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Casado P, Cutillas PR. Proteomic Characterization of Acute Myeloid Leukemia for Precision Medicine. Mol Cell Proteomics 2023; 22:100517. [PMID: 36805445 PMCID: PMC10152134 DOI: 10.1016/j.mcpro.2023.100517] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 02/07/2023] [Accepted: 02/13/2023] [Indexed: 02/19/2023] Open
Abstract
Acute myeloid leukemia (AML) is a highly heterogeneous cancer of the hematopoietic system with no cure for most patients. In addition to chemotherapy, treatment options for AML include recently approved therapies that target proteins with roles in AML pathobiology, such as FLT3, BLC2, and IDH1/2. However, due to disease complexity, these therapies produce very diverse responses, and survival rates are still low. Thus, despite considerable advances, there remains a need for therapies that target different aspects of leukemic biology and for associated biomarkers that define patient populations likely to respond to each available therapy. To meet this need, drugs that target different AML vulnerabilities are currently in advanced stages of clinical development. Here, we review proteomics and phosphoproteomics studies that aimed to provide insights into AML biology and clinical disease heterogeneity not attainable with genomic approaches. To place the discussion in context, we first provide an overview of genetic and clinical aspects of the disease, followed by a summary of proteins targeted by compounds that have been approved or are under clinical trials for AML treatment and, if available, the biomarkers that predict responses. We then discuss proteomics and phosphoproteomics studies that provided insights into AML pathogenesis, from which potential biomarkers and drug targets were identified, and studies that aimed to rationalize the use of synergistic drug combinations. When considered as a whole, the evidence summarized here suggests that proteomics and phosphoproteomics approaches can play a crucial role in the development and implementation of precision medicine for AML patients.
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Affiliation(s)
- Pedro Casado
- Cell Signalling & Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Pedro R Cutillas
- Cell Signalling & Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom; The Alan Turing Institute, The British Library, London, United Kingdom; Digital Environment Research Institute (DERI), Queen Mary University of London, London, United Kingdom.
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Affiliation(s)
- Gary B Smejkal
- a Core Services Laboratory , Focus Proteomics , Hudson , NH , USA
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Yang N, Anapindi KDB, Romanova EV, Rubakhin SS, Sweedler JV. Improved identification and quantitation of mature endogenous peptides in the rodent hypothalamus using a rapid conductive sample heating system. Analyst 2018; 142:4476-4485. [PMID: 29098220 DOI: 10.1039/c7an01358b] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Measurement, identification, and quantitation of endogenous peptides in tissue samples by mass spectrometry (MS) contribute to our understanding of the complex molecular mechanisms of numerous biological phenomena. For accurate results, it is essential to arrest the postmortem degradation of ubiquitous proteins in samples prior to performing peptidomic measurements. Doing so ensures that the detection of endogenous peptides, typically present at relatively low levels of abundance, is not overwhelmed by protein degradation products. Heat stabilization has been shown to inactivate the enzymes in tissue samples and minimize the presence of protein degradation products in the subsequent peptide extracts. However, the efficacy of different heat treatments to preserve the integrity of full-length endogenous peptides has not been well documented; prior peptidomic studies of heat stabilization methods have not distinguished between the full-length (mature) and numerous truncated (possible artifacts of sampling) forms of endogenous peptides. We show that thermal sample treatment via rapid conductive heat transfer is effective for detection of mature endogenous peptides in fresh and frozen rodent brain tissues. Freshly isolated tissue processing with the commercial Stabilizor T1 heat stabilization system resulted in the confident identification of 65% more full-length mature neuropeptides compared to widely used sample treatment in a hot water bath. This finding was validated by a follow-up quantitative multiple reaction monitoring MS analysis of select neuropeptides. The rapid conductive heating in partial vacuum provided by the Stabilizor T1 effectively reduces protein degradation and decreases the chemical complexity of the sample, as assessed by determining total protein content. This system enabled the detection, identification, and quantitation of neuropeptides related to 22 prohormones expressed in individual rat hypothalami and suprachiasmatic nuclei.
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Affiliation(s)
- Ning Yang
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana 61801, USA.
