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Selheim F, Aasebø E, Reikvam H, Bruserud Ø, Hernandez-Valladares M. Monocytic Differentiation of Human Acute Myeloid Leukemia Cells: A Proteomic and Phosphoproteomic Comparison of FAB-M4/M5 Patients with and without Nucleophosmin 1 Mutations. Int J Mol Sci 2024; 25:5080. [PMID: 38791118 PMCID: PMC11121526 DOI: 10.3390/ijms25105080] [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: 12/20/2023] [Revised: 04/14/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
Even though morphological signs of differentiation have a minimal impact on survival after intensive cytotoxic therapy for acute myeloid leukemia (AML), monocytic AML cell differentiation (i.e., classified as French/American/British (FAB) subtypes M4/M5) is associated with a different responsiveness both to Bcl-2 inhibition (decreased responsiveness) and possibly also bromodomain inhibition (increased responsiveness). FAB-M4/M5 patients are heterogeneous with regard to genetic abnormalities, even though monocytic differentiation is common for patients with Nucleophosmin 1 (NPM1) insertions/mutations; to further study the heterogeneity of FAB-M4/M5 patients we did a proteomic and phosphoproteomic comparison of FAB-M4/M5 patients with (n = 13) and without (n = 12) NPM1 mutations. The proteomic profile of NPM1-mutated FAB-M4/M5 patients was characterized by increased levels of proteins involved in the regulation of endocytosis/vesicle trafficking/organellar communication. In contrast, AML cells without NPM1 mutations were characterized by increased levels of several proteins involved in the regulation of cytoplasmic translation, including a large number of ribosomal proteins. The phosphoproteomic differences between the two groups were less extensive but reflected similar differences. To conclude, even though FAB classification/monocytic differentiation are associated with differences in responsiveness to new targeted therapies (e.g., Bcl-2 inhibition), our results shows that FAB-M4/M5 patients are heterogeneous with regard to important biological characteristics of the leukemic cells.
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Affiliation(s)
- Frode Selheim
- Proteomics Unit of University of Bergen (PROBE), University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Elise Aasebø
- Acute Leukemia Research Group, Department of Clinical Science, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway; (E.A.); (H.R.); (Ø.B.)
| | - Håkon Reikvam
- Acute Leukemia Research Group, Department of Clinical Science, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway; (E.A.); (H.R.); (Ø.B.)
- Section for Hematology, Department of Medicine, Haukeland University Hospital, 5009 Bergen, Norway
| | - Øystein Bruserud
- Acute Leukemia Research Group, Department of Clinical Science, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway; (E.A.); (H.R.); (Ø.B.)
- Section for Hematology, Department of Medicine, Haukeland University Hospital, 5009 Bergen, Norway
| | - Maria Hernandez-Valladares
- Proteomics Unit of University of Bergen (PROBE), University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
- Department of Physical Chemistry, University of Granada, Avenida de la Fuente Nueva S/N, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18012 Granada, Spain
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2
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Punetha A, Kotiya D. Advancements in Oncoproteomics Technologies: Treading toward Translation into Clinical Practice. Proteomes 2023; 11:2. [PMID: 36648960 PMCID: PMC9844371 DOI: 10.3390/proteomes11010002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/12/2023] Open
Abstract
Proteomics continues to forge significant strides in the discovery of essential biological processes, uncovering valuable information on the identity, global protein abundance, protein modifications, proteoform levels, and signal transduction pathways. Cancer is a complicated and heterogeneous disease, and the onset and progression involve multiple dysregulated proteoforms and their downstream signaling pathways. These are modulated by various factors such as molecular, genetic, tissue, cellular, ethnic/racial, socioeconomic status, environmental, and demographic differences that vary with time. The knowledge of cancer has improved the treatment and clinical management; however, the survival rates have not increased significantly, and cancer remains a major cause of mortality. Oncoproteomics studies help to develop and validate proteomics technologies for routine application in clinical laboratories for (1) diagnostic and prognostic categorization of cancer, (2) real-time monitoring of treatment, (3) assessing drug efficacy and toxicity, (4) therapeutic modulations based on the changes with prognosis and drug resistance, and (5) personalized medication. Investigation of tumor-specific proteomic profiles in conjunction with healthy controls provides crucial information in mechanistic studies on tumorigenesis, metastasis, and drug resistance. This review provides an overview of proteomics technologies that assist the discovery of novel drug targets, biomarkers for early detection, surveillance, prognosis, drug monitoring, and tailoring therapy to the cancer patient. The information gained from such technologies has drastically improved cancer research. We further provide exemplars from recent oncoproteomics applications in the discovery of biomarkers in various cancers, drug discovery, and clinical treatment. Overall, the future of oncoproteomics holds enormous potential for translating technologies from the bench to the bedside.
