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Sun Z, Feng D, Jiang L, Tian J, Wang J, Zhu W. Integrated proteomic and metabolomic analysis of plasma reveals regulatory pathways and key elements in thyroid cancer. Mol Omics 2023; 19:800-809. [PMID: 37642188 DOI: 10.1039/d3mo00142c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Thyroid cancer (TC) is the most common endocrine malignancy with increasing incidence in recent years. Fine-needle aspiration biopsy (FNAB), as a gold standard for the initial evaluation of thyroid nodules, fails to cover all the cytopathologic conditions resulting in overdiagnosis. There is an urgent need for a better classification of thyroid cancer from benign thyroid nodules (BTNs). Here, data independent acquisition (DIA)-based proteomics and untargeted metabolomics in plasma samples of 10 patients with TC and 15 patients with BTNs were performed. Key proteins and metabolites were identified specific to TC, and an independent cohort was used to validate the potential biomarkers using enzyme-linked immunosorbent assay (ELISA). In total, 1429 proteins and 1172 metabolites were identified. Principal component analysis showed a strong overlap at the proteomic level and a significant discrimination at the metabolomic level between the two groups, indicating a more drastic disturbance in the metabolome of thyroid cancer. Integrated analysis of proteomics and metabolomics shows glycerophospholipid metabolism and arachidonic acid metabolism as key regulatory pathways. Furthermore, a multi-omics biomarker panel was developed consisting of LCAT, GPX3 and leukotriene B4. Based on the AUC value for the discovery set, the classification performance was 0.960. The AUC value of the external validation set was 0.930. Altogether, our results will contribute to the clinical application of potential biomarkers in the diagnosis of thyroid cancer.
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Affiliation(s)
- Zijian Sun
- Key Laboratory for Molecular Medicine and Chinese Medicine Preparations, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, China.
| | - Dongdong Feng
- Department of Head and Neck Surgery, Center of Otolaryngology-head and neck surgery, Zhejiang Provincial People's Hospital (People's Hospital of Hangzhou Medical College), Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, Hangzhou, 310014, China.
| | - Liehao Jiang
- Department of Head and Neck Surgery, Center of Otolaryngology-head and neck surgery, Zhejiang Provincial People's Hospital (People's Hospital of Hangzhou Medical College), Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, Hangzhou, 310014, China.
| | - Jingkui Tian
- Key Laboratory for Molecular Medicine and Chinese Medicine Preparations, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, China.
| | - Jiafeng Wang
- Department of Head and Neck Surgery, Center of Otolaryngology-head and neck surgery, Zhejiang Provincial People's Hospital (People's Hospital of Hangzhou Medical College), Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, Hangzhou, 310014, China.
| | - Wei Zhu
- Key Laboratory for Molecular Medicine and Chinese Medicine Preparations, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, China.
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2
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Liu Y, Zhang M, Liu Z, Li S, Liu H, Huang R, Yi F, Zhou J. A strategy can be used to analyze intracellular interaction proteomics of cell-surface receptors. Amino Acids 2023; 55:263-273. [PMID: 36539546 DOI: 10.1007/s00726-022-03223-8] [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: 05/30/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022]
Abstract
Comprehensive knowledge of the intracellular protein interactions of cell-surface receptors will greatly advance our comprehension of the underlying trafficking mechanisms. Hence, development of effective and high-throughput approaches is highly desired. In this work, we presented a strategy aiming to tailor toward the analysis of intracellular protein interactome of cell-surface receptors. We used α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors subunit GluA1 as an example to illustrate the methodological application. To capture intracellular proteins that interact with GluA1, after surface biotinylation of the prepared hippocampal neurons and slices, the non-biotinylated protein components as intracellular protein-enriched fraction were unconventionally applied for the following co-immunoprecipitation. The co-immuno-precipitated proteins were then analyzed through mass spectrometry-based proteomics and bioinformatics platforms. The detailed localizations indicated that intracellular proteins accounted for up to 93.7 and 90.3% of the analyzed proteins in the neurons and slices, respectively, suggesting that our protein preparation was highly effective to characterize intracellular interactome of GluA1. Further, we systematically revealed the protein functional profile of GluA1 intracellular interactome, thereby providing complete overview and better comprehension of diverse intracellular biological processes correlated with the complex GluA1 trafficking. All experimental results demonstrated that our methodology would be applicable and useful for intracellular interaction proteomics of general cell-surface receptors.
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Affiliation(s)
- Yanchen Liu
- Institute of Neuroscience, Basic Medical College, Chongqing Medical University, Yuzhong District, 1 Yixueyuan Road, Chongqing, 400016, China
| | - Mingming Zhang
- Institute of Neuroscience, Basic Medical College, Chongqing Medical University, Yuzhong District, 1 Yixueyuan Road, Chongqing, 400016, China
| | - Zhao Liu
- Institute of Neuroscience, Basic Medical College, Chongqing Medical University, Yuzhong District, 1 Yixueyuan Road, Chongqing, 400016, China
| | - Shuiming Li
- Shenzhen Key Laboratory of Microbiology and Gene Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Hangfei Liu
- Shenzhen Wininnovate Bio-Tech Co., Ltd,, Shenzhen, 518073, China
| | - Rongzhong Huang
- ChuangXu Institute of Life Science, Chongqing, 400016, China.,Chongqing Institute of Life Science, Chongqing, 400016, China
| | - Faping Yi
- Institute of Neuroscience, Basic Medical College, Chongqing Medical University, Yuzhong District, 1 Yixueyuan Road, Chongqing, 400016, China.
| | - Jian Zhou
- Institute of Neuroscience, Basic Medical College, Chongqing Medical University, Yuzhong District, 1 Yixueyuan Road, Chongqing, 400016, China.
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3
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Herbst SA, Vesterlund M, Helmboldt AJ, Jafari R, Siavelis I, Stahl M, Schitter EC, Liebers N, Brinkmann BJ, Czernilofsky F, Roider T, Bruch PM, Iskar M, Kittai A, Huang Y, Lu J, Richter S, Mermelekas G, Umer HM, Knoll M, Kolb C, Lenze A, Cao X, Österholm C, Wahnschaffe L, Herling C, Scheinost S, Ganzinger M, Mansouri L, Kriegsmann K, Kriegsmann M, Anders S, Zapatka M, Del Poeta G, Zucchetto A, Bomben R, Gattei V, Dreger P, Woyach J, Herling M, Müller-Tidow C, Rosenquist R, Stilgenbauer S, Zenz T, Huber W, Tausch E, Lehtiö J, Dietrich S. Proteogenomics refines the molecular classification of chronic lymphocytic leukemia. Nat Commun 2022; 13:6226. [PMID: 36266272 PMCID: PMC9584885 DOI: 10.1038/s41467-022-33385-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 09/14/2022] [Indexed: 12/24/2022] Open
Abstract
Cancer heterogeneity at the proteome level may explain differences in therapy response and prognosis beyond the currently established genomic and transcriptomic-based diagnostics. The relevance of proteomics for disease classifications remains to be established in clinically heterogeneous cancer entities such as chronic lymphocytic leukemia (CLL). Here, we characterize the proteome and transcriptome alongside genetic and ex-vivo drug response profiling in a clinically annotated CLL discovery cohort (n = 68). Unsupervised clustering of the proteome data reveals six subgroups. Five of these proteomic groups are associated with genetic features, while one group is only detectable at the proteome level. This new group is characterized by accelerated disease progression, high spliceosomal protein abundances associated with aberrant splicing, and low B cell receptor signaling protein abundances (ASB-CLL). Classifiers developed to identify ASB-CLL based on its characteristic proteome or splicing signature in two independent cohorts (n = 165, n = 169) confirm that ASB-CLL comprises about 20% of CLL patients. The inferior overall survival in ASB-CLL is also independent of both TP53- and IGHV mutation status. Our multi-omics analysis refines the classification of CLL and highlights the potential of proteomics to improve cancer patient stratification beyond genetic and transcriptomic profiling.
