1
|
Almarzooqi S, Campbell C. Genetic Research Using Archival Tissue: Ethical, Social, and Legal Considerations in the United Arab Emirates. Asian Bioeth Rev 2018; 10:219-230. [PMID: 33717288 DOI: 10.1007/s41649-018-0062-z] [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: 10/18/2017] [Accepted: 07/02/2018] [Indexed: 10/26/2022] Open
Abstract
Pathological archival tissue has been used as a source of research material for many years. The advancement in molecular techniques led to an escalated interest in genetic research on archival tissue. Research on archival tissue has been used without obtaining consents from patients, although the ethical justification for such a practice is unlikely to apply for genetic research that involves whole genome sequencing, for instance. Issues of confidentiality and patients' autonomy are being raised as institutions consider when approval for this type of research should be granted. In addition, patients' advocate is mandating some of these changes. In the context of the United Arab Emirates, this paper makes clear the current uncertainties arising from the use of archival tissue in genetic research, as it could be highly invasive of privacy interests and also fails to respect autonomous choice. It further explains what needs to change in order to support such research that is directed at promoting public good, but in a way that is not detrimental to the welfare of patients as research participants.
Collapse
Affiliation(s)
- Saeeda Almarzooqi
- Pathology Department, College of Medicine and Health Sciences, United Arab Emirates University, P.O. Box 17666, Al Ain, United Arab Emirates
| | - Carol Campbell
- College of Natural and Health Sciences, Zayed University, P.O. Box 144534, Abu Dhabi, United Arab Emirates
| |
Collapse
|
2
|
Taverna D, Mignogna C, Gabriele C, Santise G, Donato G, Cuda G, Gaspari M. An optimized procedure for on-tissue localized protein digestion and quantification using hydrogel discs and isobaric mass tags: analysis of cardiac myxoma. Anal Bioanal Chem 2017; 409:2919-2930. [PMID: 28190108 DOI: 10.1007/s00216-017-0237-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 01/20/2017] [Accepted: 01/31/2017] [Indexed: 01/22/2023]
Abstract
An optimized workflow for multiplexed and spatially localized on-tissue quantitative protein analysis is here presented. The method is based on the use of an enzyme delivery platform, a polymeric hydrogel disc, allowing for a localized digestion directly onto the tissue surface coupled with an isobaric mass tag strategy for peptide labeling and relative quantification. The digestion occurs within such hydrogels, followed by peptide solvent extraction and identification by liquid chromatography coupled to high-resolution tandem mass spectrometry (LC-MS/MS). Since this is a histology-directed on-tissue analysis, multiple hydrogels were placed onto morphologically and spatially different regions of interest (ROIs) within the tissue surface, e.g., cardiac myxoma tumor vascularized region and the adjacent hypocellular area. After a microwave digestion step (2 min), enzymatically cleaved peptides were labeled using TMT reagents with isobaric mass tags, enabling analysis of multiple samples per experiment. Thus, N = 8 hydrogel-digested samples from cardiac myxoma serial tissue sections (N = 4 from the vascularized ROIs and N = 4 from the adjacent hypocellular areas) were processed and then combined before a single LC-MS/MS analysis. Regulated proteins from both cardiac myxoma regions were assayed in a single experiment. Graphical abstract The workflow for histology-guided on-tissue localized protein digestion followed by isobaric mass tagging and LC-MS/MS analysis for proteins quantification is here summarized.
Collapse
Affiliation(s)
- Domenico Taverna
- Research Center for Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Campus "S. Venuta", Viale Europa, Loc. Germaneto, 88100, Catanzaro, Italy.
| | - Chiara Mignogna
- Department of Health Science, Magna Graecia University of Catanzaro, Viale Europa, 88100, Catanzaro, Italy
| | - Caterina Gabriele
- Research Center for Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Campus "S. Venuta", Viale Europa, Loc. Germaneto, 88100, Catanzaro, Italy
| | - Gianluca Santise
- Cardiothoracic Surgery Unit, Sant'Anna Hospital, Via Pio X, 111, 88100, Catanzaro, Italy
| | - Giuseppe Donato
- Department of Health Science, Magna Graecia University of Catanzaro, Viale Europa, 88100, Catanzaro, Italy
| | - Giovanni Cuda
- Research Center for Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Campus "S. Venuta", Viale Europa, Loc. Germaneto, 88100, Catanzaro, Italy
| | - Marco Gaspari
- Research Center for Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Campus "S. Venuta", Viale Europa, Loc. Germaneto, 88100, Catanzaro, Italy
| |
Collapse
|
3
|
Taverna D, Pollins AC, Nanney LB, Sindona G, Caprioli RM. Histology-guided protein digestion/extraction from formalin-fixed and paraffin-embedded pressure ulcer biopsies. Exp Dermatol 2015; 25:143-6. [PMID: 26440596 DOI: 10.1111/exd.12870] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2015] [Indexed: 12/24/2022]
Abstract
Herein we present a simple, reproducible and versatile approach for in situ protein digestion and identification on formalin-fixed and paraffin-embedded (FFPE) tissues. This adaptation is based on the use of an enzyme delivery platform (hydrogel discs) that can be positioned on the surface of a tissue section. By simultaneous deposition of multiple hydrogels over select regions of interest within the same tissue section, multiple peptide extracts can be obtained from discrete histological areas. After enzymatic digestion, the hydrogel extracts are submitted for LC-MS/MS analysis followed by database inquiry for protein identification. Further, imaging mass spectrometry (IMS) is used to reveal the spatial distribution of the identified peptides within a serial tissue section. Optimization was achieved using cutaneous tissue from surgically excised pressure ulcers that were subdivided into two prime regions of interest: the wound bed and the adjacent dermal area. The robust display of tryptic peptides within these spectral analyses of histologically defined tissue regions suggests that LC-MS/MS in combination with IMS can serve as useful exploratory tools.
