1
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Shoff T, Van Orman B, Onwudiwe VC, Genereux JC, Julian RR. Determination of Trends Underlying Aspartic Acid Isomerization in Intact Proteins Reveals Unusually Rapid Isomerization of Tau. ACS Chem Neurosci 2025; 16:673-686. [PMID: 39881547 PMCID: PMC11843600 DOI: 10.1021/acschemneuro.4c00721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2024] [Revised: 01/08/2025] [Accepted: 01/14/2025] [Indexed: 01/31/2025] Open
Abstract
Spontaneous chemical modifications in long-lived proteins can potentially change protein structure in ways that impact proteostasis and cellular health. For example, isomerization of aspartic acid interferes with protein turnover and is anticorrelated with cognitive acuity in Alzheimer's disease. However, few isomerization rates have been determined for Asp residues in intact proteins. To remedy this deficiency, we used protein extracts from SH-SY5Y neuroblastoma cells as a source of a complex, brain-relevant proteome with no baseline isomerization. Cell lysates were aged in vitro to generate isomers, and extracted proteins were analyzed by data-independent acquisition (DIA) liquid chromatography-mass spectrometry (LC-MS). Although no Asp isomers were detected at day 0, isomerization increased over time and was quantifiable for 105 proteins by day 50. Data analysis revealed that the isomerization rate is influenced by both primary sequence and secondary structure, suggesting that steric hindrance and backbone rigidity modulate isomerization. Additionally, we examined lysates extracted under gentle conditions to preserve protein complexes and found that protein-protein interactions often slow isomerization. Base catalysis was explored as a means to accelerate Asp isomerization due to findings of accelerated asparagine deamidation. However, no substantial rate enhancement was found for isomerization, suggesting fundamental differences in acid-base chemistry. With an enhanced understanding of Asp isomerization in proteins in general, we next sought to better understand Asp isomerization in tau. In vitro aging of monomeric and aggregated recombinant tau revealed that tau isomerizes significantly faster than any similar protein within our data set, which is likely related to its correlation with cognition in Alzheimer's disease.
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Affiliation(s)
- Thomas
A. Shoff
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Brielle Van Orman
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Vivian C. Onwudiwe
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Joseph C. Genereux
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Ryan R. Julian
- Department of Chemistry, University of California, Riverside, California 92521, United States
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2
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Frostadottir D, Welinder C, Perez R, Dahlin LB. Refinement of Protein Extraction Protocols for Human Peripheral Nerve Tissue. ACS OMEGA 2025; 10:5111-5118. [PMID: 39959086 PMCID: PMC11822717 DOI: 10.1021/acsomega.4c11373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2024] [Revised: 01/14/2025] [Accepted: 01/23/2025] [Indexed: 02/18/2025]
Abstract
Our aim was to establish an effective method for protein extraction from freshly frozen human peripheral nerves, determine the minimum amount required for consistent protein extraction outcomes, and assess which method produced the highest number of protein identities. Five extraction methods were compared using 8 M urea and Ripa buffer using either the Bullet Blender or Bioruptor. Out of the total 2619 identified proteins, protein extraction using the Ripa buffer combined with either Bioruptor or Bullet Blender resulted in the identification of 1582 (60%) and 1615 (62%) proteins, respectively. In contrast, using 8 M urea and Bioruptor for protein extraction resulted in 1022 proteins (39%), whereas employing Bullet Blender yielded 1446 proteins (55%). Sample amounts, ranging from 0.6 to 10 mg, were prepared with consistent protein extraction outcome obtained for samples ≥1.2 mg. Combining Ripa and 8 M urea with Bullet Blender increased protein identification to 2126 (81%). Proteins were classified by their cell components, molecular functions, and biological processes. Furthermore, a subclassification of proteins involved in the extracellular matrix (ECM) was introduced. We recommend the use of Ripa buffer, in combination with 8 M urea and Bullet Blender for extracting proteins from fresh-frozen human nerves weighing ≥1.2 mg.
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Affiliation(s)
- Drifa Frostadottir
- Department
of Translational Medicine − Hand Surgery, Lund University, Malmö S-20502, Sweden
- Department
of Hand Surgery, Skane University Hospital, Malmö S-20502, Sweden
| | - Charlotte Welinder
- Faculty of
Medicine, Department of Clinical Sciences Lund, Mass Spectrometry, Lund University, Lund S-20502, Sweden
| | - Raquel Perez
- Department
of Translational Medicine − Hand Surgery, Lund University, Malmö S-20502, Sweden
- Unit for
Social Epidemiology, Department of Clinical Sciences Malmö, Lund University, Malmö S-20502, Sweden
| | - Lars B. Dahlin
- Department
of Translational Medicine − Hand Surgery, Lund University, Malmö S-20502, Sweden
- Department
of Hand Surgery, Skane University Hospital, Malmö S-20502, Sweden
- Department
of Biomedical and Clinical Sciences, Linköping
University, SE-581 83 Linköping, Sweden
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3
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Moon C, Park CS, Jeong CM, Lee HS, Kim K, Byeon H, Eom D, Kim HH. LC-MS/MS analysis of surface and lysate N-glycans of CHO-K1 cells: Structure, relative quantity, and absolute quantity. J Chromatogr B Analyt Technol Biomed Life Sci 2025; 1252:124441. [PMID: 39756143 DOI: 10.1016/j.jchromb.2024.124441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2024] [Revised: 12/20/2024] [Accepted: 12/24/2024] [Indexed: 01/07/2025]
Abstract
Chinese hamster ovary (CHO)-K1 cells are widely used in biomedical research relevant to cancer, toxicity screening, and viruses, as well as in the production of recombinant proteins for biopharmaceuticals. In this study, liquid chromatography (LC)-electrospray ionization (ESI)-higher energy collisional dissociation (HCD)-tandem mass spectrometry (MS/MS) was used to characterize the surface and lysate N-glycans of CHO-K1 cells and analyze their structures. The relative quantity (%) of each N-glycan and absolute quantity (pmol) of total N-glycans were also obtained. In total, 37 surface and 30 lysate N-glycans were identified. Each of these two fractions contained eight high-mannose type (required for protection against proteolysis and N-glycosylation of recombinant proteins) at 28.8 % (the sum of the relative quantities of each N-glycan) and 66.5 %, respectively. Additionally, the surface and lysate N-glycans differed in their levels of sialyation (affect cell-cell interactions; 48.1 % and 13.5 %), fucosylation (affect cell signaling; 37.9 % and 25.5 %), and terminal-galactosylation (prerequisite for subsequent sialylation; 36.6 % and 20.9 %). These results indicate that the lysate of CHO-K1 cells contained more mannosylated (2.3-fold) N-glycans compared to the surface, which contained relatively more sialylated (3.6-fold), slightly more highly fucosylated (1.5-fold), and more terminal-galactosylated (1.8-fold) N-glycans. The sum of the absolute quantity of each N-glycan was obtained as a ratio of 1 (1,778.7 pmol; surface):2.2 (3,887.3 pmol; lysate) from approximately 5 × 106 CHO-K1 cells. This study is the first to compare the surface and lysate N-glycans of CHO-K1 cells using LC-ESI-HCD-MS/MS. The results can be used to control and optimize biotechnology and biomedical research using CHO-K1 cells.
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Affiliation(s)
- Chulmin Moon
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Chi Soo Park
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Chang Myeong Jeong
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Han Seul Lee
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Kyuran Kim
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Haeun Byeon
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Daeun Eom
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Ha Hyung Kim
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea.
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4
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Meirelles MG, Fénero CIM, Nornberg BF, Camara NOS, Marins LF. In Vivo Measurement of Intestinal Permeability to Macromolecules in Adult Zebrafish ( Danio rerio). Zebrafish 2025; 22:1-10. [PMID: 39895322 DOI: 10.1089/zeb.2024.0167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2025] Open
Abstract
Intestinal permeability plays a crucial role in intestinal barrier function. Altered intestinal permeability is well documented in numerous chronic diseases and may serve as a risk factor for disease onset as well as a target for innovative therapeutic strategies. While reliable and sensitive approaches for studying intestinal permeability have been established in animal models, such as mice and zebrafish larvae, methods for investigating this in adult zebrafish remain a considerable challenge. The zebrafish has emerged as a valuable model for studying intestinal development, physiology, and disease. Moreover, zebrafish offer certain advantages over rodent models, such as the ability to evaluate the dynamic interactions of labeled markers in vivo and in real time. In this study, we present a comprehensive pipeline for assessing in vivo intestinal permeability in adult zebrafish using fluorescent-labeled dextran. Detailed protocols for fish handling, reagent preparation, optimization of reagent dosage and delivery routes, and quantification of fluorescent markers in extraintestinal sites are provided. Our findings suggest that zebrafish hold promise as an alternative model for in vivo investigations of intestinal permeability induced by genetic, pathophysiological, and/or pharmacological events.
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Affiliation(s)
- Marcela G Meirelles
- LEGENE-Research Group in Genetic Engineering and Biotechnology, Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Rio Grande-FURG, Rio Grande, Brazil
| | - Camila I M Fénero
- Department of Immunology, Institute of Biomedical Science, University of São Paulo-USP, São Paulo, Brazil
| | - Bruna F Nornberg
- LEGENE-Research Group in Genetic Engineering and Biotechnology, Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Rio Grande-FURG, Rio Grande, Brazil
| | - Niels Olsen S Camara
- Department of Immunology, Institute of Biomedical Science, University of São Paulo-USP, São Paulo, Brazil
| | - Luis Fernando Marins
- LEGENE-Research Group in Genetic Engineering and Biotechnology, Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Rio Grande-FURG, Rio Grande, Brazil
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5
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Jang JY, Moon C, Kim K, Park CS, Jang L, Jeong CM, Lee HS, Byeon H, Kim HH. Structural and quantitative characterization of membrane N-glycans from MIN6 mouse pancreatic beta cells using liquid chromatography-quadrupole-Orbitrap tandem mass spectrometry. J Pharm Biomed Anal 2025; 252:116494. [PMID: 39369550 DOI: 10.1016/j.jpba.2024.116494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Revised: 09/25/2024] [Accepted: 09/29/2024] [Indexed: 10/08/2024]
Abstract
MIN6, a mouse pancreatic beta cell line, is used in diabetes research, and the cellular N-glycoproteins in membrane are important in regulating the metabolism of insulin secretion. However, the identities of N-glycans in MIN6 cells are yet to be fully elucidated. In this study, the structures of N-glycans were analyzed using liquid chromatography-electrospray ionization-higher energy collisional dissociation-tandem mass spectrometry. The abundances (%) of each N-glycan relative to the total N-glycans (100 %) were also obtained. Fifty N-glycans (with relative abundance of each > 0.5 %) were obtained, revealing 22 bisecting N-acetylglucosamine (GlcNAc; associated with cell adhesion and growth; sum of relative abundance of each: 27.1 %), 21 core-fucosylated (associated with glucose sensing and insulin secretion regulation; 28.3 %), and 16 sialylated (N-acetylneuraminic acid; related to the expression of glucose transporters and diabetes;15.5 %) N-glycans. Membranes contained higher bisecting GlcNAc and core-fucosylation, similar sialylation, but less high-mannosylation than the lysate (the cellular contents). Notably, all bisecting GlcNAc N-glycans were categorized into structures with (16.6 %) or without (10.5 %) core-fucosylation and with (6.9 %) or without (20.2 %) sialylation. The bisecting GlcNAc structures were not found in human islets; moreover, sialylation levels were 6.9 times higher than for human islets. These structural characteristics of N-glycans affect their cell adhesion and distribution through homologous interactions between beta cells, leading to increased insulin secretion efficiency. This study is the first to identify the structures and quantities of 50 N-glycans in MIN6 cell membranes that may play an important role in regulating the functions of pancreatic beta cells.
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Affiliation(s)
- Ji Yeon Jang
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Chulmin Moon
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Kyuran Kim
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Chi Soo Park
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Leeseul Jang
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Chang Myeong Jeong
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Han Seul Lee
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Haeun Byeon
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Ha Hyung Kim
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea.
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6
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Shoff TA, Van Orman B, Onwudiwe VC, Genereux JC, Julian RR. Unusually Rapid Isomerization of Aspartic Acid in Tau. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.04.626870. [PMID: 39677806 PMCID: PMC11643016 DOI: 10.1101/2024.12.04.626870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/17/2024]
Abstract
Spontaneous chemical modifications in long-lived proteins can potentially change protein structure in ways that impact proteostasis and cellular health. For example, isomerization of aspartic acid interferes with protein turnover and is anticorrelated with cognitive acuity in Alzheimer's disease. However, few isomerization rates have been determined for Asp residues in intact proteins. To remedy this deficiency, we used protein extracts from SH-SY5Y neuroblastoma cells as a source of a complex, brain-relevant proteome with no baseline isomerization. Cell lysates were aged in vitro to generate isomers, and extracted proteins were analyzed by data-independent acquisition (DIA) liquid chromatography-mass spectrometry (LC-MS). Although no Asp isomers were detected at Day 0, isomerization increased across time and was quantifiable for 105 proteins by Day 50. Data analysis revealed that isomerization rate is influenced by both primary sequence and secondary structure, suggesting that steric hindrance and backbone rigidity modulate isomerization. Additionally, we examined lysates extracted under gentle conditions to preserve protein complexes and found that protein-protein interactions often slow isomerization. Base catalysis was explored as a means to accelerate Asp isomerization due to findings of accelerated asparagine deamidation. However, no substantial rate enhancement was found for isomerization, suggesting fundamental differences in acid-base chemistry. With an enhanced understanding of Asp isomerization in proteins in general, we next sought to better understand Asp isomerization in tau. In vitro aging of monomeric and aggregated recombinant tau revealed that tau isomerizes significantly faster than any similar protein within our dataset, which is likely related to its correlation with cognition in Alzheimer's disease.
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Affiliation(s)
- Thomas A. Shoff
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Brielle Van Orman
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Vivian C. Onwudiwe
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Joseph C. Genereux
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Ryan R. Julian
- Department of Chemistry, University of California, Riverside, California 92521, United States
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7
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Bano N, Kainat KM, Ansari MI, Pal A, Sarkar S, Sharma PK. Identification of chemoresistance targets in doxorubicin-resistant lung adenocarcinoma cells using LC-MS/MS-based proteomics. J Chemother 2024:1-15. [PMID: 39101797 DOI: 10.1080/1120009x.2024.2385267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 07/03/2024] [Accepted: 07/24/2024] [Indexed: 08/06/2024]
Abstract
Acquired chemoresistance remains a significant challenge in the clinics as most of the treated cancers eventually emerge as hard-to-treat phenotypes. Therefore, identifying chemoresistance targets is highly warranted to manage the disease better. In this study, we employed a label-free LC-MS/MS-based quantitative proteomics analysis to identify potential targets and signaling pathways underlying acquired chemoresistance in a sub-cell line (A549DR) derived from the parental lung adenocarcinoma cells (A549) treated with gradually increasing doses of doxorubicin (DOX). Our proteomics analysis identified 146 upregulated and 129 downregulated targets in A549DR cells. The KEGG pathway and Gene ontology (GO) analysis of differentially expressed upregulated and downregulated proteins showed that most abundant upregulated pathways were related to metabolic pathways, cellular senescence, cell cycle, and p53 signaling. Meanwhile, the downregulated pathways were related to spliceosome, nucleotide metabolism, DNA replication, nucleotide excision repair, and nuclear-cytoplasmic transport. Further, STRING analysis of upregulated biological processes showed a protein-protein interaction (PPI) between CDK1, AKT2, SRC, STAT1, HDAC1, FDXR, FDX1, NPC1, ALDH2, GPx1, CDK4, and B2M, proteins. The identified proteins in this study might be the potential therapeutic targets for mitigating DOX resistance.