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Affiliation(s)
- Sophie A. Herbst
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory (EMBL), Heidelberg, Germany ,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany ,grid.461742.20000 0000 8855 0365Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Mattias Vesterlund
- grid.452834.c0000 0004 5911 2402Department of Oncology-Pathology, Karolinska Institute and Science for Life Laboratory, Stockholm, Sweden
| | - Alexander J. Helmboldt
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Rozbeh Jafari
- grid.452834.c0000 0004 5911 2402Department of Oncology-Pathology, Karolinska Institute and Science for Life Laboratory, Stockholm, Sweden
| | - Ioannis Siavelis
- grid.452834.c0000 0004 5911 2402Department of Oncology-Pathology, Karolinska Institute and Science for Life Laboratory, Stockholm, Sweden
| | - Matthias Stahl
- grid.452834.c0000 0004 5911 2402Department of Oncology-Pathology, Karolinska Institute and Science for Life Laboratory, Stockholm, Sweden
| | - Eva C. Schitter
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Nora Liebers
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory (EMBL), Heidelberg, Germany ,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany ,grid.461742.20000 0000 8855 0365Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Berit J. Brinkmann
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory (EMBL), Heidelberg, Germany ,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felix Czernilofsky
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Tobias Roider
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory (EMBL), Heidelberg, Germany ,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Peter-Martin Bruch
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory (EMBL), Heidelberg, Germany ,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Murat Iskar
- grid.7497.d0000 0004 0492 0584Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Adam Kittai
- grid.261331.40000 0001 2285 7943Department of Internal Medicine, Division of Hematology, The Ohio State University, Columbus, OH USA
| | - Ying Huang
- grid.261331.40000 0001 2285 7943Department of Internal Medicine, Division of Hematology, The Ohio State University, Columbus, OH USA
| | - Junyan Lu
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory (EMBL), Heidelberg, Germany ,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Sarah Richter
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Georgios Mermelekas
- grid.452834.c0000 0004 5911 2402Department of Oncology-Pathology, Karolinska Institute and Science for Life Laboratory, Stockholm, Sweden
| | - Husen Muhammad Umer
- grid.452834.c0000 0004 5911 2402Department of Oncology-Pathology, Karolinska Institute and Science for Life Laboratory, Stockholm, Sweden
| | - Mareike Knoll
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Carolin Kolb
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Angela Lenze
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Xiaofang Cao
- grid.452834.c0000 0004 5911 2402Department of Oncology-Pathology, Karolinska Institute and Science for Life Laboratory, Stockholm, Sweden
| | - Cecilia Österholm
- grid.4714.60000 0004 1937 0626Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Linus Wahnschaffe
- grid.6190.e0000 0000 8580 3777Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf (CIO ABCD), Excellence Cluster for Cellular Stress Response and Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Carmen Herling
- grid.6190.e0000 0000 8580 3777Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf (CIO ABCD), Excellence Cluster for Cellular Stress Response and Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Sebastian Scheinost
- grid.461742.20000 0000 8855 0365Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthias Ganzinger
- grid.7700.00000 0001 2190 4373Institute of Medical Biometry and Informatics, Heidelberg University, Heidelberg, Germany
| | - Larry Mansouri
- grid.4714.60000 0004 1937 0626Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Katharina Kriegsmann
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Mark Kriegsmann
- grid.7700.00000 0001 2190 4373Institute of Pathology, University of Heidelberg, Heidelberg, Germany
| | - Simon Anders
- grid.7700.00000 0001 2190 4373Center for Molecular Biology of the University of Heidelberg (ZMBH), Heidelberg, Germany
| | - Marc Zapatka
- grid.7497.d0000 0004 0492 0584Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Giovanni Del Poeta
- grid.6530.00000 0001 2300 0941Division of Hematology, University of Tor Vergata, Rome, Italy
| | - Antonella Zucchetto
- grid.418321.d0000 0004 1757 9741Clinical and Experimental Onco-Hematology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Riccardo Bomben
- grid.418321.d0000 0004 1757 9741Clinical and Experimental Onco-Hematology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Valter Gattei
- grid.418321.d0000 0004 1757 9741Clinical and Experimental Onco-Hematology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Peter Dreger
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Jennifer Woyach
- grid.261331.40000 0001 2285 7943Department of Internal Medicine, Division of Hematology, The Ohio State University, Columbus, OH USA
| | - Marco Herling
- grid.6190.e0000 0000 8580 3777Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf (CIO ABCD), Excellence Cluster for Cellular Stress Response and Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Carsten Müller-Tidow
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory (EMBL), Heidelberg, Germany ,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Richard Rosenquist
- grid.4714.60000 0004 1937 0626Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden ,grid.24381.3c0000 0000 9241 5705Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Stephan Stilgenbauer
- grid.6582.90000 0004 1936 9748Department of Internal Medicine III, University of Ulm, Ulm, Germany
| | - Thorsten Zenz
- grid.461742.20000 0000 8855 0365Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.412004.30000 0004 0478 9977Department of Medical Oncology and Hematology, University Hospital Zürich, Zürich, Switzerland
| | - Wolfgang Huber
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory (EMBL), Heidelberg, Germany ,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Eugen Tausch
- grid.6582.90000 0004 1936 9748Department of Internal Medicine III, University of Ulm, Ulm, Germany
| | - Janne Lehtiö
- grid.452834.c0000 0004 5911 2402Department of Oncology-Pathology, Karolinska Institute and Science for Life Laboratory, Stockholm, Sweden
| | - Sascha Dietrich
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory (EMBL), Heidelberg, Germany ,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany ,grid.461742.20000 0000 8855 0365Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.14778.3d0000 0000 8922 7789Department of Hematolgy, Oncology and Immunolgy, University Hospital of Düsseldorf, Düsseldorf, Germany
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4
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Linley AJ, Karydis LI, Mondru AK, D'Avola A, Al Shmrany H, Cicconi S, Griffin R, Forconi F, Pettitt AR, Kalakonda N, Rawstron AC, Hillmen P, Steele AJ, MacEwan DJ, Packham G, Prior IA, Slupsky JR. Kinobead Profiling Reveals Reprogramming of BCR Signaling in Response to Therapy within Primary CLL Cells. Clin Cancer Res 2021; 27:5647-5659. [PMID: 34380642 PMCID: PMC9662893 DOI: 10.1158/1078-0432.ccr-21-0161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 04/15/2021] [Accepted: 07/30/2021] [Indexed: 01/07/2023]
Abstract
PURPOSE B-cell receptor (BCR) signaling is critical for the pathogenesis of chronic lymphocytic leukemia (CLL), promoting both malignant cell survival and disease progression. Although vital, understanding of the wider signaling network associated with malignant BCR stimulation is poor. This is relevant with respect to potential changes in response to therapy, particularly involving kinase inhibitors. In the current study, we describe a novel high-resolution approach to investigate BCR signaling in primary CLL cells and track the influence of therapy on signaling response. EXPERIMENTAL DESIGN A kinobead/mass spectrometry-based protocol was used to study BCR signaling in primary CLL cells. Longitudinal analysis of samples donated by clinical trial patients was used to investigate the impact of chemoimmunotherapy and ibrutinib on signaling following surface IgM engagement. Complementary Nanostring and immunoblotting analysis was used to verify our findings. RESULTS Our protocol isolated a unique, patient-specific signature of over 30 kinases from BCR-stimulated CLL cells. This signature was associated with 13 distinct Kyoto Encyclopedia of Genes and Genomes pathways and showed significant change in cells from treatment-naïve patients compared with those from patients who had previously undergone therapy. This change was validated by longitudinal analysis of clinical trials samples where BCR-induced kinome responses in CLL cells altered between baseline and disease progression in patients failing chemoimmunotherapy and between baseline and treatment in patients taking ibrutinib. CONCLUSIONS These data comprise the first comprehensive proteomic investigation of the BCR signaling response within CLL cells and reveal unique evidence that these cells undergo adaptive reprogramming of this signaling in response to therapy.
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Affiliation(s)
- Adam J Linley
- Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom.
