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Espejo C, Lyons B, Woods GM, Wilson R. Early Cancer Biomarker Discovery Using DIA-MS Proteomic Analysis of EVs from Peripheral Blood. Methods Mol Biol 2023; 2628:127-152. [PMID: 36781783 DOI: 10.1007/978-1-0716-2978-9_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
One of the cornerstones of effective cancer treatment is early diagnosis. In this context, the identification of proteins that can serve as cancer biomarkers in bodily fluids ("liquid biopsies") has gained attention over the last decade. Plasma and serum fractions of blood are the most commonly investigated sources of potential cancer liquid biopsy biomarkers. However, the high complexity and dynamic range typical of these fluids hinders the sensitivity of protein detection by the most commonly used mass spectrometry technology (data-dependent acquisition mass spectrometry (DDA-MS)). Recently, data-independent acquisition mass spectrometry (DIA-MS) techniques have overcome the limitations of DDA-MS, increasing sensitivity and proteome coverage. In addition to DIA-MS, isolating extracellular vesicles (EVs) can help to increase the depth of serum/plasma proteome coverage by improving the identification of low-abundance proteins which are a potential treasure trove of diagnostic molecules. EVs, the nano-sized membrane-enclosed vesicles present in most bodily fluids, contain proteins which may serve as potential biomarkers for various cancers. Here, we describe a detailed protocol that combines DIA-MS and EV methodologies for discovering and validating early cancer biomarkers using blood serum. The pipeline includes size exclusion chromatography methods to isolate serum-derived extracellular vesicles and subsequent EV sample preparation for liquid chromatography and mass spectrometry analysis. Procedures for spectral library generation by DDA-MS incorporate methods for off-line peptide separation by microflow HPLC with automated fraction concatenation. Analysis of the samples by DIA-MS includes recommended protocols for data processing and statistical methods. This pipeline will provide a guide to discovering and validating EV-associated proteins that can serve as sensitive and specific biomarkers for early cancer detection and other diseases.
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Affiliation(s)
- Camila Espejo
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, TAS, Australia
| | - Bruce Lyons
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, TAS, Australia
| | - Gregory M Woods
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, TAS, Australia
| | - Richard Wilson
- Central Science Laboratory, University of Tasmania, Hobart, TAS, Australia.
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2
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Reale A, Khong T, Spencer A. Extracellular Vesicles and Their Roles in the Tumor Immune Microenvironment. J Clin Med 2022; 11:jcm11236892. [PMID: 36498469 PMCID: PMC9737553 DOI: 10.3390/jcm11236892] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/15/2022] [Accepted: 11/15/2022] [Indexed: 11/24/2022] Open
Abstract
Tumor cells actively incorporate molecules (e.g., proteins, lipids, RNA) into particles named extracellular vesicles (EVs). Several groups have demonstrated that EVs can be transferred to target (recipient) cells, making EVs an important means of intercellular communication. Indeed, EVs are able to modulate the functions of target cells by reprogramming signaling pathways. In a cancer context, EVs promote the formation of a supportive tumor microenvironment (TME) and (pre)metastatic niches. Recent studies have revealed that immune cells, tumor cells and their secretome, including EVs, promote changes in the TME and immunosuppressive functions of immune cells (e.g., natural killer, dendritic cells, T and B cells, monocytes, macrophages) that allow tumor cells to establish and propagate. Despite the growing knowledge on EVs and on their roles in cancer and as modulators of the immune response/escape, the translation into clinical practice remains in its early stages, hence requiring improved translational research in the EVs field. Here, we comprehensively review the current knowledge and most recent research on the roles of EVs in tumor immune evasion and immunosuppression in both solid tumors and hematological malignancies. We also highlight the clinical utility of EV-mediated immunosuppression targeting and EV-engineering. Importantly, we discuss the controversial role of EVs in cancer biology, current limitations and future perspectives to further the EV knowledge into clinical practice.