Collapse
Affiliation(s)
- Domenico Taverna
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Arcavacata di Rende, Italy.,Mass Spectrometry Research Center, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Alonda C Pollins
- Department of Plastic Surgery, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Lillian B Nanney
- Department of Plastic Surgery, Vanderbilt School of Medicine, Nashville, TN, USA.,Department of Cell & Developmental Biology, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Giovanni Sindona
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Arcavacata di Rende, Italy
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt School of Medicine, Nashville, TN, USA.,Department of Biochemistry, Vanderbilt School of Medicine, Nashville, TN, USA
| |
Collapse
|
4
|
Pelekanos RA, Sardesai VS, Dekker Nitert M, Callaway LK, Fisk NM, Jeffery PL. Rapid method for growth hormone receptor exon 3 delete (GHRd3) SNP genotyping from archival human placental samples. Endocrine 2015; 49:643-52. [PMID: 26067082 DOI: 10.1007/s12020-015-0647-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 06/01/2015] [Indexed: 12/15/2022]
Abstract
Analysis of archival samples from cohorts of pregnant women may be key to discovering prognosticators of stillbirth and pregnancy/perinatal complications. Growth hormone (GH) and its receptor (GHR) are pivotal in feto-placental development and pregnancy maintenance. We report a rapid, optimized method for genotyping the GHR full-length versus exon 3-deleted isoform (GHRd3). TaqMan single nucleotide polymorphism (SNP) genotyping proved superior to standard multiplex polymerase chain reaction (PCR) in allele detection and GHR genotyping from archived samples, including those with poor genomic deoxyribonucleic acid quality/quantity such as formalin fixed, paraffin embedded, blood, and serum. Furthermore, this assay is suitable for high through put 96 or 384-well plate quantitative PCR machines with automated genotype calling software. The TaqMan genotyping assay can increase the data obtained from precious archival human samples.
Collapse
Affiliation(s)
- Rebecca A Pelekanos
- Experimental Fetal Medicine Group, UQ Centre for Clinical Research, The University of Queensland, Herston, QLD, 4029, Australia,
| | | | | | | | | | | |
Collapse
|
5
|
Tanca A, Uzzau S, Addis MF. Full-length protein extraction protocols and gel-based downstream applications in formalin-fixed tissue proteomics. Methods Mol Biol 2015; 1295:117-134. [PMID: 25820719 DOI: 10.1007/978-1-4939-2550-6_11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Archival formalin-fixed, paraffin-embedded (FFPE) tissue repositories and their associated clinical information can represent a valuable resource for tissue proteomics. In order to make these tissues available for protein biomarker discovery and validation studies, dedicated sample preparation procedures overcoming the intermolecular cross-links introduced by formalin need to be implemented. This chapter describes a full-length protein extraction protocol optimized for downstream gel-based proteomics applications. Using the procedures detailed here, SDS-PAGE, western immunoblotting, GeLC-MS/MS, 2D-PAGE, and 2D-DIGE can be carried out on FFPE tissues. Technical tips, critical aspects, and drawbacks of the method are presented and discussed.
Collapse
Affiliation(s)
- Alessandro Tanca
- Porto Conte Ricerche, Loc, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio, Alghero (SS), 07041, Italy
| | | | | |
Collapse
|
6
|
Taverna D, Norris JL, Caprioli RM. Histology-directed microwave assisted enzymatic protein digestion for MALDI MS analysis of mammalian tissue. Anal Chem 2014; 87:670-6. [PMID: 25427280 PMCID: PMC4287167 DOI: 10.1021/ac503479a] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
![]()
This study presents on-tissue proteolytic
digestion using a microwave
irradiation and peptide extraction method for in situ analysis of proteins from spatially defined regions of a tissue
section. The methodology utilizes hydrogel discs (1 mm diameter) embedded
with trypsin solution. The enzyme-laced hydrogel discs are applied
to a tissue section, directing enzymatic digestion to a spatially
confined area of the tissue. By applying microwave radiation, protein
digestion is performed in 2 min on-tissue, and the extracted peptides
are then analyzed by matrix assisted laser desorption/ionization mass
spectrometry (MALDI MS) and liquid chromatography tandem mass spectrometry
(LC-MS/MS). The reliability and reproducibility of the microwave assisted
hydrogel mediated on-tissue digestion is demonstrated by the comparison
with other on-tissue digestion strategies, including comparisons with
conventional heating and in-solution digestion. LC-MS/MS data were
evaluated considering the number of identified proteins as well as
the number of protein groups and distinct peptides. The results of
this study demonstrate that rapid and reliable protein digestion can
be performed on a single thin tissue section while preserving the
relationship between the molecular information obtained and the tissue
architecture, and the resulting peptides can be extracted in sufficient
abundance to permit analysis using LC-MS/MS. This approach will be
most useful for samples that have limited availability but are needed
for multiple analyses, especially for the correlation of proteomics
data with histology and immunohistochemistry.
Collapse
Affiliation(s)
- Domenico Taverna
- Department of Chemistry and Technological Chemistry, University of Calabria , Arcavacata di Rende, Cosenza 87036, Italy
| | | | | |
Collapse
|
7
|
Zen Y, Britton D, Mitra V, Brand A, Jung S, Loessner C, Ward M, Pike I, Heaton N, Quaglia A. Protein expression profiles of chemo-resistant mixed phenotype liver tumors using laser microdissection and LC–MS/MS proteomics. EUPA OPEN PROTEOMICS 2013. [DOI: 10.1016/j.euprot.2013.10.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|