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Affiliation(s)
- Nuzhat Bano
- Food Toxicology Group, Food, Drug & Chemical, Environment, and Systems Toxicology (FEST) Division, CSIR-Indian Institute of Toxicology Research, Lucknow, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - K M Kainat
- Food Toxicology Group, Food, Drug & Chemical, Environment, and Systems Toxicology (FEST) Division, CSIR-Indian Institute of Toxicology Research, Lucknow, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Mohammad Imran Ansari
- Food Toxicology Group, Food, Drug & Chemical, Environment, and Systems Toxicology (FEST) Division, CSIR-Indian Institute of Toxicology Research, Lucknow, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Anjali Pal
- Food Toxicology Group, Food, Drug & Chemical, Environment, and Systems Toxicology (FEST) Division, CSIR-Indian Institute of Toxicology Research, Lucknow, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sana Sarkar
- Systems Toxicology Group, Food, Drug & Chemical, Environment and Systems Toxicology (FEST) Division, CSIR- Indian Institute of Toxicology Research, Lucknow, Uttar Pradesh, India
| | - Pradeep Kumar Sharma
- Food Toxicology Group, Food, Drug & Chemical, Environment, and Systems Toxicology (FEST) Division, CSIR-Indian Institute of Toxicology Research, Lucknow, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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8
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El Feky SE, Fakhry KA, Hussain AM, Ibrahim FAR, Morsi MI. MLKL regulates radiation-induced death in breast cancer cells: an interplay between apoptotic and necroptotic signals. Med Oncol 2024; 41:172. [PMID: 38862702 DOI: 10.1007/s12032-024-02415-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 05/25/2024] [Indexed: 06/13/2024]
Abstract
Resistance to caspase-dependent apoptosis is often responsible for treatments failure in cancer. Necroptosis is a type of programmed necrosis that occurs under caspase-deficient conditions that could overcome apoptosis resistance. Our purpose was to investigate the interrelationship between apoptotic and necroptotic death pathways and their influence on the response of breast cancer cells to radiotherapy in vitro. Human BC cell lines MCF-7 and MDA-MB-231 were treated with ionizing radiation, and then several markers of apoptosis, necroptosis, and survival were assessed in the presence and absence of necroptosis inhibition. MLKL knockdown was achieved by siRNA transfection. Our main findings emphasize the role of necroptosis in cellular response to radiation represented in the dose- and time-dependent elevated expression of necroptotic markers RIPK1, RIPK3, and MLKL. Knockdown of necroptotic marker MLKL by siRNA led to a significant elevation in MDA-MB-231 and MCF-7 survival with a dose modifying factor (DMF) of 1.23 and 1.61, respectively. Apoptotic markers Caspase 8 and TRADD showed transitory or delayed upregulation, indicating that apoptosis was not the main mechanism by which cells respond to radiation exposure. Apoptotic markers also showed a significant elevation following MLKL knockdown, suggesting its role either as a secondary or death alternative pathway. The result of our study emphasizes the critical role of the necroptotic pathway in regulating breast cancer cells responses to radiotherapy and suggests a promising utilization of its key modulator, MLKL, as a treatment strategy to improve the response to radiotherapy.
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Affiliation(s)
- Shaymaa E El Feky
- Radiation Sciences Department, Medical Research Institute, University of Alexandria, Alexandria, Egypt.
| | - Karen Adel Fakhry
- Radiation Sciences Department, Medical Research Institute, University of Alexandria, Alexandria, Egypt
| | - Amr M Hussain
- Cancer Management and Research Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Fawziya A R Ibrahim
- Applied Medical Chemistry Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Mohamed Ibrahim Morsi
- Radiation Sciences Department, Medical Research Institute, University of Alexandria, Alexandria, Egypt
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9
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Zhang J, Wei L, Miao J, Yu Y, Yu N, Hu Q, Chen H, Chen Y. Authenticity identification of animal species in characteristic milk by integration of shotgun proteomics and scheduled multiple reaction monitoring (MRM) based on tandem mass spectrometry. Food Chem 2024; 436:137736. [PMID: 37863000 DOI: 10.1016/j.foodchem.2023.137736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/19/2023] [Accepted: 10/09/2023] [Indexed: 10/22/2023]
Abstract
Milk is one of the oldest natural dairies with high value, which has different species including cow, camel, donkey, goat, sheep, buffalo, yak and et al. However, economically motivated adulteration of non-cow milk with cheaper cow milk occurs frequently. To develop a high-throughput approach for milk species authentication, integration of shotgun proteomics and scheduled multiple reaction monitoring (MRM) was developed. In total, 37 specific peptides were screened as unique to different species. Specific peptides processing stability was investigated under different treatment (heat, pressure, fermentation). Subsequently, four quantitative ion pairs of peptides from cow milk and six quantitative ion pairs of peptides from six non-cow milks were selected for the adulteration quantitative analysis. The method is capable of detection adulteration in the range of 1%-100%, and the quantitative recoveries ranged from 91.07% to 111.75%. The results suggested that combination of shotgun proteomics and MRM had potential for the milk species authentication.
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Affiliation(s)
- Jiukai Zhang
- Chinese Academy of Inspection and Quarantine, Beijing 100176, PR China
| | - Liyang Wei
- Chinese Academy of Inspection and Quarantine, Beijing 100176, PR China
| | - Jinliang Miao
- Chinese Academy of Inspection and Quarantine, Beijing 100176, PR China
| | - Yue Yu
- Chinese Academy of Inspection and Quarantine, Beijing 100176, PR China; School of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, PR China
| | - Ning Yu
- Chinese Academy of Inspection and Quarantine, Beijing 100176, PR China
| | - Qian Hu
- Chinese Academy of Inspection and Quarantine, Beijing 100176, PR China
| | - He Chen
- Institute of Quality Standard & Testing Technology for Agro-products, Xinjiang Academy of Agricultural Sciences, 830091, PR China
| | - Ying Chen
- Chinese Academy of Inspection and Quarantine, Beijing 100176, PR China.
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10
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Koutsilieri S, Mickols E, Végvári Á, Lauschke VM. Proteomic workflows for deep phenotypic profiling of 3D organotypic liver models. Biotechnol J 2024; 19:e2300684. [PMID: 38509783 DOI: 10.1002/biot.202300684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 02/07/2024] [Accepted: 02/15/2024] [Indexed: 03/22/2024]
Abstract
Organotypic human tissue models constitute promising systems to facilitate drug discovery and development. They allow to maintain native cellular phenotypes and functions, which enables long-term pharmacokinetic and toxicity studies, as well as phenotypic screening. To trace relevant phenotypic changes back to specific targets or signaling pathways, comprehensive proteomic profiling is the gold-standard. A multitude of proteomic workflows have been applied on 3D tissue models to quantify their molecular phenotypes; however, their impact on analytical results and biological conclusions in this context has not been evaluated. The performance of twelve mass spectrometry-based global proteomic workflows that differed in the amount of cellular input, lysis protocols and quantification methods was compared for the analysis of primary human liver spheroids. Results differed majorly between protocols in the total number and subcellular compartment bias of identified proteins, which is particularly relevant for the reliable quantification of transporters and drug metabolizing enzymes. Using a model of metabolic dysfunction-associated steatotic liver disease, we furthermore show that critical disease pathways are robustly identified using a standardized high throughput-compatible workflow based on thermal lysis, even using only individual spheroids (1500 cells) as input. The results increase the applicability of proteomic profiling to phenotypic screens in organotypic microtissues and provide a scalable platform for deep phenotyping from limited biological material.
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Affiliation(s)
- Stefania Koutsilieri
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Evgeniya Mickols
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Department of Pharmacy, Uppsala University, Uppsala, Sweden
| | - Ákos Végvári
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Volker M Lauschke
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
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11
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Akkurt Arslan M, Rabut G, Chardonnet S, Pionneau C, Kobal A, Gratas Pelletier M, Harfouche N, Réaux La Goazigo A, Baudouin C, Brignole-Baudouin F, Kessal K. Expanded biochemical analyses of human tear fluid: Polyvalent faces of the schirmer strip. Exp Eye Res 2023; 237:109679. [PMID: 37858607 DOI: 10.1016/j.exer.2023.109679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 09/27/2023] [Accepted: 10/16/2023] [Indexed: 10/21/2023]
Abstract
The tear film forms a protective barrier between the ocular surface and the external environment. Despite its small volume, recent advancements in preanalytical and analytical procedures have enabled its in-depth analysis using multiple approaches. However, the diversity of tear film collection methods and the lack of standardization in pre-analytical methods represent the main obstacles to reproducible results and comparison among different studies. In this study, we first improved the pre-analytical procedures for the extraction of various molecular entities from Schirmer strips (ScS). Subsequently, our investigation focused on analyzing the molecular variances that might occur between two primary tear collection methods: capillary tube (CT) and ScS. Additionally, we examined different parts of the ScS to underscore these variations, which could serve as crucial factors for developing a standardized, optimized protocol for sample processing. Our results show that the inclusion of surfactants in the extraction process enhanced both the yield of protein extraction and the number of proteins identified in ScS, by effectively lysing the cells and improving the solubility of several intracellular proteins. In addition to proteins, nucleic acids could also be recovered for gene expression analyses, particularly from the bulb region of the ScS which is placed in the cul-de-sac. Despite their diluted nature, extracts from ScS remain a suitable material for retrieving tear proteins such as IL-17A at levels as low as the fg/mL range, thanks to highly sensitive immunoassays. Collection methods can affect measured tear protein levels. Lactoferrin is found in higher percentages in capillary electrophoresis analysis of tears collected using ScS compared to tears collected by CT (39.6 ± 4.8% versus 31 ± 4.4%).
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Affiliation(s)
- Murat Akkurt Arslan
- Institut National de La Santé et de La Recherche Médicale INSERM UMRS 968, CNRS, UMR 7210, Institut de La Vision, IHU ForeSight, Sorbonne Université UM80, 75012, Paris, France.
| | - Ghislaine Rabut
- Hôpital National de La Vision des 15-20, Service 3, 75012, Paris, France.
| | - Solenne Chardonnet
- Sorbonne Université, INSERM, UMS Production et Analyse des Données en Sciences de La Vie et en Santé, PASS, Plateforme Post-génomique de La Pitié-Salpêtrière, P3S, 75013, Paris, France.
| | - Cédric Pionneau
- Sorbonne Université, INSERM, UMS Production et Analyse des Données en Sciences de La Vie et en Santé, PASS, Plateforme Post-génomique de La Pitié-Salpêtrière, P3S, 75013, Paris, France.
| | - Alfred Kobal
- Hôpital National de La Vision des 15-20, Laboratoire d'Ophtalmobiologie, 75012, Paris, France.
| | | | - Nouara Harfouche
- Hôpital National de La Vision des 15-20, Laboratoire d'Ophtalmobiologie, 75012, Paris, France.
| | - Annabelle Réaux La Goazigo
- Institut National de La Santé et de La Recherche Médicale INSERM UMRS 968, CNRS, UMR 7210, Institut de La Vision, IHU ForeSight, Sorbonne Université UM80, 75012, Paris, France.
| | - Christophe Baudouin
- Institut National de La Santé et de La Recherche Médicale INSERM UMRS 968, CNRS, UMR 7210, Institut de La Vision, IHU ForeSight, Sorbonne Université UM80, 75012, Paris, France; Hôpital National de La Vision des 15-20, Service 3, 75012, Paris, France; Hôpital National de La Vision des 15-20, INSERM-DGOS CIC 1423, IHU FOReSIGHT, 75012, Paris, France; Hôpital Ambroise Paré, Assistance Publique-Hôpitaux de Paris APHP, Service d'Ophtalmologie, Université Versailles Saint-Quentin-en-Yvelines, Paris Saclay, 92100, Boulogne, France.
| | - Françoise Brignole-Baudouin
- Institut National de La Santé et de La Recherche Médicale INSERM UMRS 968, CNRS, UMR 7210, Institut de La Vision, IHU ForeSight, Sorbonne Université UM80, 75012, Paris, France; Hôpital National de La Vision des 15-20, Laboratoire d'Ophtalmobiologie, 75012, Paris, France; Hôpital National de La Vision des 15-20, INSERM-DGOS CIC 1423, IHU FOReSIGHT, 75012, Paris, France; Faculté de Pharmacie de Paris, Université Paris Cité, 75006 Paris, France.
| | - Karima Kessal
- Institut National de La Santé et de La Recherche Médicale INSERM UMRS 968, CNRS, UMR 7210, Institut de La Vision, IHU ForeSight, Sorbonne Université UM80, 75012, Paris, France; Hôpital National de La Vision des 15-20, Laboratoire d'Ophtalmobiologie, 75012, Paris, France; Hôpital National de La Vision des 15-20, INSERM-DGOS CIC 1423, IHU FOReSIGHT, 75012, Paris, France.
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12
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Riisom M, Jamieson SMF, Hartinger CG. Critical evaluation of cell lysis methods for metallodrug studies in cancer cells. Metallomics 2023; 15:mfad048. [PMID: 37596065 DOI: 10.1093/mtomcs/mfad048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/01/2023] [Indexed: 08/20/2023]
Abstract
Intracellular accumulation studies are a key step in metallodrug development but often variable results are obtained. Therefore, we aimed here to investigate different protocols for efficient and reproducible lysis of cancer cells in terms of protein content in lysates and in cell uptake studies of the Ru anticancer complex [chlorido(8-oxyquinolinato)(η6-p-cymene)ruthenium(II)] ([Ru(cym)(HQ)Cl]). The physical lysis methods osmosis and sonication were chosen for comparison with chemical lysis with the radioimmunoprecipitation assay (RIPA) buffer. Based on the protein content and the total Ru accumulated in the lysates, the latter determined using inductively coupled plasma-mass spectrometry, RIPA buffer was the most efficient lysis method. Measurements of plastic adsorption blanks revealed that the higher Ru content determined in the RIPA buffer lysis samples may be due a higher amount of Ru extracted from the plastic incubation plates compared with osmosis and sonication. Overall, we found that the choice of lysis method needs to be matched to the information sought and we suggest the least disruptive osmosis method might be the best choice for labile drug-biomolecule adducts. Minimal differences were found for experiments aimed at measuring the overall cell uptake of the Ru complex.
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Affiliation(s)
- Mie Riisom
- School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
- Auckland Cancer Society Research Centre, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Stephen M F Jamieson
- Auckland Cancer Society Research Centre, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
- Department of Pharmacology and Clinical Pharmacology, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Christian G Hartinger
- School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
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13
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Sule R, Rivera G, Gomes AV. Western blotting (immunoblotting): history, theory, uses, protocol and problems. Biotechniques 2023; 75:99-114. [PMID: 36971113 DOI: 10.2144/btn-2022-0034] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
Western blotting (immunoblotting) is a powerful and commonly used technique that is capable of detecting or semiquantifying an individual protein from complex mixtures of proteins extracted from cells or tissues. The history surrounding the origin of western blotting, the theory behind the western blotting technique, a comprehensive protocol and the uses of western blotting are presented. Lesser known and significant problems in the western blotting field and troubleshooting of common problems are highlighted and discussed. This work is a comprehensive primer and guide for new western blotting researchers and those interested in a better understanding of the technique or getting better results.
