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Abstract
Characterization of proteins that mediate mechanotransduction by hair cells, the sensory cells of the inner ear, is hampered by the scarcity of these cells and their sensory organelle, the hair bundle. Mass spectrometry, with its high sensitivity and identification precision, is the ideal method for determining which proteins are present in bundles and what proteins they interact with. We describe here the isolation of mouse hair bundles, as well as preparation of bundle protein samples for mass spectrometry. We also describe protocols for data-dependent (shotgun) and parallel reaction monitoring (targeted) mass spectrometry that allow us to identify and quantify proteins of the hair bundle. These sensitive methods are particularly useful for comparing proteomes of wild-type mice and mice with deafness mutations affecting hair-bundle proteins.
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Affiliation(s)
- J F Krey
- Oregon Hearing Research Center, Oregon Health & Science University, Portland, OR, United States; Vollum Institute, Oregon Health & Science University, Portland, OR, United States
| | - P A Wilmarth
- Oregon Health & Science University, Portland, OR, United States
| | - L L David
- Oregon Health & Science University, Portland, OR, United States
| | - P G Barr-Gillespie
- Oregon Hearing Research Center, Oregon Health & Science University, Portland, OR, United States; Vollum Institute, Oregon Health & Science University, Portland, OR, United States; Oregon Health & Science University, Portland, OR, United States.
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Huan J, Hornick NI, Goloviznina NA, Kamimae-Lanning AN, David LL, Wilmarth PA, Mori T, Chevillet JR, Narla A, Roberts CT, Loriaux MM, Chang BH, Kurre P. Coordinate regulation of residual bone marrow function by paracrine trafficking of AML exosomes. Leukemia 2015; 29:2285-95. [PMID: 26108689 DOI: 10.1038/leu.2015.163] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 05/19/2015] [Accepted: 06/11/2015] [Indexed: 12/20/2022]
Abstract
We recently demonstrated that acute myeloid leukemia (AML) cell lines and patient-derived blasts release exosomes that carry RNA and protein; following an in vitro transfer, AML exosomes produce proangiogenic changes in bystander cells. We reasoned that paracrine exosome trafficking may have a broader role in shaping the leukemic niche. In a series of in vitro studies and murine xenografts, we demonstrate that AML exosomes downregulate critical retention factors (Scf, Cxcl12) in stromal cells, leading to hematopoietic stem and progenitor cell (HSPC) mobilization from the bone marrow. Exosome trafficking also regulates HSPC directly, and we demonstrate declining clonogenicity, loss of CXCR4 and c-Kit expression, and the consistent repression of several hematopoietic transcription factors, including c-Myb, Cebp-β and Hoxa-9. Additional experiments using a model of extramedullary AML or direct intrafemoral injection of purified exosomes reveal that the erosion of HSPC function can occur independent of direct cell-cell contact with leukemia cells. Finally, using a novel multiplex proteomics technique, we identified candidate pathways involved in the direct exosome-mediated modulation of HSPC function. In aggregate, this work suggests that AML exosomes participate in the suppression of residual hematopoietic function that precedes widespread leukemic invasion of the bone marrow directly and indirectly via stromal components.
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Affiliation(s)
- J Huan
- Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA.,Papé Family Pediatric Research Institute, Oregon Health & Science University, Portland, OR, USA.,Oregon Stem Cell Center, Oregon Health & Science University, Portland, OR, USA
| | - N I Hornick
- Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA.,Papé Family Pediatric Research Institute, Oregon Health & Science University, Portland, OR, USA.,Oregon Stem Cell Center, Oregon Health & Science University, Portland, OR, USA
| | - N A Goloviznina
- Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA.,Papé Family Pediatric Research Institute, Oregon Health & Science University, Portland, OR, USA.,Oregon Stem Cell Center, Oregon Health & Science University, Portland, OR, USA
| | - A N Kamimae-Lanning
- Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA.,Papé Family Pediatric Research Institute, Oregon Health & Science University, Portland, OR, USA.,Oregon Stem Cell Center, Oregon Health & Science University, Portland, OR, USA
| | - L L David
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR, USA
| | - P A Wilmarth
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR, USA
| | - T Mori
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - J R Chevillet
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - A Narla
