| 1. |
- Malm, Johan, et al.
(författare)
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Developments in biobanking workflow standardization providing sample integrity and stability
- 2013
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Ingår i: Journal of Proteomics. - : Elsevier BV. - 1874-3919 .- 1876-7737. ; 95:SI, s. 38-45
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Tidskriftsartikel (refereegranskat)abstract
- Recommendations and outlines for standardization in biobanking processes are presented by a research team with long-term experience in clinical studies. These processes have important bearing on the use of samples in developing assays. These measurements are useful to document states of health and disease that are beneficial for academic research, commercial healthcare, drug development industry and government regulating agencies. There is a need for increasing awareness within proteomic and genomic communities regarding the basic concepts of collecting, storing and utilizing clinical samples. Quality control and sample suitability for analysis need to be documented and validated to ensure data integrity and establish contexts for interpretation of results. Standardized methods in proteomics and genomics are required to be practiced throughout the community allowing datasets to be comparable and shared for analysis. For example, sample processing of thousands of clinical samples, performed in 384 high-density sample tube systems in a fully automated workflow, preserves sample content and is presented showing validation criteria. Large studies will be accompanied by biological and molecular information with corresponding clinical records from patients and healthy donors. These developments position biobanks of human patient samples as an increasingly recognized major asset in disease research, future drug development and within patient care. Biological significance: The current manuscript is of major relevance to the proteomic and genomic fields, as it outlines the standardization aspects of biobanking and the requirements that are needed to run future clinical studies that will benefit the patients where OMICS science will play a major role. A global view of the field is given where best practice and conventional acceptances are presented along with ongoing large-scale biobanking projects. The authors represent broadly stakeholders that cover the academic, pharma, biotech and healthcare fields with extensive experience and deliveries. This contribution will be a milestone paper to the proteomic and genomic scientists to present data in the future that will have impact to the life science area.This article is part of a Special Issue entitled: Standardization and Quality Control in Proteomics.
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| 2. |
- Donnarumma, Fabrizio, et al.
(författare)
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Accessing microenvironment compartments in formalin-fixed paraffin-embedded tissues by protein expression analysis.
- 2013
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Ingår i: Bioanalysis. - : Future Science Ltd. - 1757-6180 .- 1757-6199. ; 5:21, s. 2647-2659
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Tidskriftsartikel (refereegranskat)abstract
- Background: Formalin-fixed paraffin-embedded (FFPE) samples are an outstanding source of new information regarding disease evolvements. Current research on new biomarkers and diseases features has recently invested resources in FFPE-related projects. Results: In order to initiate clinical protein-expression studies using minute amount of biological material, a workflow based on the combination of filter-assisted sample preparation with MS analysis and label-free quantification was developed. Xenograft lung tumor tissue was investigated as a model system. The workflow was optimized and characterized in terms of its reproducibility from a quantitative and qualitative point of view. We proposed a modification of the original filter-assisted sample preparation protocol to improve reproducibility and highlight its potential for the investigation of hydrophobic proteins. Conclusions: Altogether the presented workflow allows analysis of FFPE samples with improvements in the analytical time and performance, and we show its application for lung cancer xenograft tissue samples.
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| 3. |
- Fehniger, Thomas, et al.
(författare)
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Direct demonstration of tissue uptake of an inhaled drug: proof-of-principle study using matrix assisted laser desorption ionization mass spectrometry imaging
- 2011
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Ingår i: Analytical Chemistry. - : American Chemical Society (ACS). - 1520-6882 .- 0003-2700. ; 83:21, s. 8329-8336
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Tidskriftsartikel (refereegranskat)abstract
- Drug therapy is often directed to specific organ and tissue compartments where the mode of action of the compound effects specifically targeted biological processes. However, the direct measurement of drug uptake in terms of a time kinetic and concentrations attained at the local sites has not been readily available as a clinical index for most drugs. A proof-of-principle study was conducted to test the utility of applying MALDI mass spectrometry imaging (MALDI-MSI) to demonstrate the qualitative distribution pattern of a locally administered drug within tissue sites of targeted action. Here we have measured the occurrence of an inhaled bronchodilator, the muscarinic receptor antagonist ipratropium, within human bronchial biopsies obtained by fiber optic bronchoscopy shortly after dosing exposure. Cryo-preserved biopsy samples from five subjects being evaluated for airway obstruction or potential tumor development were prepared as thin frozen sections. Samples coated with a MALDI matrix were analyzed by a MALDI LTQ Orbitrap XL mass spectrometer at large (100 μm) and small (30 μm) raster size. Our results demonstrate that ipratropium is rapidly absorbed into the airway wall. Ipratropium parent ion (m/z 332.332) and daughter ions (m/z 166.2 and 290.2) were coincidently partitioned within submucosal spaces containing targeted airway smooth muscle in 4/5 subjects. The signal intensity of ipratropium fragment ions provided estimates that local drug concentrations between 3-80 nM were achieved within the airway wall. To our knowledge, this is the first reported study in man applying MALDI-MSI to demonstrate the localization of a drug administered at therapeutic levels. The study highlights the potential benefit of MALDI-MSI to provide important measurements of drug efficacy in clinical settings.