| | - Laura I Karydis
- School of Cancer Sciences, Cancer Research UK Centre, University of Southampton, Southampton, United Kingdom
| | - Anil K Mondru
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Annalisa D'Avola
- School of Cancer Sciences, Cancer Research UK Centre, University of Southampton, Southampton, United Kingdom
| | - Humood Al Shmrany
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Silvia Cicconi
- Cancer Research Clinical Trials Unit, University of Liverpool, Liverpool, United Kingdom
| | - Rebecca Griffin
- Cancer Research Clinical Trials Unit, University of Liverpool, Liverpool, United Kingdom
| | - Francesco Forconi
- School of Cancer Sciences, Cancer Research UK Centre, University of Southampton, Southampton, United Kingdom
| | - Andrew R Pettitt
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Nagesh Kalakonda
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Andrew C Rawstron
- Department of Haematology, Leeds Teaching Hospitals NHS Trust, Leeds, United Kingdom
| | - Peter Hillmen
- Faculty of Medicine and Health, School of Medicine, University of Leeds, Wellcome Trust Brenner Building, Leeds, United Kingdom
| | - Andrew J Steele
- School of Cancer Sciences, Cancer Research UK Centre, University of Southampton, Southampton, United Kingdom
| | - David J MacEwan
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Graham Packham
- School of Cancer Sciences, Cancer Research UK Centre, University of Southampton, Southampton, United Kingdom
| | - Ian A Prior
- Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Joseph R Slupsky
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
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5
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Beckmann L, Berg V, Dickhut C, Sun C, Merkel O, Bloehdorn J, Robrecht S, Seifert M, da Palma Guerreiro A, Claasen J, Loroch S, Oliverio M, Underbayev C, Vaughn L, Thomalla D, Hülsemann MF, Tausch E, Fischer K, Fink AM, Eichhorst B, Sickmann A, Wendtner CM, Stilgenbauer S, Hallek M, Wiestner A, Zahedi RP, Frenzel LP. MARCKS affects cell motility and response to BTK inhibitors in CLL. Blood 2021; 138:544-556. [PMID: 33735912 PMCID: PMC8377477 DOI: 10.1182/blood.2020009165] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 03/18/2021] [Accepted: 03/06/2021] [Indexed: 12/26/2022] Open
Abstract
Bruton tyrosine kinase (BTK) inhibitors are highly active drugs for the treatment of chronic lymphocytic leukemia (CLL). To understand the response to BTK inhibitors on a molecular level, we performed (phospho)proteomic analyses under ibrutinib treatment. We identified 3466 proteins and 9184 phosphopeptides (representing 2854 proteins) in CLL cells exhibiting a physiological ratio of phosphorylated serines (pS), threonines (pT), and tyrosines (pY) (pS:pT:pY). Expression of 83 proteins differed between unmutated immunoglobulin heavy-chain variable region (IGHV) CLL (UM-CLL) and mutated IGHV CLL (M-CLL). Strikingly, UM-CLL cells showed higher basal phosphorylation levels than M-CLL samples. Effects of ibrutinib on protein phosphorylation levels were stronger in UM-CLL, especially on phosphorylated tyrosines. The differentially regulated phosphopeptides and proteins clustered in pathways regulating cell migration, motility, cytoskeleton composition, and survival. One protein, myristoylated alanine-rich C-kinase substrate (MARCKS), showed striking differences in expression and phosphorylation level in UM-CLL vs M-CLL. MARCKS sequesters phosphatidylinositol-4,5-bisphosphate, thereby affecting central signaling pathways and clustering of the B-cell receptor (BCR). Genetically induced loss of MARCKS significantly increased AKT signaling and migratory capacity. CD40L stimulation increased expression of MARCKS. BCR stimulation induced phosphorylation of MARCKS, which was reduced by BTK inhibitors. In line with our in vitro findings, low MARCKS expression is associated with significantly higher treatment-induced leukocytosis and more pronounced decrease of nodal disease in patients with CLL treated with acalabrutinib.
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Affiliation(s)
- Laura Beckmann
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Valeska Berg
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Clarissa Dickhut
- Leibniz-Institut für Analytische Wissenschaften (ISAS) eV, Dortmund, Germany
| | - Clare Sun
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Olaf Merkel
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | | | - Sandra Robrecht
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
| | - Marc Seifert
- Institute of Cell Biology (Cancer Research), Medical Faculty, University of Duisburg-Essen, Essen, Germany
| | - Alexandra da Palma Guerreiro
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Julia Claasen
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Stefan Loroch
- Leibniz-Institut für Analytische Wissenschaften (ISAS) eV, Dortmund, Germany
| | - Matteo Oliverio
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Chingiz Underbayev
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Lauren Vaughn
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Daniel Thomalla
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Malte F Hülsemann
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Eugen Tausch
- Department of Internal Medicine III, Ulm University, Ulm, Germany
| | - Kirsten Fischer
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
| | - Anna Maria Fink
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
| | - Barbara Eichhorst
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften (ISAS) eV, Dortmund, Germany
| | - Clemens M Wendtner
- Department I of Internal Medicine and
- Munich Clinic Schwabing, Academic Teaching Hospital, Ludwig Maximilian University (LMU), Munich, Germany
| | - Stephan Stilgenbauer
- Department of Internal Medicine III, Ulm University, Ulm, Germany
- Department of Internal Medicine I, Saarland University, Homburg, Germany
| | - Michael Hallek
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Adrian Wiestner
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - René P Zahedi
- Leibniz-Institut für Analytische Wissenschaften (ISAS) eV, Dortmund, Germany
- Segal Cancer Proteomics Centre, Lady Davis Institute and
- Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, QC, Canada; and
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Lukas P Frenzel
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
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6
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Global effects of RAB3GAP1 dysexpression on the proteome of mouse cortical neurons. Amino Acids 2021; 53:1339-1350. [PMID: 34363538 DOI: 10.1007/s00726-021-03058-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 07/30/2021] [Indexed: 12/15/2022]
Abstract
Mounting studies have demonstrated that RAB3GAP1 expression is modified in brain diseases with multiple neurobiological functions and processes and acts as a potentially significant target. However, the cellular and molecular events arising from RAB3GAP1 dysexpression are still incompletely understood. In this work, underexpression and overexpression of RAB3GAP1 were first induced into cultured mouse cortical neurons by transfection with lentivirus plasmids. Then we globally explored the effects of RAB3GAP1 dysexpression on the proteome of the neurons through the use of isobaric tag for relative and absolute quantitation (iTRAQ)-based quantitative proteomics with bioinformatics. A total of 364 proteins in the RAB3GAP1-underexpression group and 314 proteins in the RAB3GAP1-overexpression group were identified to be differentially expressed. Subsequent bioinformatics analysis indicated that the proteome functional expression profiles induced by RAB3GAP1 underexpression and overexpression were different, suggesting the potential differences in biological processes and cellular effects. Subsequent intergroup cross-comparison revealed some candidate target proteins regulated directly by RAB3GAP1. Further parallel reaction monitoring (PRM) analysis illustrated that Sub1, Ssrp1, and Top1 proteins might serve as new potentially important linkers in the RAB3GAP1-mediated autophagy pathway in the cortical neurons. Collectively, the current proteomics data furnished new valuable insights to better understand the regulatory molecular mechanism of neuronal RAB3GAP1.
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7
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Bagacean C, Iuga CA, Bordron A, Tempescul A, Pralea IE, Bernard D, Cornen M, Bergot T, Le Dantec C, Brooks W, Saad H, Ianotto JC, Pers JO, Zdrenghea M, Berthou C, Renaudineau Y. Identification of altered cell signaling pathways using proteomic profiling in stable and progressive chronic lymphocytic leukemia. J Leukoc Biol 2021; 111:313-325. [PMID: 34288092 DOI: 10.1002/jlb.4hi0620-392r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) is characterized by significant biologic and clinical heterogeneity. This study was designed to explore CLL B-cells' proteomic profile in order to identify biologic processes affected at an early stage and during disease evolution as stable or progressive. Purified B cells from 11 untreated CLL patients were tested at two time points by liquid chromatography-tandem mass spectrometry. Patients included in the study evolved to either progressive (n = 6) or stable disease (n = 5). First, at an early stage of the disease (Binet stage A), based on the relative abundance levels of 389 differentially expressed proteins (DEPs), samples were separated into stable and progressive clusters with the main differentiating factor being the RNA splicing pathway. Next, in order to test how the DEPs affect RNA splicing, a RNA-Seq study was conducted showing 4217 differentially spliced genes between the two clusters. Distinct longitudinal evolutions were observed with predominantly proteomic modifications in the stable CLL group and spliced genes in the progressive CLL group. Splicing events were shown to be six times more frequent in the progressive CLL group. The main aberrant biologic processes controlled by DEPs and spliced genes in the progressive group were cytoskeletal organization, Wnt/β-catenin signaling, and mitochondrial and inositol phosphate metabolism with a downstream impact on CLL B-cell survival and migration. This study suggests that proteomic profiles at the early stage of CLL can discriminate progressive from stable disease and that RNA splicing dysregulation underlies CLL evolution, which opens new perspectives in terms of biomarkers and therapy.