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Affiliation(s)
- Ankita Punetha
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Rutgers University, 225 Warren St., Newark, NJ 07103, USA
| | - Deepak Kotiya
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, 900 South Limestone St., Lexington, KY 40536, USA
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3
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Tislevoll BS, Hellesøy M, Fagerholt OHE, Gullaksen SE, Srivastava A, Birkeland E, Kleftogiannis D, Ayuda-Durán P, Piechaczyk L, Tadele DS, Skavland J, Panagiotis B, Hovland R, Andresen V, Seternes OM, Tvedt THA, Aghaeepour N, Gavasso S, Porkka K, Jonassen I, Fløisand Y, Enserink J, Blaser N, Gjertsen BT. Early response evaluation by single cell signaling profiling in acute myeloid leukemia. Nat Commun 2023; 14:115. [PMID: 36611026 PMCID: PMC9825407 DOI: 10.1038/s41467-022-35624-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 12/13/2022] [Indexed: 01/09/2023] Open
Abstract
Aberrant pro-survival signaling is a hallmark of cancer cells, but the response to chemotherapy is poorly understood. In this study, we investigate the initial signaling response to standard induction chemotherapy in a cohort of 32 acute myeloid leukemia (AML) patients, using 36-dimensional mass cytometry. Through supervised and unsupervised machine learning approaches, we find that reduction of extracellular-signal-regulated kinase (ERK) 1/2 and p38 mitogen-activated protein kinase (MAPK) phosphorylation in the myeloid cell compartment 24 h post-chemotherapy is a significant predictor of patient 5-year overall survival in this cohort. Validation by RNA sequencing shows induction of MAPK target gene expression in patients with high phospho-ERK1/2 24 h post-chemotherapy, while proteomics confirm an increase of the p38 prime target MAPK activated protein kinase 2 (MAPKAPK2). In this study, we demonstrate that mass cytometry can be a valuable tool for early response evaluation in AML and elucidate the potential of functional signaling analyses in precision oncology diagnostics.
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Affiliation(s)
- Benedicte Sjo Tislevoll
- Centre for Cancer Biomarkers (CCBIO), Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Monica Hellesøy
- Department of Internal Medicine, Hematology Section, Haukeland University Hospital, Helse Bergen HF, Bergen, Norway
| | - Oda Helen Eck Fagerholt
- Centre for Cancer Biomarkers (CCBIO), Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Stein-Erik Gullaksen
- Department of Internal Medicine, Hematology Section, Haukeland University Hospital, Helse Bergen HF, Bergen, Norway
| | - Aashish Srivastava
- Genome Core Facility, Clinical Laboratory, K2 Haukeland University Hospital, Bergen, Norway
| | - Even Birkeland
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, Bergen, Norway
| | - Dimitrios Kleftogiannis
- Centre for Cancer Biomarkers (CCBIO), Department of Clinical Science, University of Bergen, Bergen, Norway.,Centre for Cancer Biomarkers and Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Pilar Ayuda-Durán
- Department of Molecular Cell Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Montebello, 0379, Oslo, Norway.,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0318, Oslo, Norway
| | - Laure Piechaczyk
- Department of Molecular Cell Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Montebello, 0379, Oslo, Norway.,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0318, Oslo, Norway.,Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Dagim Shiferaw Tadele
- Department of Molecular Genetics, Division of Laboratory Medicine, Oslo University Hospital, Oslo, Norway.,Department of Translational Hematology and Oncology Research, Cleveland Clinic, OH, 44106, USA
| | - Jørn Skavland