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Affiliation(s)
- Antonia Reale
- Myeloma Research Group, Australian Centre for Blood Diseases, Central Clinical School, Monash University—Alfred Health, Melbourne, VIC 3004, Australia
- Correspondence: (A.R.); (A.S.)
| | - Tiffany Khong
- Myeloma Research Group, Australian Centre for Blood Diseases, Central Clinical School, Monash University—Alfred Health, Melbourne, VIC 3004, Australia
| | - Andrew Spencer
- Myeloma Research Group, Australian Centre for Blood Diseases, Central Clinical School, Monash University—Alfred Health, Melbourne, VIC 3004, Australia
- Malignant Haematology and Stem Cell Transplantation, Department of Haematology, Alfred Hospital, Melbourne, VIC 3004, Australia
- Department of Clinical Hematology, Monash University, Melbourne, VIC 3004, Australia
- Correspondence: (A.R.); (A.S.)
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3
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Laurenzana I, Trino S, Lamorte D, De Stradis A, Santodirocco M, Sgambato A, De Luca L, Caivano A. Multiple Myeloma-Derived Extracellular Vesicles Impair Normal Hematopoiesis by Acting on Hematopoietic Stem and Progenitor Cells. Front Med (Lausanne) 2022; 8:793040. [PMID: 34977093 PMCID: PMC8716627 DOI: 10.3389/fmed.2021.793040] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 11/08/2021] [Indexed: 12/17/2022] Open
Abstract
Multiple myeloma (MM) is characterized by the abnormal proliferation of clonal plasma cells (PCs) in bone marrow (BM). MM-PCs progressively occupy and likely alter BM niches where reside hematopoietic stem and progenitor cells (HSPCs) whose viability, self-renewal, proliferation, commitment, and differentiation are essential for normal hematopoiesis. Extracellular vesicles (EVs) are particles released by normal and neoplastic cells, such as MM cells. They are important cell-to-cell communicators able to modify the phenotype, genotype, and the fate of the recipient cells. Investigation of mechanisms and mediators underlying HSPC-MM-PC crosstalk is warranted to better understand the MM hematopoietic impairment and for the identification of novel therapeutic strategies against this incurable malignancy. This study is aimed to evaluate whether EVs released by MM-PCs interact with HSPCs, what effects they exert, and the underlying mechanisms involved. Therefore, we investigated the viability, cell cycle, phenotype, clonogenicity, and microRNA profile of HSPCs exposed to MM cell line-released EVs (MM-EVs). Our data showed that: (i) MM cells released a heterogeneous population of EVs; (ii) MM-EVs caused a dose-dependent reduction of HSPCs viability; (iii) MM-EVs caused a redistribution of the HSPC pool characterized by a significant increase in the frequency of stem and early precursors accompanied by a reduction of late precursor cells, such as common myeloid progenitors (CMPs), megakaryocyte erythroid progenitors (MEPs), B and NK progenitors, and a slight increase of granulocyte macrophage progenitors (GMPs); (iv) MM-EVs caused an increase of stem and early precursors in S phase with a decreased number of cells in G0/G1 phase in a dose-dependent manner; (v) MM-EVs reduced the HSPC colony formation; and (vi) MM-EVs caused an increased expression level of C-X-C motif chemokine receptor type 4 (CXCR4) and activation of miRNAs. In conclusion, MM cells through the release of EVs, by acting directly on normal HSPCs, negatively dysregulate normal hematopoiesis, and this could have important therapeutic implications.
