USA; Department of Integrative Systems Biology, George Washington University, Washington DC, USA
| | - Yi-Wen Chen
- Center for Genetic Medicine Research, Children's National Health System, Washington DC, USA; Department of Integrative Systems Biology, George Washington University, Washington DC, USA
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13
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Staal JA, Lau LS, Zhang H, Ingram WJ, Hallahan AR, Northcott PA, Pfister SM, Wechsler-Reya RJ, Rusert JM, Taylor MD, Cho YJ, Packer RJ, Brown KJ, Rood BR. Proteomic profiling of high risk medulloblastoma reveals functional biology. Oncotarget 2016; 6:14584-95. [PMID: 25970789 PMCID: PMC4546489 DOI: 10.18632/oncotarget.3927] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [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: 04/03/2015] [Accepted: 04/08/2015] [Indexed: 12/11/2022] Open
Abstract
Genomic characterization of medulloblastoma has improved molecular risk classification but struggles to define functional biological processes, particularly for the most aggressive subgroups. We present here a novel proteomic approach to this problem using a reference library of stable isotope labeled medulloblastoma-specific proteins as a spike-in standard for accurate quantification of the tumor proteome. Utilizing high-resolution mass spectrometry, we quantified the tumor proteome of group 3 medulloblastoma cells and demonstrate that high-risk MYC amplified tumors can be segregated based on protein expression patterns. We cross-validated the differentially expressed protein candidates using an independent transcriptomic data set and further confirmed them in a separate cohort of medulloblastoma tissue samples to identify the most robust proteogenomic differences. Interestingly, highly expressed proteins associated with MYC-amplified tumors were significantly related to glycolytic metabolic pathways via alternative splicing of pyruvate kinase (PKM) by heterogeneous ribonucleoproteins (HNRNPs). Furthermore, when maintained under hypoxic conditions, these MYC-amplified tumors demonstrated increased viability compared to non-amplified tumors within the same subgroup. Taken together, these findings highlight the power of proteomics as an integrative platform to help prioritize genetic and molecular drivers of cancer biology and behavior.
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Affiliation(s)
- Jerome A Staal
- Center for Cancer and Immunology Research, Children's National Medical Center, Washington DC, USA
| | - Ling San Lau
- Center for Cancer and Immunology Research, Children's National Medical Center, Washington DC, USA
| | - Huizhen Zhang
- Center for Cancer and Immunology Research, Children's National Medical Center, Washington DC, USA
| | - Wendy J Ingram
- UQ Child Health Research Centre, The University of Queensland and Queensland Children's Medical Research Institute, Children's Health, Queensland, Australia
| | - Andrew R Hallahan
- UQ Child Health Research Centre, The University of Queensland and Queensland Children's Medical Research Institute, Children's Health, Queensland, Australia
| | - Paul A Northcott
- Division of Pediatric Neurooncology, German Cancer Research Center, Heidleberg, Germany
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, German Cancer Research Center, Heidleberg, Germany
| | | | - Jessica M Rusert
- Sanford-Burnham Medical Research Institute, La Jolla, California, USA
| | - Michael D Taylor
- Department of Neurosurgery, Hospital for Sick Children, Toronto, Canada
| | - Yoon-Jae Cho
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
| | - Roger J Packer
- Center for Neuroscience and Behavioral Medicine, Children's National Medical Center, Washington DC, USA
| | - Kristy J Brown
- Center for Genetic Medicine, Children's National Medical Center, Washington DC, USA
| | - Brian R Rood
- Center for Cancer and Immunology Research, Children's National Medical Center, Washington DC, USA
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14
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Hathout Y, Seol H, Han MHJ, Zhang A, Brown KJ, Hoffman EP. Clinical utility of serum biomarkers in Duchenne muscular dystrophy. Clin Proteomics 2016; 13:9. [PMID: 27051355 PMCID: PMC4820909 DOI: 10.1186/s12014-016-9109-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [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: 01/05/2016] [Accepted: 03/16/2016] [Indexed: 12/14/2022] Open
Abstract
Assessments of disease progression and response to therapies in Duchenne muscular dystrophy (DMD) patients remain challenging. Current DMD patient assessments include complex physical tests and invasive procedures such as muscle biopsies, which are not suitable for young children. Defining alternative, less invasive and objective outcome measures to assess disease progression and response to therapy will aid drug development and clinical trials in DMD. In this review we highlight advances in development of non-invasive blood circulating biomarkers as a means to assess disease progression and response to therapies in DMD.
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Affiliation(s)
- Yetrib Hathout
- Center for Genetic Medicine, Children's National Healthy System, Washington, DC USA
| | - Haeri Seol
- Center for Genetic Medicine, Children's National Healthy System, Washington, DC USA
| | - Meng Hsuan J Han
- Center for Genetic Medicine, Children's National Healthy System, Washington, DC USA
| | - Aiping Zhang
- Center for Genetic Medicine, Children's National Healthy System, Washington, DC USA
| | - Kristy J Brown
- Center for Genetic Medicine, Children's National Healthy System, Washington, DC USA
| | - Eric P Hoffman
- Center for Genetic Medicine, Children's National Healthy System, Washington, DC USA
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15
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Punetha J, Mansoor S, Bertorini TE, Kesari A, Brown KJ, Hoffman EP. Somatic mosaicism due to a reversion variant causing hemi-atrophy: a novel variant of dystrophinopathy. Eur J Hum Genet 2016; 24:1511-4. [PMID: 26956251 DOI: 10.1038/ejhg.2016.22] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 02/04/2016] [Accepted: 02/10/2016] [Indexed: 11/09/2022] Open
Abstract
We describe a case of hemi-atrophy in a young adult male, with a positive family history of three maternal uncles with Duchenne muscular dystrophy (DMD). The patient showed progressive weakness localized to the left side, an abnormal electromyography, and creatine kinase levels >3000 IU/l. Muscle biopsy showed both dystrophin-positive and -negative myofibers. An out-of-frame duplication variant in DMD, that is, c.(93+1_94-1)_(649+1_650-1)dup(p.?) resulting in duplication of exons 3-7 was inherited, but the muscle biopsy showed dystrophin mRNA with and without the duplication. Dystrophin quantification using mass spectrometry showed 25% normal dystrophin protein levels in the muscle biopsy from the stronger right side. Sex chromosome aneuploidy was ruled out. We conclude that the patient inherited the duplication variant, but early in development an inner cell mass underwent a somatic recombination event removing the duplication and restoring dystrophin expression. To our knowledge, this is the first report of a reversion leading to somatic mosaicism in DMD.
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Affiliation(s)
- Jaya Punetha
- Department of Integrative Systems Biology, The George Washington University School of Medicine, Washington, DC, USA.,Research Center for Genetic Medicine, Children's National Medical Center, Washington, DC, USA
| | - Simin Mansoor
- Department of Neurology, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Tulio E Bertorini
- Department of Neurology, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Akanchha Kesari
- Research Center for Genetic Medicine, Children's National Medical Center, Washington, DC, USA
| | - Kristy J Brown
- Research Center for Genetic Medicine, Children's National Medical Center, Washington, DC, USA
| | - Eric P Hoffman
- Department of Integrative Systems Biology, The George Washington University School of Medicine, Washington, DC, USA.,Research Center for Genetic Medicine, Children's National Medical Center, Washington, DC, USA
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16
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Val S, Burgett K, Brown KJ, Preciado D. SuperSILAC Quantitative Proteome Profiling of Murine Middle Ear Epithelial Cell Remodeling with NTHi. PLoS One 2016; 11:e0148612. [PMID: 26859300 PMCID: PMC4747582 DOI: 10.1371/journal.pone.0148612] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [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: 05/20/2015] [Accepted: 01/20/2016] [Indexed: 12/12/2022] Open
Abstract
Background Chronic Otitis Media with effusion (COME) develops after sustained inflammation and is characterized by secretory middle ear epithelial metaplasia and effusion, most frequently mucoid. Non-typeable Haemophilus influenzae (NTHi), the most common acute Otitis Media (OM) pathogen, is postulated to promote middle ear epithelial remodeling in the progression of OM from acute to chronic. The goals of this study were to examine histopathological and quantitative proteomic epithelial effects of NTHi challenge in a murine middle ear epithelial cell line. Methods NTHi lysates were generated and used to stimulate murine epithelial cells (mMEEC) cultured at air-liquid interface over 48 hours– 1 week. Conditional quantitative Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC) of cell lysates was performed to interrogate the global protein production in the cells, using the SuperSILAC technique. Histology of the epithelium over time was done to measure bacterial dependent remodeling. Results Mass spectrometry analysis identified 2,565 proteins across samples, of which 74 exhibited differential enrichment or depletion in cell lysates (+/-2.0 fold-change; p value<0.05). The key molecular functions regulated by NTHi lysates exposure were related to cell proliferation, death, migration, adhesion and inflammation. Finally, chronic exposure induced significant epithelial thickening of cells grown at air liquid interface. Conclusions NTHi lysates drive pathways responsible of cell remodeling in murine middle ear epithelium which likely contributes to observed epithelial hyperplasia in vitro. Further elucidation of these mediators will be critical in understanding the progression of OM from acute to chronic at the molecular level.
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Affiliation(s)
- Stéphanie Val
- Sheikh Zayed Center for Pediatric Surgical Innovation, Children’s National Health System, Washington, DC, United States of America
| | - Katelyn Burgett
- Sheikh Zayed Center for Pediatric Surgical Innovation, Children’s National Health System, Washington, DC, United States of America
| | - Kristy J. Brown
- Center for Genetic Medicine Research, Children’s National Health System, Washington, DC, United States of America
| | - Diego Preciado
- Sheikh Zayed Center for Pediatric Surgical Innovation, Children’s National Health System, Washington, DC, United States of America
- Division of Pediatric Otolaryngology, Children’s National Health System, Washington, DC, United States of America
- * E-mail:
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17
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Vila MC, Klimek MB, Novak JS, Rayavarapu S, Uaesoontrachoon K, Boehler JF, Fiorillo AA, Hogarth MW, Zhang A, Shaughnessy C, Gordish-Dressman H, Burki U, Straub V, Lu QL, Partridge TA, Brown KJ, Hathout Y, van den Anker J, Hoffman EP, Nagaraju K. Elusive sources of variability of dystrophin rescue by exon skipping. Skelet Muscle 2015; 5:44. [PMID: 26634117 PMCID: PMC4667482 DOI: 10.1186/s13395-015-0070-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [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: 10/16/2015] [Accepted: 11/24/2015] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Systemic delivery of anti-sense oligonucleotides to Duchenne muscular dystrophy (DMD) patients to induce de novo dystrophin protein expression in muscle (exon skipping) is a promising therapy. Treatment with Phosphorodiamidate morpholino oligomers (PMO) lead to shorter de novo dystrophin protein in both animal models and DMD boys who otherwise lack dystrophin; however, restoration of dystrophin has been observed to be highly variable. Understanding the factors causing highly variable induction of dystrophin expression in pre-clinical models would likely lead to more effective means of exon skipping in both pre-clinical studies and human clinical trials. METHODS In the present study, we investigated possible factors that might lead to the variable success of exon skipping using morpholino drugs in the mdx mouse model. We tested whether specific muscle groups or fiber types showed better success than others and also correlated residual PMO concentration in muscle with the amount of de novo dystrophin protein 1 month after a single high-dose morpholino injection (800 mg/kg). We compared the results from six muscle groups using three different methods of dystrophin quantification: immunostaining, immunoblotting, and mass spectrometry assays. RESULTS The triceps muscle showed the greatest degree of rescue (average 38±28 % by immunostaining). All three dystrophin detection methods were generally concordant for all muscles. We show that dystrophin rescue occurs in a sporadic patchy pattern with high geographic variability across muscle sections. We did not find a correlation between residual morpholino drug in muscle tissue and the degree of dystrophin expression. CONCLUSIONS While we found some evidence of muscle group enhancement and successful rescue, our data also suggest that other yet-undefined factors may underlie the observed variability in the success of exon skipping. Our study highlights the challenges associated with quantifying dystrophin in clinical trials where a single small muscle biopsy is taken from a DMD patient.