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Affiliation(s)
- Cristina Bagacean
- Univ Brest, INSERM, UMR1227, B Lymphocytes and Autoimmunity, Brest, France.,Department of Hematology, University Hospital of Brest, Brest, France
| | - Cristina Adela Iuga
- Department of Drug Analysis, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Department of Proteomics and Metabolomics, MedFuture Research Center for Advanced Medicine-MedFUTURE, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Anne Bordron
- Univ Brest, INSERM, UMR1227, B Lymphocytes and Autoimmunity, Brest, France
| | - Adrian Tempescul
- Univ Brest, INSERM, UMR1227, B Lymphocytes and Autoimmunity, Brest, France.,Department of Hematology, University Hospital of Brest, Brest, France
| | - Ioana-Ecaterina Pralea
- Department of Proteomics and Metabolomics, MedFuture Research Center for Advanced Medicine-MedFUTURE, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | | | - Melanie Cornen
- Univ Brest, INSERM, UMR1227, B Lymphocytes and Autoimmunity, Brest, France
| | | | | | - Wesley Brooks
- Department of Chemistry, University of South Florida, Tampa, Florida, USA
| | - Hussam Saad
- Department of Hematology, University Hospital of Brest, Brest, France
| | | | | | - Mihnea Zdrenghea
- "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Christian Berthou
- Univ Brest, INSERM, UMR1227, B Lymphocytes and Autoimmunity, Brest, France.,Department of Hematology, University Hospital of Brest, Brest, France
| | - Yves Renaudineau
- Univ Brest, INSERM, UMR1227, B Lymphocytes and Autoimmunity, Brest, France.,Laboratory of Immunology and Immunotherapy, University Hospital of Brest, Brest, France
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8
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Mavridou D, Psatha K, Aivaliotis M. Proteomics and Drug Repurposing in CLL towards Precision Medicine. Cancers (Basel) 2021; 13:cancers13143391. [PMID: 34298607 PMCID: PMC8303629 DOI: 10.3390/cancers13143391] [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] [Received: 05/06/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 11/30/2022] Open
Abstract
Simple Summary Despite continued efforts, the current status of knowledge in CLL molecular pathobiology, diagnosis, prognosis and treatment remains elusive and imprecise. Proteomics approaches combined with advanced bioinformatics and drug repurposing promise to shed light on the complex proteome heterogeneity of CLL patients and mitigate, improve, or even eliminate the knowledge stagnation. In relation to this concept, this review presents a brief overview of all the available proteomics and drug repurposing studies in CLL and suggests the way such studies can be exploited to find effective therapeutic options combined with drug repurposing strategies to adopt and accost a more “precision medicine” spectrum. Abstract CLL is a hematological malignancy considered as the most frequent lymphoproliferative disease in the western world. It is characterized by high molecular heterogeneity and despite the available therapeutic options, there are many patient subgroups showing the insufficient effectiveness of disease treatment. The challenge is to investigate the individual molecular characteristics and heterogeneity of these patients. Proteomics analysis is a powerful approach that monitors the constant state of flux operators of genetic information and can unravel the proteome heterogeneity and rewiring into protein pathways in CLL patients. This review essences all the available proteomics studies in CLL and suggests the way these studies can be exploited to find effective therapeutic options combined with drug repurposing approaches. Drug repurposing utilizes all the existing knowledge of the safety and efficacy of FDA-approved or investigational drugs and anticipates drug alignment to crucial CLL therapeutic targets, leading to a better disease outcome. The drug repurposing studies in CLL are also discussed in this review. The next goal involves the integration of proteomics-based drug repurposing in precision medicine, as well as the application of this procedure into clinical practice to predict the most appropriate drugs combination that could ensure therapy and the long-term survival of each CLL patient.
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Affiliation(s)
- Dimitra Mavridou
- Laboratory of Biochemistry, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece;
- Functional Proteomics and Systems Biology (FunPATh)—Center for Interdisciplinary Research and Innovation (CIRI-AUTH), GR-57001 Thessaloniki, Greece
- Basic and Translational Research Unit, Special Unit for Biomedical Research and Education, School of Medicine, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece
| | - Konstantina Psatha
- Laboratory of Biochemistry, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece;
- Functional Proteomics and Systems Biology (FunPATh)—Center for Interdisciplinary Research and Innovation (CIRI-AUTH), GR-57001 Thessaloniki, Greece
- Basic and Translational Research Unit, Special Unit for Biomedical Research and Education, School of Medicine, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology, GR-70013 Heraklion, Greece
- Correspondence: (K.P.); (M.A.)
| | - Michalis Aivaliotis
- Laboratory of Biochemistry, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece;
- Functional Proteomics and Systems Biology (FunPATh)—Center for Interdisciplinary Research and Innovation (CIRI-AUTH), GR-57001 Thessaloniki, Greece
- Basic and Translational Research Unit, Special Unit for Biomedical Research and Education, School of Medicine, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology, GR-70013 Heraklion, Greece
- Correspondence: (K.P.); (M.A.)
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9
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Alsagaby SA, Brewis IA, Vijayakumar R, Alhumaydhi FA, Alwashmi AS, Alharbi NK, Al Abdulmonem W, Premanathan M, Pratt G, Fegan C, Pepper C, Brennan P. Proteomics-based identification of cancer-associated proteins in chronic lymphocytic leukaemia. ELECTRON J BIOTECHN 2021. [DOI: 10.1016/j.ejbt.2021.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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10
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The Protein Landscape of Chronic Lymphocytic Leukemia (CLL). Blood 2021; 138:2514-2525. [PMID: 34189564 DOI: 10.1182/blood.2020009741] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 06/09/2021] [Indexed: 11/20/2022] Open
Abstract
Many functional consequences of mutations on tumor phenotypes in chronic lymphocytic leukemia (CLL) are unknown. This may be in part due to a scarcity of information on the proteome of CLL. We profiled the proteome of 117 CLL patient samples with data-independent acquisition mass spectrometry (DIA-MS) and integrated the results with genomic, transcriptomic, ex vivo drug response and clinical outcome data. We found trisomy 12, IGHV mutational status, mutated SF3B1, trisomy 19, del(17)(p13), del(11)(q22.3), mutated DDX3X, and MED12 to influence protein expression (FDR < 5%). Trisomy 12 and IGHV status were the major determinants of protein expression variation in CLL as shown by principal component analysis (1055 and 542 differentially expressed proteins, FDR=5%). Gene set enrichment analyses of CLL with trisomy 12 implicated BCR/PI3K/AKT signaling as a tumor driver. These findings were supported by analyses of protein abundance buffering and protein complex formation, which identified limited protein abundance buffering and an upregulated protein complex involved in BCR, AKT, MAPK and PI3K signaling in trisomy 12 CLL. A survey of proteins associated with trisomy 12/IGHV-independent drug response linked STAT2 protein expression with response to kinase inhibitors including BTK and MEK inhibitors. STAT2 was upregulated in U-CLL, trisomy 12 CLL and required for chemokine/cytokine signaling (interferon response). This study highlights the importance of protein abundance data as a non-redundant layer of information in tumor biology, and provides a protein expression reference map for CLL.
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11
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Cuesta-Mateos C, Brown JR, Terrón F, Muñoz-Calleja C. Of Lymph Nodes and CLL Cells: Deciphering the Role of CCR7 in the Pathogenesis of CLL and Understanding Its Potential as Therapeutic Target. Front Immunol 2021; 12:662866. [PMID: 33841445 PMCID: PMC8024566 DOI: 10.3389/fimmu.2021.662866] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/09/2021] [Indexed: 01/13/2023] Open
Abstract
The lymph node (LN) is an essential tissue for achieving effective immune responses but it is also critical in the pathogenesis of chronic lymphocytic leukemia (CLL). Within the multitude of signaling pathways aberrantly regulated in CLL the homeostatic axis composed by the chemokine receptor CCR7 and its ligands is the main driver for directing immune cells to home into the LN. In this literature review, we address the roles of CCR7 in the pathophysiology of CLL, and how this chemokine receptor is of critical importance to develop more rational and effective therapies for this malignancy.
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Affiliation(s)
- Carlos Cuesta-Mateos
- Immunology Department, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria- Instituto de La Princesa (IIS-IP), Madrid, Spain.,IMMED S.L., Immunological and Medicinal Products, Madrid, Spain.,Catapult Therapeutics BV, Lelystad, Netherlands
| | - Jennifer R Brown
- Chronic Lymphocytic Leukemia (CLL) Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Fernando Terrón
- IMMED S.L., Immunological and Medicinal Products, Madrid, Spain.,Catapult Therapeutics BV, Lelystad, Netherlands
| | - Cecilia Muñoz-Calleja
- Immunology Department, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria- Instituto de La Princesa (IIS-IP), Madrid, Spain.,School of Medicine, Universidad Autónoma de Madrid, Madrid, Spain
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12
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Eagle GL, Herbert JMJ, Zhuang J, Oates M, Khan UT, Kitteringham NR, Clarke K, Park BK, Pettitt AR, Jenkins RE, Falciani F. Assessing technical and biological variation in SWATH-MS-based proteomic analysis of chronic lymphocytic leukaemia cells. Sci Rep 2021; 11:2932. [PMID: 33536534 PMCID: PMC7858606 DOI: 10.1038/s41598-021-82609-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 01/11/2021] [Indexed: 12/18/2022] Open
Abstract
Chronic lymphocytic leukaemia (CLL) exhibits variable clinical course and response to therapy, but the molecular basis of this variability remains incompletely understood. Data independent acquisition (DIA)-MS technologies, such as SWATH (Sequential Windowed Acquisition of all THeoretical fragments), provide an opportunity to study the pathophysiology of CLL at the proteome level. Here, a CLL-specific spectral library (7736 proteins) is described alongside an analysis of sample replication and data handling requirements for quantitative SWATH-MS analysis of clinical samples. The analysis was performed on 6 CLL samples, incorporating biological (IGHV mutational status), sample preparation and MS technical replicates. Quantitative information was obtained for 5169 proteins across 54 SWATH-MS acquisitions: the sources of variation and different computational approaches for batch correction were assessed. Functional enrichment analysis of proteins associated with IGHV mutational status showed significant overlap with previous studies based on gene expression profiling. Finally, an approach to perform statistical power analysis in proteomics studies was implemented. This study provides a valuable resource for researchers working on the proteomics of CLL. It also establishes a sound framework for the design of sufficiently powered clinical proteomics studies. Indeed, this study shows that it is possible to derive biologically plausible hypotheses from a relatively small dataset.
