1
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Weke K, Kote S, Faktor J, Al Shboul S, Uwugiaren N, Brennan PM, Goodlett DR, Hupp TR, Dapic I. DIA-MS proteome analysis of formalin-fixed paraffin-embedded glioblastoma tissues. Anal Chim Acta 2022; 1204:339695. [DOI: 10.1016/j.aca.2022.339695] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 03/04/2022] [Accepted: 03/05/2022] [Indexed: 12/11/2022]
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2
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Weke K, Singh A, Uwugiaren N, Alfaro JA, Wang T, Hupp TR, O'Neill JR, Vojtesek B, Goodlett DR, Williams SM, Zhou M, Kelly RT, Zhu Y, Dapic I. MicroPOTS Analysis of Barrett's Esophageal Cell Line Models Identifies Proteomic Changes after Physiologic and Radiation Stress. J Proteome Res 2021; 20:2195-2205. [PMID: 33491460 PMCID: PMC8155554 DOI: 10.1021/acs.jproteome.0c00629] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Moving from macroscale
preparative systems in proteomics to micro-
and nanotechnologies offers researchers the ability to deeply profile
smaller numbers of cells that are more likely to be encountered in
clinical settings. Herein a recently developed microscale proteomic
method, microdroplet processing in one pot for trace samples (microPOTS),
was employed to identify proteomic changes in ∼200 Barrett’s
esophageal cells following physiologic and radiation stress exposure.
From this small population of cells, microPOTS confidently identified
>1500 protein groups, and achieved a high reproducibility with
a Pearson’s
correlation coefficient value of R > 0.9 and over
50% protein overlap from replicates. A Barrett’s cell line
model treated with either lithocholic acid (LCA) or X-ray had 21 (e.g.,
ASNS, RALY, FAM120A, UBE2M, IDH1, ESD) and 32 (e.g., GLUL, CALU, SH3BGRL3,
S100A9, FKBP3, AGR2) overexpressed proteins, respectively, compared
to the untreated set. These results demonstrate the ability of microPOTS
to routinely identify and quantify differentially expressed proteins
from limited numbers of cells.
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Affiliation(s)
- Kenneth Weke
- University of Gdansk, International Centre for Cancer Vaccine Science, ul. Kładki 24, 80-822 Gdansk, Poland
| | - Ashita Singh
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH4 2XR, U.K.,Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| | - Naomi Uwugiaren
- University of Gdansk, International Centre for Cancer Vaccine Science, ul. Kładki 24, 80-822 Gdansk, Poland
| | - Javier A Alfaro
- University of Gdansk, International Centre for Cancer Vaccine Science, ul. Kładki 24, 80-822 Gdansk, Poland.,Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH4 2XR, U.K
| | - Tongjie Wang
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH4 2XR, U.K
| | - Ted R Hupp
- University of Gdansk, International Centre for Cancer Vaccine Science, ul. Kładki 24, 80-822 Gdansk, Poland.,Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH4 2XR, U.K
| | - J Robert O'Neill
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH4 2XR, U.K.,Cambridge Oesophagogastric Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, U.K
| | - Borek Vojtesek
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| | - David R Goodlett
- University of Gdansk, International Centre for Cancer Vaccine Science, ul. Kładki 24, 80-822 Gdansk, Poland.,University of Victoria - Genome British Columbia Proteomics Centre, Victoria, BC V8Z 7X8, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Sarah M Williams
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Ryan T Kelly
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Irena Dapic
- University of Gdansk, International Centre for Cancer Vaccine Science, ul. Kładki 24, 80-822 Gdansk, Poland
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Zhou M, Uwugiaren N, Williams SM, Moore RJ, Zhao R, Goodlett D, Dapic I, Paša-Tolić L, Zhu Y. Sensitive Top-Down Proteomics Analysis of a Low Number of Mammalian Cells Using a Nanodroplet Sample Processing Platform. Anal Chem 2020; 92:7087-7095. [PMID: 32374172 DOI: 10.1021/acs.analchem.0c00467] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Top-down proteomics is a powerful tool for characterizing genetic variations and post-translational modifications at intact protein level. However, one significant technical gap of top-down proteomics is the inability to analyze a low amount of biological samples, which limits its access to isolated rare cells, fine needle aspiration biopsies, and tissue substructures. Herein, we developed an ultrasensitive top-down platform by incorporating a microfluidic sample preparation system, termed nanoPOTS (nanodroplet processing in one pot for trace samples), into a top-down proteomic workflow. A unique combination of a nonionic detergent dodecyl-β-d-maltopyranoside (DDM) with urea as protein extraction buffer significantly improved both protein extraction efficiency and sample recovery. We hypothesize that the DDM detergent improves protein recovery by efficiently reducing nonspecific adsorption of intact proteins on container surfaces, while urea serves as a strong denaturant to disrupt noncovalent complexes and release intact proteins for downstream analysis. The nanoPOTS-based top-down platform reproducibly and quantitatively identified ∼170 to ∼620 proteoforms from ∼70 to ∼770 HeLa cells containing ∼10 to ∼115 ng of total protein. A variety of post-translational modifications including acetylation, myristoylation, and iron binding were identified using only less than 800 cells. We anticipate the nanoPOTS top-down proteomics platform will be broadly applicable in biomedical research, particularly where clinical specimens are not available in amounts amenable to standard workflows.