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Affiliation(s)
- Rasheed Sule
- Department of Neurobiology, Physiology & Behavior, University of California, Davis, Davis, CA 95616, USA
| | - Gabriela Rivera
- Department of Neurobiology, Physiology & Behavior, University of California, Davis, Davis, CA 95616, USA
| | - Aldrin V Gomes
- Department of Neurobiology, Physiology & Behavior, University of California, Davis, Davis, CA 95616, USA
- Department of Physiology & Membrane Biology, University of California, Davis, Davis, CA 95616, USA
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14
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Sebastian S, Hoffmann MK, Howard D, Young C, Washington J, Unterweger H, Alexiou C, Turnbull T, D’Andrea R, Hoffmann P, Kempson I. Kinetic Effects of Transferrin-Conjugated Gold Nanoparticles on the Antioxidant Glutathione-Thioredoxin Pathway. Antioxidants (Basel) 2023; 12:1617. [PMID: 37627612 PMCID: PMC10451790 DOI: 10.3390/antiox12081617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/08/2023] [Accepted: 08/13/2023] [Indexed: 08/27/2023] Open
Abstract
Nanoparticle-based therapeutics are being clinically translated for treating cancer. Even when thought to be biocompatible, nanoparticles are being increasingly identified as altering cell regulation and homeostasis. Antioxidant pathways are important for maintaining cell redox homeostasis and play important roles by maintaining ROS levels within tolerable ranges. Here, we sought to understand how a model of a relatively inert nanoparticle without any therapeutic agent itself could antagonize a cancer cell lines' antioxidant mechanism. A label-free protein expression approach was used to assess the glutathione-thioredoxin antioxidative pathway in a prostate cancer cell line (PC-3) after exposure to gold nanoparticles conjugated with a targeting moiety (transferrin). The impact of the nanoparticles was also corroborated through morphological analysis with TEM and classification of pro-apoptotic cells by way of the sub-G0/G1 population via the cell cycle and annexin V apoptosis assay. After a two-hour exposure to nanoparticles, major proteins associated with the glutathione-thioredoxin antioxidant pathway were downregulated. However, this response was acute, and in terms of protein expression, cells quickly recovered within 24 h once nanoparticle exposure ceased. The impact on PRDX-family proteins appears as the most influential factor in how these nanoparticles induced an oxidative stress response in the PC-3 cells. An apparent adaptive response was observed if exposure to nanoparticles continued. Acute exposure was observed to have a detrimental effect on cell viability compared to continuously exposed cells. Nanoparticle effects on cell regulation likely provide a compounding therapeutic advantage under some circumstances, in addition to the action of any cytotoxic agents; however, any therapeutic advantage offered by nanoparticles themselves with regard to vulnerabilities specific to the glutathione-thioredoxin antioxidative pathway is highly temporal.
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Affiliation(s)
- Sonia Sebastian
- Future Industries Institute, University of South Australia, Adelaide, SA 5095, Australia; (S.S.); (D.H.); (T.T.)
- Clinical Health Sciences, University of South Australia, Adelaide, SA 5000, Australia; (M.K.H.); (C.Y.); (P.H.)
| | - Manuela Klingler Hoffmann
- Clinical Health Sciences, University of South Australia, Adelaide, SA 5000, Australia; (M.K.H.); (C.Y.); (P.H.)
- Mass Spectrometry & Proteomics Group, Clinical Health Sciences, University of South Australia, Adelaide, SA 5000, Australia
| | - Douglas Howard
- Future Industries Institute, University of South Australia, Adelaide, SA 5095, Australia; (S.S.); (D.H.); (T.T.)
| | - Clifford Young
- Clinical Health Sciences, University of South Australia, Adelaide, SA 5000, Australia; (M.K.H.); (C.Y.); (P.H.)
- Mass Spectrometry & Proteomics Group, Clinical Health Sciences, University of South Australia, Adelaide, SA 5000, Australia
| | - Jenni Washington
- Clinical Health Sciences, University of South Australia, Adelaide, SA 5000, Australia; (M.K.H.); (C.Y.); (P.H.)
- Mass Spectrometry & Proteomics Group, Clinical Health Sciences, University of South Australia, Adelaide, SA 5000, Australia
| | - Harald Unterweger
- Department of Otorhinolaryngology, Head and Neck Surgery, Section of Experimental Oncology and Nanomedicine (SEON), Else Kröner-Fresenius-Stiftung Professorship, Universitätsklinikum Erlangen, 91054 Erlangen, Germany; (H.U.); (C.A.)
| | - Christoph Alexiou
- Department of Otorhinolaryngology, Head and Neck Surgery, Section of Experimental Oncology and Nanomedicine (SEON), Else Kröner-Fresenius-Stiftung Professorship, Universitätsklinikum Erlangen, 91054 Erlangen, Germany; (H.U.); (C.A.)
| | - Tyron Turnbull
- Future Industries Institute, University of South Australia, Adelaide, SA 5095, Australia; (S.S.); (D.H.); (T.T.)
| | - Richard D’Andrea
- Centre for Cancer Biology, University of South Australia, Adelaide, SA 5000, Australia;
| | - Peter Hoffmann
- Clinical Health Sciences, University of South Australia, Adelaide, SA 5000, Australia; (M.K.H.); (C.Y.); (P.H.)
- Mass Spectrometry & Proteomics Group, Clinical Health Sciences, University of South Australia, Adelaide, SA 5000, Australia
| | - Ivan Kempson
- Future Industries Institute, University of South Australia, Adelaide, SA 5095, Australia; (S.S.); (D.H.); (T.T.)
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15
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Billinger K, Okai CA, Russ M, Koy C, Röwer C, Opuni KFM, Illges H, Pecks U, Glocker MO. Dried serum spots on pre-punched filter paper discs are ready-to-use storage and shipping devices for blood-borne antigens and antibodies. J Immunol Methods 2023; 519:113519. [PMID: 37419022 DOI: 10.1016/j.jim.2023.113519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/09/2023]
Abstract
Dried serum spots that are well prepared can be attractive alternatives to frozen serum samples for shelving specimens in a medical or research center's biobank and mailing freshly prepared serum to specialized laboratories. During the pre-analytical phase, complications can arise which are often challenging to identify or are entirely overlooked. These complications can lead to reproducibility issues, which can be avoided in serum protein analysis by implementing optimized storage and transfer procedures. With a method that ensures accurate loading of filter paper discs with donor or patient serum, a gap in dried serum spot preparation and subsequent serum analysis shall be filled. Pre-punched filter paper discs with a 3 mm diameter are loaded within seconds in a highly reproducible fashion (approximately 10% standard deviation) when fully submerged in 10 μl of serum, named the "Submerge and Dry" protocol. Such prepared dried serum spots can store several hundred micrograms of proteins and other serum components. Serum-borne antigens and antibodies are reproducibly released in 20 μl elution buffer in high yields (approximately 90%). Dried serum spot-stored and eluted antigens kept their epitopes and antibodies their antigen binding abilities as was assessed by SDS-PAGE, 2D gel electrophoresis-based proteomics, and Western blot analysis, suggesting pre-punched filter paper discs as handy solution for serological tests.
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Affiliation(s)
- Kira Billinger
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Schillingallee 69, 18057 Rostock, Germany
| | - Charles A Okai
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Schillingallee 69, 18057 Rostock, Germany
| | - Manuela Russ
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Schillingallee 69, 18057 Rostock, Germany
| | - Cornelia Koy
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Schillingallee 69, 18057 Rostock, Germany
| | - Claudia Röwer
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Schillingallee 69, 18057 Rostock, Germany
| | - Kwabena F M Opuni
- Department of Pharmaceutical Chemistry, School of Pharmacy, College of Health Science, University of Ghana, P. O. Box LG43, Legon, Ghana
| | - Harald Illges
- Department of Applied Natural Sciences, Immunology and Cell Biology, Institute of Functional Gene Analytics, University of Applied Sciences Bonn-Rhein-Sieg, von-Liebig-Str. 20, 53359 Rheinbach, Germany
| | - Ulrich Pecks
- Department of Obstetrics and Gynecology, Medical Faculty, University of Schleswig-Holstein, Campus Kiel, Arnold-Heller-Straße 3, 24105 Kiel, Germany
| | - Michael O Glocker
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Schillingallee 69, 18057 Rostock, Germany.
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16
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Cheng L, Xu Y, Zhu K, Liang B, Zhang S, Liu P. Protein sample preparation for tissue distribution study. Proteomics Clin Appl 2023; 17:e2200088. [PMID: 36333925 DOI: 10.1002/prca.202200088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 10/18/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022]
Abstract
PURPOSE The distribution and expression level of a protein among animal tissues is indicative of its possible roles. It is important to establish a generally applicable method to prepare protein samples with high-quality and achieve near 100% recovery of proteins from animal tissues. EXPERIMENTAL DESIGN During preparation, to sufficiently dissolve and maintain stability of almost all proteins from tissues, as well as to avoid most contaminations affecting protein detection, 2×SDS Sample Buffer, sonication and trichloroacetic acid precipitation are applied. RESULTS Here we provide a relatively simple, reproducible, and broadly applicable method for studying protein distribution in most tissues, in which the issues resulting from protein degradation and modification during sample preparation and assay interference by other cellular components like neutral lipids and glycogen could be overcome. Furthermore, this method represents the protein content by equal wet tissue mass, which is a better means to present the expression level of a protein in various tissues. High-quality protein samples from almost all tissues could be prepared. CONCLUSIONS AND CLINICAL RELEVANCE The samples produced are amenable to tissue distribution analysis by Western blotting and for silver/Coomassie staining, proteomics, and other protein analyses, which would contribute to potential biomarkers or treatments for a disease.
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Affiliation(s)
- Linjia Cheng
- Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China.,Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yilu Xu
- School of Basic Medical Sciences, Southwest Medical University, Luzhou, China.,Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Kangling Zhu
- Huazhong University of Science and Technology, Wuhan, China
| | - Bin Liang
- Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Shuyan Zhang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,Institute of Infectious Diseases, Beijing Key Laboratory of Emerging Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China.,Beijing Institute of Infectious Diseases, Beijing, China.,National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Pingsheng Liu
- School of Basic Medical Sciences, Southwest Medical University, Luzhou, China.,Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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17
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Pandya PH, Jannu AJ, Bijangi-Vishehsaraei K, Dobrota E, Bailey BJ, Barghi F, Shannon HE, Riyahi N, Damayanti NP, Young C, Malko R, Justice R, Albright E, Sandusky GE, Wurtz LD, Collier CD, Marshall MS, Gallagher RI, Wulfkuhle JD, Petricoin EF, Coy K, Trowbridge M, Sinn AL, Renbarger JL, Ferguson MJ, Huang K, Zhang J, Saadatzadeh MR, Pollok KE. Integrative Multi-OMICs Identifies Therapeutic Response Biomarkers and Confirms Fidelity of Clinically Annotated, Serially Passaged Patient-Derived Xenografts Established from Primary and Metastatic Pediatric and AYA Solid Tumors. Cancers (Basel) 2022; 15:259. [PMID: 36612255 PMCID: PMC9818438 DOI: 10.3390/cancers15010259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 01/04/2023] Open
Abstract
Establishment of clinically annotated, molecularly characterized, patient-derived xenografts (PDXs) from treatment-naïve and pretreated patients provides a platform to test precision genomics-guided therapies. An integrated multi-OMICS pipeline was developed to identify cancer-associated pathways and evaluate stability of molecular signatures in a panel of pediatric and AYA PDXs following serial passaging in mice. Original solid tumor samples and their corresponding PDXs were evaluated by whole-genome sequencing, RNA-seq, immunoblotting, pathway enrichment analyses, and the drug−gene interaction database to identify as well as cross-validate actionable targets in patients with sarcomas or Wilms tumors. While some divergence between original tumor and the respective PDX was evident, majority of alterations were not functionally impactful, and oncogenic pathway activation was maintained following serial passaging. CDK4/6 and BETs were prioritized as biomarkers of therapeutic response in osteosarcoma PDXs with pertinent molecular signatures. Inhibition of CDK4/6 or BETs decreased osteosarcoma PDX growth (two-way ANOVA, p < 0.05) confirming mechanistic involvement in growth. Linking patient treatment history with molecular and efficacy data in PDX will provide a strong rationale for targeted therapy and improve our understanding of which therapy is most beneficial in patients at diagnosis and in those already exposed to therapy.
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Affiliation(s)
- Pankita H. Pandya
- Department of Pediatrics, Hematology/Oncology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Asha Jacob Jannu
- Department of Biostatistics & Health Data Science Indiana, University School of Medicine, Indianapolis, IN 46202, USA
| | - Khadijeh Bijangi-Vishehsaraei
- Department of Pediatrics, Hematology/Oncology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Erika Dobrota
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Barbara J. Bailey
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Farinaz Barghi
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Harlan E. Shannon
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Niknam Riyahi
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Nur P. Damayanti
- Department of Neurological Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Courtney Young
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Rada Malko
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Ryli Justice
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Eric Albright
- Department of Pathology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - George E. Sandusky
- Department of Pathology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - L. Daniel Wurtz
- Department of Orthopedics Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Christopher D. Collier
- Department of Orthopedics Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Mark S. Marshall
- Department of Pediatrics, Hematology/Oncology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Rosa I. Gallagher
- Center for Applied Proteomics and Molecular Medicine, Institute for Biomedical Innovation, George Mason University, Manassas, VA 20110, USA
| | - Julia D. Wulfkuhle
- Center for Applied Proteomics and Molecular Medicine, Institute for Biomedical Innovation, George Mason University, Manassas, VA 20110, USA
| | - Emanuel F. Petricoin
- Center for Applied Proteomics and Molecular Medicine, Institute for Biomedical Innovation, George Mason University, Manassas, VA 20110, USA
| | - Kathy Coy
- Preclinical Modeling and Therapeutics Core, Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Melissa Trowbridge
- Preclinical Modeling and Therapeutics Core, Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Anthony L. Sinn
- Preclinical Modeling and Therapeutics Core, Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Jamie L. Renbarger
- Department of Pediatrics, Hematology/Oncology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Michael J. Ferguson
- Department of Pediatrics, Hematology/Oncology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Kun Huang
- Department of Biostatistics & Health Data Science Indiana, University School of Medicine, Indianapolis, IN 46202, USA
| | - Jie Zhang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - M. Reza Saadatzadeh
- Department of Pediatrics, Hematology/Oncology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Karen E. Pollok
- Department of Pediatrics, Hematology/Oncology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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18
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Watson MC, Williams C, Wang RM, Perreault LR, Sullivan KE, Stoppel WL, Black LD. Extracellular matrix and cyclic stretch alter fetal cardiomyocyte proliferation and maturation in a rodent model of heart hypoplasia. Front Cardiovasc Med 2022; 9:993310. [PMID: 36518682 PMCID: PMC9744115 DOI: 10.3389/fcvm.2022.993310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 10/10/2022] [Indexed: 01/22/2024] Open
Abstract
Introduction Birth defects, particularly those that affect development of the heart, are a leading cause of morbidity and mortality in infants and young children. Babies born with heart hypoplasia (heart hypoplasia) disorders often have a poor prognosis. It remains unclear whether cardiomyocytes from hypoplastic hearts retain the potential to recover growth, although this knowledge would be beneficial for developing therapies for heart hypoplasia disorders. The objective of this study was to determine the proliferation and maturation potential of cardiomyocytes from hypoplastic hearts and whether these behaviors are influenced by biochemical signaling from the extracellular matrix (ECM) and cyclic mechanical stretch. Method Congenital diaphragmatic hernia (CDH)-associated heart hypoplasia was induced in rat fetuses by maternal exposure to nitrofen. Hearts were isolated from embryonic day 21 nitrofen-treated fetuses positive for CDH (CDH+) and from fetuses without nitrofen administration during gestation. Results and discussion CDH+ hearts were smaller and had decreased myocardial proliferation, along with evidence of decreased maturity compared to healthy hearts. In culture, CDH+ cardiomyocytes remained immature and demonstrated increased proliferative capacity compared to their healthy counterparts. Culture on ECM derived from CDH+ hearts led to a significant reduction in proliferation for both CDH+ and healthy cardiomyocytes. Healthy cardiomyocytes were dosed with exogenous nitrofen to examine whether nitrofen may have an aberrant effect on the proliferative ability of cardiomyocyte, yet no significant change in proliferation was observed. When subjected to stretch, CDH+ cardiomyocytes underwent lengthening of sarcomeres while healthy cardiomyocyte sarcomeres were unaffected. Taken together, our results suggest that alterations to environmental cues such as ECM and stretch may be important factors in the pathological progression of heart hypoplasia.