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| 4. |
- Fehniger, Thomas, et al.
(författare)
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International Biobanking for Lung Cancer and COPD as the Future Resource for Clinical Protein Research
- 2013
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Ingår i: EuPA Open Proteomics. - : Elsevier BV. - 2212-9685. ; 1, s. 3-7
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Tidskriftsartikel (refereegranskat)abstract
- Characterized tissue with pathological grading and blood samples as well as other biofluids forms the basis for all biobanks as a resource in modern life science. Biobanks are accessed to measure biological components that can be used to monitor the status of health and disease in individual samples and population groups. The biomarker diagnostics area, predicting drug efficacy, stratification of patient groups, can benefit from the continuous qualitative developments, where Proteomics can make a difference in lung cancer and COPD. This in turn can provide key treasures to novel drugs for personalized medicine in the future.
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| 5. |
- Fehniger, Thomas, et al.
(författare)
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Queries of MALDI-Imaging Global Datasets Identifying Ion Mass Signatures Associated with Tissue Compartments
- 2014
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Ingår i: Proteomics. - : Wiley. - 1615-9861 .- 1615-9853. ; 14:7-8, s. 862-871
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Tidskriftsartikel (refereegranskat)abstract
- Scanning mass spectrometry by matrix assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) creates large volumetric global datasets that describe the location and identity of ions registered at each sampling location. While thousands of ion peaks are recorded in a typical whole tissue analysis, only a fraction of these measured molecules are purposefully scrutinized within a given experimental design. To address this need, we recently reported new methods to query the full volume of MALDI-MSI data that correlate all ion masses to one another. As an example of this utility we demonstrate that specific ion peak m/z signatures can be used to localize similar histological structures within tissue samples. In this study we use the example of ion peak masses that are associated with tissue spaces occupied by airway bronchioles in rat lung samples. The volume of raw data was pre-processed into structures of 0.1 mass unit bins containing metadata collected at each sampling position. Interactive visualization in Paraview identified ion peaks that especially showed strong association with airway bronchioles but not vascular or parenchymal tissue compartments. Further iterative statistical correlation queries provided ranked indices of all m/z values in the global dataset regarding co-incident distributions at any given X,Y position in the histological spaces occupied by bronchioles The study further provides methods for extracting important information contained in global datasets that previously was unseen or inaccessible. This article is protected by copyright. All rights reserved.
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| 6. |
- Lee, Sujin, et al.
(författare)
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Aptamer/ISET-MS: A New Affinity-Based MALDI Technique for Improved Detection of Biomarkers
- 2014
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Ingår i: Analytical Chemistry. - : American Chemical Society (ACS). - 1520-6882 .- 0003-2700. ; 86:15, s. 7627-7634
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Tidskriftsartikel (refereegranskat)abstract
- With the rapid progress in the development of new clinical biomarkers there is an unmet need of fast and sensitive multiplex analysis methods for disease specific protein monitoring. Immunoaffinity extraction integrated with matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) analysis offers a route to rapid and sensitive protein analysis and potentially multiplex biomarker analysis. In this study, the previously reported integrated selective enrichment target (ISET)-MALDI-MS analysis was implemented with ssDNA aptamer functionalized microbeads to address the specific capturing of thrombin in complex samples. The main objective for using an aptamer as the capturing ligand was to avoid the inherently high background components, which are produced during the digestion step following the target extraction when antibodies are used. By applying a thrombin specific aptamer linked to ISET-MALDI-MS detection, a proof of concept of antibody fragment background reduction in the ISET-MALDI-MS readout is presented. Detection sensitivity was significantly increased compared to the corresponding system based on antibody-specific binding as the aptamer ligand does not induce any interfering background residues from the antibodies. The limit of detection for thrombin was 10 fmol in buffer using the aptamer/ISET-MALDI-MS configuration as confirmed by MS/MS fragmentation. The aptamer/ISET-MALDI-MS platform also displayed a limit of detection of 10 fmol for thrombin in five different human serum samples (1/10 diluted), demonstrating the applicability of the aptamer/ISET-MALDI-MS analysis in clinical samples.
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| 7. |
- Lichti, Cheryl F., et al.
(författare)
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Integrated Chromosome 19 Transcriptomic and Proteomic Data Sets Derived from Glioma Cancer Stem-Cell Lines
- 2014
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Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 13:1, s. 191-199
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Tidskriftsartikel (refereegranskat)abstract
- One subproject within the global Chromosome 19 Consortium is to define chromosome 19 gene and protein expression in glioma-derived cancer stem cells (GSCs). Chromosome 19 is notoriously linked to glioma by 1p/19q codeletions, and clinical tests are established to detect that specific aberration. GSCs are tumor-initiating cells and are hypothesized to provide a repository of cells in tumors that can self-replicate and be refractory to radiation and chemotherapeutic agents developed for the treatment of tumors. In this pilot study, we performed RNA-Seq, label-free quantitative protein measurements in six GSC lines, and targeted transcriptomic analysis using a chromosome 19-specific microarray in an additional six GSC lines. The data have been deposited to the ProteomeXchange with identifier PXD000563. Here we present insights into differences in GSC gene and protein expression, including the identification of proteins listed as having no or low evidence at the protein level in the Human Protein Atlas, as correlated to chromosome 19 and GSC subtype. Furthermore, the upregulation of proteins downstream of adenovirus-associated integration site 1 (AAVS1) in GSC11 in response to oncolytic adenovirus treatment was demonstrated. Taken together, our results may indicate new roles for chromosome 19, beyond the 1p/19q codeletion, in the future of personalized medicine for glioma patients.