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Affiliation(s)
- Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Naomi Uwugiaren
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Sarah M Williams
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Rui Zhao
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - David Goodlett
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland.,Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland 21201, United States
| | - Irena Dapic
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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4
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Dapic I, Baljeu-Neuman L, Uwugiaren N, Kers J, Goodlett DR, Corthals GL. Proteome analysis of tissues by mass spectrometry. Mass Spectrom Rev 2019; 38:403-441. [PMID: 31390493 DOI: 10.1002/mas.21598] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 06/17/2019] [Indexed: 06/10/2023]
Abstract
Tissues and biofluids are important sources of information used for the detection of diseases and decisions on patient therapies. There are several accepted methods for preservation of tissues, among which the most popular are fresh-frozen and formalin-fixed paraffin embedded methods. Depending on the preservation method and the amount of sample available, various specific protocols are available for tissue processing for subsequent proteomic analysis. Protocols are tailored to answer various biological questions, and as such vary in lysis and digestion conditions, as well as duration. The existence of diverse tissue-sample protocols has led to confusion in how to choose the best protocol for a given tissue and made it difficult to compare results across sample types. Here, we summarize procedures used for tissue processing for subsequent bottom-up proteomic analysis. Furthermore, we compare protocols for their variations in the composition of lysis buffers, digestion procedures, and purification steps. For example, reports have shown that lysis buffer composition plays an important role in the profile of extracted proteins: the most common are tris(hydroxymethyl)aminomethane, radioimmunoprecipitation assay, and ammonium bicarbonate buffers. Although, trypsin is the most commonly used enzyme for proteolysis, in some protocols it is supplemented with Lys-C and/or chymotrypsin, which will often lead to an increase in proteome coverage. Data show that the selection of the lysis procedure might need to be tissue-specific to produce distinct protocols for individual tissue types. Finally, selection of the procedures is also influenced by the amount of sample available, which range from biopsies or the size of a few dozen of mm2 obtained with laser capture microdissection to much larger amounts that weight several milligrams.