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Affiliation(s)
- Maria Candida Vila
- Research Center for Genetic Medicine, Children's National Health System, 111 Michigan Avenue N.W., Washington, DC, 20010 USA.,Institute of Biomedical Sciences, The George Washington University, Washington, DC, USA
| | - Margaret Benny Klimek
- Research Center for Genetic Medicine, Children's National Health System, 111 Michigan Avenue N.W., Washington, DC, 20010 USA
| | - James S Novak
- Research Center for Genetic Medicine, Children's National Health System, 111 Michigan Avenue N.W., Washington, DC, 20010 USA
| | - Sree Rayavarapu
- Research Center for Genetic Medicine, Children's National Health System, 111 Michigan Avenue N.W., Washington, DC, 20010 USA
| | - Kitipong Uaesoontrachoon
- Research Center for Genetic Medicine, Children's National Health System, 111 Michigan Avenue N.W., Washington, DC, 20010 USA
| | - Jessica F Boehler
- Research Center for Genetic Medicine, Children's National Health System, 111 Michigan Avenue N.W., Washington, DC, 20010 USA.,Institute of Biomedical Sciences, The George Washington University, Washington, DC, USA
| | - Alyson A Fiorillo
- Research Center for Genetic Medicine, Children's National Health System, 111 Michigan Avenue N.W., Washington, DC, 20010 USA
| | - Marshall W Hogarth
- Research Center for Genetic Medicine, Children's National Health System, 111 Michigan Avenue N.W., Washington, DC, 20010 USA
| | - Aiping Zhang
- Research Center for Genetic Medicine, Children's National Health System, 111 Michigan Avenue N.W., Washington, DC, 20010 USA
| | - Conner Shaughnessy
- Research Center for Genetic Medicine, Children's National Health System, 111 Michigan Avenue N.W., Washington, DC, 20010 USA
| | - Heather Gordish-Dressman
- Research Center for Genetic Medicine, Children's National Health System, 111 Michigan Avenue N.W., Washington, DC, 20010 USA.,Institute of Biomedical Sciences, The George Washington University, Washington, DC, USA
| | - Umar Burki
- The John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases at Newcastle, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Volker Straub
- The John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases at Newcastle, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Qi Long Lu
- McColl-Lockwood Laboratory for Muscular Dystrophy Research, Neuromuscular/ALS Center, Department of Neurology, Carolinas Medical Center, Charlotte, NC USA
| | - Terence A Partridge
- Research Center for Genetic Medicine, Children's National Health System, 111 Michigan Avenue N.W., Washington, DC, 20010 USA.,Institute of Biomedical Sciences, The George Washington University, Washington, DC, USA
| | - Kristy J Brown
- Research Center for Genetic Medicine, Children's National Health System, 111 Michigan Avenue N.W., Washington, DC, 20010 USA.,Institute of Biomedical Sciences, The George Washington University, Washington, DC, USA
| | - Yetrib Hathout
- Research Center for Genetic Medicine, Children's National Health System, 111 Michigan Avenue N.W., Washington, DC, 20010 USA.,Institute of Biomedical Sciences, The George Washington University, Washington, DC, USA
| | - John van den Anker
- Research Center for Genetic Medicine, Children's National Health System, 111 Michigan Avenue N.W., Washington, DC, 20010 USA.,Center for Translational Science, Children's National Health System, Washington, DC, USA
| | - Eric P Hoffman
- Research Center for Genetic Medicine, Children's National Health System, 111 Michigan Avenue N.W., Washington, DC, 20010 USA.,Institute of Biomedical Sciences, The George Washington University, Washington, DC, USA
| | - Kanneboyina Nagaraju
- Research Center for Genetic Medicine, Children's National Health System, 111 Michigan Avenue N.W., Washington, DC, 20010 USA.,Institute of Biomedical Sciences, The George Washington University, Washington, DC, USA
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18
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Sherman LS, Schrankel CS, Brown KJ, Smith LC. Extraordinary Diversity of Immune Response Proteins among Sea Urchins: Nickel-Isolated Sp185/333 Proteins Show Broad Variations in Size and Charge. PLoS One 2015; 10:e0138892. [PMID: 26406912 PMCID: PMC4583492 DOI: 10.1371/journal.pone.0138892] [Citation(s) in RCA: 19] [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] [Received: 06/24/2015] [Accepted: 09/04/2015] [Indexed: 11/18/2022] Open
Abstract
Effective protection against pathogens requires the host to produce a wide range of immune effector proteins. The Sp185/333 gene family, which is expressed by the California purple sea urchin Strongylocentrotus purpuratus in response to bacterial infection, encodes a highly diverse repertoire of anti-pathogen proteins. A subset of these proteins can be isolated by affinity to metal ions based on multiple histidines, resulting in one to four bands of unique molecular weight on standard Western blots, which vary depending on the individual sea urchin. Two dimensional gel electrophoresis (2DE) of nickel-isolated protein samples followed by Western blot was employed to detect nickel-isolated Sp185/333 (Ni-Sp185/333) proteins and to evaluate protein diversity in animals before and after immune challenge with marine bacteria. Ni-Sp185/333 proteins of the same molecular weight on standard Western blots appear as a broad complex of variants that differ in pI on 2DE Western blots. The Ni-Sp185/333 protein repertoire is variable among animals, and shows a variety of changes among individual sea urchins in response to immune challenges with both the same and different species of bacteria. The extraordinary diversity of the Ni-Sp185/333 proteins may provide significant anti-pathogen capabilities for sea urchins that survive solely on innate immunity.
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Affiliation(s)
- Lauren S Sherman
- Department of Biological Sciences, George Washington University, Washington DC, United States of America
| | - Catherine S Schrankel
- Department of Biological Sciences, George Washington University, Washington DC, United States of America
| | - Kristy J Brown
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC, United States of America
| | - L Courtney Smith
- Department of Biological Sciences, George Washington University, Washington DC, United States of America
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19
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Fiorillo AA, Heier CR, Novak JS, Tully CB, Brown KJ, Uaesoontrachoon K, Vila MC, Ngheim PP, Bello L, Kornegay JN, Angelini C, Partridge TA, Nagaraju K, Hoffman EP. TNF-α-Induced microRNAs Control Dystrophin Expression in Becker Muscular Dystrophy. Cell Rep 2015; 12:1678-90. [PMID: 26321630 DOI: 10.1016/j.celrep.2015.07.066] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [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] [Received: 04/07/2015] [Revised: 06/28/2015] [Accepted: 07/29/2015] [Indexed: 12/22/2022] Open
Abstract
The amount and distribution of dystrophin protein in myofibers and muscle is highly variable in Becker muscular dystrophy and in exon-skipping trials for Duchenne muscular dystrophy. Here, we investigate a molecular basis for this variability. In muscle from Becker patients sharing the same exon 45-47 in-frame deletion, dystrophin levels negatively correlate with microRNAs predicted to target dystrophin. Seven microRNAs inhibit dystrophin expression in vitro, and three are validated in vivo (miR-146b/miR-374a/miR-31). microRNAs are expressed in dystrophic myofibers and increase with age and disease severity. In exon-skipping-treated mdx mice, microRNAs are significantly higher in muscles with low dystrophin rescue. TNF-α increases microRNA levels in vitro whereas NFκB inhibition blocks this in vitro and in vivo. Collectively, these data show that microRNAs contribute to variable dystrophin levels in muscular dystrophy. Our findings suggest a model where chronic inflammation in distinct microenvironments induces pathological microRNAs, initiating a self-sustaining feedback loop that exacerbates disease progression.
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Affiliation(s)
- Alyson A Fiorillo
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC 20010, USA
| | - Christopher R Heier
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC 20010, USA
| | - James S Novak
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC 20010, USA
| | - Christopher B Tully
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC 20010, USA
| | - Kristy J Brown
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC 20010, USA; Department of Integrative Systems Biology, George Washington University School of Medicine and Health Sciences, Washington, DC 20010, USA
| | - Kitipong Uaesoontrachoon
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC 20010, USA
| | - Maria C Vila
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC 20010, USA
| | - Peter P Ngheim
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC 20010, USA
| | - Luca Bello
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC 20010, USA; Fondazione Ospedale S. Camillo, IRCCS, Lido Venice 30126, Italy
| | - Joe N Kornegay
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77845, USA
| | | | - Terence A Partridge
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC 20010, USA; Department of Integrative Systems Biology, George Washington University School of Medicine and Health Sciences, Washington, DC 20010, USA
| | - Kanneboyina Nagaraju
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC 20010, USA; Department of Integrative Systems Biology, George Washington University School of Medicine and Health Sciences, Washington, DC 20010, USA
| | - Eric P Hoffman
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC 20010, USA; Department of Integrative Systems Biology, George Washington University School of Medicine and Health Sciences, Washington, DC 20010, USA.
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Peters-Hall JR, Brown KJ, Pillai DK, Tomney A, Garvin LM, Wu X, Rose MC. Quantitative proteomics reveals an altered cystic fibrosis in vitro bronchial epithelial secretome. Am J Respir Cell Mol Biol 2015; 53:22-32. [PMID: 25692303 PMCID: PMC4566109 DOI: 10.1165/rcmb.2014-0256rc] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [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] [Received: 07/03/2014] [Accepted: 02/05/2015] [Indexed: 12/25/2022] Open
Abstract
Alterations in epithelial secretions and mucociliary clearance contribute to chronic bacterial infection in cystic fibrosis (CF) lung disease, but whether CF lungs are unchanged in the absence of infection remains controversial. A proteomic comparison of airway secretions from subjects with CF and control subjects shows alterations in key biological processes, including immune response and proteolytic activity, but it is unclear if these are due to mutant CF transmembrane conductance regulator (CFTR) and/or chronic infection. We hypothesized that the CF lung apical secretome is altered under constitutive conditions in the absence of inflammatory cells and pathogens. To test this, we performed quantitative proteomics of in vitro apical secretions from air-liquid interface cultures of three life-extended CF (ΔF508/ΔF508) and three non-CF human bronchial epithelial cells after labeling of CF cells by stable isotope labeling with amino acids in cell culture. Mass spectrometry analysis identified and quantitated 666 proteins across samples, of which 70 exhibited differential enrichment or depletion in CF secretions (±1.5-fold change; P < 0.05). The key molecular functions were innate immunity (24%), cytoskeleton/extracellular matrix organization (24%), and protease/antiprotease activity (17%). Oxidative proteins and classical complement pathway proteins that are altered in CF secretions in vivo were not altered in vitro. Specific differentially increased proteins-MUC5AC and MUC5B mucins, fibronectin, and matrix metalloproteinase-9-were validated by antibody-based assays. Overall, the in vitro CF secretome data are indicative of a constitutive airway epithelium with altered innate immunity, suggesting that downstream consequences of mutant CFTR set the stage for chronic inflammation and infection in CF airways.