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Affiliation(s)
- Matthew C. Watson
- Department of Biomedical Engineering, Tufts University, Medford, MA, United States
- Department of Mechanical Engineering, Tufts University, Medford, MA, United States
| | - Corin Williams
- Department of Biomedical Engineering, Tufts University, Medford, MA, United States
| | - Raymond M. Wang
- Department of Biomedical Engineering, Tufts University, Medford, MA, United States
| | - Luke R. Perreault
- Department of Biomedical Engineering, Tufts University, Medford, MA, United States
| | - Kelly E. Sullivan
- Department of Biomedical Engineering, Tufts University, Medford, MA, United States
| | - Whitney L. Stoppel
- Department of Biomedical Engineering, Tufts University, Medford, MA, United States
| | - Lauren D. Black
- Department of Biomedical Engineering, Tufts University, Medford, MA, United States
- Cellular, Molecular, and Developmental Biology Program, Sackler School for Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, MA, United States
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19
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del Olmo I, Verdes A, Álvarez‐Campos P. Distinct patterns of gene expression during regeneration and asexual reproduction in the annelid Pristina leidyi. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2022; 338:405-420. [PMID: 35604322 PMCID: PMC9790225 DOI: 10.1002/jez.b.23143] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 04/03/2022] [Accepted: 05/04/2022] [Indexed: 12/30/2022]
Abstract
Regeneration, the ability to replace lost body parts, is a widespread phenomenon in the animal kingdom often connected to asexual reproduction or fission, since the only difference between the two appears to be the stimulus that triggers them. Both developmental processes have largely been characterized; however, the molecular toolkit and genetic mechanisms underlying these events remain poorly unexplored. Annelids, in particular the oligochaete Pristina leidyi, provide a good model system to investigate these processes as they show diverse ways to regenerate, and can reproduce asexually through fission under laboratory conditions. Here, we used a comparative transcriptomics approach based on RNA-sequencing and differential gene expression analyses to understand the molecular mechanisms involved in anterior regeneration and asexual reproduction. We found 291 genes upregulated during anterior regeneration, including several regeneration-related genes previously reported in other annelids such as frizzled, paics, and vdra. On the other hand, during asexual reproduction, 130 genes were found upregulated, and unexpectedly, many of them were related to germline development during sexual reproduction. We also found important differences between anterior regeneration and asexual reproduction, with the latter showing a gene expression profile more similar to that of control individuals. Nevertheless, we identified 35 genes that were upregulated in both conditions, many of them related to cell pluripotency, stem cells, and cell proliferation. Overall, our results shed light on the molecular mechanisms that control anterior regeneration and asexual reproduction in annelids and reveal similarities with other animals, suggesting that the genetic machinery controlling these processes is conserved across metazoans.
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Affiliation(s)
- Irene del Olmo
- Department of Biology (Zoology)Universidad Autónoma de MadridMadridSpain
| | - Aida Verdes
- Department of Biodiversity and Evolutionary BiologyMuseo Nacional de Ciencias Naturales de MadridMadridSpain
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20
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Generation of cell-type-specific proteomes of neurodevelopment from human cerebral organoids. STAR Protoc 2022; 3:101774. [PMID: 36313540 PMCID: PMC9597183 DOI: 10.1016/j.xpro.2022.101774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Characterization of cerebral organoids has been challenging due to their heterogeneous nature. Here, we optimized a protocol to streamline the generation of FACS-purified cell populations from human cerebral organoids for proteomic analysis with liquid chromatography tandem mass spectrometry (LC-MS/MS). We describe the procedures for enzymatic dissociation of organoids into single-cell suspension, the generation of cell-type-specific lysates, peptide extraction, and proteomic analysis. This generalizable approach can be used to study temporal and cell-type-specific protein dynamics in developing cerebral organoids. For complete details on the use and execution of this protocol, please refer to Melliou et al. (2022).
A streamlined protocol covering human organoid cell sorting, lysis, and LC-MS/MS analysis Enzymatic dissociation of organoids into single-cell suspension for downstream analysis Generation of FACS-purified cell populations derived from cerebral organoids Label-free quantification of cell-type-specific populations within organoid cultures Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
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21
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Christodoulou P, Boutsikos P, Neophytou CM, Kyriakou TC, Christodoulou MI, Papageorgis P, Stephanou A, Patrikios I. Amygdalin as a chemoprotective agent in co-treatment with cisplatin. Front Pharmacol 2022; 13:1013692. [PMID: 36204233 PMCID: PMC9531591 DOI: 10.3389/fphar.2022.1013692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 09/06/2022] [Indexed: 11/13/2022] Open
Abstract
Amygdalin is a naturally occurring glycoside used in traditional Chinese medicine and is known to have anti-cancer properties. Even though the anti-cancer properties of amygdalin are well known, its effect on normal cells has not been thoroughly investigated. The aim of the present study was to investigate a possible chemo-protective role of amygdalin against the cytotoxic effects of chemotherapy for normal human cells. Specifically, it was tested in combination with a strong chemotherapeutic drug cisplatin. Human non-tumorigenic MCF12F epithelial cell line, human fibroblasts cells, human breast cancer MCF7 and MDA-MB-231 cells were treated with cisplatin in a dose- and time-depended manner in the absence or presence of amygdalin. When MCF12F cells and fibroblasts underwent pre-treatment with amygdalin followed by cisplatin treatment (24 h amygdalin + 24 h cisplatin), the cell viability was increased (22%, p < 0.001) as indicated using MTT assay. As attested by flow cytometry, combination treatment was associated with decreased the percentage of late apoptotic cells compared with monotherapy (fold-change of decrease = 1.6 and 4.5 for 15 and 20 μΜ, respectively). Also, the proteins expression of PUMA, p53, phospho-p53 and Bax decreased, when a combination treatment was used vs. cisplatin alone, while the proapoptotic proteins Bcl-2 and Bcl-xL exhibited an increased tendency in the presence of amygdalin. Moreover, the levels of pro-apoptotic genes PUMA, p53, and BAX mRNA were significantly downregulated (∼83%, ∼66%, and ∼44%, respectively) vs. cisplatin alone, while the mRNA levels of anti-apoptotic genes BCl-2 and Bcl-XL were upregulated (∼44.5% and ∼51%, respectively), vs. cisplatin alone after 24 h of combination treatment. The study on the Combination index (CI) assay indicated that amygdalin could be possibly considered as an antagonist to cisplatin (2.2 and 2.3) for MCF12F and fibroblast cells, respectively. In contrast, for the breast cancer MCF7 and MDA-MB-231 cells, amygdalin and cisplatin indicated a synergistic effect (0.8 and 0.65), respectively. Our present findings suggest that amygdalin has chemo-modulatory effect when used in co-treatment with cisplatin and is able to protect normal breast cells as well as the fibroblasts during chemotherapy treatment, indicating a strong selective chemoprotective ability and may contribute to a better quality of life for cancer patients.
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Affiliation(s)
- Panayiota Christodoulou
- School of Medicine, European University Cyprus, Nicosia, Cyprus
- Tumor Immunology and Biomarkers Laboratory, Basic and Translational Cancer Research Center, Department of Life Sciences, European University Cyprus, Nicosia, Cyprus
- *Correspondence: Panayiota Christodoulou,
| | | | - Christiana M. Neophytou
- Tumor Microenvironment, Metastasis and Experimental Therapeutics Laboratory, Basic and Translational Cancer Research Center, Department of Life Sciences, European University Cyprus, Nicosia, Cyprus
| | - Theodora-Christina Kyriakou
- School of Medicine, European University Cyprus, Nicosia, Cyprus
- Tumor Microenvironment, Metastasis and Experimental Therapeutics Laboratory, Basic and Translational Cancer Research Center, Department of Life Sciences, European University Cyprus, Nicosia, Cyprus
| | - Maria-Ioanna Christodoulou
- Tumor Immunology and Biomarkers Laboratory, Basic and Translational Cancer Research Center, Department of Life Sciences, European University Cyprus, Nicosia, Cyprus
| | - Panagiotis Papageorgis
- Tumor Microenvironment, Metastasis and Experimental Therapeutics Laboratory, Basic and Translational Cancer Research Center, Department of Life Sciences, European University Cyprus, Nicosia, Cyprus
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22
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Setiawati A, Jeong S, Brillian AI, Lee SH, Shim JG, Jung KH, Shin K. Fabrication of a Tailored, Hybrid Extracellular Matrix Composite. Macromol Biosci 2022; 22:e2200106. [PMID: 35765216 DOI: 10.1002/mabi.202200106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/24/2022] [Indexed: 11/10/2022]
Abstract
The extracellular matrix (ECM) is a network of connective fibers that supports cells living in their surroundings. Native ECM, generated by the secretory products of each tissue's resident cells, has a unique architecture with different protein composition depending on the tissue. Therefore, it is very difficult to artificially design in vivo architecture in tissue engineering. In this study, we fabricated a hybrid ECM scaffold from the basic structure of fibroblast-derived cellular ECMs by adding major ECM components of fibronectin (FN) and collagen (COL I) externally. It was confirmed that while maintaining the basic structure of the native ECM, major protein components can be regulated. Then, decellularization was performed to prepare hybrid ECM scaffolds with various protein compositions and we demonstrated that a liver-mimicking fibronectin (FN)-rich hybrid ECM promoted successful settling of H4IIE rat hepatoma cells. We believe that our method holds promise for the fabrication of scaffolds that provide a tailored cellular microenvironment for specific organs and serve as novel pathways for the replacement or regeneration of specific organ tissues. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Agustina Setiawati
- Department of Chemistry and Institute of Biological Interfaces, 35-Baekbeom-ro, Sogang University, Mapo-gu, Seoul, 04107, Republic of Korea.,Department of Life Science, 35-Baekbeom-ro, Sogang University, Mapo-gu, Seoul, 04107, Republic of Korea.,Faculty of Pharmacy, Paingan, Maguwoharjo, Depok, Sanata Dharma University, Sleman, Yogyakarta, 55284, Indonesia
| | - Sungwoo Jeong
- Department of Chemistry and Institute of Biological Interfaces, 35-Baekbeom-ro, Sogang University, Mapo-gu, Seoul, 04107, Republic of Korea
| | - Albertus Ivan Brillian
- Department of Chemistry and Institute of Biological Interfaces, 35-Baekbeom-ro, Sogang University, Mapo-gu, Seoul, 04107, Republic of Korea
| | - Sang Ho Lee
- Department of Chemistry and Institute of Biological Interfaces, 35-Baekbeom-ro, Sogang University, Mapo-gu, Seoul, 04107, Republic of Korea
| | - Jin-Gon Shim
- Department of Life Science, 35-Baekbeom-ro, Sogang University, Mapo-gu, Seoul, 04107, Republic of Korea
| | - Kwang-Hwan Jung
- Department of Life Science, 35-Baekbeom-ro, Sogang University, Mapo-gu, Seoul, 04107, Republic of Korea
| | - Kwanwoo Shin
- Department of Chemistry and Institute of Biological Interfaces, 35-Baekbeom-ro, Sogang University, Mapo-gu, Seoul, 04107, Republic of Korea
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23
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Mu R, Yuan J, Huang Y, Meissen JK, Mou S, Liang M, Rosenbaum AI. Bioanalytical Methods and Strategic Perspectives Addressing the Rising Complexity of Novel Bioconjugates and Delivery Routes for Biotherapeutics. BioDrugs 2022; 36:181-196. [PMID: 35362869 PMCID: PMC8972746 DOI: 10.1007/s40259-022-00518-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2022] [Indexed: 12/20/2022]
Abstract
In recent years, an increase in the discovery and development of biotherapeutics employing new modalities, such as bioconjugates or novel routes of delivery, has created bioanalytical challenges. The inherent complexity of conjugated molecular structures means that quantification of the bioconjugate and its multiple components is critical for preclinical/clinical studies to inform drug discovery and development. Moreover, bioconjugates involve additional multifactorial complexity because of the potential for in vivo catabolism and biotransformation, which may require thorough investigations in multiple biological matrices. Furthermore, excipients that enhance absorption are frequently evaluated and employed for the development of oral and inhaled biotherapeutics. Risk-benefit assessments are required for novel or existing excipients that utilize dosages above previously approved levels. Bioanalytical methods that can measure both excipients and potential drug metabolites in biological matrices are highly relevant to these emerging bioanalysis challenges. We discuss the bioanalytical strategies for analyzing bioconjugates such as antibody-drug conjugates and antibody-oligonucleotide conjugates and review recent advances in bioanalytical methods for the quantification and characterization of novel bioconjugates. We also discuss bioanalytical considerations for both biotherapeutics and excipients through novel administration routes and review analyses in various biological matrices, from the extensively studied serum or plasma to tissue biopsy in the context of preclinical and clinical studies from both technical and regulatory perspectives.
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Affiliation(s)
- Ruipeng Mu
- Integrated Bioanalysis, Clinical Pharmacology and Quantitative Pharmacology, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, South San Francisco, CA, USA
| | - Jiaqi Yuan
- Integrated Bioanalysis, Clinical Pharmacology and Quantitative Pharmacology, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, South San Francisco, CA, USA
| | - Yue Huang
- Integrated Bioanalysis, Clinical Pharmacology and Quantitative Pharmacology, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, South San Francisco, CA, USA
| | - John K Meissen
- Integrated Bioanalysis, Clinical Pharmacology and Quantitative Pharmacology, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, South San Francisco, CA, USA
| | - Si Mou
- Integrated Bioanalysis, Clinical Pharmacology and Quantitative Pharmacology, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, South San Francisco, CA, USA
| | - Meina Liang
- Integrated Bioanalysis, Clinical Pharmacology and Quantitative Pharmacology, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, South San Francisco, CA, USA
| | - Anton I Rosenbaum
- Integrated Bioanalysis, Clinical Pharmacology and Quantitative Pharmacology, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, South San Francisco, CA, USA.