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| 8. |
- Malm, Johan, et al.
(författare)
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Blood Plasma Reference Material – A Global Resource for Proteomic Research
- 2013
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Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 12:7, s. 3087-3092
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Tidskriftsartikel (refereegranskat)abstract
- There is an ever-increasing awareness and interest within the clinical research field that has creating a large demand for blood fraction samples as well as other clinical samples. The translational research area is another field that demanding for blood samples, used widely in proteomics, genomics, as well as metabolomics. Blood samples are the global most common biological samples that find its use in a broad variety of applications in Life Science. We hereby introduce a new reference blood plasma (EDTA) that is aimed as a global resource for the Proteomics community. We have developed these reference plasma standards by defining the Control group as those with CRP levels <3mg/L and a Disease group with CRP ranges >30 mg/L. In these references we have used both newborn children 1-2 weeks, as well as youngsters 10-15 years, and middle aged 30-50 years, and elderly patients at the ages of 65+. The total number of these reference plasma pools was 80 patients in each group. We provide data on the developments and characteristics of the reference blood plasma standards, as well as what is used by the team members at the respective laboratories. The standards have been evaluated by pilot sample processing in biobanking operations, and are currently a resource that allows the Proteomic society to perform quantitative proteomic studies. By the use of high quality reference plasma samples, global initiatives, such as the Chromosome Human Proteome Project (C-HPP), will benefit as one scientific program when the entire human proteome is mapped and linked to human diseases.
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| 9. |
- Malm, Johan, et al.
(författare)
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Large Scale Biobanking of Blood – The Importance of High Density Sample Processing Procedures
- 2012
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Ingår i: Journal of Proteomics. - : Elsevier BV. - 1874-3919. ; 76:1, s. 116-124
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Tidskriftsartikel (refereegranskat)abstract
- We introduce a novel automated sample-processing concept that will be of mandatory importance to proteomics and future clinical research, performing patient studies from resulting blood fractions in various disease areas. Biobank storage of small sample volumes allows for high replicate numbers to be processed and aliquoted, where each sample aliquot can be used for a dedicated clinical analysis and end-point measurement. In order to preserve sample integrity and value over time, the principle of single usage is gaining recognition. We hereby present a 384-format sample tube system for the preservation and archiving of clinical patient samples that will form the basis for future proteomics studies. This high density scaling allows for reproducible aliquoting 70-µL volumes of blood fractions. Blood plasma with EDTA, Li-heparin, and citrate, as anti-coagulants, are fractioned along with the buffy coat and the erythrocyte fraction, in addition to the serum fraction. We demonstrate an automated sample handling for biobanking: samples from patients were processed and aliquoted in both 96- and 384-sample racks by liquid handling robotics and Laboratory Intelligence Management System (LIMS) overview and control. Within this study, the blood samples were analyzed by the Clinical Chemistry department at the Southern University Hospital in Malmö, using standard biomarker assays, quantifying 23 common markers used in everyday healthcare around the world. We were able to prove that the 384-format using an aluminum foil with a thin polymer film coating for sealing, is stable and can reproducibly be processed for automated biobank freezer units.
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| 10. |
- Malm, Johan, et al.
(författare)
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Stardardization Developments for Large Scale Biobanks in Smoking Related Diseases - A Model System for Blood Sample Processing and Storage
- 2013
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Ingår i: Translational Respiratory Medicine. - : Springer Science and Business Media LLC. - 2213-0802. ; 1
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Tidskriftsartikel (refereegranskat)abstract
- Biobank samples stored in biobanks give researchers and respiratory healthcare institutions access to datasets of analytes valuable for both diagnostic and research practices. The usefulness of these samples in clinical decision-making is highly dependent on their quality and integrity. New procedures that better preserve sample integrity and reduce degradation are being developed to meet the needs of both present and future biobanking. Hereby we present an automatic sample workflow scheme that is designed to handle high numbers of blood samples. Blood fractions are aliquoted, heat sealed using novel technology, and stored in 384 tube high-density sample arrays. The newly developed 384 biobank rack system is especially suited for preserving identical small aliquots. This technology development allows rapid access to a given sample in the frozen archive while maintaining individual sample integrity with sample tube confinement and quality management. We provide data on robotic processing of clinical samples at -80°C, following initial processing, analysis and shipping between laboratories throughout Europe. Subsequent to unpacking, re-sorting, and storage at these sites, the samples have been returned for analysis. Biomarker analysis of 13 common tests in the clinical chemistry unit of the hospital provides evidence of qualitative and stable logistics using the 384-sample tube system.
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