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Affiliation(s)
| | - Kristy J. Brown
- Departments of Integrative Systems Biology and
- Pediatrics, George Washington University School of Medicine, Washington, DC; and
- Research Center for Genetic Medicine and
| | - Dinesh K. Pillai
- Departments of Integrative Systems Biology and
- Pediatrics, George Washington University School of Medicine, Washington, DC; and
- Research Center for Genetic Medicine and
- Division of Pulmonary and Sleep Medicine, Children's National, Washington, DC
| | | | - Lindsay M. Garvin
- Departments of Integrative Systems Biology and
- Research Center for Genetic Medicine and
| | - Xiaofang Wu
- Departments of Integrative Systems Biology and
- Pediatrics, George Washington University School of Medicine, Washington, DC; and
- Research Center for Genetic Medicine and
| | - Mary C. Rose
- Departments of Integrative Systems Biology and
- Pediatrics, George Washington University School of Medicine, Washington, DC; and
- Research Center for Genetic Medicine and
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21
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Zhang A, Uaesoontrachoon K, Shaughnessy C, Das JR, Rayavarapu S, Brown KJ, Ray PE, Nagaraju K, van den Anker JN, Hoffman EP, Hathout Y. The use of urinary and kidney SILAM proteomics to monitor kidney response to high dose morpholino oligonucleotides in the mdx mouse. Toxicol Rep 2015. [PMID: 26213685 PMCID: PMC4512206 DOI: 10.1016/j.toxrep.2015.05.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [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] [Indexed: 12/20/2022] Open
Abstract
Phosphorodiamidate morpholino oligonucleotides (PMO) are used as a promising exon-skipping gene therapy for Duchenne Muscular Dystrophy (DMD). One potential complication of high dose PMO therapy is its transient accumulation in the kidneys. Therefore new urinary biomarkers are needed to monitor this treatment. Here, we carried out a pilot proteomic profiling study using stable isotope labeling in mammals (SILAM) strategy to identify new biomarkers to monitor the effect of PMO on the kidneys of the dystrophin deficient mouse model for DMD (mdx-23). We first assessed the baseline renal status of the mdx-23 mouse compared to the wild type (C57BL10) mouse, and then followed the renal outcome of mdx-23 mouse treated with a single high dose intravenous PMO injection (800 mg/kg). Surprisingly, untreated mdx-23 mice showed evidence of renal injury at baseline, which was manifested by albuminuria, increased urine output, and changes in established urinary biomarker of acute kidney injury (AKI). The PMO treatment induced further transient renal injury, which peaked at 7 days, and returned to almost the baseline status at 30 days post-treatment. In the kidney, the SILAM approach followed by western blot validation identified changes in Meprin A subunit alpha at day 2, then returned to normal levels at day 7 and 30 after PMO injection. In the urine, SILAM approach identified an increase in Clusterin and γ-glutamyl transpeptidase 1 as potential candidates to monitor the transient renal accumulation of PMO. These results, which were confirmed by Western blots or ELISA, demonstrate the value of the SILAM approach to identify new candidate biomarkers of renal injury in mdx-23 mice treated with high dose PMO. Chemical compounds studied in this article: Phosphorodiamidate morpholino (PubChem CID: 22140692); isoflurane (PubChem CID: 3763); formic acid (PubChem CID: 284); acetonitrile (PubChem CID: 6342); acetone (PubChem CID: 180); methanol (PubChem CID: 887).
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Affiliation(s)
- Aiping Zhang
- The Centers for Genetic Medicine Research and Translational Science, Children's Research Institute, Children's National Medical Center, 111 Michigan Avenue, NW, Washington, DC 20010, USA
| | - Kitipong Uaesoontrachoon
- The Centers for Genetic Medicine Research and Translational Science, Children's Research Institute, Children's National Medical Center, 111 Michigan Avenue, NW, Washington, DC 20010, USA
| | - Conner Shaughnessy
- The Centers for Genetic Medicine Research and Translational Science, Children's Research Institute, Children's National Medical Center, 111 Michigan Avenue, NW, Washington, DC 20010, USA
| | - Jharna R Das
- The Centers for Genetic Medicine Research and Translational Science, Children's Research Institute, Children's National Medical Center, 111 Michigan Avenue, NW, Washington, DC 20010, USA
| | - Sree Rayavarapu
- The Centers for Genetic Medicine Research and Translational Science, Children's Research Institute, Children's National Medical Center, 111 Michigan Avenue, NW, Washington, DC 20010, USA
| | - Kristy J Brown
- The Centers for Genetic Medicine Research and Translational Science, Children's Research Institute, Children's National Medical Center, 111 Michigan Avenue, NW, Washington, DC 20010, USA
| | - Patricio E Ray
- The Centers for Genetic Medicine Research and Translational Science, Children's Research Institute, Children's National Medical Center, 111 Michigan Avenue, NW, Washington, DC 20010, USA
| | - Kanneboyina Nagaraju
- The Centers for Genetic Medicine Research and Translational Science, Children's Research Institute, Children's National Medical Center, 111 Michigan Avenue, NW, Washington, DC 20010, USA
| | - John N van den Anker
- The Centers for Genetic Medicine Research and Translational Science, Children's Research Institute, Children's National Medical Center, 111 Michigan Avenue, NW, Washington, DC 20010, USA
| | - Eric P Hoffman
- The Centers for Genetic Medicine Research and Translational Science, Children's Research Institute, Children's National Medical Center, 111 Michigan Avenue, NW, Washington, DC 20010, USA
| | - Yetrib Hathout
- The Centers for Genetic Medicine Research and Translational Science, Children's Research Institute, Children's National Medical Center, 111 Michigan Avenue, NW, Washington, DC 20010, USA
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22
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Scheffer LL, Sreetama SC, Sharma N, Medikayala S, Brown KJ, Defour A, Jaiswal JK. Mechanism of Ca²⁺-triggered ESCRT assembly and regulation of cell membrane repair. Nat Commun 2014; 5:5646. [PMID: 25534348 PMCID: PMC4333728 DOI: 10.1038/ncomms6646] [Citation(s) in RCA: 223] [Impact Index Per Article: 22.3] [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] [Received: 04/02/2014] [Accepted: 10/22/2014] [Indexed: 12/11/2022] Open
Abstract
In muscle and other mechanically active tissue, cell membranes are constantly injured, and their repair depends on the injury-induced increase in cytosolic calcium. Here, we show that injury-triggered Ca(2+) increase results in assembly of ESCRT III and accessory proteins at the site of repair. This process is initiated by the calcium-binding protein-apoptosis-linked gene (ALG)-2. ALG-2 facilitates accumulation of ALG-2-interacting protein X (ALIX), ESCRT III and Vps4 complex at the injured cell membrane, which in turn results in cleavage and shedding of the damaged part of the cell membrane. Lack of ALG-2, ALIX or Vps4B each prevents shedding, and repair of the injured cell membrane. These results demonstrate Ca(2+)-dependent accumulation of ESCRT III-Vps4 complex following large focal injury to the cell membrane and identify the role of ALG-2 as the initiator of sequential ESCRT III-Vps4 complex assembly that facilitates scission and repair of the injured cell membrane.
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Affiliation(s)
- Luana L Scheffer
- Children's National Medical Center, Center for Genetic Medicine Research, 111 Michigan Avenue, NW, Washington DC 20010-2970, USA
| | - Sen Chandra Sreetama
- Children's National Medical Center, Center for Genetic Medicine Research, 111 Michigan Avenue, NW, Washington DC 20010-2970, USA
| | - Nimisha Sharma
- Children's National Medical Center, Center for Genetic Medicine Research, 111 Michigan Avenue, NW, Washington DC 20010-2970, USA
| | - Sushma Medikayala
- Children's National Medical Center, Center for Genetic Medicine Research, 111 Michigan Avenue, NW, Washington DC 20010-2970, USA
| | - Kristy J Brown
- 1] Children's National Medical Center, Center for Genetic Medicine Research, 111 Michigan Avenue, NW, Washington DC 20010-2970, USA [2] Department of Integrative Systems Biology, George Washington University School of Medicine and Health Sciences, Washington DC, USA
| | - Aurelia Defour
- Children's National Medical Center, Center for Genetic Medicine Research, 111 Michigan Avenue, NW, Washington DC 20010-2970, USA
| | - Jyoti K Jaiswal
- 1] Children's National Medical Center, Center for Genetic Medicine Research, 111 Michigan Avenue, NW, Washington DC 20010-2970, USA [2] Department of Integrative Systems Biology, George Washington University School of Medicine and Health Sciences, Washington DC, USA
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23
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Hathout Y, Marathi RL, Rayavarapu S, Zhang A, Brown KJ, Seol H, Gordish-Dressman H, Cirak S, Bello L, Nagaraju K, Partridge T, Hoffman EP, Takeda S, Mah JK, Henricson E, McDonald C. Discovery of serum protein biomarkers in the mdx mouse model and cross-species comparison to Duchenne muscular dystrophy patients. Hum Mol Genet 2014; 23:6458-69. [PMID: 25027324 DOI: 10.1093/hmg/ddu366] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
It is expected that serum protein biomarkers in Duchenne muscular dystrophy (DMD) will reflect disease pathogenesis, progression and aid future therapy developments. Here, we describe use of quantitative in vivo stable isotope labeling in mammals to accurately compare serum proteomes of wild-type and dystrophin-deficient mdx mice. Biomarkers identified in serum from two independent dystrophin-deficient mouse models (mdx-Δ52 and mdx-23) were concordant with those identified in sera samples of DMD patients. Of the 355 mouse sera proteins, 23 were significantly elevated and 4 significantly lower in mdx relative to wild-type mice (P-value < 0.001). Elevated proteins were mostly of muscle origin: including myofibrillar proteins (titin, myosin light chain 1/3, myomesin 3 and filamin-C), glycolytic enzymes (aldolase, phosphoglycerate mutase 2, beta enolase and glycogen phosphorylase), transport proteins (fatty acid-binding protein, myoglobin and somatic cytochrome-C) and others (creatine kinase M, malate dehydrogenase cytosolic, fibrinogen and parvalbumin). Decreased proteins, mostly of extracellular origin, included adiponectin, lumican, plasminogen and leukemia inhibitory factor receptor. Analysis of sera from 1 week to 7 months old mdx mice revealed age-dependent changes in the level of these biomarkers with most biomarkers acutely elevated at 3 weeks of age. Serum analysis of DMD patients, with ages ranging from 4 to 15 years old, confirmed elevation of 20 of the murine biomarkers in DMD, with similar age-related changes. This study provides a panel of biomarkers that reflect muscle activity and pathogenesis and should prove valuable tool to complement natural history studies and to monitor treatment efficacy in future clinical trials.