- Centre for Cancer Biomarkers (CCBIO), Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Baliakas Panagiotis
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Randi Hovland
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Vibeke Andresen
- Centre for Cancer Biomarkers (CCBIO), Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Ole Morten Seternes
- Department of Pharmacy, UiT-The Arctic University of Norway, 9037, Tromsø, Norway
| | | | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, 94121, USA.,Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94121, USA.,Department of Biomedical Informatics, Stanford University School of Medicine, Stanford, CA, 94121, USA
| | - Sonia Gavasso
- Centre for Cancer Biomarkers (CCBIO), Department of Clinical Science, University of Bergen, Bergen, Norway.,Centre for Clinical Treatment Research (NeuroSysMed), Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Kimmo Porkka
- Department of Hematology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - Inge Jonassen
- Centre for Cancer Biomarkers and Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Yngvar Fløisand
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0318, Oslo, Norway.,Department of Hematology, Oslo University Hospital, Oslo, Norway
| | - Jorrit Enserink
- Department of Molecular Cell Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Montebello, 0379, Oslo, Norway.,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0318, Oslo, Norway.,Section for Biochemistry and Molecular Biology, Faculty of Mathematics and Natural Sciences, University of Oslo, 0037, Oslo, Norway
| | - Nello Blaser
- Department of Informatics, University of Bergen, Bergen, Norway.
| | - Bjørn Tore Gjertsen
- Centre for Cancer Biomarkers (CCBIO), Department of Clinical Science, University of Bergen, Bergen, Norway. .,Department of Internal Medicine, Hematology Section, Haukeland University Hospital, Helse Bergen HF, Bergen, Norway.
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4
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Grey W, Rio-Machin A, Casado-Izquierdo P, Grönroos E, Ali S, Miettinen JJ, Bewicke-Copley F, Parsons A, Heckman CA, Swanton C, Cutillas P, Gribben J, Fitzgibbon J, Bonnet D. CKS1 inhibition depletes leukemic stem cells and protects healthy hematopoietic stem cells in acute myeloid leukemia. Sci Transl Med 2022; 14:eabn3248. [PMID: 35731890 PMCID: PMC7612983 DOI: 10.1126/scitranslmed.abn3248] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Acute myeloid leukemia (AML) is an aggressive hematological disorder comprising a hierarchy of quiescent leukemic stem cells (LSCs) and proliferating blasts with limited self-renewal ability. AML has a dismal prognosis, with extremely low 2-year survival rates in the poorest cytogenetic risk patients, primarily due to the failure of intensive chemotherapy protocols to deplete LSCs and toxicity of therapy toward healthy hematopoietic cells. We studied the role of cyclin-dependent kinase regulatory subunit 1 (CKS1)-dependent protein degradation in primary human AML and healthy hematopoiesis xenograft models in vivo. Using a small-molecule inhibitor (CKS1i), we demonstrate a dual role for CKS1-dependent protein degradation in reducing patient-derived AML blasts in vivo and, importantly, depleting LSCs, whereas inhibition of CKS1 has the opposite effect on normal hematopoiesis, protecting normal hematopoietic stem cells from chemotherapeutic toxicity. Proteomic analysis of responses to CKS1i in our patient-derived xenograft mouse model demonstrate that inhibition of CKS1 in AML leads to hyperactivation of RAC1 and accumulation of lethal reactive oxygen species, whereas healthy hematopoietic cells enter quiescence in response to CKS1i, protecting hematopoietic stem cells. Together, these findings demonstrate that CKS1-dependent proteostasis is a key vulnerability in malignant stem cell biology.