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Affiliation(s)
- Gina L Eagle
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - John M J Herbert
- Computational Biology Facility, University of Liverpool, Liverpool, UK
| | - Jianguo Zhuang
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Melanie Oates
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Umair T Khan
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.,Department of Haemato-Oncology, Clatterbridge Cancer Centre NHS Foundation Trust, Liverpool, UK
| | - Neil R Kitteringham
- Department Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, MRC Centre for Drug Safety Science, University of Liverpool, Liverpool, UK
| | - Kim Clarke
- Computational Biology Facility, University of Liverpool, Liverpool, UK
| | - B Kevin Park
- Department Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, MRC Centre for Drug Safety Science, University of Liverpool, Liverpool, UK
| | - Andrew R Pettitt
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.,Department of Haemato-Oncology, Clatterbridge Cancer Centre NHS Foundation Trust, Liverpool, UK
| | - Rosalind E Jenkins
- Department Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, MRC Centre for Drug Safety Science, University of Liverpool, Liverpool, UK.
| | - Francesco Falciani
- Computational Biology Facility, University of Liverpool, Liverpool, UK. .,Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
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13
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Hippocampal proteomic changes of susceptibility and resilience to depression or anxiety in a rat model of chronic mild stress. Transl Psychiatry 2019; 9:260. [PMID: 31624233 PMCID: PMC6797788 DOI: 10.1038/s41398-019-0605-4] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 07/15/2019] [Accepted: 08/01/2019] [Indexed: 01/21/2023] Open
Abstract
Chronic stressful occurrences are documented as a vital cause of both depression and anxiety disorders. However, the stress-induced molecular mechanisms underlying the common and distinct pathophysiology of these disorders remains largely unclear. We utilized a chronic mild stress (CMS) rat model to differentiate and subgroup depression-susceptible, anxiety-susceptible, and insusceptible rats. The hippocampus was analyzed for differential proteomes by combining mass spectrometry and the isobaric tags for relative and absolute quantitation (iTRAQ) labeling technique. Out of 2593 quantified proteins, 367 were aberrantly expressed. These hippocampal protein candidates might be associated with susceptibility to stress-induced depression or anxiety and stress resilience. They provide the potential protein systems involved in various metabolic pathways as novel investigative protein targets. Further, independent immunoblot analysis identified changes in Por, Idh2 and Esd; Glo1, G6pdx, Aldh2, and Dld; Dlat, Ogdhl, Anxal, Tpp2, and Sdha that were specifically associated to depression-susceptible, anxiety-susceptible, or insusceptible groups respectively, suggesting that identical CMS differently impacted the mitochondrial and metabolic processes in the hippocampus. Collectively, the observed alterations to protein abundance profiles of the hippocampus provided significant and novel insights into the stress regulation mechanism in a CMS rat model. This might serve as the molecular basis for further studies that would contributed to a better understanding of the similarities and differences in pathophysiologic mechanisms underlying stress-induced depression or anxiety, and stress resiliency.
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14
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Cancerous inhibitor of protein phosphatase 2A (CIP2A) modifies energy metabolism via 5' AMP-activated protein kinase signalling in malignant cells. Biochem J 2019; 476:2255-2269. [PMID: 31350330 DOI: 10.1042/bcj20190121] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 07/09/2019] [Accepted: 07/26/2019] [Indexed: 12/25/2022]
Abstract
Cancerous inhibitor of protein phosphatase 2A (CIP2A) is an adverse biomarker across many malignancies. Using K562 cells engineered to have high or low CIP2A expression, we show that high CIP2A levels significantly bias cellular energy production towards oxidative phosphorylation (OXPHOS) rather than glycolysis. Mass spectrometric analysis of CIP2A interactors and isobaric tagging for relative and absolute protein quantitation (ITRAQ) experiments identified many associated proteins, several of which co-vary with CIP2A level. Many of these CIP2A associating and co-varying proteins are involved in energy metabolism including OXPHOS, or in 5' AMP-activated protein kinase (AMPK) signalling, and manipulating AMPK activity mimics the effects of low/high CIP2A on OXPHOS. These effects are dependent on the availability of nutrients, driven by metabolic changes caused by CIP2A. CIP2A level did not affect starvation-induced AMPK phosphorylation of Unc-51 autophagy activating kinase 1 (ULK-1) at Ser555, but autophagy activity correlated with an increase in AMPK activity, to suggest that some AMPK processes are uncoupled by CIP2A, likely via its inhibition of protein phosphatase 2A (PP2A). The data demonstrate that AMPK mediates this novel CIP2A effect on energy generation in malignant cells.
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15
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Alsagaby SA, Alhumaydhi FA. Proteomics insights into the pathology and prognosis of chronic lymphocytic leukemia. Saudi Med J 2019; 40:317-327. [PMID: 30957124 PMCID: PMC6506661 DOI: 10.15537/smj.2019.4.23598] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Chronic lymphocytic leukemia (CLL) is an incurable malignant disease of B-lymphocytes characterized by drastically heterogeneous clinical courses. Proteomics is an advanced approach that allows a global profiling of protein expression, providing a valuable chance for the discovery of disease-related proteins. In the last 2 decades, several proteomics studies were conducted on CLL to identify aberrant protein expression underpinning the malignant transformation and progression of the disease. Overall, these studies provided insights into the pathology and prognosis of CLL and reveal protein candidates with the potential to serve as biomarkers and/or therapeutic targets of the tumor. The major findings reported in these studies are discussed here.
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MESH Headings
- Biomarkers, Tumor
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/pathology
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Leukemia, Lymphocytic, Chronic, B-Cell/therapy
- Molecular Targeted Therapy
- Prognosis
- Proteomics/trends
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Affiliation(s)
- Suliman A Alsagaby
- Department of Medical Laboratories Sciences, Faculty of Applied Medical Sciences, Majmaah University, Majmaah, Kingdom of Saudi Arabia. E-mail.
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16
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Redondo-Muñoz J, García-Pardo A, Teixidó J. Molecular Players in Hematologic Tumor Cell Trafficking. Front Immunol 2019; 10:156. [PMID: 30787933 PMCID: PMC6372527 DOI: 10.3389/fimmu.2019.00156] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 01/17/2019] [Indexed: 12/20/2022] Open
Abstract
The trafficking of neoplastic cells represents a key process that contributes to progression of hematologic malignancies. Diapedesis of neoplastic cells across endothelium and perivascular cells is facilitated by adhesion molecules and chemokines, which act in concert to tightly regulate directional motility. Intravital microscopy provides spatio-temporal views of neoplastic cell trafficking, and is crucial for testing and developing therapies against hematologic cancers. Multiple myeloma (MM), chronic lymphocytic leukemia (CLL), and acute lymphoblastic leukemia (ALL) are hematologic malignancies characterized by continuous neoplastic cell trafficking during disease progression. A common feature of these neoplasias is the homing and infiltration of blood cancer cells into the bone marrow (BM), which favors growth and survival of the malignant cells. MM cells traffic between different BM niches and egress from BM at late disease stages. Besides the BM, CLL cells commonly home to lymph nodes (LNs) and spleen. Likewise, ALL cells also infiltrate extramedullary organs, such as the central nervous system, spleen, liver, and testicles. The α4β1 integrin and the chemokine receptor CXCR4 are key molecules for MM, ALL, and CLL cell trafficking into and out of the BM. In addition, the chemokine receptor CCR7 controls CLL cell homing to LNs, and CXCR4, CCR7, and CXCR3 contribute to ALL cell migration across endothelia and the blood brain barrier. Some of these receptors are used as diagnostic markers for relapse and survival in ALL patients, and their level of expression allows clinicians to choose the appropriate treatments. In CLL, elevated α4β1 expression is an established adverse prognostic marker, reinforcing its role in the disease expansion. Combining current chemotherapies with inhibitors of malignant cell trafficking could represent a useful therapy against these neoplasias. Moreover, immunotherapy using humanized antibodies, CAR-T cells, or immune check-point inhibitors together with agents targeting the migration of tumor cells could also restrict their survival. In this review, we provide a view of the molecular players that regulate the trafficking of neoplastic cells during development and progression of MM, CLL, and ALL, together with current therapies that target the malignant cells.