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Affiliation(s)
- Yetrib Hathout
- Research Center for Genetic Medicine, Children's National Medical Center, Washington, DC 20010, USA,
| | - Ramya L Marathi
- Research Center for Genetic Medicine, Children's National Medical Center, Washington, DC 20010, USA
| | - Sree Rayavarapu
- Research Center for Genetic Medicine, Children's National Medical Center, Washington, DC 20010, USA
| | - Aiping Zhang
- Research Center for Genetic Medicine, Children's National Medical Center, Washington, DC 20010, USA
| | - Kristy J Brown
- Research Center for Genetic Medicine, Children's National Medical Center, Washington, DC 20010, USA
| | - Haeri Seol
- Research Center for Genetic Medicine, Children's National Medical Center, Washington, DC 20010, USA
| | - Heather Gordish-Dressman
- Research Center for Genetic Medicine, Children's National Medical Center, Washington, DC 20010, USA
| | - Sebahattin Cirak
- Research Center for Genetic Medicine, Children's National Medical Center, Washington, DC 20010, USA
| | - Luca Bello
- Research Center for Genetic Medicine, Children's National Medical Center, Washington, DC 20010, USA
| | - Kanneboyina Nagaraju
- Research Center for Genetic Medicine, Children's National Medical Center, Washington, DC 20010, USA
| | - Terry Partridge
- Research Center for Genetic Medicine, Children's National Medical Center, Washington, DC 20010, USA
| | - Eric P Hoffman
- Research Center for Genetic Medicine, Children's National Medical Center, Washington, DC 20010, USA
| | - Shin'ichi Takeda
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Ogawa-higashi, Kodaira Tokyo 187-0031, Japan
| | - Jean K Mah
- Department of Pediatrics, Alberta Children's Hospital, Calgary, AB, Canada T3B 6A8 and
| | - Erik Henricson
- Department of Physical Medicine and Rehabilitation, University of California, Davis School of Medicine, Davis, CA 95618, USA
| | - Craig McDonald
- Department of Physical Medicine and Rehabilitation, University of California, Davis School of Medicine, Davis, CA 95618, USA
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24
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Nghiem PP, Hoffman EP, Mittal P, Brown KJ, Schatzberg SJ, Ghimbovschi S, Wang Z, Kornegay JN. Sparing of the dystrophin-deficient cranial sartorius muscle is associated with classical and novel hypertrophy pathways in GRMD dogs. Am J Pathol 2014; 183:1411-24. [PMID: 24160322 DOI: 10.1016/j.ajpath.2013.07.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Revised: 07/19/2013] [Accepted: 07/22/2013] [Indexed: 12/28/2022]
Abstract
Both Duchenne and golden retriever muscular dystrophy (GRMD) are caused by dystrophin deficiency. The Duchenne muscular dystrophy sartorius muscle and orthologous GRMD cranial sartorius (CS) are relatively spared/hypertrophied. We completed hierarchical clustering studies to define molecular mechanisms contributing to this differential involvement and their role in the GRMD phenotype. GRMD dogs with larger CS muscles had more severe deficits, suggesting that selective hypertrophy could be detrimental. Serial biopsies from the hypertrophied CS and other atrophied muscles were studied in a subset of these dogs. Myostatin showed an age-dependent decrease and an inverse correlation with the degree of GRMD CS hypertrophy. Regulators of myostatin at the protein (AKT1) and miRNA (miR-539 and miR-208b targeting myostatin mRNA) levels were altered in GRMD CS, consistent with down-regulation of myostatin signaling, CS hypertrophy, and functional rescue of this muscle. mRNA and proteomic profiling was used to identify additional candidate genes associated with CS hypertrophy. The top-ranked network included α-dystroglycan and like-acetylglucosaminyltransferase. Proteomics demonstrated increases in myotrophin and spectrin that could promote hypertrophy and cytoskeletal stability, respectively. Our results suggest that multiple pathways, including decreased myostatin and up-regulated miRNAs, α-dystroglycan/like-acetylglucosaminyltransferase, spectrin, and myotrophin, contribute to hypertrophy and functional sparing of the CS. These data also underscore the muscle-specific responses to dystrophin deficiency and the potential deleterious effects of differential muscle involvement.
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Affiliation(s)
- Peter P Nghiem
- Department of Integrative Systems Biology, George Washington University School of Medicine, Washington, District of Columbia; Research Center for Genetic Medicine, Children's National Medical Center, Washington, District of Columbia
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25
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Cuadrado E, Vanderver A, Brown KJ, Sandza A, Takanohashi A, Jansen MH, Anink J, Herron B, Orcesi S, Olivieri I, Rice GI, Aronica E, Lebon P, Crow YJ, Hol EM, Kuijpers TW. Aicardi–Goutières syndrome harbours abundant systemic and brain-reactive autoantibodies. Ann Rheum Dis 2014; 74:1931-9. [DOI: 10.1136/annrheumdis-2014-205396] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 05/22/2014] [Indexed: 01/02/2023]
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26
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Pillai DK, Sankoorikal BJV, Johnson E, Seneviratne AN, Zurko J, Brown KJ, Hathout Y, Rose MC. Directional secretomes reflect polarity-specific functions in an in vitro model of human bronchial epithelium. Am J Respir Cell Mol Biol 2014; 50:292-300. [PMID: 24010916 DOI: 10.1165/rcmb.2013-0188oc] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The polarity of the conducting airway epithelium is responsible for its directional secretion. This is an essential characteristic of lung integrity and function that dictates interactions between the external environment (apical) and subepithelial structures (basolateral). Defining the directional secretomes in the in vitro human bronchial epithelial (HBE) differentiated model could bring valuable insights into lung biology and pulmonary diseases. Normal primary HBE cells (n = 3) were differentiated into respiratory tract epithelium. Apical and basolateral secretions (24 h) were processed for proteome profiling and pathway analysis. A total of 243 proteins were identified in secretions from all HBE cultures combined. Of these, 51% were classified as secreted proteins, including true secreted proteins (36%) and exosomal proteins (15%). Close examination revealed consistent secretion of 69 apical proteins and 13 basolateral proteins and differential secretion of 25 proteins across all donors. Expression of Annexin A4 in apical secretions and Desmoglein-2 in basolateral secretions was validated using Western blot or ELISA in triplicate independent experiments. To the best of our knowledge, this is the first study defining apical and basolateral secretomes in the in vitro differentiated HBE model. The data demonstrate that epithelial polarity directs protein secretion with different patterns of biological processes to the apical and basolateral surfaces that are consistent with normal bronchial epithelium homeostatic functions. Applying this in vitro directional secretome model to lung diseases may elucidate their molecular pathophysiology and help define potential therapeutic targets.
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27
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Thaivalappil S, Bauman N, Saieg A, Movius E, Brown KJ, Preciado D. Propranolol-mediated attenuation of MMP-9 excretion in infants with hemangiomas. JAMA Otolaryngol Head Neck Surg 2014; 139:1026-31. [PMID: 24135743 DOI: 10.1001/jamaoto.2013.4773] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
IMPORTANCE Infantile hemangiomas (IHs) vary substantially in localization and extent of tissue involvement, but IH biological progression is remarkably unique and predictable. Propranolol is an effective treatment for symptomatic IH, but its mechanism of action remains unknown and understudied. OBJECTIVE To compare excreted proteins in infants with IH being treated with propranolol vs prednisolone. DESIGN, SETTING, AND PARTICIPANTS Exploratory urine proteomics profiling of patients with IH from July 2010 to September 2012 at a tertiary pediatric hospital. Participants were infants with IH treated at our institution who were participating in a blinded, randomized trial comparing prednisolone vs propranolol. They ranged in age from 14 days to 15 months at enrollment. Exclusion criteria included a history of diabetes mellitus, asthma, and/or cardiovascular disease including hypertension or hypotension. Urine samples were longitudinally collected from all participants. Specimens were desalted, concentrated, and gel fractionated, and the protein content was identified using liquid chromatography tandem mass spectrometry. Western blot analyses and enzyme-linked immunosorbent assays (ELISAs) were performed to validate mass spectrometry findings. INTERVENTION Treatment with propranolol or prednisolone administered starting before the age of 6 months. MAIN OUTCOMES AND MEASURES Proteins present in urine samples and change in urinary levels of proteins over time. RESULTS Samples were obtained from 3 patients treated with prednisolone, 3 patients treated with propranolol, and 5 untreated controls with IH. More than 1000 urinary proteins were identified by proteomics. Patients treated with propranolol demonstrated attenuation of excreted matrix metalloproteinase 9 (MMP-9) in urine over the proliferative phase of the condition compared with prednisolone-treated patients. These findings were validated with Western blot analysis and quantified with ELISA, which confirmed mean urinary MMP-9 levels in the first year of life to be significantly lower in propranolol-treated patients with IH compared with prednisolone-treated patients with IH (0.118 vs 0.501 ng/mL; P = .03) or with nontreated patients with IH (0.118 vs 3.69 ng/mL; P = .02). CONCLUSIONS AND RELEVANCE Propranolol treatment decreases urinary excretion of MMP-9 in patients with IH. Matrix metalloproteinase 9 may be a biomarker for IH propranolol responsiveness, and its signaling pathways may represent the molecular target of this drug.
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Affiliation(s)
- Silpa Thaivalappil
- Sheik Zayed Center for Pediatric Surgical Innovation, Children's National Medical Center, Washington, DC
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28
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Rayavarapu S, Coley W, Van der Meulen JH, Cakir E, Tappeta K, Kinder TB, Dillingham BC, Brown KJ, Hathout Y, Nagaraju K. Activation of the ubiquitin proteasome pathway in a mouse model of inflammatory myopathy: a potential therapeutic target. ACTA ACUST UNITED AC 2014; 65:3248-58. [PMID: 24022788 DOI: 10.1002/art.38180] [Citation(s) in RCA: 22] [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] [Received: 01/07/2013] [Accepted: 08/27/2013] [Indexed: 01/01/2023]
Abstract
OBJECTIVE Myositis is characterized by severe muscle weakness. We and others have previously shown that endoplasmic reticulum (ER) stress plays a role in the pathogenesis of myositis. The present study was undertaken to identify perturbed pathways and assess their contribution to muscle disease in a mouse myositis model. METHODS Stable isotope labeling with amino acids in cell culture (SILAC) was used to identify alterations in the skeletal muscle proteome of myositic mice in vivo. Differentially altered protein levels identified in the initial comparisons were validated using a liquid chromatography tandem mass spectrometry spike-in strategy and further confirmed by immunoblotting. In addition, we evaluated the effect of a proteasome inhibitor, bortezomib, on the disease phenotype, using well-standardized functional, histologic, and biochemical assessments. RESULTS With the SILAC technique we identified significant alterations in levels of proteins belonging to the ER stress response, ubiquitin proteasome pathway (UPP), oxidative phosphorylation, glycolysis, cytoskeleton, and muscle contractile apparatus categories. We validated the myositis-related changes in the UPP and demonstrated a significant increase in the ubiquitination of muscle proteins as well as a specific increase in ubiquitin carboxyl-terminal hydrolase isozyme L1 (UCHL-1) in myositis, but not in muscle affected by other dystrophies or normal muscle. Inhibition of the UPP with bortezomib significantly improved muscle function and also significantly reduced tumor necrosis factor α expression in the skeletal muscle of mice with myositis. CONCLUSION Our findings indicate that ER stress activates downstream UPPs and contributes to muscle degeneration and that UCHL-1 is a potential biomarker for disease progression. UPP inhibition offers a potential therapeutic strategy for myositis.