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Affiliation(s)
- William Grey
- Haematopoietic Stem Cell Laboratory, The Francis Crick Institute, London, U.K
| | - Ana Rio-Machin
- Centre for Genomics and Computational Biology, Bart’s Cancer Institute, London, U.K
| | - Pedro Casado-Izquierdo
- Cell signalling and proteomics group, Centre for Genomics and Computational Biology, Barts Cancer Institute, London, U.K
| | - Eva Grönroos
- Cancer evolution and genome instability laboratory, The Francis Crick Institute, London, U.K
| | - Sara Ali
- Haematopoietic Stem Cell Laboratory, The Francis Crick Institute, London, U.K
| | - Juho J. Miettinen
- Institute for Molecular Medicine Finland – FINN, HiLIFE – Helsinki Institute of Life Science, iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | | | - Alun Parsons
- Institute for Molecular Medicine Finland – FINN, HiLIFE – Helsinki Institute of Life Science, iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Caroline A. Heckman
- Institute for Molecular Medicine Finland – FINN, HiLIFE – Helsinki Institute of Life Science, iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Charles Swanton
- Cancer evolution and genome instability laboratory, The Francis Crick Institute, London, U.K
| | - Pedro Cutillas
- Cell signalling and proteomics group, Centre for Genomics and Computational Biology, Barts Cancer Institute, London, U.K
| | - John Gribben
- Centre for Haemato-Oncology, Bart’s Cancer Institute, London, U.K
| | - Jude Fitzgibbon
- Centre for Genomics and Computational Biology, Bart’s Cancer Institute, London, U.K
| | - Dominique Bonnet
- Haematopoietic Stem Cell Laboratory, The Francis Crick Institute, London, U.K
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5
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Aasebø E, Brenner AK, Hernandez-Valladares M, Birkeland E, Berven FS, Selheim F, Bruserud Ø. Proteomic Comparison of Bone Marrow Derived Osteoblasts and Mesenchymal Stem Cells. Int J Mol Sci 2021; 22:ijms22115665. [PMID: 34073480 PMCID: PMC8198503 DOI: 10.3390/ijms22115665] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/21/2021] [Accepted: 05/22/2021] [Indexed: 02/07/2023] Open
Abstract
Mesenchymal stem cells (MSCs) can differentiate into osteoblasts, and therapeutic targeting of these cells is considered both for malignant and non-malignant diseases. We analyzed global proteomic profiles for osteoblasts derived from ten and MSCs from six healthy individuals, and we quantified 5465 proteins for the osteoblasts and 5420 proteins for the MSCs. There was a large overlap in the profiles for the two cell types; 156 proteins were quantified only in osteoblasts and 111 proteins only for the MSCs. The osteoblast-specific proteins included several extracellular matrix proteins and a network including 27 proteins that influence intracellular signaling (Wnt/Notch/Bone morphogenic protein pathways) and bone mineralization. The osteoblasts and MSCs showed only minor age- and sex-dependent proteomic differences. Finally, the osteoblast and MSC proteomic profiles were altered by ex vivo culture in serum-free media. We conclude that although the proteomic profiles of osteoblasts and MSCs show many similarities, we identified several osteoblast-specific extracellular matrix proteins and an osteoblast-specific intracellular signaling network. Therapeutic targeting of these proteins will possibly have minor effects on MSCs. Furthermore, the use of ex vivo cultured osteoblasts/MSCs in clinical medicine will require careful standardization of the ex vivo handling of the cells.
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Affiliation(s)
- Elise Aasebø
- Department of Clinical Science, University of Bergen, 5020 Bergen, Norway; (E.A.); (A.K.B.)
- Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5020 Bergen, Norway; (M.H.-V.); (E.B.); (F.S.B.); (F.S.)
| | - Annette K. Brenner
- Department of Clinical Science, University of Bergen, 5020 Bergen, Norway; (E.A.); (A.K.B.)
| | - Maria Hernandez-Valladares
- Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5020 Bergen, Norway; (M.H.-V.); (E.B.); (F.S.B.); (F.S.)
| | - Even Birkeland
- Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5020 Bergen, Norway; (M.H.-V.); (E.B.); (F.S.B.); (F.S.)
| | - Frode S. Berven
- Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5020 Bergen, Norway; (M.H.-V.); (E.B.); (F.S.B.); (F.S.)
| | - Frode Selheim
- Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5020 Bergen, Norway; (M.H.-V.); (E.B.); (F.S.B.); (F.S.)
| | - Øystein Bruserud
- Department of Clinical Science, University of Bergen, 5020 Bergen, Norway; (E.A.); (A.K.B.)
- Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway
- Correspondence:
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6
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Kang KW, Kim H, Hur W, Jung JH, Jeong SJ, Shin H, Seo D, Jeong H, Choi B, Hong S, Kim HK, Choi Y, Park JH, Lee KY, Kim KP, Park Y. A Proteomic Approach to Understand the Clinical Significance of Acute Myeloid Leukemia-Derived Extracellular Vesicles Reflecting Essential Characteristics of Leukemia. Mol Cell Proteomics 2020; 20:100017. [PMID: 33592500 PMCID: PMC7949255 DOI: 10.1074/mcp.ra120.002169] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 11/12/2020] [Accepted: 11/30/2020] [Indexed: 01/08/2023] Open
Abstract
Extracellular vesicle (EV) proteins from acute myeloid leukemia (AML) cell lines were analyzed using mass spectrometry. The analyses identified 2450 proteins, including 461 differentially expressed proteins (290 upregulated and 171 downregulated). CD53 and CD47 were upregulated and were selected as candidate biomarkers. The association between survival of patients with AML and the expression levels of CD53 and CD47 at diagnosis was analyzed using mRNA expression data from The Cancer Genome Atlas database. Patients with higher expression levels showed significantly inferior survival than those with lower expression levels. ELISA results of the expression levels of CD53 and CD47 from EVs in the bone marrow of patients with AML at diagnosis and at the time of complete remission with induction chemotherapy revealed that patients with downregulated CD53 and CD47 expression appeared to relapse less frequently. Network model analysis of EV proteins revealed several upregulated kinases, including LYN, CSNK2A1, SYK, CSK, and PTK2B. The potential cytotoxicity of several clinically applicable drugs that inhibit these kinases was tested in AML cell lines. The drugs lowered the viability of AML cells. The collective data suggest that AML cell-derived EVs could reflect essential leukemia biology.
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Affiliation(s)
- Ka-Won Kang
- Division of Hematology-Oncology, Department of Internal Medicine, Korea University College of Medicine, Seoul, South Korea
| | - Hyoseon Kim
- Department of Applied Chemistry, Institute of Natural Science, Global Center for Pharmaceutical Ingredient Materials, Kyung Hee University, Yongin, South Korea; Department of Biomedical Science and Technology, Kyung Hee Medical Science Research Institute, Kyung Hee University, Seoul, South Korea
| | - Woojune Hur
- Division of Hematology-Oncology, Department of Internal Medicine, Korea University College of Medicine, Seoul, South Korea
| | - Jik-Han Jung
- Department of Bio and Brain Bioengineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Su Jin Jeong
- Department of Statistics Support, Medical Science Research Institute, Kyung Hee University Hospital, Seoul, South Korea
| | - Hyunku Shin
- Department of Bio-convergence Engineering, Korea University, Seoul, South Korea
| | - Dongkwon Seo
- Department of Bio-convergence Engineering, Korea University, Seoul, South Korea
| | - Hyesun Jeong
- School of Biosystem and Biomedical Science, Korea University, Seoul, South Korea
| | - ByeongHyeon Choi
- Department of Thoracic and Cardiovascular Surgery, Korea University College of Medicine, Seoul, South Korea
| | - Sunghoi Hong
- School of Biosystem and Biomedical Science, Korea University, Seoul, South Korea
| | - Hyun Koo Kim
- Department of Thoracic and Cardiovascular Surgery, Korea University College of Medicine, Seoul, South Korea
| | - Yeonho Choi
- Department of Bio-convergence Engineering, Korea University, Seoul, South Korea
| | - Ji-Ho Park
- Department of Bio and Brain Bioengineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Kil Yeon Lee
- Department of Surgery, College of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Kwang Pyo Kim
- Department of Applied Chemistry, Institute of Natural Science, Global Center for Pharmaceutical Ingredient Materials, Kyung Hee University, Yongin, South Korea; Department of Biomedical Science and Technology, Kyung Hee Medical Science Research Institute, Kyung Hee University, Seoul, South Korea.
| | - Yong Park
- Division of Hematology-Oncology, Department of Internal Medicine, Korea University College of Medicine, Seoul, South Korea.