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Affiliation(s)
- Javier Redondo-Muñoz
- Department of Immunology, Ophthalmology and ERL, Hospital 12 de Octubre Health Research Institute (imas12), School of Medicine, Complutense University, Madrid, Spain.,Manchester Collaborative Centre for Inflammation Research, Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, United Kingdom
| | - Angeles García-Pardo
- Department of Molecular Biomedicine, Centro de Investigaciones Biológicas (CSIC), Madrid, Spain
| | - Joaquin Teixidó
- Department of Molecular Biomedicine, Centro de Investigaciones Biológicas (CSIC), Madrid, Spain
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17
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Thurgood LA, Dwyer ES, Lower KM, Chataway TK, Kuss BJ. Altered expression of metabolic pathways in CLL detected by unlabelled quantitative mass spectrometry analysis. Br J Haematol 2019; 185:65-78. [PMID: 30656643 DOI: 10.1111/bjh.15751] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 11/26/2018] [Indexed: 12/27/2022]
Abstract
Chronic lymphocytic leukaemia (CLL) remains the most common incurable malignancy of B cells in the western world. Patient outcomes are heterogeneous and can be difficult to predict with current prognostic markers. Here, we used a quantitative label-free proteomic technique to ascertain differences in the B-cell proteome from healthy donors and CLL patients with either mutated (M-CLL) or unmutated (UM-CLL) IGHV to identify new prognostic markers. In peripheral B-CLL cells, 349 (22%) proteins were differentially expressed between normal B cells and B-CLL cells and 189 (12%) were differentially expressed between M-CLL and UM-CLL. We also examined the proteome of proliferating CLL cells in the lymph nodes, and identified 76 (~8%) differentially expressed proteins between healthy and CLL lymph nodes. B-CLL cells show over-expression of proteins involved in lipid and cholesterol metabolism. A comprehensive lipidomic analysis highlighted large differences in glycolipids and sphingolipids. A shift was observed from the pro-apoptotic lipid ceramide towards the anti-apoptotic/chemoresistant lipid, glucosylceramide, which was more evident in patients with aggressive disease (UM-CLL). This study details a novel quantitative proteomic technique applied for the first time to primary patient samples in CLL and highlights that primary CLL lymphocytes display markers of a metabolic shift towards lipid synthesis and breakdown.
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Affiliation(s)
- Lauren A Thurgood
- Discipline Molecular Medicine and Pathology, College of Medicine and Public Health, Flinders University, Adelaide, South Australia, Australia
| | - Eveline S Dwyer
- Discipline Molecular Medicine and Pathology, College of Medicine and Public Health, Flinders University, Adelaide, South Australia, Australia
| | - Karen M Lower
- Discipline Molecular Medicine and Pathology, College of Medicine and Public Health, Flinders University, Adelaide, South Australia, Australia
| | - Tim K Chataway
- Flinders Proteomic Facility, Department of Human Physiology, College of Medicine and Public Health, Flinders University, Adelaide, South Australia, Australia
| | - Bryone J Kuss
- Discipline Molecular Medicine and Pathology, College of Medicine and Public Health, Flinders University, Adelaide, South Australia, Australia.,Haematology, Molecular Medicine and Pathology, SA Pathology, Flinders Medical Centre, Adelaide, South Australia, Australia
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18
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Zaprazna K, Reblova K, Svobodova V, Radova L, Bystry V, Baloun J, Durechova K, Tom N, Loja T, Buresova M, Stranska K, Oltova A, Doubek M, Atchison ML, Trbusek M, Malcikova J, Pospisilova S. Activation-induced deaminase and its splice variants associate with trisomy 12 in chronic lymphocytic leukemia. Ann Hematol 2018; 98:423-435. [PMID: 30368590 DOI: 10.1007/s00277-018-3520-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Accepted: 10/09/2018] [Indexed: 11/26/2022]
Abstract
Activation-induced cytidine deaminase (AID) is a mutator enzyme essential for somatic hypermutation (SHM) and class switch recombination (CSR) during effective adaptive immune responses. Its aberrant expression and activity have been detected in lymphomas, leukemias, and solid tumors. In chronic lymphocytic leukemia (CLL) increased expression of alternatively spliced AID variants has been documented. We used real-time RT-PCR to quantify the expression of AID and its alternatively spliced transcripts (AIDΔE4a, AIDΔE4, AIDivs3, and AIDΔE3E4) in 149 CLL patients and correlated this expression to prognostic markers including recurrent chromosomal aberrations, the presence of complex karyotype, mutation status of the immunoglobulin heavy chain variable gene, and recurrent mutations. We report a previously unappreciated association between higher AID transcript levels and trisomy of chromosome 12. Functional analysis of AID splice variants revealed loss of their activity with respect to SHM, CSR, and induction of double-strand DNA breaks. In silico modeling provided insight into the molecular interactions and structural dynamics of wild-type AID and a shortened AID variant closely resembling AIDΔE4, confirming its loss-of-function phenotype.
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MESH Headings
- Aged
- Alternative Splicing
- Animals
- Chromosomes, Human, Pair 12/enzymology
- Chromosomes, Human, Pair 12/genetics
- Computer Simulation
- Cytidine Deaminase/biosynthesis
- Cytidine Deaminase/chemistry
- Cytidine Deaminase/genetics
- Female
- Gene Expression Regulation, Enzymologic
- Gene Expression Regulation, Neoplastic
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/enzymology
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Male
- Mice
- Mice, Knockout
- Middle Aged
- Models, Biological
- Molecular Dynamics Simulation
- Neoplasm Proteins/biosynthesis
- Neoplasm Proteins/chemistry
- Neoplasm Proteins/genetics
- Trisomy/genetics
- Trisomy/pathology
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Affiliation(s)
- Kristina Zaprazna
- Central European Institute of Technology, Center of Molecular Medicine, Masaryk University, Kamenice 5/A35, 625 00, Brno, Czech Republic.
| | - Kamila Reblova
- Central European Institute of Technology, Center of Molecular Medicine, Masaryk University, Kamenice 5/A35, 625 00, Brno, Czech Republic
| | - Veronika Svobodova
- Central European Institute of Technology, Center of Molecular Medicine, Masaryk University, Kamenice 5/A35, 625 00, Brno, Czech Republic
| | - Lenka Radova
- Central European Institute of Technology, Center of Molecular Medicine, Masaryk University, Kamenice 5/A35, 625 00, Brno, Czech Republic
| | - Vojtech Bystry
- Central European Institute of Technology, Center of Molecular Medicine, Masaryk University, Kamenice 5/A35, 625 00, Brno, Czech Republic
| | - Jiri Baloun
- Central European Institute of Technology, Center of Molecular Medicine, Masaryk University, Kamenice 5/A35, 625 00, Brno, Czech Republic
| | - Kristina Durechova
- Department of Internal Medicine - Hematology and Oncology, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Nikola Tom
- Central European Institute of Technology, Center of Molecular Medicine, Masaryk University, Kamenice 5/A35, 625 00, Brno, Czech Republic
| | - Tomas Loja
- Central European Institute of Technology, Center of Molecular Medicine, Masaryk University, Kamenice 5/A35, 625 00, Brno, Czech Republic
| | - Martina Buresova
- Central European Institute of Technology, Center of Molecular Medicine, Masaryk University, Kamenice 5/A35, 625 00, Brno, Czech Republic
- Department of Internal Medicine - Hematology and Oncology, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Kamila Stranska
- Central European Institute of Technology, Center of Molecular Medicine, Masaryk University, Kamenice 5/A35, 625 00, Brno, Czech Republic
- Department of Internal Medicine - Hematology and Oncology, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Alexandra Oltova
- Department of Internal Medicine - Hematology and Oncology, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Michael Doubek
- Central European Institute of Technology, Center of Molecular Medicine, Masaryk University, Kamenice 5/A35, 625 00, Brno, Czech Republic
- Department of Internal Medicine - Hematology and Oncology, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Michael L Atchison
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Martin Trbusek
- Department of Internal Medicine - Hematology and Oncology, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Jitka Malcikova
- Central European Institute of Technology, Center of Molecular Medicine, Masaryk University, Kamenice 5/A35, 625 00, Brno, Czech Republic
- Department of Internal Medicine - Hematology and Oncology, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Sarka Pospisilova
- Central European Institute of Technology, Center of Molecular Medicine, Masaryk University, Kamenice 5/A35, 625 00, Brno, Czech Republic.