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24
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Meinicke A, Härtig W, Winter K, Puchta J, Mages B, Michalski D, Emmer A, Otto M, Hoffmann KT, Reimann W, Krause M, Schob S. Surfactant Protein-G in Wildtype and 3xTg-AD Mice: Localization in the Forebrain, Age-Dependent Hippocampal Dot-like Deposits and Brain Content. Biomolecules 2022; 12:biom12010096. [PMID: 35053244 PMCID: PMC8773979 DOI: 10.3390/biom12010096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 12/30/2021] [Accepted: 12/31/2021] [Indexed: 11/16/2022] Open
Abstract
The classic surfactant proteins (SPs) A, B, C, and D were discovered in the lungs, where they contribute to host defense and regulate the alveolar surface tension during breathing. Their additional importance for brain physiology was discovered decades later. SP-G, a novel amphiphilic SP, was then identified in the lungs and is mostly linked to inflammation. In the brain, it is also present and significantly elevated after hemorrhage in premature infants and in distinct conditions affecting the cerebrospinal fluid circulation of adults. However, current knowledge on SP-G-expression is limited to ependymal cells and some neurons in the subventricular and superficial cortex. Therefore, we primarily focused on the distribution of SP-G-immunoreactivity (ir) and its spatial relationships with components of the neurovascular unit in murine forebrains. Triple fluorescence labeling elucidated SP-G-co-expressing neurons in the habenula, infundibulum, and hypothalamus. Exploring whether SP-G might play a role in Alzheimer’s disease (AD), 3xTg-AD mice were investigated and displayed age-dependent hippocampal deposits of β-amyloid and hyperphosphorylated tau separately from clustered, SP-G-containing dots with additional Reelin-ir—which was used as established marker for disease progression in this specific context. Semi-quantification of those dots, together with immunoassay-based quantification of intra- and extracellular SP-G, revealed a significant elevation in old 3xTg mice when compared to age-matched wildtype animals. This suggests a role of SP-G for the pathophysiology of AD, but a confirmation with human samples is required.
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Affiliation(s)
- Anton Meinicke
- Paul Flechsig Institute for Brain Research, University of Leipzig, Liebigstr. 19, 04103 Leipzig, Germany; (A.M.); (W.H.); (J.P.); (W.R.)
- Institute of Neuroradiology, University Hospital Leipzig, Liebigstr. 20, 04103 Leipzig, Germany;
| | - Wolfgang Härtig
- Paul Flechsig Institute for Brain Research, University of Leipzig, Liebigstr. 19, 04103 Leipzig, Germany; (A.M.); (W.H.); (J.P.); (W.R.)
| | - Karsten Winter
- Institute of Anatomy, University of Leipzig, Liebigstr. 13, 04103 Leipzig, Germany; (K.W.); (B.M.)
| | - Joana Puchta
- Paul Flechsig Institute for Brain Research, University of Leipzig, Liebigstr. 19, 04103 Leipzig, Germany; (A.M.); (W.H.); (J.P.); (W.R.)
- Institute of Neuroradiology, University Hospital Leipzig, Liebigstr. 20, 04103 Leipzig, Germany;
| | - Bianca Mages
- Institute of Anatomy, University of Leipzig, Liebigstr. 13, 04103 Leipzig, Germany; (K.W.); (B.M.)
| | - Dominik Michalski
- Department of Neurology, University Hospital Leipzig, Liebigstr. 20, 04103 Leipzig, Germany;
| | - Alexander Emmer
- Department of Neurology, University Hospital Halle, Ernst-Grube-Str. 40, 06120 Halle (Saale), Germany; (A.E.); (M.O.)
| | - Markus Otto
- Department of Neurology, University Hospital Halle, Ernst-Grube-Str. 40, 06120 Halle (Saale), Germany; (A.E.); (M.O.)
| | - Karl-Titus Hoffmann
- Institute of Neuroradiology, University Hospital Leipzig, Liebigstr. 20, 04103 Leipzig, Germany;
| | - Willi Reimann
- Paul Flechsig Institute for Brain Research, University of Leipzig, Liebigstr. 19, 04103 Leipzig, Germany; (A.M.); (W.H.); (J.P.); (W.R.)
- Institute of Neuroradiology, University Hospital Leipzig, Liebigstr. 20, 04103 Leipzig, Germany;
| | - Matthias Krause
- Department of Neurosurgery, University Hospital Leipzig, Liebigstr. 20, 04103 Leipzig, Germany;
| | - Stefan Schob
- Department of Neuroradiology, Clinic and Policlinic of Radiology, University Hospital Halle, Ernst-Grube-Str. 40, 06120 Halle (Saale), Germany
- Correspondence: ; Tel.: +49-345-557-2432
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25
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Analysis of Epithelial Cell Responses to Microbial Pathogens. Methods Mol Biol 2021. [PMID: 33405031 DOI: 10.1007/978-1-0716-1182-1_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The epithelial cell is usually the first host cell that interacts with the microbiota present at mucosal surfaces. Although initially thought of as "bystander" cells with barrier function, the epithelial cell is now known to be a sentinel cell in the recognition and discrimination of commensal and pathogenic microorganisms and a key cell in initiating subsequent innate and adaptive immune responses. Here, we describe the main assays utilized in analyzing the activation of epithelial cell signaling (western blotting), transcription factors (TransAm), gene expression (quantitative reverse transcription PCR (qRT-PCR)), cytokine responses (ELISA, Luminex), and damage induction (lactate dehydrogenase (LDH) release). While our laboratory focuses on the epithelial response to Candida pathogens, these assays can be applied universally to analyze the activation of epithelial cells in response to any microbial pathogen.
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26
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Hossen MN, Elechalawar CK, Sjoelund V, Moore K, Mannel R, Bhattacharya R, Mukherjee P. Experimental conditions influence the formation and composition of the corona around gold nanoparticles. Cancer Nanotechnol 2021; 12:1. [PMID: 33456622 PMCID: PMC7788026 DOI: 10.1186/s12645-020-00071-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 12/01/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Ovarian cancer is one of the deadliest gynecological malignancies. While the overall survival of ovarian cancer patients has slightly improved in recent years in the developed world, it remains clinically challenging due to its frequent late diagnosis and the lack of reliable diagnostic and/or prognostic markers. The aim of this study was to identify potential new molecular target proteins (NMTPs) responsible for the poor outcomes. When nanoparticles (NP) are exposed to biological fluids, a protein coat, termed the protein corona (PC), forms around the NP, and the PC represents a tool to identify NMTPs. This study investigates the influence of pre-processing conditions, such as lysis conditions and serum/plasma treatment, on the PC composition and the resulting identification of NMTPs. RESULTS Using gel electrophoresis, pre-processing conditions, including cell-lysis techniques and enrichment of low-abundance proteins (LAPs) by immunocentrifugation of serum/plasma, were shown to alter the relative amounts and compositions of proteins. PCs formed when 20 nm gold-NPs (GNPs) were incubated with lysate proteins from either RIPA- or urea lysis. Proteomic analysis of these PCs showed 2-22-fold enrichment of NMTPs in PCs from urea lysates as compared to RIPA lysates. Enriched NMTPs were then classified as cellular components, biological and molecular functions-associated proteins. The impact of enriched LAPs (eLAPs) on both PC composition and NMTP identification was shown by comparative proteomic analysis of original plasma, eLAPs, and PCs derived from eLAPs; eLAPs-PCs enhanced the abundance of NMTPs approximately 13%. Several NMTPs, including gasdermin-B, dermcidin, and kallistatin, were identified by this method demonstrating the potential use of this PC approach for molecular target discovery. CONCLUSION The current study showed that the pre-processing conditions modulate PC composition and can be used to enhance identification of NMTPs.
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Affiliation(s)
- Md. Nazir Hossen
- Peggy and Charles Stephenson Cancer Laboratory Research, Oklahoma Stanton L. Young Biomedical Research Center, University of Oklahoma Health Sciences Center, 975 N.E., Suite # 1409 10th Street, Oklahoma City, OK 73104 USA
- Department of Pathology, University of Oklahoma Health Science Center, Oklahoma City, OK USA
| | - Chandra Kumar Elechalawar
- Peggy and Charles Stephenson Cancer Laboratory Research, Oklahoma Stanton L. Young Biomedical Research Center, University of Oklahoma Health Sciences Center, 975 N.E., Suite # 1409 10th Street, Oklahoma City, OK 73104 USA
- Department of Pathology, University of Oklahoma Health Science Center, Oklahoma City, OK USA
| | - Virginie Sjoelund
- Department of Cell Biology, Mass Spectroscopy/Proteomic Core, University of Oklahoma Health Science Center, Oklahoma City, OK 73104 USA
| | - Kathleen Moore
- Department of Obstetrics and Gynecology, University of Oklahoma Health Science Center, Oklahoma City, OK USA
| | - Robert Mannel
- Department of Obstetrics and Gynecology, University of Oklahoma Health Science Center, Oklahoma City, OK USA
| | - Resham Bhattacharya
- Department of Obstetrics and Gynecology, University of Oklahoma Health Science Center, Oklahoma City, OK USA
| | - Priyabrata Mukherjee
- Peggy and Charles Stephenson Cancer Laboratory Research, Oklahoma Stanton L. Young Biomedical Research Center, University of Oklahoma Health Sciences Center, 975 N.E., Suite # 1409 10th Street, Oklahoma City, OK 73104 USA
- Department of Pathology, University of Oklahoma Health Science Center, Oklahoma City, OK USA
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27
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Grist SM, Mourdoukoutas AP, Herr AE. 3D projection electrophoresis for single-cell immunoblotting. Nat Commun 2020; 11:6237. [PMID: 33277486 PMCID: PMC7718224 DOI: 10.1038/s41467-020-19738-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 10/20/2020] [Indexed: 12/21/2022] Open
Abstract
Immunoassays and mass spectrometry are powerful single-cell protein analysis tools; however, interfacing and throughput bottlenecks remain. Here, we introduce three-dimensional single-cell immunoblots to detect both cytosolic and nuclear proteins. The 3D microfluidic device is a photoactive polyacrylamide gel with a microwell array-patterned face (xy) for cell isolation and lysis. Single-cell lysate in each microwell is "electrophoretically projected" into the 3rd dimension (z-axis), separated by size, and photo-captured in the gel for immunoprobing and confocal/light-sheet imaging. Design and analysis are informed by the physics of 3D diffusion. Electrophoresis throughput is > 2.5 cells/s (70× faster than published serial sampling), with 25 immunoblots/mm2 device area (>10× increase over previous immunoblots). The 3D microdevice design synchronizes analyses of hundreds of cells, compared to status quo serial analyses that impart hours-long delay between the first and last cells. Here, we introduce projection electrophoresis to augment the heavily genomic and transcriptomic single-cell atlases with protein-level profiling.
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Affiliation(s)
- Samantha M Grist
- Department of Bioengineering, University of California, Berkeley, USA
| | - Andoni P Mourdoukoutas
- Department of Bioengineering, University of California, Berkeley, USA
- UC Berkeley - UCSF Graduate Program in Bioengineering, Berkeley, USA
| | - Amy E Herr
- Department of Bioengineering, University of California, Berkeley, USA.
- UC Berkeley - UCSF Graduate Program in Bioengineering, Berkeley, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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28
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Othman N, Sasidharan S. Validation of target proteins of down-regulated miR-221-5p in HeLa cells treated with Polyalthia longifolia leaf extract using label-free quantitative proteomics approaches. 3 Biotech 2020; 10:399. [PMID: 32850286 DOI: 10.1007/s13205-020-02396-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 08/12/2020] [Indexed: 12/14/2022] Open
Abstract
The current study was conducted to validate the target proteins of down-regulated miR-221-5p in HeLa cells treated with P. longifolia leaf extract. The validation was done by label-free quantitative proteomics approaches, Gene Ontology (GO) and protein-protein interaction analyses after the cells transfected with miRNA mimics or miRNA inhibitor. The LC-ESI-MS/MS identified a total of 1061, 668, 564 and 940 proteins from untransfected and untreated HeLa cells, untransfected P. longifolia leaf extract-treated HeLa cells, miR-221-5p mimic-transfected P. longifolia leaf extract-treated HeLa cells and anti-miR-221-5p-transfected P. longifolia leaf extract-treated HeLa cells, respectively. The proteomic, GO and protein-protein interaction analyses showed that P. longifolia treatment regulated various protein expressions in HeLa cells, namely tropomyosin, PRKC apoptosis WT1 regulator protein (PAWR), alpha-enolase and beta-enolase, which induced apoptotic cell death after the down-regulation of miR-221-5p. Conclusively, this study showed P. longifolia leaf extract's vital contribution in regulating various protein expressions in HeLa cervical cancer cells to induce apoptotic cell death after downregulation miR-221-5p.
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Affiliation(s)
- Nurulhasanah Othman
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia (USM), 11800 Gelugor, Pulau Pinang Malaysia
| | - Sreenivasan Sasidharan
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia (USM), 11800 Gelugor, Pulau Pinang Malaysia
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29
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Mansor M, Al-Obaidi JR, Jaafar NN, Ismail IH, Zakaria AF, Abidin MAZ, Selamat J, Radu S, Jambari NN. Optimization of Protein Extraction Method for 2DE Proteomics of Goat's Milk. Molecules 2020; 25:2625. [PMID: 32516945 PMCID: PMC7321142 DOI: 10.3390/molecules25112625] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/23/2020] [Accepted: 04/24/2020] [Indexed: 11/17/2022] Open
Abstract
Two-dimensional electrophoretic (2DE)-based proteomics remains a powerful tool for allergenomic analysis of goat's milk but requires effective extraction of proteins to accurately profile the overall causative allergens. However, there are several current issues with goat's milk allergenomic analysis, and among these are the absence of established standardized extraction method for goat's milk proteomes and the complexity of goat's milk matrix that may hamper the efficacy of protein extraction. This study aimed to evaluate the efficacies of three different protein extraction methods, qualitatively and quantitatively, for the 2DE-proteomics, using milk from two commercial dairy goats in Malaysia, Saanen, and Jamnapari. Goat's milk samples from both breeds were extracted by using three different methods: a milk dilution in urea/thiourea based buffer (Method A), a triphasic separation protocol in methanol/chloroform solution (Method B), and a dilution in sulfite-based buffer (Method C). The efficacies of the extraction methods were assessed further by performing the protein concentration assay and 1D and 2D SDS-PAGE profiling, as well as identifying proteins by MALDI-TOF/TOF MS/MS. The results showed that method A recovered the highest amount of proteins (72.68% for Saanen and 71.25% for Jamnapari) and produced the highest number of protein spots (199 ± 16.1 and 267 ± 10.6 total spots for Saanen and Jamnapari, respectively) with superior gel resolution and minimal streaking. Six milk protein spots from both breeds were identified based on the positive peptide mass fingerprinting matches with ruminant milk proteins from public databases, using the Mascot software. These results attest to the fitness of the optimized protein extraction protocol, method A, for 2DE proteomic and future allergenomic analysis of the goat's milk.
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Affiliation(s)
- Muzammeer Mansor
- Laboratory of Food Safety and Food Integrity, Institute of Tropical Agriculture and Food Security, Universti Putra Malaysia, Serdang 43400 UPM, Selangor, Malaysia; (M.M.); (N.N.J.); (J.S.); (S.R.)
| | - Jameel R. Al-Obaidi
- Department of Biology, Faculty of Science and Mathematics, Universiti Pendidikan Sultan Idris, Tanjong Malim 35900, Perak, Malaysia
| | - Nurain Nadiah Jaafar
- Laboratory of Food Safety and Food Integrity, Institute of Tropical Agriculture and Food Security, Universti Putra Malaysia, Serdang 43400 UPM, Selangor, Malaysia; (M.M.); (N.N.J.); (J.S.); (S.R.)
| | - Intan Hakimah Ismail
- Department of Paediatrics, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang 43400 UPM, Selangor, Malaysia; (I.H.I.); (M.A.Z.A.)
| | - Atiqah Farah Zakaria
- Department of Otorhinolaryngology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang 43400 UPM, Selangor, Malaysia;
| | - Mohd Azri Zainal Abidin
- Department of Paediatrics, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang 43400 UPM, Selangor, Malaysia; (I.H.I.); (M.A.Z.A.)
| | - Jinap Selamat
- Laboratory of Food Safety and Food Integrity, Institute of Tropical Agriculture and Food Security, Universti Putra Malaysia, Serdang 43400 UPM, Selangor, Malaysia; (M.M.); (N.N.J.); (J.S.); (S.R.)