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Affiliation(s)
- Irena Dapic
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | | | - Naomi Uwugiaren
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Jesper Kers
- Department of Pathology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam Cardiovascular Sciences (ACS), Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | - David R Goodlett
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
- University of Maryland, 20N. Pine Street, Baltimore, MD 21201
| | - Garry L Corthals
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
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5
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Domínguez Pardo JJ, Koorengevel MC, Uwugiaren N, Weijers J, Kopf AH, Jahn H, van Walree CA, van Steenbergen MJ, Killian JA. Membrane Solubilization by Styrene-Maleic Acid Copolymers: Delineating the Role of Polymer Length. Biophys J 2018; 115:129-138. [PMID: 29972804 PMCID: PMC6035298 DOI: 10.1016/j.bpj.2018.05.032] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [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: 02/27/2018] [Revised: 05/10/2018] [Accepted: 05/21/2018] [Indexed: 12/18/2022] Open
Abstract
Styrene-maleic acid (SMA) copolymers have attracted interest in membrane research because they allow the solubilization and purification of membrane-spanning proteins from biological membranes in the form of native-like nanodisks. However, our understanding of the underlying SMA-lipid interactions is hampered by the fact that SMA preparations are very polydisperse. Here, we obtained fractions of the two most commonly used SMA preparations: SMA 2:1 and SMA 3:1 (both with specified Mw ∼10 kD), with different number-average molecular weight (Mn) and styrene content. The fractionation is based on the differential solubility of styrene-maleic anhydride (SMAnh) in hexane and acetone mixtures. SMAnh fractions were hydrolyzed to SMA and added to lipid self-assemblies. It was found that SMA fractions inserted in monolayers and solubilized vesicles to a different extent, with the highest efficiency being observed for low-Mn SMA polymers. Electron microscopy and dynamic light scattering size analyses confirmed the presence of nanodisks independent of the Mn of the SMA polymers forming the belt, and it was shown that the nanodisks all have approximately the same size. However, nanodisks bounded by high-Mn SMA polymers were more stable than those bounded by low-Mn polymers, as indicated by a better retention of the native lipid thermotropic properties and by slower exchange rates of lipids between nanodisks. In conclusion, we here present a simple method to separate SMAnh molecules based on their Mn from commercial SMAnh blends, which allowed us to obtain insights into the importance of SMA length for polymer-lipid interactions.
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Affiliation(s)
- Juan J Domínguez Pardo
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, the Netherlands.
| | - Martijn C Koorengevel
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Naomi Uwugiaren
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Jeroen Weijers
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Adrian H Kopf
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Helene Jahn
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Cornelis A van Walree
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Mies J van Steenbergen
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - J Antoinette Killian
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, the Netherlands.
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6
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Dapic I, Uwugiaren N, Jansen PJ, Corthals GL. Fast and Simple Protocols for Mass Spectrometry-Based Proteomics of Small Fresh Frozen Uterine Tissue Sections. Anal Chem 2017; 89:10769-10775. [PMID: 28910098 PMCID: PMC5647562 DOI: 10.1021/acs.analchem.7b01937] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
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Human
tissues are an important link between organ-specific spatial
molecular information, patient pathology, and patient treatment options.
However, patient tissues are uniquely obtained by time and location,
and limited in their availability and size. Currently, little knowledge
exists about appropriate and simplified protocols for routine MS-based
analysis of the various types and sizes of tissues. Following standard
procedures used in pathology, we selected small fresh frozen uterine
tissue samples to investigate how the tissue preparation protocol
affected the subsequent proteomics analysis. First, we observed that
protein extraction with 0.1% SDS followed by extraction with a 30%
ACN/urea resulted in a decrease in the number of identified proteins,
when compared to extraction with 30% ACN/urea only. The decrease in
the number of proteins was approximately 55% and 20%, for 10 and 16
μm thick tissue, respectively. Interestingly, the relative abundance
of the proteins shared between the two methods was higher when SDS/ACN/urea
was used, compared to the 30% ACN/urea extraction, indicating the
role of SDS to be beneficial for protein solubility. Second, the influence
of tissue thickness was investigated by comparing the results obtained
for 10, 16, and 20 μm thick (1 mm2) tissue using
urea/30% ACN. We observed an increase in the number of identified
proteins and corresponding quantity with an increase in the tissue
thickness. Finally, by analyzing very small amounts of tissues (∼0.2
mm2) of 10, 16, and 20 μm thickness, we observed
that the increase in tissue thickness resulted in a higher number
of protein identifications and corresponding quantitative values.
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Affiliation(s)
- Irena Dapic
- University of Amsterdam, Van 't Hoff Institute for Molecular Sciences (HIMS) , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Naomi Uwugiaren
- University of Amsterdam, Van 't Hoff Institute for Molecular Sciences (HIMS) , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Petra J Jansen
- University of Amsterdam, Van 't Hoff Institute for Molecular Sciences (HIMS) , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Garry L Corthals
- University of Amsterdam, Van 't Hoff Institute for Molecular Sciences (HIMS) , Science Park 904, 1098 XH Amsterdam, The Netherlands
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