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Adamczyk B, Jin C, Polom K, Muñoz P, Rojas-Macias MA, Zeeberg D, Borén M, Roviello F, Karlsson NG. Sample handling of gastric tissue and O-glycan alterations in paired gastric cancer and non-tumorigenic tissues. Sci Rep 2018; 8:242. [PMID: 29321476 PMCID: PMC5762837 DOI: 10.1038/s41598-017-18299-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 12/07/2017] [Indexed: 12/13/2022] Open
Abstract
Sample collection, handling and storage are the most critical steps for ensuring the highest preservation of specimens. Pre-analytical variability can influence the results as protein signatures alter rapidly after tissue excision or during long-term storage. Hence, we evaluated current state-of-the-art biobank preservation methods from a glycomics perspective and analyzed O-glycan alterations occurring in the gastric cancer tissues. Paired tumor and adjacent normal tissue samples were obtained from six patients undergoing gastric cancer surgery. Collected samples (n = 24) were either snap-frozen or heat stabilized and then homogenized. Glycans were released from extracted glycoproteins and analyzed by LC-MS/MS. In total, the relative abundance of 83 O-glycans and 17 derived structural features were used for comparison. There was no statistically significant difference found in variables between snap frozen and heat-stabilized samples, which indicated the two preservation methods were comparable. The data also showed significant changes between normal and cancerous tissue. In addition to a shift from high sialylation in the cancer area towards blood group ABO in the normal area, we also detected that the LacdiNAc epitope (N,N'-diacetyllactosamine) was significantly decreased in cancer samples. The O-glycan alterations that are presented here may provide predictive power for the detection and prognosis of gastric cancer.
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Affiliation(s)
- Barbara Adamczyk
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Chunsheng Jin
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Karol Polom
- Department General Surgery and Surgical Oncology, University of Siena, Siena, Italy
- Department of Surgical Oncology, Medical University of Gdansk, Gdansk, Poland
| | - Pedro Muñoz
- Department of Biochemistry and Molecular Biology III, School of Medicine, Complutense University of Madrid, Madrid, Spain
| | - Miguel A Rojas-Macias
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | | | - Mats Borén
- Denator AB, Uppsala Science Park, Uppsala, Sweden
| | - Franco Roviello
- Department of Medicine, Surgery and Neurosciences, University of Siena, Siena, Italy
| | - Niclas G Karlsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
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Kanshin E, Tyers M, Thibault P. Sample Collection Method Bias Effects in Quantitative Phosphoproteomics. J Proteome Res 2015; 14:2998-3004. [PMID: 26040406 DOI: 10.1021/acs.jproteome.5b00404] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Current advances in selective enrichment, fractionation, and MS detection of phosphorylated peptides allowed identification and quantitation of tens of thousands phosphosites from minute amounts of biological material. One of the major challenges in the field is preserving the in vivo phosphorylation state of the proteins throughout the sample preparation workflow. This is typically achieved by using phosphatase inhibitors and denaturing conditions during cell lysis. Here we determine if the upstream cell collection techniques could introduce changes in protein phosphorylation. To evaluate the effect of sample collection protocols on the global phosphorylation status of the cell, we compared different sample workflows by metabolic labeling and quantitative mass spectrometry on Saccharomyces cerevisiae cell cultures. We identified highly similar phosphopeptides for cells harvested in ice cold isotonic phosphate buffer, cold ethanol, trichloroacetic acid, and liquid nitrogen. However, quantitative analyses revealed that the commonly used phosphate buffer unexpectedly activated signaling events. Such effects may introduce systematic bias in phosphoproteomics measurements and biochemical analysis.
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Affiliation(s)
- Evgeny Kanshin
- †Institute for Research in Immunology and Cancer, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, Québec H3C 3J7, Canada
| | - Michael Tyers
- †Institute for Research in Immunology and Cancer, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, Québec H3C 3J7, Canada.,‡Department of Medicine, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, Québec H3C 3J7, Canada
| | - Pierre Thibault
- †Institute for Research in Immunology and Cancer, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, Québec H3C 3J7, Canada.,§Department of Chemistry, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, Québec H3C 3J7, Canada
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Borén M. Sample preservation through heat stabilization of proteins: principles and examples. Methods Mol Biol 2015; 1295:21-32. [PMID: 25820710 DOI: 10.1007/978-1-4939-2550-6_2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Due to post-sampling changes, caused by residual enzyme activity in the sample, levels of analytes can change from their in vivo levels so that they no longer accurately reflect conditions in the living system. The Stabilizor(™) system accomplishes elimination of enzyme activity through heat-induced denaturation of enzymes by permanently altering the 3D protein structure of the enzymes. Heat stabilization can be introduced in the workflow either directly after sampling, with the instrument just next to where the sample is taken, or prior to sample homogenization and extraction, when samples are heat denatured directly from a frozen state. Initially, heat stabilization was developed to enable mass spectrometric analysis of neuropeptides. Heat stabilization has since been further developed and applied to a range of samples and downstream protein analysis techniques such as western blot, 2D gels and phosphorylation analysis with LC-MS.