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Affiliation(s)
- Sree Rayavarapu
- Children's National Medical Center and George Washington University, Washington DC
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29
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Leymarie N, Griffin PJ, Jonscher K, Kolarich D, Orlando R, McComb M, Zaia J, Aguilan J, Alley WR, Altmann F, Ball LE, Basumallick L, Bazemore-Walker CR, Behnken H, Blank MA, Brown KJ, Bunz SC, Cairo CW, Cipollo JF, Daneshfar R, Desaire H, Drake RR, Go EP, Goldman R, Gruber C, Halim A, Hathout Y, Hensbergen PJ, Horn DM, Hurum D, Jabs W, Larson G, Ly M, Mann BF, Marx K, Mechref Y, Meyer B, Möginger U, Neusüβ C, Nilsson J, Novotny MV, Nyalwidhe JO, Packer NH, Pompach P, Reiz B, Resemann A, Rohrer JS, Ruthenbeck A, Sanda M, Schulz JM, Schweiger-Hufnagel U, Sihlbom C, Song E, Staples GO, Suckau D, Tang H, Thaysen-Andersen M, Viner RI, An Y, Valmu L, Wada Y, Watson M, Windwarder M, Whittal R, Wuhrer M, Zhu Y, Zou C. Interlaboratory study on differential analysis of protein glycosylation by mass spectrometry: the ABRF glycoprotein research multi-institutional study 2012. Mol Cell Proteomics 2013; 12:2935-51. [PMID: 23764502 PMCID: PMC3790302 DOI: 10.1074/mcp.m113.030643] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [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] [Received: 05/03/2013] [Revised: 06/11/2013] [Indexed: 11/06/2022] Open
Abstract
One of the principal goals of glycoprotein research is to correlate glycan structure and function. Such correlation is necessary in order for one to understand the mechanisms whereby glycoprotein structure elaborates the functions of myriad proteins. The accurate comparison of glycoforms and quantification of glycosites are essential steps in this direction. Mass spectrometry has emerged as a powerful analytical technique in the field of glycoprotein characterization. Its sensitivity, high dynamic range, and mass accuracy provide both quantitative and sequence/structural information. As part of the 2012 ABRF Glycoprotein Research Group study, we explored the use of mass spectrometry and ancillary methodologies to characterize the glycoforms of two sources of human prostate specific antigen (PSA). PSA is used as a tumor marker for prostate cancer, with increasing blood levels used to distinguish between normal and cancer states. The glycans on PSA are believed to be biantennary N-linked, and it has been observed that prostate cancer tissues and cell lines contain more antennae than their benign counterparts. Thus, the ability to quantify differences in glycosylation associated with cancer has the potential to positively impact the use of PSA as a biomarker. We studied standard peptide-based proteomics/glycomics methodologies, including LC-MS/MS for peptide/glycopeptide sequencing and label-free approaches for differential quantification. We performed an interlaboratory study to determine the ability of different laboratories to correctly characterize the differences between glycoforms from two different sources using mass spectrometry methods. We used clustering analysis and ancillary statistical data treatment on the data sets submitted by participating laboratories to obtain a consensus of the glycoforms and abundances. The results demonstrate the relative strengths and weaknesses of top-down glycoproteomics, bottom-up glycoproteomics, and glycomics methods.
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Affiliation(s)
- Nancy Leymarie
- From the ‡Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts 02118
| | - Paula J. Griffin
- §Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts 02118
| | - Karen Jonscher
- ¶Department of Anesthesiology University of Colorado, Aurora, Colorado 80045
| | - Daniel Kolarich
- ‖Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, 14476, Germany
| | - Ron Orlando
- **Complex Carbohydrates Research Center, University of Georgia, Athens, Georgia, 30602
| | - Mark McComb
- From the ‡Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts 02118
| | - Joseph Zaia
- From the ‡Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts 02118
| | - Jennifer Aguilan
- §§Laboratory for Macromolecular Analysis and Proteomics Facility, Albert Einstein College of Medicine, Bronx, New York 10461
| | - William R. Alley
- ¶¶Department of Chemistry, Indiana University, Bloomington, Indiana 47405
| | - Friederich Altmann
- ‖‖Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, A-1180, Austria
| | - Lauren E. Ball
- MUSC Proteomic Center, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Lipika Basumallick
- Applications Development, Dionex Products, Thermo Fisher Scientific, Sunnyvale, California 94085
| | | | - Henning Behnken
- Organic Chemistry, University of Hamburg, Hamburg, 20146, Germany
| | | | - Kristy J. Brown
- Center for Genetic Medicine, Children's National Medical Center, Washington, D.C. 20310
| | | | - Christopher W. Cairo
- Department of Chemistry, University of Alberta, Edmonton, T6G 2G2, Canada
- Alberta Glycomics Centre, University of Alberta, Edmonton, T6G 2G2, Canada
| | - John F. Cipollo
- Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland 20993
| | - Rambod Daneshfar
- Department of Chemistry, University of Alberta, Edmonton, T6G 2G2, Canada
- Alberta Glycomics Centre, University of Alberta, Edmonton, T6G 2G2, Canada
| | | | - Richard R. Drake
- MUSC Proteomic Center, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Eden P. Go
- University of Kansas, Lawrence, Kansas 66045
| | - Radoslav Goldman
- Department of Oncology, Georgetown University, Washington, D.C. 20007
| | - Clemens Gruber
- ‖‖Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, A-1180, Austria
| | - Adnan Halim
- Department of Clinical Chemistry and Transfusion Medicine, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, 41345, Sweden
| | - Yetrib Hathout
- Center for Genetic Medicine, Children's National Medical Center, Washington, D.C. 20310
| | - Paul J. Hensbergen
- Biomolecular Mass Spectrometry Unit, Leiden University Medical Center, Leiden, 233ZA, The Netherlands
| | - David M. Horn
- Thermo Fisher Scientific, San Jose, California 95134
| | - Deanna Hurum
- Applications Development, Dionex Products, Thermo Fisher Scientific, Sunnyvale, California 94085
| | | | - Göran Larson
- Department of Clinical Chemistry and Transfusion Medicine, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, 41345, Sweden
| | - Mellisa Ly
- Agilent Laboratories, Agilent Technologies, Santa Clara, California 95051
| | - Benjamin F. Mann
- ¶¶Department of Chemistry, Indiana University, Bloomington, Indiana 47405
| | | | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409
| | - Bernd Meyer
- Organic Chemistry, University of Hamburg, Hamburg, 20146, Germany
| | - Uwe Möginger
- ‖Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, 14476, Germany
| | | | - Jonas Nilsson
- Department of Clinical Chemistry and Transfusion Medicine, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, 41345, Sweden
| | - Milos V. Novotny
- ¶¶Department of Chemistry, Indiana University, Bloomington, Indiana 47405
| | - Julius O. Nyalwidhe
- Department of Microbiology and Molecular Cell Biology, Leroy T. Canoles Jr Cancer Research Center, Eastern Virginia Medical School, Norfolk, Virginia 23507
| | - Nicolle H. Packer
- Biomolecular Frontiers Research Centre, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Petr Pompach
- Department of Oncology, Georgetown University, Washington, D.C. 20007
| | - Bela Reiz
- Department of Chemistry, University of Alberta, Edmonton, T6G 2G2, Canada
| | | | - Jeffrey S. Rohrer
- Applications Development, Dionex Products, Thermo Fisher Scientific, Sunnyvale, California 94085
| | | | - Miloslav Sanda
- Department of Oncology, Georgetown University, Washington, D.C. 20007
| | - Jan Mirco Schulz
- Organic Chemistry, University of Hamburg, Hamburg, 20146, Germany
| | | | - Carina Sihlbom
- Proteomics Core Facility, Gothenburg University, Gothenburg, 413 90, Sweden
| | - Ehwang Song
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409
| | - Gregory O. Staples
- Agilent Laboratories, Agilent Technologies, Santa Clara, California 95051
| | | | - Haixu Tang
- School of informatics, Indiana University, Bloomington, Indiana 47405
| | - Morten Thaysen-Andersen
- Biomolecular Frontiers Research Centre, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Rosa I. Viner
- Thermo Fisher Scientific, San Jose, California 95134
| | - Yanming An
- Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland 20993
| | - Leena Valmu
- Finnish Red Cross Blood Service, Helsinki, 00310, Finland
| | - Yoshinao Wada
- Research Institute, Osaka Medical Center for Maternal and Child Health, Izumi, Osaka, 594–1101, Japan
| | - Megan Watson
- Department of Microbiology and Molecular Cell Biology, Leroy T. Canoles Jr Cancer Research Center, Eastern Virginia Medical School, Norfolk, Virginia 23507
| | - Markus Windwarder
- ‖‖Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, A-1180, Austria
| | - Randy Whittal
- Department of Chemistry, University of Alberta, Edmonton, T6G 2G2, Canada
| | - Manfred Wuhrer
- Biomolecular Mass Spectrometry Unit, Leiden University Medical Center, Leiden, 233ZA, The Netherlands
| | - Yiying Zhu
- Department of Chemistry, Brown University, Providence, Rhode Island 02912
| | - Chunxia Zou
- Department of Chemistry, University of Alberta, Edmonton, T6G 2G2, Canada
- Alberta Glycomics Centre, University of Alberta, Edmonton, T6G 2G2, Canada
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30
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Duguez S, Duddy W, Johnston H, Lainé J, Le Bihan MC, Brown KJ, Bigot A, Hathout Y, Butler-Browne G, Partridge T. Dystrophin deficiency leads to disturbance of LAMP1-vesicle-associated protein secretion. Cell Mol Life Sci 2013; 70:2159-74. [PMID: 23344255 PMCID: PMC11113779 DOI: 10.1007/s00018-012-1248-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [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] [Received: 07/31/2012] [Revised: 12/13/2012] [Accepted: 12/17/2012] [Indexed: 01/06/2023]
Abstract
Duchenne muscular dystrophy results from loss of the protein dystrophin, which links the intracellular cytoskeletal network with the extracellular matrix, but deficiency in this function does not fully explain the onset or progression of the disease. While some intracellular events involved in the degeneration of dystrophin-deficient muscle fibers have been well characterized, changes in their secretory profile are undescribed. To analyze the secretome profile of mdx myotubes independently of myonecrosis, we labeled the proteins of mdx and wild-type myotubes with stable isotope-labeled amino acids (SILAC), finding marked enrichment of vesicular markers in the mdx secretome. These included the lysosomal-associated membrane protein, LAMP1, that co-localized in vesicles with an over-secreted cytoskeletal protein, myosin light chain 1. These LAMP1/MLC1-3-positive vesicles accumulated in the cytosol of mdx myotubes and were secreted into the culture medium in a range of abnormal densities. Restitution of dystrophin expression, by exon skipping, to some 30 % of the control value, partially normalized the secretome profile and the excess LAMP1 accumulation. Together, our results suggest that a lack of dystrophin leads to a general dysregulation of vesicle trafficking. We hypothesize that disturbance of the export of proteins through vesicles occurs before, and then concurrently with, the myonecrotic cascade and contributes chronically to the pathophysiology of DMD, thereby presenting us with a range of new potential therapeutic targets.