- Department of Internal Medicine - Hematology and Oncology, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic.
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19
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Zhan S, Li J, Wang T, Ge W. Quantitative Proteomics Analysis of Sporadic Medullary Thyroid Cancer Reveals FN1 as a Potential Novel Candidate Prognostic Biomarker. Oncologist 2018; 23:1415-1425. [PMID: 29739896 DOI: 10.1634/theoncologist.2017-0399] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 03/23/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Sporadic medullary thyroid cancer (MTC) is a rare neuroendocrine tumor. Currently, although the diagnosis of sporadic MTC is relatively simple, the need to discover novel candidate prognostic biomarkers for sporadic MTC and investigate the underlying mechanism involved in this rare disease is urgent. MATERIALS AND METHODS We employed tandem mass tag-based liquid chromatography-mass spectrometry to identify and analyze differentially expressed proteins (DEPs) in sporadic MTC. Western blotting was used to validate the DEPs. Immunohistochemistry was performed to investigate FN1 and RPS6KA3 in an independent set of sporadic MTC tissues. Immunohistochemical data were analyzed by different statistical methods. RESULTS Three hundred eighty-eight DEPs were identified in mass spectrometry, mainly involved in the extracellular matrix, cytoskeletal remodeling, or oxidoreductase activity. Among them, THBS1, MMP9, FN1, RPS6KA3, SYT1, and carcinoembryonic antigen were successfully validated by Western blot. In addition, FN1 and RPS6KA3, enriched in extracellular matrix (ECM) remodeling and the mitogen-activated protein kinase (MAPK) signaling pathway, respectively, were investigated in an independent set of sporadic MTC tissues. Receiver-operator characteristic curve analysis showed that FN1 and RPS6KA3 can be used for discriminating sporadic MTC tumorous tissues from paired normal thyroid tissues, and the clinical biomarker calcitonin was positively correlated with FN1 and RPS6KA3 in tumorous tissues. Furthermore, the immunohistochemical scores of FN1 in tumorous tissue showed an inverse relationship with tumor classification, lymph node classification, and American Joint Committee on Cancer stage. Through univariate and multivariate analysis for progression-free survival, we also found that low FN1 expression in tumorous tissues was an independent worse prognostic factor for progression-free survival. CONCLUSION We identified that the pathophysiology of sporadic MTC involve numerous pathways, including the synaptic vesicle pathway, the MAPK signaling pathway, and the ECM remodeling pathway. Furthermore, our study also identified FN1 as novel prognostic biomarkers related to the pathophysiologic changes in sporadic MTC. IMPLICATIONS FOR PRACTICE Proteomic dissection and prognostic biomarkers are scarce in sporadic medullary thyroid cancer (MTC). This article reports the use of proteomics technology to comprehensively investigate the molecular mechanisms of sporadic MTC, which resulted in the identification of FN1 as a novel candidate prognostic biomarker.
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Affiliation(s)
- Shaohua Zhan
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, National Key Laboratory of Medical Molecular Biology & Department of Immunology, Beijing, People's Republic of China
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China
| | - Tianxiao Wang
- Key Laboratory of Carcinogenesis and Translational Research, Department of Head and Neck Surgery, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
| | - Wei Ge
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, National Key Laboratory of Medical Molecular Biology & Department of Immunology, Beijing, People's Republic of China
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20
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Johnston HE, Carter MJ, Larrayoz M, Clarke J, Garbis SD, Oscier D, Strefford JC, Steele AJ, Walewska R, Cragg MS. Proteomics Profiling of CLL Versus Healthy B-cells Identifies Putative Therapeutic Targets and a Subtype-independent Signature of Spliceosome Dysregulation. Mol Cell Proteomics 2018; 17:776-791. [PMID: 29367434 PMCID: PMC5880099 DOI: 10.1074/mcp.ra117.000539] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Indexed: 12/30/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) is a heterogeneous B-cell cancer exhibiting a wide spectrum of disease courses and treatment responses. Molecular characterization of RNA and DNA from CLL cases has led to the identification of important driver mutations and disease subtypes, but the precise mechanisms of disease progression remain elusive. To further our understanding of CLL biology we performed isobaric labeling and mass spectrometry proteomics on 14 CLL samples, comparing them with B-cells from healthy donors (HDB). Of 8694 identified proteins, ∼6000 were relatively quantitated between all samples (q<0.01). A clear CLL signature, independent of subtype, of 544 significantly overexpressed proteins relative to HDB was identified, highlighting established hallmarks of CLL (e.g. CD5, BCL2, ROR1 and CD23 overexpression). Previously unrecognized surface markers demonstrated overexpression (e.g. CKAP4, PIGR, TMCC3 and CD75) and three of these (LAX1, CLEC17A and ATP2B4) were implicated in B-cell receptor signaling, which plays an important role in CLL pathogenesis. Several other proteins (e.g. Wee1, HMOX1/2, HDAC7 and INPP5F) were identified with significant overexpression that also represent potential targets. Western blotting confirmed overexpression of a selection of these proteins in an independent cohort. mRNA processing machinery were broadly upregulated across the CLL samples. Spliceosome components demonstrated consistent overexpression (p = 1.3 × 10-21) suggesting dysregulation in CLL, independent of SF3B1 mutations. This study highlights the potential of proteomics in the identification of putative CLL therapeutic targets and reveals a subtype-independent protein expression signature in CLL.
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Affiliation(s)
- Harvey E Johnston
- From the ‡Antibody and Vaccine Group, Cancer Sciences Unit, Faculty of Medicine, General Hospital, University of Southampton, Southampton, UK
- §Centre for Proteomic Research, Institute for Life Sciences, University of Southampton, Highfield Campus, Southampton, UK
| | - Matthew J Carter
- From the ‡Antibody and Vaccine Group, Cancer Sciences Unit, Faculty of Medicine, General Hospital, University of Southampton, Southampton, UK
| | - Marta Larrayoz
- ¶Cancer Genomics, Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - James Clarke
- ‖Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Spiro D Garbis
- §Centre for Proteomic Research, Institute for Life Sciences, University of Southampton, Highfield Campus, Southampton, UK
- **Clinical and Experimental Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - David Oscier
- ‡‡Department of Molecular Pathology, Royal Bournemouth Hospital, Bournemouth, UK
| | - Jonathan C Strefford
- ¶Cancer Genomics, Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Andrew J Steele
- §§Leukemia and Lymphoma Molecular Mechanisms and Therapy Group, Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Renata Walewska
- ¶¶Department of Haematology, Royal Bournemouth Hospital, Bournemouth, UK
| | - Mark S Cragg
- From the ‡Antibody and Vaccine Group, Cancer Sciences Unit, Faculty of Medicine, General Hospital, University of Southampton, Southampton, UK;
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21
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Proteomic and network analysis of human serum albuminome by integrated use of quick crosslinking and two-step precipitation. Sci Rep 2017; 7:9856. [PMID: 28851998 PMCID: PMC5575314 DOI: 10.1038/s41598-017-09563-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 07/24/2017] [Indexed: 11/23/2022] Open
Abstract
Affinity- and chemical-based methods are usually employed to prepare human serum albuminome; however, these methods remain technically challenging. Herein, we report the development of a two-step precipitation (TSP) method by combined use of polyethylene glycol (PEG) and ethanol. PEG precipitation was newly applied to remove immunoglobulin G for albuminome preparation, which is simple, cost effective, efficient and compatible with downstream ethanol precipitation. Nonetheless, chemical extraction using TSP may disrupt weak and transient protein interactions with human serum albumin (HSA) leading to an incomplete albuminome. Accordingly, rapid fixation based on formaldehyde crosslinking (FC) was introduced into the TSP procedure. The developed FC-TSP method increased the number of identified proteins, probably by favouring real-time capture of weakly bound proteins in the albuminome. A total of 171 proteins excluding HSA were identified from the fraction obtained with FC-TSP. Further interaction network and cluster analyses revealed 125 HSA-interacting proteins and 14 highly-connected clusters. Compared with five previous studies, 55 new potential albuminome proteins including five direct and 50 indirect binders were only identified by our strategy and 12 were detected as common low-abundance proteins. Thus, this new strategy has the potential to effectively survey the human albuminome, especially low-abundance proteins of clinical interest.