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Affiliation(s)
- Mats Borén
- Denator AB, Dag Hammarskjöldsv. 10A, 753 81, Uppsala, Sweden,
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Smejkal GB. Genomics and proteomics: of hares, tortoises and the complexity of tortoises. Expert Rev Proteomics 2014. [DOI: 10.1586/epr.12.48] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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Sköld K, Alm H, Scholz B. The impact of biosampling procedures on molecular data interpretation. Mol Cell Proteomics 2013; 12:1489-501. [PMID: 23382104 PMCID: PMC3675808 DOI: 10.1074/mcp.r112.024869] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 01/17/2013] [Indexed: 01/06/2023] Open
Abstract
The separation between biological and technical variation without extensive use of technical replicates is often challenging, particularly in the context of different forms of protein and peptide modifications. Biosampling procedures in the research laboratory are easier to conduct within a shorter time frame and under controlled conditions as compared with clinical sampling, with the latter often having issues of reproducibility. But is the research laboratory biosampling really less variable? Biosampling introduces within minutes rapid tissue-specific changes in the cellular microenvironment, thus inducing a range of different pathways associated with cell survival. Biosampling involves hypoxia and, depending on the circumstances, hypothermia, circumstances for which there are evolutionarily conserved defense strategies in the range of species and also are relevant for the range of biomedical conditions. It remains unclear to what extent such adaptive processes are reflected in different biosampling procedures or how important they are for the definition of sample quality. Lately, an increasing number of comparative studies on different biosampling approaches, post-mortem effects and pre-sampling biological state, have investigated such immediate early biosampling effects. Commonalities between biosampling effects and a range of ischemia/reperfusion- and hypometabolism/anoxia-associated biological phenomena indicate that even small variations in post-sampling time intervals are likely to introduce a set of nonrandom and tissue-specific effects of experimental importance (both in vivo and in vitro). This review integrates the information provided by these comparative studies and discusses how an adaptive biological perspective in biosampling procedures may be relevant for sample quality issues.
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Affiliation(s)
- Karl Sköld
- From ‡Denator AB, Uppsala Science Park, SE-75183 Uppsala and
| | - Henrik Alm
- the §Department of Pharmaceutical Biosciences, Division of Drug Safety and Toxicology, Uppsala University, SE-75124 Uppsala, Sweden
| | - Birger Scholz
- the §Department of Pharmaceutical Biosciences, Division of Drug Safety and Toxicology, Uppsala University, SE-75124 Uppsala, Sweden
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Blessborn D, Sköld K, Zeeberg D, Kaewkhao K, Sköld O, Ahnoff M. Heat stabilization of blood spot samples for determination of metabolically unstable drug compounds. Bioanalysis 2013; 5:31-9. [PMID: 23256470 PMCID: PMC4024484 DOI: 10.4155/bio.12.294] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Sample stability is critical for accurate analysis of drug compounds in biosamples. The use of additives to eradicate the enzymatic activity causing loss of these analytes has its limitations. RESULTS A novel technique for sample stabilization by rapid, high-temperature heating was used. The stability of six commercial drugs in blood and blood spots was investigated under various conditions with or without heat stabilization at 95°C. Oseltamivir, cefotaxime and ribavirin were successfully stabilized by heating whereas significant losses were seen in unheated samples. Amodiaquine was stable with and without heating. Artemether and dihydroartemisinin were found to be very heat sensitive and began to decompose even at 60°C. CONCLUSION Heat stabilization is a viable technique to maintain analytes in blood spot samples, without the use of chemical additives, by stopping the enzymatic activity that causes sample degradation.
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Affiliation(s)
- Daniel Blessborn
- Mahidol Oxford Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | | | | | - Karnrawee Kaewkhao
- Mahidol Oxford Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | | | - Martin Ahnoff
- Denator AB, Gothenburg, Sweden
- Regulatory Bioanalysis, AstraZeneca R&D Mölndal, Sweden
- Chemistry & Molecular Biology, University of Gothenburg, Sweden
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Freeman E, Ivanov AR. Proteomics under Pressure: Development of Essential Sample Preparation Techniques in Proteomics Using Ultrahigh Hydrostatic Pressure. J Proteome Res 2011; 10:5536-46. [DOI: 10.1021/pr200805u] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Emily Freeman
- HSPH Proteomics Resource, Department of Genetics and Complex Diseases, Harvard School of Public Health, Harvard University, 655 Huntington Avenue, SPH-1 Room 409, Boston, Massachusetts 02115, United States
| | - Alexander R. Ivanov
- HSPH Proteomics Resource, Department of Genetics and Complex Diseases, Harvard School of Public Health, Harvard University, 655 Huntington Avenue, SPH-1 Room 409, Boston, Massachusetts 02115, United States
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