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7
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Hernandez-Valladares M, Bruserud Ø, Selheim F. The Implementation of Mass Spectrometry-Based Proteomics Workflows in Clinical Routines of Acute Myeloid Leukemia: Applicability and Perspectives. Int J Mol Sci 2020; 21:ijms21186830. [PMID: 32957646 PMCID: PMC7556012 DOI: 10.3390/ijms21186830] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/10/2020] [Accepted: 09/15/2020] [Indexed: 02/08/2023] Open
Abstract
With the current reproducibility of proteome preparation workflows along with the speed and sensitivity of the mass spectrometers, the transition of the mass spectrometry (MS)-based proteomics technology from biomarker discovery to clinical implementation is under appraisal in the biomedicine community. Therefore, this technology might be implemented soon to detect well-known biomarkers in cancers and other diseases. Acute myeloid leukemia (AML) is an aggressive heterogeneous malignancy that requires intensive treatment to cure the patient. Leukemia relapse is still a major challenge even for patients who have favorable genetic abnormalities. MS-based proteomics could be of great help to both describe the proteome changes of individual patients and identify biomarkers that might encourage specific treatments or clinical strategies. Herein, we will review the advances and availability of the MS-based proteomics strategies that could already be used in clinical proteomics. However, the heterogeneity of complex diseases as AML requires consensus to recognize AML biomarkers and to establish MS-based workflows that allow their unbiased identification and quantification. Although our literature review appears promising towards the utilization of MS-based proteomics in clinical AML in a near future, major efforts are required to validate AML biomarkers and agree on clinically approved workflows.
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MESH Headings
- Biomarkers, Tumor/analysis
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Computational Biology
- Humans
- Leukemia, Myeloid, Acute/diagnosis
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/therapy
- Mass Spectrometry/methods
- Prognosis
- Proteome/analysis
- Proteome/metabolism
- Proteomics/methods
- Robotics/instrumentation
- Robotics/methods
- Workflow
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Affiliation(s)
- Maria Hernandez-Valladares
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
- The Proteomics Facility of the University of Bergen (PROBE), Department of Biomedicine, University of Bergen, 5009 Bergen, Norway
- Correspondence: (M.H.-V.); (Ø.B.); (F.S.); Tel.: +47-55586368 (M.H.-V.); +47-55972997 (Ø.B.); +47-55586368 (F.S.)
| | - Øystein Bruserud
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
- Correspondence: (M.H.-V.); (Ø.B.); (F.S.); Tel.: +47-55586368 (M.H.-V.); +47-55972997 (Ø.B.); +47-55586368 (F.S.)
| | - Frode Selheim
- The Proteomics Facility of the University of Bergen (PROBE), Department of Biomedicine, University of Bergen, 5009 Bergen, Norway
- The Department of Biomedicine, University of Bergen, 5009 Bergen, Norway
- Correspondence: (M.H.-V.); (Ø.B.); (F.S.); Tel.: +47-55586368 (M.H.-V.); +47-55972997 (Ø.B.); +47-55586368 (F.S.)
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8
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Aasebø E, Berven FS, Bartaula-Brevik S, Stokowy T, Hovland R, Vaudel M, Døskeland SO, McCormack E, Batth TS, Olsen JV, Bruserud Ø, Selheim F, Hernandez-Valladares M. Proteome and Phosphoproteome Changes Associated with Prognosis in Acute Myeloid Leukemia. Cancers (Basel) 2020; 12:cancers12030709. [PMID: 32192169 PMCID: PMC7140113 DOI: 10.3390/cancers12030709] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/05/2020] [Accepted: 03/13/2020] [Indexed: 12/12/2022] Open
Abstract
Acute myeloid leukemia (AML) is a hematological cancer that mainly affects the elderly. Although complete remission (CR) is achieved for the majority of the patients after induction and consolidation therapies, nearly two-thirds relapse within a short interval. Understanding biological factors that determine relapse has become of major clinical interest in AML. We utilized liquid chromatography tandem mass spectrometry (LC-MS/MS) to identify the protein changes and protein phosphorylation events associated with AML relapse in primary cells from 41 AML patients at time of diagnosis. Patients were defined as relapse-free if they had not relapsed within a five-year clinical follow-up after AML diagnosis. Relapse was associated with increased expression of RNA processing proteins and decreased expression of V-ATPase proteins. We also observed an increase in phosphorylation events catalyzed by cyclin-dependent kinases (CDKs) and casein kinase 2 (CSK2). The biological relevance of the proteome findings was supported by cell proliferation assays using inhibitors of V-ATPase (bafilomycin), CSK2 (CX-4945), CDK4/6 (abemaciclib) and CDK2/7/9 (SNS-032). While bafilomycin preferentially inhibited the cells from relapse patients, the kinase inhibitors were less efficient in these cells. This suggests that therapy against the upregulated kinases could also target the factors inducing their upregulation rather than their activity. This study, therefore, presents markers that could help predict AML relapse and direct therapeutic strategies.