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22
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Wang M, Guo Y, Wang M, Zhou T, Xue Y, Du G, Wei X, Wang J, Qi L, Zhang H, Li L, Ye L, Guo X, Wu X. The Glial Cell-Derived Neurotrophic Factor (GDNF)-responsive Phosphoprotein Landscape Identifies Raptor Phosphorylation Required for Spermatogonial Progenitor Cell Proliferation. Mol Cell Proteomics 2017; 16:982-997. [PMID: 28408662 DOI: 10.1074/mcp.m116.065797] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Revised: 03/24/2017] [Indexed: 01/15/2023] Open
Abstract
Cytokine-dependent renewal of stem cells is a fundamental requisite for tissue homeostasis and regeneration. Spermatogonial progenitor cells (SPCs) including stem cells support life-long spermatogenesis and male fertility, but pivotal phosphorylation events that regulate fate decisions in SPCs remain unresolved. Here, we described a quantitative mass-spectrometry-based proteomic and phosphoproteomic analyses of SPCs following sustained stimulation with glial cell-derived neurotrophic factor (GDNF), an extrinsic factor supporting SPC proliferation. Stimulated SPCs contained 3382 identified phosphorylated proteins and 12141 phosphorylation sites. Of them, 325 differentially phosphorylated proteins and 570 phosphorylation sites triggered by GDNF were highly enriched for ERK1/2, GSK3, CDK1, and CDK5 phosphorylating motifs. We validated that inhibition of GDNF/ERK1/2-signaling impaired SPC proliferation and increased G2/M cell cycle arrest. Significantly, we found that proliferation of SPCs requires phosphorylation of the mTORC1 component Raptor at Ser863 Tissue-specific deletion of Raptor in mouse germline cells results in impaired spermatogenesis and progressive loss of spermatogonia, but in vitro increased phosphorylation of Raptor by raptor over-expression in SPCs induced a more rapidly growth of SPCs in culture. These findings implicate previously undescribed signaling networks in governing fate decision of SPCs, which is essential for the understanding of spermatogenesis and of potential consequences of pathogenic insult for male infertility.
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Affiliation(s)
- Min Wang
- From the ‡State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Yueshuai Guo
- From the ‡State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Mei Wang
- From the ‡State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Tao Zhou
- From the ‡State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Yuanyuan Xue
- From the ‡State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Guihua Du
- From the ‡State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Xiang Wei
- From the ‡State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Jing Wang
- From the ‡State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Lin Qi
- From the ‡State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Hao Zhang
- From the ‡State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Lufan Li
- From the ‡State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Lan Ye
- From the ‡State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Xuejiang Guo
- From the ‡State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Xin Wu
- From the ‡State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China
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23
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Thurgood LA, Chataway TK, Lower KM, Kuss BJ. From genome to proteome: Looking beyond DNA and RNA in chronic lymphocytic leukemia. J Proteomics 2017; 155:73-84. [PMID: 28069558 DOI: 10.1016/j.jprot.2017.01.001] [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: 09/06/2016] [Revised: 11/11/2016] [Accepted: 01/03/2017] [Indexed: 02/07/2023]
Abstract
Chronic lymphocytic leukemia (CLL) remains the most common leukemia in the Western world. Whilst its disease course is extremely heterogeneous (ranging from indolent to aggressive), current methods are unable to accurately predict the clinical journey of each patient. There is clearly a pressing need for both improved prognostication and treatment options for patients with this disease. Whilst molecular studies have analyzed both genetic mutations and gene expression profiles of these malignant B-cells, and as a result have shed light on the pathogenesis of CLL, proteomic studies have been largely overlooked to date. This review summarizes our current knowledge of the proteomics of CLL, and discusses some of the issues in CLL proteomic research, such as reproducibility and data interpretation. In addition, we look ahead to how proteomics may significantly help in the development of a successful treatment for this currently incurable disease.
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Affiliation(s)
- Lauren A Thurgood
- Department of Haematology and Genetic Pathology, Flinders University, Adelaide, South Australia, Australia.
| | - Tim K Chataway
- Department of Physiology, Flinders University, Adelaide, South Australia, Australia
| | - Karen M Lower
- Department of Haematology and Genetic Pathology, Flinders University, Adelaide, South Australia, Australia
| | - Bryone J Kuss
- Department of Haematology and Genetic Pathology, Flinders University, Adelaide, South Australia, Australia
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24
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Díez P, Góngora R, Orfao A, Fuentes M. Functional proteomic insights in B-cell chronic lymphocytic leukemia. Expert Rev Proteomics 2016; 14:137-146. [DOI: 10.1080/14789450.2017.1275967] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Paula Díez
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Rafael Góngora
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Alberto Orfao
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Manuel Fuentes
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
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25
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Frazzi R, Auffray C, Ferrari A, Filippini P, Rutella S, Cesario A. Integrative systems medicine approaches to identify molecular targets in lymphoid malignancies. J Transl Med 2016; 14:252. [PMID: 27580852 PMCID: PMC5007715 DOI: 10.1186/s12967-016-1018-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 08/18/2016] [Indexed: 12/22/2022] Open
Abstract
Although survival rates for lymphoproliferative disorders are steadily increasing both in the US and in Europe, there is need for optimizing front-line therapies and developing more effective salvage strategies. Recent advances in molecular genetics have highlighted the biological diversity of lymphoproliferative disorders. In particular, integrative approaches including whole genome sequencing, whole exome sequencing, and transcriptome or RNA sequencing have been instrumental to the identification of molecular targets for treatment. Herein, we will discuss how genomic, epigenomic and proteomic approaches in lymphoproliferative disorders have supported the discovery of molecular lesions and their therapeutic targeting in the clinic.
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Affiliation(s)
- Raffaele Frazzi
- Laboratory of Translational Research, IRCCS "Arcispedale S. Maria Nuova", Reggio Emilia, Italy
| | - Charles Auffray
- European Institute for Systems Biology and Medicine (EISBM), Paris, France
| | - Angela Ferrari
- Division of Hematology, IRCCS "Arcispedale S. Maria Nuova", Reggio Emilia, Italy
| | - Perla Filippini
- Division of Translational Medicine, Sidra Medical and Research Centre, Doha, Qatar
| | - Sergio Rutella
- John van Geest Cancer Research Centre, College of Science and Technology, Nottingham Trent University, Clifton Campus, Nottingham, NG11 8NS, UK.
| | - Alfredo Cesario
- Clinical Governance and International Research Activities, Fondazione Policlinico Gemelli, Rome, Italy.,Division of Thoracic Surgery, Università Cattolica del Sacro Cuore, Rome, Italy.,European Association of Systems Medicine, Aachen, Germany
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26
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Alsagaby SA, Brennan P, Pepper C. Key Molecular Drivers of Chronic Lymphocytic Leukemia. CLINICAL LYMPHOMA MYELOMA & LEUKEMIA 2016; 16:593-606. [PMID: 27601002 DOI: 10.1016/j.clml.2016.08.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 06/29/2016] [Accepted: 08/02/2016] [Indexed: 01/01/2023]
Abstract
Chronic lymphocytic leukemia (CLL) is an adult neoplastic disease of B cells characterized by variable clinical outcomes. Although some patients have an aggressive form of the disease and often encounter treatment failure and short survival, others have more stable disease with long-term survival and little or no need for theraphy. In the past decade, significant advances have been made in our understanding of the molecular drivers that affect the natural pathology of CLL. The present review describes what is known about these key molecules in the context of their role in tumor pathogenicity, prognosis, and therapy.
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Affiliation(s)
- Suliman A Alsagaby
- Department of Medical Laboratory, College of Science, Majmaah University, Al-Zuli, Kingdom of Saudi Arabia; Institute of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom.
| | - Paul Brennan
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Chris Pepper
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
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27
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Zent CS. Chronic lymphocytic leukemia and proteomics: protein profiles and links with disease progression still need validation. Leuk Lymphoma 2016; 57:985-6. [PMID: 26726799 DOI: 10.3109/10428194.2015.1121263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Clive S Zent
- a Division of Hematology/Oncology , Wilmot Cancer Institute, University of Rochester Medical Center , Rochester , NY , USA
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28
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Huang PY, Mactier S, Armacki N, Giles Best O, Belov L, Kaufman KL, Pascovici D, Mulligan SP, Christopherson RI. Protein profiles distinguish stable and progressive chronic lymphocytic leukemia. Leuk Lymphoma 2015; 57:1033-43. [DOI: 10.3109/10428194.2015.1094692] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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