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, Serdang 43400 UPM, Selangor, Malaysia
| | - Son Radu
- Laboratory of Food Safety and Food Integrity, Institute of Tropical Agriculture and Food Security, Universti Putra Malaysia, Serdang 43400 UPM, Selangor, Malaysia; (M.M.); (N.N.J.); (J.S.); (S.R.)
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, Serdang 43400 UPM, Selangor, Malaysia
| | - Nuzul Noorahya Jambari
- Laboratory of Food Safety and Food Integrity, Institute of Tropical Agriculture and Food Security, Universti Putra Malaysia, Serdang 43400 UPM, Selangor, Malaysia; (M.M.); (N.N.J.); (J.S.); (S.R.)
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, Serdang 43400 UPM, Selangor, Malaysia
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Martín B, Pappa S, Díez-Villanueva A, Mallona I, Custodio J, Barrero MJ, Peinado MA, Jordà M. Tissue and cancer-specific expression of DIEXF is epigenetically mediated by an Alu repeat. Epigenetics 2020; 15:765-779. [PMID: 32041475 DOI: 10.1080/15592294.2020.1722398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Alu repeats constitute a major fraction of human genome and for a small subset of them a role in gene regulation has been described. The number of studies focused on the functional characterization of particular Alu elements is very limited. Most Alu elements are DNA methylated and then assumed to lie in repressed chromatin domains. We hypothesize that Alu elements with low or variable DNA methylation are candidates for a functional role. In a genome-wide study in normal and cancer tissues, we pinpointed an Alu repeat (AluSq2) with differential methylation located upstream of the promoter region of the DIEXF gene. DIEXF encodes a highly conserved factor essential for the development of zebrafish digestive tract. To characterize the contribution of the Alu element to the regulation of DIEXF we analysed the epigenetic landscapes of the gene promoter and flanking regions in different cell types and cancers. Alternate epigenetic profiles (DNA methylation and histone modifications) of the AluSq2 element were associated with DIEXF transcript diversity as well as protein levels, while the epigenetic profile of the CpG island associated with the DIEXF promoter remained unchanged. These results suggest that AluSq2 might directly contribute to the regulation of DIEXF transcription and protein expression. Moreover, AluSq2 was DNA hypomethylated in different cancer types, pointing out its putative contribution to DIEXF alteration in cancer and its potential as tumoural biomarker.
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Affiliation(s)
- Berta Martín
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - Stella Pappa
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - Anna Díez-Villanueva
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - Izaskun Mallona
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - Joaquín Custodio
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - María José Barrero
- Center for Regenerative Medicine in Barcelona (CMRB), Avinguda de la Granvia de l'Hospitalet , Barcelona, Spain
| | - Miguel A Peinado
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - Mireia Jordà
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
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Li QF, Wang H, Zheng L, Yang F, Li HZ, Li JX, Cheng D, Lu K, Liu Y. Effects of Modest Hypoxia and Exercise on Cardiac Function, Sleep-Activity, Negative Geotaxis Behavior of Aged Female Drosophila. Front Physiol 2020; 10:1610. [PMID: 32038290 PMCID: PMC6985434 DOI: 10.3389/fphys.2019.01610] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 12/23/2019] [Indexed: 12/13/2022] Open
Abstract
Mild normobaric hypoxia (NH) and modest exercise have multiple beneficial effects on health, but the changes in physiological function induced by NH and/or exercise remain unclear. The purpose of this investigation was to examine the specific effects of NH and/or exercise on cardiac function and myocardial structure and behavior including sleep-activity and negative geotaxis in aged Drosophila. We also assessed the survival rate of flies after hypoxia and/or exercise. One-thousand wild-type w1118 virgin female flies were randomly divided into four groups and treated with NH and/or exercise from ages 3-6 weeks. We found that exercise remarkably delayed the decline of actin and myosin and the age-related changes in cardiac structure, improved abnormal cardiac contraction, and enhanced the cardiac pumping force by inducing cardiac hypertrophy and delaying deterioration of cardiac contractility and diastolic compliance, and improved abnormal heart contraction. NH also increased the content of actin and myosin, but induced a decrease in heart diameter and heart rate, as well as an increase in the number of mitochondria and deeper sleep, which may be the manifestation of energy saving under long-term hypoxia. Both NH and exercise improved sleep quality and climbing ability of aged flies, as well as extended the maximum life span, which shows the benefits of hypoxia and exercise. Finally, the superposition of NH and exercise did not impart any obvious physiological and behavior improvement. Therefore, it is necessary to further explore the appropriate combination of hypoxia and exercise.
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Affiliation(s)
- Qiu Fang Li
- Key Laboratory of Physical Fitness and Exercise Rehabilitation of Hunan Province, Hunan Normal University, Changsha, China
| | - Hui Wang
- Key Laboratory of Physical Fitness and Exercise Rehabilitation of Hunan Province, Hunan Normal University, Changsha, China
| | - Lan Zheng
- Key Laboratory of Physical Fitness and Exercise Rehabilitation of Hunan Province, Hunan Normal University, Changsha, China
| | - Fan Yang
- Key Laboratory of Physical Fitness and Exercise Rehabilitation of Hunan Province, Hunan Normal University, Changsha, China
| | - Han Zhe Li
- Key Laboratory of Physical Fitness and Exercise Rehabilitation of Hunan Province, Hunan Normal University, Changsha, China
| | - Jin Xiu Li
- Key Laboratory of Physical Fitness and Exercise Rehabilitation of Hunan Province, Hunan Normal University, Changsha, China
| | - Dan Cheng
- Key Laboratory of Physical Fitness and Exercise Rehabilitation of Hunan Province, Hunan Normal University, Changsha, China
| | - Kai Lu
- Key Laboratory of Physical Fitness and Exercise Rehabilitation of Hunan Province, Hunan Normal University, Changsha, China
| | - Yang Liu
- Key Laboratory of Physical Fitness and Exercise Rehabilitation of Hunan Province, Hunan Normal University, Changsha, China
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Saleem S, Tariq S, Aleem I, Sadr-ul Shaheed, Tahseen M, Atiq A, Hassan S, Abu Bakar M, Khattak S, Syed AA, Ahmad AH, Hussain M, Yusuf MA, Sutton C. Proteomics analysis of colon cancer progression. Clin Proteomics 2019; 16:44. [PMID: 31889941 PMCID: PMC6935225 DOI: 10.1186/s12014-019-9264-y;] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 12/12/2019] [Indexed: 07/31/2024] Open
Abstract
BACKGROUND The aim of this pilot study was to identify proteins associated with advancement of colon cancer (CC). METHODS A quantitative proteomics approach was used to determine the global changes in the proteome of primary colon cancer from patients with non-cancer normal colon (NC), non-adenomatous colon polyp (NAP), non-metastatic tumor (CC NM) and metastatic tumor (CC M) tissues, to identify up- and down-regulated proteins. Total protein was extracted from each biopsy, trypsin-digested, iTRAQ-labeled and the resulting peptides separated using strong cation exchange (SCX) and reverse-phase (RP) chromatography on-line to electrospray ionization mass spectrometry (ESI-MS). RESULTS Database searching of the MS/MS data resulted in the identification of 2777 proteins which were clustered into groups associated with disease progression. Proteins which were changed in all disease stages including benign, and hence indicative of the earliest molecular perturbations, were strongly associated with spliceosomal activity, cell cycle division, and stromal and cytoskeleton disruption reflecting increased proliferation and expansion into the surrounding healthy tissue. Those proteins changed in cancer stages but not in benign, were linked to inflammation/immune response, loss of cell adhesion, mitochondrial function and autophagy, demonstrating early evidence of cells within the nutrient-poor solid mass either undergoing cell death or adjusting for survival. Caveolin-1, which decreased and Matrix metalloproteinase-9, which increased through the three disease stages compared to normal tissue, was selected to validate the proteomics results, but significant patient-to-patient variation obfuscated interpretation so corroborated the contradictory observations made by others. CONCLUSION Nevertheless, the study has provided significant insights into CC stage progression for further investigation.
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Affiliation(s)
- Saira Saleem
- Basic Science Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre, 7-A Block R-3, Johar Town, Lahore, 54000 Pakistan
| | - Sahrish Tariq
- Basic Science Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre, 7-A Block R-3, Johar Town, Lahore, 54000 Pakistan
| | - Iffat Aleem
- Basic Science Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre, 7-A Block R-3, Johar Town, Lahore, 54000 Pakistan
| | - Sadr-ul Shaheed
- Institute of Cancer Therapeutics, University of Bradford, Tumbling Hill Street, Bradford, BD7 1BD UK
| | - Muhammad Tahseen
- Department of Pathology, Shaukat Khanum Memorial Cancer Hospital and Research Centre, 7-A Block R-3, Johar Town, Lahore, 54000 Pakistan
| | - Aribah Atiq
- Department of Pathology, Shaukat Khanum Memorial Cancer Hospital and Research Centre, 7-A Block R-3, Johar Town, Lahore, 54000 Pakistan
| | - Sadia Hassan
- Clinical Research Office, Shaukat Khanum Memorial Cancer Hospital and Research Centre, 7-A Block R-3, Johar Town, Lahore, 54000 Pakistan
| | - Muhammad Abu Bakar
- Cancer Registry and Clinical Data Management, Shaukat Khanum Memorial Cancer Hospital and Research Centre, 7-A Block R-3, Johar Town, Lahore, 54000 Pakistan
| | - Shahid Khattak
- Department of Surgical Oncology, Shaukat Khanum Memorial Cancer Hospital and Research Centre, 7-A Block R-3, Johar Town, Lahore, 54000 Pakistan
| | - Aamir Ali Syed
- Department of Surgical Oncology, Shaukat Khanum Memorial Cancer Hospital and Research Centre, 7-A Block R-3, Johar Town, Lahore, 54000 Pakistan
| | - Asad Hayat Ahmad
- Department of Pathology, Shaukat Khanum Memorial Cancer Hospital and Research Centre, 7-A Block R-3, Johar Town, Lahore, 54000 Pakistan
| | - Mudassar Hussain
- Department of Pathology, Shaukat Khanum Memorial Cancer Hospital and Research Centre, 7-A Block R-3, Johar Town, Lahore, 54000 Pakistan
| | - Muhammed Aasim Yusuf
- Department of Internal Medicine, Shaukat Khanum Mmemorial Cancer Hospital and Research Centre, 7-A Block R-3, Johar Town, Lahore, 54000 Pakistan
| | - Chris Sutton
- Institute of Cancer Therapeutics, University of Bradford, Tumbling Hill Street, Bradford, BD7 1BD UK
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Saleem S, Tariq S, Aleem I, Sadr-ul Shaheed, Tahseen M, Atiq A, Hassan S, Abu Bakar M, Khattak S, Syed AA, Ahmad AH, Hussain M, Yusuf MA, Sutton C. Proteomics analysis of colon cancer progression. Clin Proteomics 2019; 16:44. [PMID: 31889941 PMCID: PMC6935225 DOI: 10.1186/s12014-019-9264-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 12/12/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The aim of this pilot study was to identify proteins associated with advancement of colon cancer (CC). METHODS A quantitative proteomics approach was used to determine the global changes in the proteome of primary colon cancer from patients with non-cancer normal colon (NC), non-adenomatous colon polyp (NAP), non-metastatic tumor (CC NM) and metastatic tumor (CC M) tissues, to identify up- and down-regulated proteins. Total protein was extracted from each biopsy, trypsin-digested, iTRAQ-labeled and the resulting peptides separated using strong cation exchange (SCX) and reverse-phase (RP) chromatography on-line to electrospray ionization mass spectrometry (ESI-MS). RESULTS Database searching of the MS/MS data resulted in the identification of 2777 proteins which were clustered into groups associated with disease progression. Proteins which were changed in all disease stages including benign, and hence indicative of the earliest molecular perturbations, were strongly associated with spliceosomal activity, cell cycle division, and stromal and cytoskeleton disruption reflecting increased proliferation and expansion into the surrounding healthy tissue. Those proteins changed in cancer stages but not in benign, were linked to inflammation/immune response, loss of cell adhesion, mitochondrial function and autophagy, demonstrating early evidence of cells within the nutrient-poor solid mass either undergoing cell death or adjusting for survival. Caveolin-1, which decreased and Matrix metalloproteinase-9, which increased through the three disease stages compared to normal tissue, was selected to validate the proteomics results, but significant patient-to-patient variation obfuscated interpretation so corroborated the contradictory observations made by others. CONCLUSION Nevertheless, the study has provided significant insights into CC stage progression for further investigation.
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Affiliation(s)
- Saira Saleem
- Basic Science Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre, 7-A Block R-3, Johar Town, Lahore, 54000 Pakistan
| | - Sahrish Tariq
- Basic Science Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre, 7-A Block R-3, Johar Town, Lahore, 54000 Pakistan
| | - Iffat Aleem
- Basic Science Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre, 7-A Block R-3, Johar Town, Lahore, 54000 Pakistan
| | - Sadr-ul Shaheed
- Institute of Cancer Therapeutics, University of Bradford, Tumbling Hill Street, Bradford, BD7 1BD UK
| | - Muhammad Tahseen
- Department of Pathology, Shaukat Khanum Memorial Cancer Hospital and Research Centre, 7-A Block R-3, Johar Town, Lahore, 54000 Pakistan
| | - Aribah Atiq
- Department of Pathology, Shaukat Khanum Memorial Cancer Hospital and Research Centre, 7-A Block R-3, Johar Town, Lahore, 54000 Pakistan
| | - Sadia Hassan
- Clinical Research Office, Shaukat Khanum Memorial Cancer Hospital and Research Centre, 7-A Block R-3, Johar Town, Lahore, 54000 Pakistan
| | - Muhammad Abu Bakar
- Cancer Registry and Clinical Data Management, Shaukat Khanum Memorial Cancer Hospital and Research Centre, 7-A Block R-3, Johar Town, Lahore, 54000 Pakistan
| | - Shahid Khattak
- Department of Surgical Oncology, Shaukat Khanum Memorial Cancer Hospital and Research Centre, 7-A Block R-3, Johar Town, Lahore, 54000 Pakistan
| | - Aamir Ali Syed
- Department of Surgical Oncology, Shaukat Khanum Memorial Cancer Hospital and Research Centre, 7-A Block R-3, Johar Town, Lahore, 54000 Pakistan
| | - Asad Hayat Ahmad
- Department of Pathology, Shaukat Khanum Memorial Cancer Hospital and Research Centre, 7-A Block R-3, Johar Town, Lahore, 54000 Pakistan
| | - Mudassar Hussain
- Department of Pathology, Shaukat Khanum Memorial Cancer Hospital and Research Centre, 7-A Block R-3, Johar Town, Lahore, 54000 Pakistan
| | - Muhammed Aasim Yusuf
- Department of Internal Medicine, Shaukat Khanum Mmemorial Cancer Hospital and Research Centre, 7-A Block R-3, Johar Town, Lahore, 54000 Pakistan
| | - Chris Sutton
- Institute of Cancer Therapeutics, University of Bradford, Tumbling Hill Street, Bradford, BD7 1BD UK
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Golberg A, Sheviryov J, Solomon O, Anavy L, Yakhini Z. Molecular harvesting with electroporation for tissue profiling. Sci Rep 2019; 9:15750. [PMID: 31673038 PMCID: PMC6823461 DOI: 10.1038/s41598-019-51634-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 10/03/2019] [Indexed: 01/01/2023] Open
Abstract
Recent developments in personalized medicine are based on molecular measurement steps that guide personally adjusted medical decisions. A central approach to molecular profiling consists of measuring DNA, RNA, and/or proteins in tissue samples, most notably in and around tumors. This measurement yields molecular biomarkers that are potentially predictive of response and of tumor type. Current methods in cancer therapy mostly use tissue biopsy as the starting point of molecular profiling. Tissue biopsies involve a physical resection of a small tissue sample, leading to localized tissue injury, bleeding, inflammation and stress, as well as to an increased risk of metastasis. Here we developed a technology for harvesting biomolecules from tissues using electroporation. We show that tissue electroporation, achieved using a combination of high-voltage short pulses, 50 pulses 500 V cm-1, 30 µs, 1 Hz, with low-voltage long pulses 50 pulses 50 V cm-1, 10 ms, delivered at 1 Hz, allows for tissue-specific extraction of RNA and proteins. We specifically tested RNA and protein extraction from excised kidney and liver samples and from excised HepG2 tumors in mice. Further in vivo development of extraction methods based on electroporation can drive novel approaches to the molecular profiling of tumors and of tumor environment and to related diagnosis practices.