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Affiliation(s)
- Elise Aasebø
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (E.A.); (S.B.-B.); (T.S.); (M.V.); (Ø.B.)
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5009 Bergen, Norway; (F.S.B.); (F.S.)
| | - Frode S. Berven
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5009 Bergen, Norway; (F.S.B.); (F.S.)
- The Department of Biomedicine, University of Bergen, 5009 Bergen, Norway;
| | - Sushma Bartaula-Brevik
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (E.A.); (S.B.-B.); (T.S.); (M.V.); (Ø.B.)
| | - Tomasz Stokowy
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (E.A.); (S.B.-B.); (T.S.); (M.V.); (Ø.B.)
- Department for Medical Genetics, Haukeland University Hospital, 5021 Bergen, Norway;
| | - Randi Hovland
- Department for Medical Genetics, Haukeland University Hospital, 5021 Bergen, Norway;
- Department of Biological Sciences, University of Bergen, 5006 Bergen, Norway
| | - Marc Vaudel
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (E.A.); (S.B.-B.); (T.S.); (M.V.); (Ø.B.)
| | | | - Emmet McCormack
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway;
| | - Tanveer S. Batth
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark; (T.S.B.); (J.V.O.)
| | - Jesper V. Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark; (T.S.B.); (J.V.O.)
| | - Øystein Bruserud
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (E.A.); (S.B.-B.); (T.S.); (M.V.); (Ø.B.)
| | - Frode Selheim
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5009 Bergen, Norway; (F.S.B.); (F.S.)
- The Department of Biomedicine, University of Bergen, 5009 Bergen, Norway;
| | - Maria Hernandez-Valladares
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (E.A.); (S.B.-B.); (T.S.); (M.V.); (Ø.B.)
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5009 Bergen, Norway; (F.S.B.); (F.S.)
- Correspondence: ; Tel.: +47-5558-6368
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High Constitutive Cytokine Release by Primary Human Acute Myeloid Leukemia Cells Is Associated with a Specific Intercellular Communication Phenotype. J Clin Med 2019; 8:jcm8070970. [PMID: 31277464 PMCID: PMC6678419 DOI: 10.3390/jcm8070970] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 06/20/2019] [Accepted: 07/01/2019] [Indexed: 12/18/2022] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease, and this heterogeneity includes the capacity of constitutive release of extracellular soluble mediators by AML cells. We investigated whether this capacity is associated with molecular genetic abnormalities, and we compared the proteomic profiles of AML cells with high and low release. AML cells were derived from 71 consecutive patients that showed an expected frequency of cytogenetic and molecular genetic abnormalities. The constitutive extracellular release of 34 soluble mediators (CCL and CXCL chemokines, interleukins, proteases, and protease regulators) was investigated for an unselected subset of 62 patients, and they could be classified into high/intermediate/low release subsets based on their general capacity of constitutive secretion. FLT3-ITD was more frequent among patients with high constitutive mediator release, but our present study showed no additional associations between the capacity of constitutive release and 53 other molecular genetic abnormalities. We compared the proteomic profiles of two contrasting patient subsets showing either generally high or low constitutive release. A network analysis among cells with high release levels demonstrated high expression of intracellular proteins interacting with integrins, RAC1, and SYK signaling. In contrast, cells with low release showed high expression of several transcriptional regulators. We conclude that AML cell capacity of constitutive mediator release is characterized by different expression of potential intracellular therapeutic targets.
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