- Division of Hematology/Oncology, Stanford University, Palo Alto, CA, USA
| | - C T Roberts
- Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA.,Department of Medicine, Oregon Health & Science University, Portland, OR, USA.,Oregon National Primate Research Center, Beaverton, OR, USA
| | - M M Loriaux
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.,Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - B H Chang
- Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA.,Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - P Kurre
- Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA.,Papé Family Pediatric Research Institute, Oregon Health & Science University, Portland, OR, USA.,Oregon Stem Cell Center, Oregon Health & Science University, Portland, OR, USA.,Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
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Wilmarth PA, Tanner S, Dasari S, Nagalla SR, Riviere MA, Bafna V, Pevzner PA, David LL. Age-related changes in human crystallins determined from comparative analysis of post-translational modifications in young and aged lens: does deamidation contribute to crystallin insolubility? J Proteome Res 2006; 5:2554-66. [PMID: 17022627 PMCID: PMC2536618 DOI: 10.1021/pr050473a] [Citation(s) in RCA: 221] [Impact Index Per Article: 12.3] [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: 01/30/2023]
Abstract
We have employed recently developed blind modification search techniques to generate the most comprehensive map of post-translational modifications (PTMs) in human lens constructed to date. Three aged lenses, two of which had moderate cataract, and one young control lens were analyzed using multidimensional liquid chromatography mass spectrometry. In total, 491 modification sites in lens proteins were identified. There were 155 in vivo PTM sites in crystallins: 77 previously reported sites and 78 newly detected PTM sites. Several of these sites had modifications previously undetected by mass spectrometry in lens including carboxymethyl lysine (+58 Da), carboxyethyl lysine (+72 Da), and an arginine modification of +55 Da with yet unknown chemical structure. These new modifications were observed in all three aged lenses but were not found in the young lens. Several new sites of cysteine methylation were identified indicating this modification is more extensive in lens than previously thought. The results were used to estimate the extent of modification at specific sites by spectral counting. We tested the long-standing hypothesis that PTMs contribute to age-related loss of crystallin solubility by comparing spectral counts between the water-soluble and water-insoluble fractions of the aged lenses and found that the extent of deamidation was significantly increased in the water-insoluble fractions. On the basis of spectral counting, the most abundant PTMs in aged lenses were deamidations and methylated cysteines with other PTMs present at lower levels.
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Affiliation(s)
- P A Wilmarth
- Department of Integrative Biosciences, School of Dentistry, Oregon Health and Science University, 611 South West Campus Drive, Portland, Oregon 97239, USA.
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Toth KS, Sousa DC, Nitschke JM, Vierinen KS, Wilmarth PA. Identification of the s1/2 145Dy ground state. Phys Rev C Nucl Phys 1993; 48:436-438. [PMID: 9968839 DOI: 10.1103/physrevc.48.436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Toth KS, Wilmarth PA, Nitschke JM, Sousa DC. Observation of 146Er electron capture and beta + decay. Phys Rev C Nucl Phys 1993; 48:445-447. [PMID: 9968842 DOI: 10.1103/physrevc.48.445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Toth KS, Sousa DC, Wilmarth PA, Nitschke JM, Vierinen KS. Electron capture and beta + decay of 147Tm. Phys Rev C Nucl Phys 1993; 47:1804-1806. [PMID: 9968628 DOI: 10.1103/physrevc.47.1804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Toth KS, Vierinen KS, Kortelahti MO, Sousa DC, Nitschke JM, Wilmarth PA. Investigation of A=155 and A=151 nuclides: Identification of the 155Tm s1/2 isomer and of the 155Yb beta -decay branch. Phys Rev C Nucl Phys 1991; 44:1868-1877. [PMID: 9967607 DOI: 10.1103/physrevc.44.1868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Firestone RB, Gilat J, Nitschke JM, Wilmarth PA, Vierinen KS. Decay studies of neutron deficient nuclei near the Z=64 subshell: 142Dy, 140,142Tb, 140,142Gd, 140,142Eu, 142Sm, and 142Pm. Phys Rev C Nucl Phys 1991; 43:1066-1085. [PMID: 9967150 DOI: 10.1103/physrevc.43.1066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Chasteler RM, Nitschke JM, Firestone RB, Vierinen KS, Wilmarth PA. Decay studies of the neutron-rich isotopes 168Dy and 168Hog and the identification of the new isomer 168Hom. Phys Rev C Nucl Phys 1990; 42:1796-1799. [PMID: 9966916 DOI: 