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Affiliation(s)
- Alexander Golberg
- Porter School of Environment and Earth Sciences, Tel Aviv University, Tel Aviv, Israel.
| | - Julia Sheviryov
- Porter School of Environment and Earth Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Oz Solomon
- School of Computer Science, Herzliya Interdisciplinary Center, Herzliya, Israel
| | - Leon Anavy
- Computer Science Department, Technion, Haifa, Israel
| | - Zohar Yakhini
- School of Computer Science, Herzliya Interdisciplinary Center, Herzliya, Israel.
- Computer Science Department, Technion, Haifa, Israel.
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SILAC-Based Quantification of TGFBR2-Regulated Protein Expression in Extracellular Vesicles of Microsatellite Unstable Colorectal Cancers. Int J Mol Sci 2019; 20:ijms20174162. [PMID: 31454892 PMCID: PMC6747473 DOI: 10.3390/ijms20174162] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/21/2019] [Accepted: 08/23/2019] [Indexed: 12/13/2022] Open
Abstract
Microsatellite unstable (MSI) colorectal cancers (CRCs) are characterized by mutational inactivation of Transforming Growth Factor Beta Receptor Type 2 (TGFBR2). TGFBR2-deficient CRCs present altered target gene and protein expression. Such cellular alterations modulate the content of CRC-derived extracellular vesicles (EVs). EVs function as couriers of proteins, nucleic acids, and lipids in intercellular communication. At a qualitative level, we have previously shown that TGFBR2 deficiency causes overall alterations in the EV protein content. To deepen the basic understanding of altered protein dynamics, this work aimed to determine TGFBR2-dependent EV protein signatures in a quantitative manner. Using a stable isotope labeling with amino acids in cell culture (SILAC) approach for mass spectrometry-based quantification, 48 TGFBR2-regulated proteins were identified in MSI CRC-derived EVs. Overall, TGFBR2 deficiency caused upregulation of several EV proteins related to the extracellular matrix and nucleosome as well as downregulation of proteasome-associated proteins. The present study emphasizes the general overlap of proteins between EVs and their parental CRC cells but also highlights the impact of TGFBR2 deficiency on EV protein composition. From a clinical perspective, TGFBR2-regulated quantitative differences of protein expression in EVs might nominate novel biomarkers for liquid biopsy-based MSI typing in the future.
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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 SPECTROMETRY REVIEWS 2019; 38:403-441. [PMID: 31390493 DOI: 10.1002/mas.21598] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [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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Xylose rich heteroglycan from flaxseed gum mediates the immunostimulatory effects on macrophages via TLR2 activation. Carbohydr Polym 2019; 213:59-69. [DOI: 10.1016/j.carbpol.2019.02.080] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 02/12/2019] [Accepted: 02/22/2019] [Indexed: 12/18/2022]
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38
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Biofabrication of a vascularized islet organ for type 1 diabetes. Biomaterials 2019; 199:40-51. [PMID: 30735895 DOI: 10.1016/j.biomaterials.2019.01.035] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 11/27/2018] [Accepted: 01/18/2019] [Indexed: 12/17/2022]
Abstract
Islet transplantation is superior to extrinsic insulin supplementation in the treating severe Type 1 diabetes. However, its efficiency and longevity are limited by substantial islet loss post-transplantation due to lack of engraftment and vascular supply. To overcome these limitations, we developed a novel approach to bio-fabricate functional, vascularized islet organs (VIOs) ex vivo. We endothelialized acellular lung matrixes to provide a biocompatible multicompartment scaffold with an intact hierarchical vascular tree as a backbone for islet engraftment. Over seven days of culture, islets anatomically and functionally integrated into the surrounding bio-engineered vasculature, generating a functional perfusable endocrine organ. When exposed to supra-physiologic arterial glucose levels in vivo and ex vivo, mature VIOs responded with a physiologic insulin release from the vein and provided more efficient reduction of hyperglycemia compared to intraportally transplanted fresh islets. In long-term transplants in diabetic mice, subcutaneously implanted VIOs achieved normoglycemia significantly faster and more efficiently compared to islets that were transplanted in deviceless fashion. We conclude that ex vivo bio-fabrication of VIOs enables islet engraftment and vascularization before transplantation, and thereby helps to overcome limited islet survival and function observed in conventional islet transplantation. Given recent progress in stem cells, this technology may enable assembly of functional personalized endocrine organs.
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Metabolic glycan labeling and chemoselective functionalization of native biomaterials. Biomaterials 2018; 182:127-134. [PMID: 30118980 DOI: 10.1016/j.biomaterials.2018.08.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 08/01/2018] [Accepted: 08/03/2018] [Indexed: 01/01/2023]
Abstract
Decellularized native extracellular matrix (ECM) biomaterials are widely used in tissue engineering and have reached clinical application as biomesh implants. To enhance their regenerative properties and postimplantation performance, ECM biomaterials could be functionalized via immobilization of bioactive molecules. To facilitate ECM functionalization, we developed a metabolic glycan labeling approach using physiologic pathways to covalently incorporate click-reactive azide ligands into the native ECM of a wide variety of rodent tissues and organs in vivo, and into the ECM of isolated rodent and porcine lungs cultured ex vivo. The incorporated azides within the ECM were preserved after decellularization and served as chemoselective ligands for subsequent bioconjugation via click chemistry. As proof of principle, we generated alkyne-modified heparin, immobilized it onto azide-incorporated acellular lungs, and demonstrated its bioactivity by Antithrombin III immobilization and Factor Xa inhibition. The herein reported metabolic glycan labeling approach represents a novel platform technology for manufacturing click-reactive native ECM biomaterials, thereby enabling efficient and chemoselective functionalization of these materials to facilitate tissue regeneration and repair.
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Carmody M, Zimmer JT, Cushman CH, Nguyen T, Lawson TG. The ubiquitin-protein ligase E6AP/UBE3A supports early encephalomyocarditis virus replication. Virus Res 2018; 252:48-57. [PMID: 29782878 DOI: 10.1016/j.virusres.2018.05.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 05/03/2018] [Accepted: 05/15/2018] [Indexed: 12/28/2022]
Abstract
Many viruses make use of, and even direct, the ubiquitin-proteasome system to facilitate the generation of a cellular environment favorable for virus replication, while host cells use selected protein ubiquitylation pathways for antiviral defense. Relatively little information has been acquired, however, regarding the extent to which protein ubiquitylation determines the replication success of picornaviruses. Here we report that the ubiquitin-protein ligase E6AP/UBE3A, recently shown to be a participant in encephalomyocarditis virus (EMCV) 3C protease concentration regulation, also facilitates the early stages of EMCV replication, probably by a mechanism that does not involve 3C protease ubiquitylation. Using stably transfected E6AP knockdown cells, we found that reduced E6AP concentration extends the time required for infected cells to undergo the morphological changes caused by virally induced pathogenesis and to begin the production of infectious virions. This lag in virion production is accompanied by a corresponding delay in the appearance of detectable levels of viral proteins and RNA. We also found, by using both immunofluorescence microscopy and cell fractionation, that E6AP is partially redistributed from the nucleus to the cytoplasm in EMCV-infected cells, thereby increasing its availability to participate in cytoplasmic virus replication processes.
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Affiliation(s)
- Marybeth Carmody
- Department of Chemistry and Biochemistry, Bates College, Lewiston, ME, 04240, USA
| | - Joshua T Zimmer
- Department of Chemistry and Biochemistry, Bates College, Lewiston, ME, 04240, USA
| | - Camille H Cushman
- Department of Chemistry and Biochemistry, Bates College, Lewiston, ME, 04240, USA
| | - Thao Nguyen
- Department of Chemistry and Biochemistry, Bates College, Lewiston, ME, 04240, USA
| | - T Glen Lawson
- Department of Chemistry and Biochemistry, Bates College, Lewiston, ME, 04240, USA.
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41
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Abstract
Posttranslational modification (PTM) of proteins has emerged as a major regulatory mechanism in all three domains of life. One emerging PTM is Nε-lysine acetylation-the acetylation of the epsilon amino group of lysine residues. Nε-lysine acetylation is known to regulate multiple cellular processes. In eukaryotes, it regulates chromatin structure, transcription, metabolism, signal transduction, and the cytoskeleton. Recently, multiple groups have detected Nε-lysine acetylation in diverse bacterial phyla, but no work on protein acetylation in Borrelia burgdorferi has been reported. Here, we describe a step-by-step protocol to identify Nε-lysine acetylated proteins in B. burgdorferi.
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42
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Iqbal SM, Aufy M, Shabbir W, Lemmens-Gruber R. Identification of phosphorylation sites and binding pockets for modulation of Na V 1.5 channel by Fyn tyrosine kinase. FEBS J 2018; 285:2520-2530. [PMID: 29734505 DOI: 10.1111/febs.14496] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/05/2018] [Accepted: 04/30/2018] [Indexed: 11/26/2022]
Abstract
Cardiac sodium channel NaV 1.5 is the predominant form of sodium channels in cardiomyocytes, which exists as a macromolecular complex and interacts with multiple protein partners. Fyn kinase is one of the interacting proteins which colocalize, phosphorylate and modulate the NaV 1.5 channel. To elaborate this interaction we created expression vectors for the N-terminal, intracellular loop, and C-terminal regions of the NaV 1.5 channel, to express in HEK-293 cells. By co-immunoprecipitation and anti-phosphotyrosine blotting, we identified proline-rich binding sites for Fyn kinase in the N-terminal, IC-loopi-ii and C-terminal. After binding, Fyn kinase phosphorylates tyrosine residues present in the N- and C-terminal, which produce a depolarizing shift of 7 mV in fast inactivation. The functional relevance of these binding and phosphorylation sites was further underpinned by creating full length mutants masking these sites sequentially. An activation and inactivation curves were recorded with or without co-expressed Fyn kinase which indicates that phosphorylation of tyrosine residues at positions 68, 87, 112 in the N-terminal and at positions 1811 and 1889 in the C-terminal creates a depolarizing shift in fast inactivation of NaV 1.5 channel.
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Affiliation(s)
- Shahid Muhammad Iqbal
- Department of Pharmacology and Toxicology, University of Vienna, Vienna, Austria.,Drugs Regulatory Authority of Pakistan, Islamabad, Pakistan
| | - Mohammed Aufy
- Department of Pharmacology and Toxicology, University of Vienna, Vienna, Austria
| | - Waheed Shabbir
- Department of Pharmacology and Toxicology, University of Vienna, Vienna, Austria
| | - Rosa Lemmens-Gruber
- Department of Pharmacology and Toxicology, University of Vienna, Vienna, Austria
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43
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Drayman N, Ben-Nun-Shaul O, Butin-Israeli V, Srivastava R, Rubinstein AM, Mock CS, Elyada E, Ben-Neriah Y, Lahav G, Oppenheim A. p53 elevation in human cells halt SV40 infection by inhibiting T-ag expression. Oncotarget 2018; 7:52643-52660. [PMID: 27462916 PMCID: PMC5288138 DOI: 10.18632/oncotarget.10769] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 07/14/2016] [Indexed: 11/25/2022] Open
Abstract
SV40 large T-antigen (T-ag) has been known for decades to inactivate the tumor suppressor p53 by sequestration and additional mechanisms. Our present study revealed that the struggle between p53 and T-ag begins very early in the infection cycle. We found that p53 is activated early after SV40 infection and defends the host against the infection. Using live cell imaging and single cell analyses we found that p53 dynamics are variable among individual cells, with only a subset of cells activating p53 immediately after SV40 infection. This cell-to-cell variabilty had clear consequences on the outcome of the infection. None of the cells with elevated p53 at the beginning of the infection proceeded to express T-ag, suggesting a p53-dependent decision between abortive and productive infection. In addition, we show that artificial elevation of p53 levels prior to the infection reduces infection efficiency, supporting a role for p53 in defending against SV40. We further found that the p53-mediated host defense mechanism against SV40 is not facilitated by apoptosis nor via interferon-stimulated genes. Instead p53 binds to the viral DNA at the T-ag promoter region, prevents its transcriptional activation by Sp1, and halts the progress of the infection. These findings shed new light on the long studied struggle between SV40 T-ag and p53, as developed during virus-host coevolution. Our studies indicate that the fate of SV40 infection is determined as soon as the viral DNA enters the nucleus, before the onset of viral gene expression.