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Affiliation(s)
- Stephanie Duguez
- Center for Genetic Medicine, Children’s Research Institute, Children’s National Medical Center, 111 Michigan Avenue, Washington, DC USA
- Institut de Myologie, UM76, Inserm U974, CNRS, UMR7215, Université Pierre et Marie Curie-Paris 6, Paris, 75013 France
| | - William Duddy
- Center for Genetic Medicine, Children’s Research Institute, Children’s National Medical Center, 111 Michigan Avenue, Washington, DC USA
- Institut de Myologie, UM76, Inserm U974, CNRS, UMR7215, Université Pierre et Marie Curie-Paris 6, Paris, 75013 France
| | - Helen Johnston
- Center for Genetic Medicine, Children’s Research Institute, Children’s National Medical Center, 111 Michigan Avenue, Washington, DC USA
| | - Jeanne Lainé
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
- Département de Physiologie, Université Pierre Et Marie Curie-Paris 06, Site Pitié-Salpêtrière, Paris, 75013 France
| | - Marie Catherine Le Bihan
- Institut de Myologie, UM76, Inserm U974, CNRS, UMR7215, Université Pierre et Marie Curie-Paris 6, Paris, 75013 France
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Kristy J. Brown
- Center for Genetic Medicine, Children’s Research Institute, Children’s National Medical Center, 111 Michigan Avenue, Washington, DC USA
| | - Anne Bigot
- Institut de Myologie, UM76, Inserm U974, CNRS, UMR7215, Université Pierre et Marie Curie-Paris 6, Paris, 75013 France
| | - Yetrib Hathout
- Center for Genetic Medicine, Children’s Research Institute, Children’s National Medical Center, 111 Michigan Avenue, Washington, DC USA
| | - Gillian Butler-Browne
- Institut de Myologie, UM76, Inserm U974, CNRS, UMR7215, Université Pierre et Marie Curie-Paris 6, Paris, 75013 France
| | - Terence Partridge
- Center for Genetic Medicine, Children’s Research Institute, Children’s National Medical Center, 111 Michigan Avenue, Washington, DC USA
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Brown KJ, Seol H, Pillai DK, Sankoorikal BJ, Formolo CA, Mac J, Edwards NJ, Rose MC, Hathout Y. The human secretome atlas initiative: implications in health and disease conditions. Biochim Biophys Acta 2013; 1834:2454-61. [PMID: 23603790 DOI: 10.1016/j.bbapap.2013.04.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 03/26/2013] [Accepted: 04/11/2013] [Indexed: 01/24/2023]
Abstract
Proteomic analysis of human body fluids is highly challenging, therefore many researchers are redirecting efforts toward secretome profiling. The goal is to define potential biomarkers and therapeutic targets in the secretome that can be traced back in accessible human body fluids. However, currently there is a lack of secretome profiles of normal human primary cells making it difficult to assess the biological meaning of current findings. In this study we sought to establish secretome profiles of human primary cells obtained from healthy donors with the goal of building a human secretome atlas. Such an atlas can be used as a reference for discovery of potential disease associated biomarkers and eventually novel therapeutic targets. As a preliminary study, secretome profiles were established for six different types of human primary cell cultures and checked for overlaps with the three major human body fluids including plasma, cerebrospinal fluid and urine. About 67% of the 1054 identified proteins in the secretome of these primary cells occurred in at least one body fluid. Furthermore, comparison of the secretome profiles of two human glioblastoma cell lines to this new human secretome atlas enabled unambiguous identification of potential brain tumor biomarkers. These biomarkers can be easily monitored in different body fluids using stable isotope labeled standard proteins. The long term goal of this study is to establish a comprehensive online human secretome atlas for future use as a reference for any disease related secretome study. This article is part of a Special Issue entitled: An Updated Secretome.
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Affiliation(s)
- Kristy J Brown
- Center for Genetic Medicine Research, Children's National Medical Center, Washington DC 20010, USA
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32
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Gutierrez JL, Many G, Panchapakesan K, Brown KJ, Hathout Y, Marathi R, Devaney J, Hoffman EP. Asymptomatic African Americans with high‐risk APOL1 genotypes have reduced urinary angiogenesis‐promoting cytokines. FASEB J 2013. [DOI: 10.1096/fasebj.27.1_supplement.lb474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Gina Many
- Center for Genetic Medicine ResearchChildren's National Medical CenterWashingtonDC
| | - Karuna Panchapakesan
- Center for Genetic Medicine ResearchChildren's National Medical CenterWashingtonDC
| | - Kristy J Brown
- Center for Genetic Medicine ResearchChildren's National Medical CenterWashingtonDC
| | - Yetrib Hathout
- Center for Genetic Medicine ResearchChildren's National Medical CenterWashingtonDC
| | - Ramya Marathi
- Center for Genetic Medicine ResearchChildren's National Medical CenterWashingtonDC
| | - Joseph Devaney
- Center for Genetic Medicine ResearchChildren's National Medical CenterWashingtonDC
| | - Eric P Hoffman
- Center for Genetic Medicine ResearchChildren's National Medical CenterWashingtonDC
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33
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Rayavarapu S, Coley W, Cakir E, Jahnke V, Takeda S, Aoki Y, Grodish-Dressman H, Jaiswal JK, Hoffman EP, Brown KJ, Hathout Y, Nagaraju K. Identification of disease specific pathways using in vivo SILAC proteomics in dystrophin deficient mdx mouse. Mol Cell Proteomics 2013; 12:1061-73. [PMID: 23297347 DOI: 10.1074/mcp.m112.023127] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is an X-linked neuromuscular disorder caused by a mutation in the dystrophin gene. DMD is characterized by progressive weakness of skeletal, cardiac, and respiratory muscles. The molecular mechanisms underlying dystrophy-associated muscle weakness and damage are not well understood. Quantitative proteomics techniques could help to identify disease-specific pathways. Recent advances in the in vivo labeling strategies such as stable isotope labeling in mouse (SILAC mouse) with (13)C6-lysine or stable isotope labeling in mammals (SILAM) with (15)N have enabled accurate quantitative analysis of the proteomes of whole organs and tissues as a function of disease. Here we describe the use of the SILAC mouse strategy to define the underlying pathological mechanisms in dystrophin-deficient skeletal muscle. Differential SILAC proteome profiling was performed on the gastrocnemius muscles of 3-week-old (early stage) dystrophin-deficient mdx mice and wild-type (normal) mice. The generated data were further confirmed in an independent set of mdx and normal mice using a SILAC spike-in strategy. A total of 789 proteins were quantified; of these, 73 were found to be significantly altered between mdx and normal mice (p < 0.05). Bioinformatics analyses using Ingenuity Pathway software established that the integrin-linked kinase pathway, actin cytoskeleton signaling, mitochondrial energy metabolism, and calcium homeostasis are the pathways initially affected in dystrophin-deficient muscle at early stages of pathogenesis. The key proteins involved in these pathways were validated by means of immunoblotting and immunohistochemistry in independent sets of mdx mice and in human DMD muscle biopsies. The specific involvement of these molecular networks early in dystrophic pathology makes them potential therapeutic targets. In sum, our findings indicate that SILAC mouse strategy has uncovered previously unidentified pathological pathways in mouse models of human skeletal muscle disease.
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Affiliation(s)
- Sree Rayavarapu
- Research Center for Genetic Medicine, Children's National Medical Center, 111 Michigan Ave NW, Washington, DC, USA
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34
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Brown KJ, Formolo CA, Seol H, Marathi RL, Duguez S, An E, Pillai D, Nazarian J, Rood BR, Hathout Y. Advances in the proteomic investigation of the cell secretome. Expert Rev Proteomics 2013; 9:337-45. [PMID: 22809211 DOI: 10.1586/epr.12.21] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Studies of the cell secretome have greatly increased in recent years owing to improvements in proteomic platforms, mass spectrometry instrumentation and to the increased interaction between analytical chemists, biologists and clinicians. Several secretome studies have been implemented in different areas of research, leading to the generation of a valuable secretome catalogs. Secreted proteins continue to be an important source of biomarkers and therapeutic target discovery and are equally valuable in the field of microbiology. Several discoveries have been achieved in vitro using cell culture systems, ex vivo using human tissue specimens and in vivo using animal models. In this review, some of the most recent advances in secretome studies and the fields that have benefited the most from this evolving technology are highlighted.
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Affiliation(s)
- Kristy J Brown
- Children's National Medical Center, Center for Genetic Medicine Research, 111 Michigan Avenue NW, Washington, DC 20010, USA
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35
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Brown KJ, Marathi R, Fiorillo AA, Ciccimaro EF, Sharma S, Rowlands DS, Rayavarapu S, Nagaraju K, Hoffman EP, Hathout Y. Accurate Quantitation of Dystrophin Protein in Human Skeletal Muscle Using Mass Spectrometry. ACTA ACUST UNITED AC 2013; Suppl 7. [PMID: 23646235 DOI: 10.4172/1948-593x.s7-001] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Quantitation of human dystrophin protein in muscle biopsies is a clinically relevant endpoint for both diagnosis and response to dystrophin-replacement therapies for dystrophinopathies. A robust and accurate assay would enable the use of dystrophin as a surrogate biomarker, particularly in exploratory Phase 2 trials. Currently available methods to quantitate dystrophin rely on immunoblot or immunohistochemistry methods that are not considered robust. Here we present a mass spectrometry based approach to accurately quantitate dystrophin protein in a total protein extract from human muscle biopsies. Our approach uses a combination of stable isotope labeled dystrophin as a spike-in standard, gel electrophoresis and high precision mass spectrometry to detect and quantitate multiple peptides of dystrophin within a complex protein mixture. The method was found highly reproducible and linear over a wide dynamic range, detecting as low as 5% of dystrophin relative to the normal amount in healthy individuals.
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Affiliation(s)
- Kristy J Brown
- Children's National Medical Center, Center for Genetic Medicine Research, USA ; Department of Integrative Systems Biology, The George Washington University, 2300 Eye Street, N.W., Ross 605, Washington, D.C. USA
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36
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Li Y, Xiao H, de Renty C, Jaramillo-Lambert A, Han Z, DePamphilis ML, Brown KJ, Zhu W. The involvement of acidic nucleoplasmic DNA-binding protein (And-1) in the regulation of prereplicative complex (pre-RC) assembly in human cells. J Biol Chem 2012; 287:42469-79. [PMID: 23093411 DOI: 10.1074/jbc.m112.404277] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA replication in all eukaryotes starts with the process of loading the replicative helicase MCM2-7 onto chromatin during late mitosis of the cell cycle. MCM2-7 is a key component of the prereplicative complex (pre-RC), which is loaded onto chromatin by the concerted action of origin recognition complex, Cdc6, and Cdt1. Here, we demonstrate that And-1 is assembled onto chromatin in late mitosis and early G(1) phase before the assembly of pre-RC in human cells. And-1 forms complexes with MCM2-7 to facilitate the assembly of MCM2-7 onto chromatin at replication origins in late mitosis and G(1) phase. We also present data to show that depletion of And-1 significantly reduces the interaction between Cdt1 and MCM7 in G(1) phase cells. Thus, human And-1 facilitates loading of the MCM2-7 helicase onto chromatin during the assembly of pre-RC.