10.1103/physrevc.42.r1796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Chasteler RM, Nitschke JM, Firestone RB, Vierinen KS, Wilmarth PA. Decay of the neutron-rich isotope 171Ho and the identification of 169Dy. Phys Rev C Nucl Phys 1990; 42:1171-1174. [PMID: 9966844 DOI: 10.1103/physrevc.42.r1171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Akovali YA, Toth KS, Goodman AL, Nitschke JM, Wilmarth PA, Moltz DM, Rao MN, Sousa DC. Single-particle states in 151Tm and 151Er: Systematics of neutron states in N=83 nuclei. Phys Rev C Nucl Phys 1990; 41:1126-1140. [PMID: 9966454 DOI: 10.1103/physrevc.41.1126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Gilat J, Nitschke JM, Wilmarth PA, Firestone RB. Decay studies of neutron-deficient nuclei near the Z=64 subshell: 141Dy, 141Tb, 141Gdg+m, and 141Eum. Phys Rev C Nucl Phys 1989; 40:2249-2259. [PMID: 9966223 DOI: 10.1103/physrevc.40.2249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Nitschke JM, Wilmarth PA, Firestone RB, Möller P, Toth KS, Gilat J. Doorway-state formation and structure in beta -delayed proton decay. Phys Rev Lett 1989; 62:2805-2808. [PMID: 10040096 DOI: 10.1103/physrevlett.62.2805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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Vierinen KS, Nitschke JM, Wilmarth PA, Chasteler RM, Shihab-Eldin AA, Firestone RB, Toth KS, Akovali YA. Identification of 145Er and 145Ho. Phys Rev C Nucl Phys 1989; 39:1972-1975. [PMID: 9955422 DOI: 10.1103/physrevc.39.1972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Kortelahti MO, Toth KS, Vierinen KS, Nitschke JM, Wilmarth PA, Firestone RB, Chasteler RM, Shihab-Eldin AA. Decay properties of 153Yb and 153Tm; Excitation energies of the s1/2 and h11/2 proton states in 153Tm. Phys Rev C Nucl Phys 1989; 39:636-644. [PMID: 9955237 DOI: 10.1103/physrevc.39.636] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Firestone RB, Nitschke JM, Wilmarth PA, Vierinen K, Gilat J, Toth KS, Akovali YA. Decay of 149Erg+m by positron and delayed proton emission and by electron capture. Phys Rev C Nucl Phys 1989; 39:219-232. [PMID: 9955180 DOI: 10.1103/physrevc.39.219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Toth KS, Wilmarth PA, Nitschke JM, Firestone RB, Vierinen K, Kortelahti MO, Avignone FT. Fine structure in 153Tm alpha decay. Phys Rev C Nucl Phys 1988; 38:1932-1935. [PMID: 9955005 DOI: 10.1103/physrevc.38.1932] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Vierinen KS, Shihab-Eldin AA, Nitschke JM, Wilmarth PA, Chasteler RM, Firestone RB, Toth KS. Beta decay of 154Lu and 154Yb. Phys Rev C Nucl Phys 1988; 38:1509-1512. [PMID: 9954959 DOI: 10.1103/physrevc.38.1509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Nitschke JM, Wilmarth PA, Gilat J, Toth KS, Avignone FT. Delayed proton emission of N=81 odd-odd precursors: 148Ho, 150Tm, and 152Lu. Phys Rev C Nucl Phys 1988; 37:2694-2703. [PMID: 9954747 DOI: 10.1103/physrevc.37.2694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Toth KS, Sousa DC, Nitschke JM, Wilmarth PA. Beta decay properties of 148Er and 148Ho. Phys Rev C Nucl Phys 1988; 37:1196-1202. [PMID: 9954558 DOI: 10.1103/physrevc.37.1196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Toth KS, Gilat J, Nitschke JM, Wilmarth PA, Vierinen K, Avignone III. Observation of 149Tm decay to 149Er levels and beta -delayed proton emission. Phys Rev C Nucl Phys 1987; 36:826-829. [PMID: 9954144 DOI: 10.1103/physrevc.36.826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Gregorich KE, Moody KJ, Lee D, Kot WK, Welch RB, Wilmarth PA, Seaborg GT. Actinide production in 136Xe bombardments of 249Cf. Phys Rev C Nucl Phys 1987; 35:2117-2124. [PMID: 9954008 DOI: 10.1103/physrevc.35.2117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Toth KS, Sousa DC, Nitschke JM, Wilmarth PA. Decay properties of 150Tm and 150Er. Phys Rev C Nucl Phys 1987; 35:620-624. [PMID: 9953806 DOI: 10.1103/physrevc.35.620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Toth KS, Sousa DC, Nitschke JM, Wilmarth PA. Investigation of A=152 radioactivities with mass-separated sources: Identification of 152Lu. Phys Rev C Nucl Phys 1987; 35:310-314. [PMID: 9953762 DOI: 10.1103/physrevc.35.310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Toth KS, Ellis-Akovali YA, Avignone FT, Moore RS, Moltz DM, Nitschke JM, Wilmarth PA, Lemmertz PK, Sousa DC, Goodman AL. Single-particle states in sup149Er and sup149Ho, and the effect of the Z=64 closure. Phys Rev C Nucl Phys 1985; 32:342-345. [PMID: 9952843 DOI: 10.1103/physrevc.32.342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Nitschke JM, Wilmarth PA, Lemmertz PK, Zeitz WD, Honkanen JA. Beta-delayed proton emission observed in new lanthanide isotopes. ACTA ACUST UNITED AC 1984. [DOI: 10.1007/bf01412274] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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