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Affiliation(s)
- Nir Drayman
- Department of Hematology, Hebrew University Faculty of Medicine and Hadassah University Hospital, Jerusalem, Israel.,Department of Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Orly Ben-Nun-Shaul
- Department of Hematology, Hebrew University Faculty of Medicine and Hadassah University Hospital, Jerusalem, Israel
| | - Veronika Butin-Israeli
- Department of Hematology, Hebrew University Faculty of Medicine and Hadassah University Hospital, Jerusalem, Israel
| | - Rohit Srivastava
- Department of Hematology, Hebrew University Faculty of Medicine and Hadassah University Hospital, Jerusalem, Israel
| | - Ariel M Rubinstein
- Department of Hematology, Hebrew University Faculty of Medicine and Hadassah University Hospital, Jerusalem, Israel
| | - Caroline S Mock
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Ela Elyada
- The Lautenberg Center for Immunology and Cancer Research, Hebrew University Faculty of Medicine, Jerusalem, Israel
| | - Yinon Ben-Neriah
- The Lautenberg Center for Immunology and Cancer Research, Hebrew University Faculty of Medicine, Jerusalem, Israel
| | - Galit Lahav
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Ariella Oppenheim
- Department of Hematology, Hebrew University Faculty of Medicine and Hadassah University Hospital, Jerusalem, Israel
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44
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González-Cruz RD, Sadick JS, Fonseca VC, Darling EM. Nuclear Lamin Protein C Is Linked to Lineage-Specific, Whole-Cell Mechanical Properties. Cell Mol Bioeng 2018; 11:131-142. [PMID: 29755599 DOI: 10.1007/s12195-018-0518-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
INTRODUCTION Lamin proteins confer nuclear integrity and relay external mechanical cues that drive changes in gene expression. However, the influence these lamins have on whole-cell mechanical properties is unknown. We hypothesized that protein expression of lamins A, B1, and C would depend on the integrity of the actin cytoskeleton and correlate with cellular elasticity and viscoelasticity. METHODS To test these hypotheses, we examined the protein expression of lamins A, B1, and C across five different cell lines with varied mechanical properties. Additionally, we treated representative "soft/stiff" cell types with cytochalasin D and LMNA siRNA to determine the effect of a more compliant whole-cell phenotype on lamin A, B1 and C protein expression. RESULTS A positive, linear correlation existed between lamin C protein expression and average cell moduli/apparent viscosity. Though moderate correlations existed between lamin A/B1 protein expression and whole-cell mechanical properties, they were statistically insignificant. Inhibition of actin polymerization, via cytochalasin D treatment, resulted in reduced cell elasticity, viscoelasticity, and lamin A and C protein expression in "stiff" MG-63 cells. In "soft" HEK-293T cells, this treatment reduced cell elasticity and viscoelasticity but did not affect lamin B1 or C protein expression. Additionally, LMNA siRNA treatment of MG-63 cells decreased whole-cell elasticity and viscoelasticity. CONCLUSION These findings suggest that lamin C protein expression is strongly associated with whole-cell mechanical properties and could potentially serve as a biomarker for mechanophenotype.
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Affiliation(s)
- Rafael D González-Cruz
- Center for Biomedical Engineering, Brown University, Providence, RI USA.,Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI USA
| | - Jessica S Sadick
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI USA
| | - Vera C Fonseca
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI USA
| | - Eric M Darling
- Center for Biomedical Engineering, Brown University, Providence, RI USA.,Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI USA.,Department of Orthopaedics, Brown University, Providence, RI USA.,School of Engineering, Brown University, Providence, RI USA
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45
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Carmody M, Notarianni TP, Sambel LA, Walsh SJ, Burke JM, Armstrong JL, Lawson TG. E6AP/UBE3A catalyzes encephalomyocarditis virus 3C protease polyubiquitylation and promotes its concentration reduction in virus-infected cells. Biochem Biophys Res Commun 2017; 494:63-69. [PMID: 29054411 PMCID: PMC5675005 DOI: 10.1016/j.bbrc.2017.10.084] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 10/16/2017] [Indexed: 12/11/2022]
Abstract
The encephalomyocarditis virus (EMCV) 3C protease (3Cpro) is one of a small number of viral proteins whose concentration is known to be regulated by the cellular ubiquitin-proteasome system. Here we report that the ubiquitin-conjugating enzyme UbcH7/UBE2L3 and the ubiquitin-protein ligase E6AP/UBE3A are components of a previously unknown EMCV 3Cpro-polyubiquitylating pathway. Following the identification of UbcH7/UBE2L3 as a participant in 3Cpro ubiquitylation, we purified a UbcH7-dependent 3Cpro-ubiquitylating activity from mouse cells, which we identified as E6AP. In vitro reconstitution assays demonstrated that E6AP catalyzes the synthesis of 3Cpro-attached Lys48-linked ubiquitin chains, known to be recognized by the 26S proteasome. We found that the 3Cpro accumulates to higher levels in EMCV-infected E6AP knockdown cells than in control cells, indicating a role for E6AP in in vivo 3Cpro concentration regulation. We also discovered that ARIH1 functions with UbcH7 to catalyze EMCV 3Cpro monoubiquitylation, but this activity does not influence the in vivo 3Cpro concentration.
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Affiliation(s)
- Marybeth Carmody
- Department of Chemistry and Biochemistry, Bates College, Lewiston, ME 04240, USA
| | - Tara P Notarianni
- Department of Chemistry and Biochemistry, Bates College, Lewiston, ME 04240, USA
| | - Larissa A Sambel
- Department of Chemistry and Biochemistry, Bates College, Lewiston, ME 04240, USA
| | - Shannon J Walsh
- Department of Chemistry and Biochemistry, Bates College, Lewiston, ME 04240, USA
| | - Jenna M Burke
- Department of Chemistry and Biochemistry, Bates College, Lewiston, ME 04240, USA
| | - Jenna L Armstrong
- Department of Chemistry and Biochemistry, Bates College, Lewiston, ME 04240, USA
| | - T Glen Lawson
- Department of Chemistry and Biochemistry, Bates College, Lewiston, ME 04240, USA.
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46
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DeCaprio J, Kohl TO. Detergent Lysis of Tissue Culture Cells for Immunoprecipitation. Cold Spring Harb Protoc 2017; 2017:pdb.prot098558. [PMID: 29196599 DOI: 10.1101/pdb.prot098558] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
This protocol describes the lysis of tissue culture cells for the solubilization of proteins of interest for immunoprecipitation. Upon collection of cells by centrifugation and depending on the use of either Tris- or phosphate-based cell lysis buffers, cells are rinsed, respectively, in either TBS or PBS before lysis. If possible, the pH of the Wash buffer should match that of the Lysis buffer. Adherent cells can be directly lysed on the plate. This is particularly useful upon lysis encompassing mild nonionic detergents, leaving the cytoskeleton intact. Alternatively, adherent cells can be scraped off the plate and directly resuspended in Lysis buffer or Wash buffer for transfer to a tube followed by the addition of Lysis buffer.
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47
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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: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
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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48
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Gedik N, Krüger M, Thielmann M, Kottenberg E, Skyschally A, Frey UH, Cario E, Peters J, Jakob H, Heusch G, Kleinbongard P. Proteomics/phosphoproteomics of left ventricular biopsies from patients with surgical coronary revascularization and pigs with coronary occlusion/reperfusion: remote ischemic preconditioning. Sci Rep 2017; 7:7629. [PMID: 28794502 PMCID: PMC5550488 DOI: 10.1038/s41598-017-07883-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 06/22/2017] [Indexed: 12/18/2022] Open
Abstract
Remote ischemic preconditioning (RIPC) by repeated brief cycles of limb ischemia/reperfusion reduces myocardial ischemia/reperfusion injury. In left ventricular (LV) biopsies from patients undergoing coronary artery bypass grafting (CABG), only the activation of signal transducer and activator of transcription 5 was associated with RIPC’s cardioprotection. We have now used an unbiased, non-hypothesis-driven proteomics and phosphoproteomics approach to analyze LV biopsies from patients undergoing CABG and from pigs undergoing coronary occlusion/reperfusion without (sham) and with RIPC. False discovery rate-based statistics identified a higher prostaglandin reductase 2 expression at early reperfusion with RIPC than with sham in patients. In pigs, the phosphorylation of 116 proteins was different between baseline and early reperfusion with RIPC and/or with sham. The identified proteins were not identical for patients and pigs, but in-silico pathway analysis of proteins with ≥2-fold higher expression/phosphorylation at early reperfusion with RIPC in comparison to sham revealed a relation to mitochondria and cytoskeleton in both species. Apart from limitations of the proteomics analysis per se, the small cohorts, the sampling/sample processing and the number of uncharacterized/unverifiable porcine proteins may have contributed to this largely unsatisfactory result.
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Affiliation(s)
- Nilgün Gedik
- Institute for Pathophysiology, West German Heart and Vascular Center Essen, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Marcus Krüger
- Institute for Genetics Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), and University of Cologne, Cologne, Germany
| | - Matthias Thielmann
- Department of Thoracic and Cardiovascular Surgery, West German Heart and Vascular Center Essen, Universitätsklinikum Essen, Universität Duisburg- Essen, Essen, Germany
| | - Eva Kottenberg
- Klinik für Anästhesiologie und Intensivmedizin, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Andreas Skyschally
- Institute for Pathophysiology, West German Heart and Vascular Center Essen, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Ulrich H Frey
- Klinik für Anästhesiologie und Intensivmedizin, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Elke Cario
- Experimental Gastroenterology, Department of Gastroenterology and Hepatology, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Jürgen Peters
- Klinik für Anästhesiologie und Intensivmedizin, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Heinz Jakob
- Department of Thoracic and Cardiovascular Surgery, West German Heart and Vascular Center Essen, Universitätsklinikum Essen, Universität Duisburg- Essen, Essen, Germany
| | - Gerd Heusch
- Institute for Pathophysiology, West German Heart and Vascular Center Essen, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Petra Kleinbongard
- Institute for Pathophysiology, West German Heart and Vascular Center Essen, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany.
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49
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Ashraf Kharaz Y, Zamboulis D, Sanders K, Comerford E, Clegg P, Peffers M. Comparison between chaotropic and detergent-based sample preparation workflow in tendon for mass spectrometry analysis. Proteomics 2017; 17:1700018. [PMID: 28547889 PMCID: PMC5575552 DOI: 10.1002/pmic.201700018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 05/16/2017] [Accepted: 05/19/2017] [Indexed: 01/12/2023]
Abstract
Exploring the tendon proteome is a challenging but important task for understanding the mechanisms of physiological/pathological processes during ageing and disease and for the development of new treatments. Several extraction methods have been utilised for tendon mass spectrometry, however different extraction methods have not been simultaneously compared. In the present study we compared protein extraction in tendon with two chaotropic agents, guanidine hydrochloride (GnHCl) and urea, a detergent, RapiGest™, and their combinations for shotgun mass spectrometry. An initial proteomic analysis was performed following urea, GnHCl, and RapiGest™ extraction of equine superficial digital flexor tendon (SDFT) tissue. Subsequently, another proteomic analysis was performed following extraction with GnHCl, Rapigest™, and their combinations. Between the two chaotropic agents, GnHCl extracted more proteins, whilst a greater number of proteins were solely identified after Rapigest™ extraction. Protein extraction with a combination of GnHCl followed by RapiGest™ on the insoluble pellet demonstrated, after label-free quantification, increased abundance of identified collagen proteins and low sample to sample variability. In contrast, GnHCl extraction on its own showed increased abundance of identified proteoglycans and cellular proteins. Therefore, the selection of protein extraction method for tendon tissue for mass spectrometry analysis should reflect the focus of the study.
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Affiliation(s)
- Yalda Ashraf Kharaz
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic DiseaseUniversity of LiverpoolLiverpoolUK
| | - Danae Zamboulis
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic DiseaseUniversity of LiverpoolLiverpoolUK
| | - Karen Sanders
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic DiseaseUniversity of LiverpoolLiverpoolUK
| | - Eithne Comerford
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic DiseaseUniversity of LiverpoolLiverpoolUK
| | - Peter Clegg
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic DiseaseUniversity of LiverpoolLiverpoolUK
- The MRC‐Arthritis Research UK Centre for Integrated research into Musculoskeletal Ageing (CIMA)LiverpoolUK
| | - Mandy Peffers
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic DiseaseUniversity of LiverpoolLiverpoolUK
- The MRC‐Arthritis Research UK Centre for Integrated research into Musculoskeletal Ageing (CIMA)LiverpoolUK
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50
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Winter M, Dokic I, Schlegel J, Warnken U, Debus J, Abdollahi A, Schnölzer M. Deciphering the Acute Cellular Phosphoproteome Response to Irradiation with X-rays, Protons and Carbon Ions. Mol Cell Proteomics 2017; 16:855-872. [PMID: 28302921 DOI: 10.1074/mcp.m116.066597] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 03/15/2017] [Indexed: 12/15/2022] Open
Abstract
Radiotherapy is a cornerstone of cancer therapy. The recently established particle therapy with raster-scanning protons and carbon ions landmarks a new era in the field of high-precision cancer medicine. However, molecular mechanisms governing radiation induced intracellular signaling remain elusive. Here, we present the first comprehensive proteomic and phosphoproteomic study applying stable isotope labeling by amino acids in cell culture (SILAC) in combination with high-resolution mass spectrometry to decipher cellular response to irradiation with X-rays, protons and carbon ions. At protein expression level limited alterations were observed 2 h post irradiation of human lung adenocarcinoma cells. In contrast, 181 phosphorylation sites were found to be differentially regulated out of which 151 sites were not hitherto attributed to radiation response as revealed by crosscheck with the PhosphoSitePlus database.Radiation-induced phosphorylation of the p(S/T)Q motif was the prevailing regulation pattern affecting proteins involved in DNA damage response signaling. Because radiation doses were selected to produce same level of cell kill and DNA double-strand breakage for each radiation quality, DNA damage responsive phosphorylation sites were regulated to same extent. However, differential phosphorylation between radiation qualities was observed for 55 phosphorylation sites indicating the existence of distinct signaling circuitries induced by X-ray versus particle (proton/carbon) irradiation beyond the canonical DNA damage response. This unexpected finding was confirmed in targeted spike-in experiments using synthetic isotope labeled phosphopeptides. Herewith, we successfully validated uniform DNA damage response signaling coexisting with altered signaling involved in apoptosis and metabolic processes induced by X-ray and particle based treatments.In summary, the comprehensive insight into the radiation-induced phosphoproteome landscape is instructive for the design of functional studies aiming to decipher cellular signaling processes in response to radiotherapy, space radiation or ionizing radiation per se Further, our data will have a significant impact on the ongoing debate about patient treatment modalities.
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Affiliation(s)
- Martin Winter
- From the ‡Functional Proteome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany.,§Translational Radiation Oncology, National Center for Tumor diseases (NCT), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 460, D-69120 Heidelberg, Germany.,¶German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Ivana Dokic
- §Translational Radiation Oncology, National Center for Tumor diseases (NCT), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 460, D-69120 Heidelberg, Germany.,¶German Cancer Consortium (DKTK), Heidelberg, Germany.,‖Heidelberg Ion Beam Therapy Center (HIT), Department of Radiation Oncology, University of Heidelberg Medical School, Im Neuenheimer Feld 450, D-69120 Heidelberg, Germany.,**Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), Heidelberg, Germany
| | - Julian Schlegel
- §Translational Radiation Oncology, National Center for Tumor diseases (NCT), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 460, D-69120 Heidelberg, Germany.,¶German Cancer Consortium (DKTK), Heidelberg, Germany.,‖Heidelberg Ion Beam Therapy Center (HIT), Department of Radiation Oncology, University of Heidelberg Medical School, Im Neuenheimer Feld 450, D-69120 Heidelberg, Germany.,**Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), Heidelberg, Germany
| | - Uwe Warnken
- From the ‡Functional Proteome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| | - Jürgen Debus
- §Translational Radiation Oncology, National Center for Tumor diseases (NCT), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 460, D-69120 Heidelberg, Germany.,¶German Cancer Consortium (DKTK), Heidelberg, Germany.,‖Heidelberg Ion Beam Therapy Center (HIT), Department of Radiation Oncology, University of Heidelberg Medical School, Im Neuenheimer Feld 450, D-69120 Heidelberg, Germany.,**Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), Heidelberg, Germany
| | - Amir Abdollahi
- §Translational Radiation Oncology, National Center for Tumor diseases (NCT), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 460, D-69120 Heidelberg, Germany.,¶German Cancer Consortium (DKTK), Heidelberg, Germany.,‖Heidelberg Ion Beam Therapy Center (HIT), Department of Radiation Oncology, University of Heidelberg Medical School, Im Neuenheimer Feld 450, D-69120 Heidelberg, Germany.,**Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), Heidelberg, Germany
| | - Martina Schnölzer
- From the ‡Functional Proteome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany;
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