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Affiliation(s)
- Yongming Li
- Department of Biochemistry and Molecular Biology, The George Washington University Medical School, Washington, D. C. 20037, USA
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37
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Sharma N, Medikayala S, Defour A, Rayavarapu S, Brown KJ, Hathout Y, Jaiswal JK. Use of quantitative membrane proteomics identifies a novel role of mitochondria in healing injured muscles. J Biol Chem 2012; 287:30455-67. [PMID: 22778268 DOI: 10.1074/jbc.m112.354415] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Skeletal muscles are proficient at healing from a variety of injuries. Healing occurs in two phases, early and late phase. Early phase involves healing the injured sarcolemma and restricting the spread of damage to the injured myofiber. Late phase of healing occurs a few days postinjury and involves interaction of injured myofibers with regenerative and inflammatory cells. Of the two phases, cellular and molecular processes involved in the early phase of healing are poorly understood. We have implemented an improved sarcolemmal proteomics approach together with in vivo labeling of proteins with modified amino acids in mice to study acute changes in the sarcolemmal proteome in early phase of myofiber injury. We find that a notable early phase response to muscle injury is an increased association of mitochondria with the injured sarcolemma. Real-time imaging of live myofibers during injury demonstrated that the increased association of mitochondria with the injured sarcolemma involves translocation of mitochondria to the site of injury, a response that is lacking in cultured myoblasts. Inhibiting mitochondrial function at the time of injury inhibited healing of the injured myofibers. This identifies a novel role of mitochondria in the early phase of healing injured myofibers.
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Affiliation(s)
- Nimisha Sharma
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC 20010, USA
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38
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Brown KJ, Vanderver A, Hoffman EP, Schiffmann R, Hathout Y. Characterization of Transferrin Glycopeptide Structures in Human Cerebrospinal Fluid. Int J Mass Spectrom 2012; 312:97-106. [PMID: 22408387 PMCID: PMC3293479 DOI: 10.1016/j.ijms.2011.06.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Transferrin in cerebrospinal fluid (CSF) exists as a mixture of silao and asialo glycoforms believed to originate from liver and brain respectively. We have previously shown that alteration in the asialo glycoform pattern could be an indication of certain anomalies in the central nervous system. Additionally, CSF asialo-transferrin has been shown to be a reliable marker to assess cerebrospinal leakage in head trauma. Therefore, the CSF transferrin glycoform pattern could be a useful diagnostic and prognostic tool. In this study we sought to characterize, in-depth, the transferrin glycovariants in cerebrospinal fluid using a combination of two-dimensional gel electrophoresis and high precision mass spectrometry analysis. Cerebrospinal fluid transferrin was detected as multiple spots (seven major spots) with different isoelectric points and slight shift in apparent molecular mass. High resolution (>60,000) and high accuracy (< 3 ppm error) mass spectrometry analysis revealed that each spot had a unique glycopeptide signature. MS(n) analysis enabled characterization of the glycan structure directly from the in-gel digested spots. The multiple spots detected for cerebrospinal fluid transferrin were mainly due to heterogeneity of di-antennary and tri-antennary glycans harboring a varying number of terminal N-acetylneuraminic acids and the existence of a high mannose and high N-acetylhexosamine glycosylated species.
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Affiliation(s)
| | | | | | - Raphael Schiffmann
- Hôpital de la Salpetriere, Paris, France
- Baylor Research Institute, Dallas, TX
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39
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Zhang A, Williamson CD, Wong DS, Bullough MD, Brown KJ, Hathout Y, Colberg-Poley AM. Quantitative proteomic analyses of human cytomegalovirus-induced restructuring of endoplasmic reticulum-mitochondrial contacts at late times of infection. Mol Cell Proteomics 2011; 10:M111.009936. [PMID: 21742798 DOI: 10.1074/mcp.m111.009936] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Endoplasmic reticulum-mitochondrial contacts, known as mitochondria-associated membranes, regulate important cellular functions including calcium signaling, bioenergetics, and apoptosis. Human cytomegalovirus is a medically important herpesvirus whose growth increases energy demand and depends upon continued cell survival. To gain insight into how human cytomegalovirus infection affects endoplasmic reticulum-mitochondrial contacts, we undertook quantitative proteomics of mitochondria-associated membranes using differential stable isotope labeling by amino acids in cell culture strategy and liquid chromatography-tandem MS analysis. This is the first reported quantitative proteomic analyses of a suborganelle during permissive human cytomegalovirus infection. Human fibroblasts were uninfected or human cytomegalovirus-infected for 72 h. Heavy mitochondria-associated membranes were isolated from paired unlabeled, uninfected cells and stable isotope labeling by amino acids in cell culture-labeled, infected cells and analyzed by liquid chromatography-tandem MS analysis. The results were verified by a reverse labeling experiment. Human cytomegalovirus infection dramatically altered endoplasmic reticulum-mitochondrial contacts by late times. Notable is the increased abundance of several fundamental networks in the mitochondria-associated membrane fraction of human cytomegalovirus-infected fibroblasts. Chaperones, including HSP60 and BiP, which is required for human cytomegalovirus assembly, were prominently increased at endoplasmic reticulum-mitochondrial contacts after infection. Minimal translational and translocation machineries were also associated with endoplasmic reticulum-mitochondrial contacts and increased after human cytomegalovirus infection as were glucose regulated protein 75 and the voltage dependent anion channel, which can form an endoplasmic reticulum-mitochondrial calcium signaling complex. Surprisingly, mitochondrial metabolic enzymes and cytosolic glycolytic enzymes were confidently detected in the mitochondria-associated membrane fraction and increased therein after infection. Finally, proapoptotic regulatory proteins, including Bax, cytochrome c, and Opa1, were augmented in endoplasmic reticulum-mitochondrial contacts after infection, suggesting attenuation of proapoptotic signaling by their increased presence therein. Together, these results suggest that human cytomegalovirus infection restructures the proteome of endoplasmic reticulum-mitochondrial contacts to bolster protein translation at these junctions, calcium signaling to mitochondria, cell survival, and bioenergetics and, thereby, allow for enhanced progeny production.
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Affiliation(s)
- Aiping Zhang
- Center for Cancer and Immunology Research, Children's Research Institute, Children's National Medical Center, 111 Michigan Avenue, NW, Washington, DC 20010, USA
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40
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Mate SE, Brown KJ, Hoffman EP. Integrated genomics and proteomics of the Torpedo californica electric organ: concordance with the mammalian neuromuscular junction. Skelet Muscle 2011; 1:20. [PMID: 21798097 PMCID: PMC3156643 DOI: 10.1186/2044-5040-1-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [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] [Received: 12/20/2010] [Accepted: 05/04/2011] [Indexed: 11/25/2022] Open
Abstract
Background During development, the branchial mesoderm of Torpedo californica transdifferentiates into an electric organ capable of generating high voltage discharges to stun fish. The organ contains a high density of cholinergic synapses and has served as a biochemical model for the membrane specialization of myofibers, the neuromuscular junction (NMJ). We studied the genome and proteome of the electric organ to gain insight into its composition, to determine if there is concordance with skeletal muscle and the NMJ, and to identify novel synaptic proteins. Results Of 435 proteins identified, 300 mapped to Torpedo cDNA sequences with ≥2 peptides. We identified 14 uncharacterized proteins in the electric organ that are known to play a role in acetylcholine receptor clustering or signal transduction. In addition, two human open reading frames, C1orf123 and C6orf130, showed high sequence similarity to electric organ proteins. Our profile lists several proteins that are highly expressed in skeletal muscle or are muscle specific. Synaptic proteins such as acetylcholinesterase, acetylcholine receptor subunits, and rapsyn were present in the electric organ proteome but absent in the skeletal muscle proteome. Conclusions Our integrated genomic and proteomic analysis supports research describing a muscle-like profile of the organ. We show that it is a repository of NMJ proteins but we present limitations on its use as a comprehensive model of the NMJ. Finally, we identified several proteins that may become candidates for signaling proteins not previously characterized as components of the NMJ.
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Affiliation(s)
- Suzanne E Mate
- Department of Biochemistry and Molecular Genetics, IBS, George Washington University, Washington DC, USA
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41
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Abstract
This chapter provides a detailed description of a method used to study temporal changes in the endoplasmic reticulum (ER) proteome of fibroblast cells exposed to ER stress agents (tunicamycin and thapsigargin). Differential stable isotope labeling by amino acids in cell culture (SILAC) is used in combination with crude ER fractionation, SDS-PAGE and LC-MS/MS to define altered protein expression in tunicamycin or thapsigargin treated cells versus untreated cells. Treated and untreated cells are harvested at different time points, mixed at a 1:1 ratio and processed for ER fractionation. Samples containing labeled and unlabeled proteins are separated by SDS-PAGE, bands are digested with trypsin and the resulting peptides analyzed by LC-MS/MS. Proteins are identified using Bioworks software and the Swiss-Prot database, whereas ratios of protein expression between treated and untreated cells are quantified using ZoomQuant software. Data visualization is facilitated by GeneSpring software.
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Affiliation(s)
- Catherine A Formolo
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC, USA
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Abstract
Chronic otitis media (COM), e.g. "glue" ear is characterized by middle ear effusion and conductive hearing loss. Although mucous glycoproteins (mucins), which contribute to increased effusion viscosity, have been analyzed in ear tissue specimens, no studies have been reported that characterize the molecular identity of secreted mucin proteins present in actual middle ear fluid. For this study, effusions from children with COM undergoing myringotomy at Children's National Medical Center, Washington, DC were collected. These were solubilized and gel fractionated, and the protein content was identified using a liquid chromatography tandem mass spectrometry (LC-MS/MS) proteomics approach. Western blot analyses with mucin specific antibodies and densitometry were performed to validate the mass spectrometry findings. LC-MS/MS results identified mucin MUC5B by >26 unique peptides in six of six middle ear effusion samples, whereas mucin MUC5AC was only identified in one of six middle ear effusions. These findings were validated by Western blot performed on the same six and on an additional 11 separate samples where densitometry revealed on average a 6.4-fold increased signal in MUC5B when compared with MUC5AC (p = 0.0009). In summary, although both MUC5AC and MUC5B mucins are detected in middle ear effusions, MUC5B seems to be predominant mucin present in COM secretions.
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Affiliation(s)
- Diego Preciado
- Department of Pediatric Otolaryngology-Head and Neck Surgery, Center for Genetic Medicine Research, Children's National Medical Center, 111 Michigan Avenue Northwest, Washington, DC 20001, USA.
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43
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Brown KJ, Jewells V, Herfarth H, Castillo M. White matter lesions suggestive of amyotrophic lateral sclerosis attributed to celiac disease. AJNR Am J Neuroradiol 2009; 31:880-1. [PMID: 19910450 DOI: 10.3174/ajnr.a1826] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [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
CD is an autoimmune-mediated disorder of the gastrointestinal tract. Initial symptom presentation is variable and can include neurologic manifestations that may comprise ataxia, neuropathy, dizziness, epilepsy, and cortical calcifications rather than gastrointestinal-hindering diagnosis and management. We present a case of a young man with progressive neurologic symptoms and brain MR imaging findings worrisome for ALS. During the diagnostic work-up, endomysium antibodies were discovered, and CD was confirmed by upper gastrointestinal endoscopy with duodenal biopsies. MR imaging findings suggestive of ALS improved after gluten-free diet institution.
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Affiliation(s)
- K J Brown
- Department of Radiology, University of North Carolina, Chapel Hill, North Carolina 27599-7510, USA.
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44
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Kok JGM, Raaymakers BW, Lagendijk JJW, Overweg J, de Graaff CHW, Brown KJ. Installation of the 1.5 T MRI accelerator next to clinical accelerators: impact of the fringe field. Phys Med Biol 2009; 54:N409-15. [PMID: 19687566 DOI: 10.1088/0031-9155/54/18/n02] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In the UMC Utrecht a prototype MRI accelerator has been installed to investigate the feasibility of real-time, MRI guided radiotherapy. The system consists of a 6 MV Elekta (Crawley, UK) accelerator and a 1.5 T Philips (Best, The Netherlands) MRI system. The system is installed in a standard radiotherapy bunker. The bunker is at the corner of a block of six bunkers, so there are three neighbouring clinical Elekta accelerators. During ramping of the magnet, the magnetic fringe field in the two nearest bunkers was measured as a function of the magnetic field strength of the MRI magnet. At 8 m, a maximum increase of 1.5 G was measured, at 12 m, 0.6 G. This is up to three times the earth's magnetic field. The clinical accelerators are needed to be re-calibrated in order to operate in such an external magnetic field. The resulting radiation field flatness of the clinical accelerators was measured and was similar to the situation before ramping the magnet.
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Affiliation(s)
- J G M Kok
- Department of Radiotherapy, University Medical Center Utrecht, Heidelberglaan 100, Utrecht 3584 CX, The Netherlands
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45
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Raaymakers BW, Lagendijk JJW, Overweg J, Kok JGM, Raaijmakers AJE, Kerkhof EM, van der Put RW, Meijsing I, Crijns SPM, Benedosso F, van Vulpen M, de Graaff CHW, Allen J, Brown KJ. Integrating a 1.5 T MRI scanner with a 6 MV accelerator: proof of concept. Phys Med Biol 2009. [PMID: 19451689 DOI: 10.1088/0031‐9155/54/12/n01] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
At the UMC Utrecht, The Netherlands, we have constructed a prototype MRI accelerator. The prototype is a modified 6 MV Elekta (Crawley, UK) accelerator next to a modified 1.5 T Philips Achieva (Best, The Netherlands) MRI system. From the initial design onwards, modifications to both systems were aimed to yield simultaneous and unhampered operation of the MRI and the accelerator. Indeed, the simultaneous operation is shown by performing diagnostic quality 1.5 T MRI with the radiation beam on. No degradation of the performance of either system was found. The integrated 1.5 T MRI system and radiotherapy accelerator allow simultaneous irradiation and MR imaging. The full diagnostic imaging capacities of the MRI can be used; dedicated sequences for MRI-guided radiotherapy treatments will be developed. This proof of concept opens the door towards a clinical prototype to start testing MRI-guided radiation therapy (MRIgRT) in the clinic.
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Affiliation(s)
- B W Raaymakers
- Department of Radiotherapy, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands.
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46
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Raaymakers BW, Lagendijk JJW, Overweg J, Kok JGM, Raaijmakers AJE, Kerkhof EM, van der Put RW, Meijsing I, Crijns SPM, Benedosso F, van Vulpen M, de Graaff CHW, Allen J, Brown KJ. Integrating a 1.5 T MRI scanner with a 6 MV accelerator: proof of concept. Phys Med Biol 2009; 54:N229-37. [PMID: 19451689 DOI: 10.1088/0031-9155/54/12/n01] [Citation(s) in RCA: 439] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
At the UMC Utrecht, The Netherlands, we have constructed a prototype MRI accelerator. The prototype is a modified 6 MV Elekta (Crawley, UK) accelerator next to a modified 1.5 T Philips Achieva (Best, The Netherlands) MRI system. From the initial design onwards, modifications to both systems were aimed to yield simultaneous and unhampered operation of the MRI and the accelerator. Indeed, the simultaneous operation is shown by performing diagnostic quality 1.5 T MRI with the radiation beam on. No degradation of the performance of either system was found. The integrated 1.5 T MRI system and radiotherapy accelerator allow simultaneous irradiation and MR imaging. The full diagnostic imaging capacities of the MRI can be used; dedicated sequences for MRI-guided radiotherapy treatments will be developed. This proof of concept opens the door towards a clinical prototype to start testing MRI-guided radiation therapy (MRIgRT) in the clinic.
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Affiliation(s)
- B W Raaymakers
- Department of Radiotherapy, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands.
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47
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Mintz M, Vanderver A, Brown KJ, Lin J, Wang Z, Kaneski C, Schiffmann R, Nagaraju K, Hoffman EP, Hathout Y. Time series proteome profiling to study endoplasmic reticulum stress response. J Proteome Res 2008; 7:2435-44. [PMID: 18435558 DOI: 10.1021/pr700842m] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [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
Time series profiling is a powerful approach for obtaining information on protein expression dynamics and prevailing biochemical pathways. To date, such information could only be obtained at the mRNA level using mature and highly parallel technologies such as microarray gene expression profiling. The generation of time series data at the protein level has lagged due to the lack of robust and highly reproducible methodologies. Using a combination of SILAC strategy, SDS-PAGE and LC-MS/MS, we demonstrate successful monitoring of expression levels of the same set of proteins across different time points within the ER compartment of human primary fibroblast cells when exposed to ER stress inducers tunicamycin and thapsigargin. Data visualization was facilitated using GeneSpring GX analysis platform that was designed to process Affymetrix microarray data. This software also facilitated the generation of important parameters such as data normalization, calculation of statistical values to extract significant changes in protein expression, and the cross comparison of data sets.
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Affiliation(s)
- Michelle Mintz
- Children's National Medical Center, Center for Genetic Medicine, Washington, D.C. 20010, USA
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48
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Sevinsky JR, Brown KJ, Cargile BJ, Bundy JL, Stephenson JL. Minimizing back exchange in 18O/16O quantitative proteomics experiments by incorporation of immobilized trypsin into the initial digestion step. Anal Chem 2007; 79:2158-62. [PMID: 17249691 PMCID: PMC2796076 DOI: 10.1021/ac0620819] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [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: 11/28/2022]
Abstract
Differential labeling of peptides via the use of the 18O-water proteolytic labeling method has been widely adopted for quantitative shotgun proteomics studies due to its simplicity and low reagent costs. In this report, the use of immobilized trypsin in the initial digestion step, in addition to the initial digestion step, is explored as a means to minimize postlabeling back exchange of 18O-labeled peptides into the 16O form when multidimensional peptide separation methods (here, isoelectric focusing of peptides) are incorporated into the sample workflow. Examples are shown with a mixture of standard proteins and a sample from an ongoing clinical proteomics study.
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Affiliation(s)
- Joel R. Sevinsky
- Mass Spectrometry Research Program, Research Triangle Institute, 3040 Cornwallis Rd, Research Triangle Park NC 27709
| | - Kristy J. Brown
- CTL Bio Services LLC, 352 Academic and Research Building, 9601 Medical Center Dr. Rockville, MD 20850
| | - Benjamin J. Cargile
- Mass Spectrometry Research Program, Research Triangle Institute, 3040 Cornwallis Rd, Research Triangle Park NC 27709
| | - Jonathan L. Bundy
- Mass Spectrometry Research Program, Research Triangle Institute, 3040 Cornwallis Rd, Research Triangle Park NC 27709
- Author to whom correspondence should be addressed: Phone: 919.485.2676; FAX: 919.541.6161,
| | - James L. Stephenson
- Mass Spectrometry Research Program, Research Triangle Institute, 3040 Cornwallis Rd, Research Triangle Park NC 27709
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49
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Pasternack GB, Brown KJ. Natural and anthropogenic geochemical signatures of floodplain and deltaic sedimentary strata, Sacramento-San Joaquin Delta, California, USA. Environ Pollut 2006; 141:295-309. [PMID: 16236412 DOI: 10.1016/j.envpol.2005.08.044] [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] [Received: 01/25/2005] [Accepted: 08/08/2005] [Indexed: 05/04/2023]
Abstract
The geochemical history of an upper deltaic plain pending tidal wetland restoration was reconstructed to assess remobilization of redox-sensitive constituents in sediment, identify depositional processes promoting geochemical retention, and determine the extent of contamination with Hg, As, Pb, Cu, and Zn. Three 12-14-m sediment cores were analyzed for bulk sediment geochemistry using ICP-AES. Rather than showing similar stratigraphic and geochemical down-core trends, cores had a unique record indicative of strong spatial gradients in deposition processes. Each strata type (e.g. basal clay, sand channel, distal floodplain, and agriculturally impacted surficial horizon) had a unique geochemical "fingerprint". The agriculturally impacted surficial layer showed high [Hg], [As], and [Pb]. The significance is that a restored upper delta will have a complex geomorphology defying conventional criteria of "success" in a restoration framework. Also, there is a significant risk of generating toxic, bio-available CH3Hg+ that would be hazardous to fish.
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Affiliation(s)
- G B Pasternack
- Department of Land, Air and Water Resources, University of California, 211 Veihmeyer Hall, One Shields Avenue, Davis, CA 95616-8628, USA.
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50
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Brown KJ, Clark JS, Grimm EC, Donovan JJ, Mueller PG, Hansen BCS, Stefanova I. Fire cycles in North American interior grasslands and their relation to prairie drought. Proc Natl Acad Sci U S A 2005; 102:8865-70. [PMID: 15956200 PMCID: PMC1150278 DOI: 10.1073/pnas.0503621102] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
High-resolution analyses of a late Holocene core from Kettle Lake in North Dakota reveal coeval fluctuations in loss-on-ignition carbonate content, percentage of grass pollen, and charcoal flux. These oscillations are indicative of climate-fuel-fire cycles that have prevailed on the Northern Great Plains (NGP) for most of the late Holocene. High charcoal flux occurred during past moist intervals when grass cover was extensive and fuel loads were high, whereas reduced charcoal flux characterized the intervening droughts when grass cover, and hence fuel loads, decreased, illustrating that fire is not a universal feature of the NGP through time but oscillates with climate. Spectral and wavelet analyses reveal that the cycles have a periodicity of approximately = 160 yr, although secular trends in the cycles are difficult to identify for the entire Holocene because the periodicity in the early Holocene ranged between 80 and 160 yr. Although the cycles are evident for most of the last 4,500 yr, their occasional muting adds further to the overall climatic complexity of the plains. These findings clearly show that the continental interior of North America has experienced short-term climatic cycles accompanied by a marked landscape response for several millennia, regularly alternating between dual landscape modes. The documentation of cycles of similar duration at other sites in the NGP, western North America, and Greenland suggests some degree of regional coherence to climatic forcing. Accordingly, the effects of global warming from increasing greenhouse gases will be superimposed on this natural variability of drought.
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Affiliation(s)
- K J Brown
- Department of Biology, Duke University, P.O. Box 90338, Durham, NC 27708, USA.
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