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Affiliation(s)
- Ilaria Laurenzana
- Laboratory of Preclinical and Translational Research, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, Italy
| | - Stefania Trino
- Laboratory of Preclinical and Translational Research, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, Italy
| | - Daniela Lamorte
- Laboratory of Preclinical and Translational Research, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, Italy
| | - Angelo De Stradis
- Institute for Sustainable Plant Protection, National Research Council (CNR), Bari, Italy
| | - Michele Santodirocco
- Trasfusional Medicine Department, Puglia CBB, Casa Sollievo Della Sofferenza Hospital, San Giovanni Rotondo, Italy
| | - Alessandro Sgambato
- Scientific Direction, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, Italy
| | - Luciana De Luca
- Unit of Clinical Pathology, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, Italy
| | - Antonella Caivano
- Unit of Clinical Pathology, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, Italy
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4
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Liquid biopsy: an evolving paradigm for the biological characterisation of plasma cell disorders. Leukemia 2021; 35:2771-2783. [PMID: 34262132 DOI: 10.1038/s41375-021-01339-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 05/14/2021] [Accepted: 06/25/2021] [Indexed: 02/06/2023]
Abstract
Liquid biopsies-a source of circulating cell-free nucleic acids, proteins and extracellular vesicles-are currently being explored for the quantitative and qualitative characterisation of the tumour genome and as a mode of non-invasive therapeutic monitoring in cancer. Emerging data suggest that liquid biopsies might offer a potentially simple, non-invasive, repeatable strategy for diagnosis, prognostication and therapeutic decision making in a genetically heterogeneous disease like multiple myeloma (MM), with particular applicability in subsets of patients where conventional markers of disease burden may be less informative. In this review, we describe the emerging utility of the evaluation of circulating tumour DNA, extracellular RNA, cell-free proteins and metabolites and extracellular vesicles in MM.
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Reale A, Khong T, Mithraprabhu S, Spencer A. Translational Potential of RNA Derived From Extracellular Vesicles in Multiple Myeloma. Front Oncol 2021; 11:718502. [PMID: 34513695 PMCID: PMC8429596 DOI: 10.3389/fonc.2021.718502] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/04/2021] [Indexed: 12/20/2022] Open
Abstract
The cross-talk between tumour cells and stromal cells is a hallmark of multiple myeloma (MM), a blood cancer that still remains incurable despite increased knowledge of its biology and advances in its treatment. Extracellular vesicles (EVs) derived from both tumour and stromal cells have been shown to play an important role in mediating this cross-talk ultimately favouring MM progression and drug resistance. Furthermore, EVs and their content including RNA (EV-RNA) have been successfully isolated from blood and are being explored as liquid biomarkers in MM with the potential to improve diagnosis and monitoring modalities with a minimally-invasive and repeatable analysis, i.e. liquid biopsy. In this review, we describe both the role of EV-RNA in defining the biological features of MM and their potential translational relevance as liquid biomarkers, therapeutic targets and delivery systems. We also discuss the limitations and technical challenges related to the isolation and characterization of EVs and provide a perspective on the future of MM-derived EV-RNA in translational research.
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Affiliation(s)
- Antonia Reale
- Myeloma Research Group, Australian Centre for Blood Diseases, Central Clinical School, Monash University/Alfred Health, Melbourne, VIC, Australia
| | - Tiffany Khong
- Myeloma Research Group, Australian Centre for Blood Diseases, Central Clinical School, Monash University/Alfred Health, Melbourne, VIC, Australia
| | - Sridurga Mithraprabhu
- Myeloma Research Group, Australian Centre for Blood Diseases, Central Clinical School, Monash University/Alfred Health, Melbourne, VIC, Australia
| | - Andrew Spencer
- Myeloma Research Group, Australian Centre for Blood Diseases, Central Clinical School, Monash University/Alfred Health, Melbourne, VIC, Australia.,Malignant Haematology and Stem Cell Transplantation, The Alfred Hospital, and Department of Clinical Haematology, Monash University, Melbourne, VIC, Australia
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6
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Mosquera-Heredia MI, Morales LC, Vidal OM, Barceló E, Silvera-Redondo C, Vélez JI, Garavito-Galofre P. Exosomes: Potential Disease Biomarkers and New Therapeutic Targets. Biomedicines 2021; 9:1061. [PMID: 34440265 PMCID: PMC8393483 DOI: 10.3390/biomedicines9081061] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 02/07/2023] Open
Abstract
Exosomes are extracellular vesicles released by cells, both constitutively and after cell activation, and are present in different types of biological fluid. Exosomes are involved in the pathogenesis of diseases, such as cancer, neurodegenerative diseases, pregnancy disorders and cardiovascular diseases, and have emerged as potential non-invasive biomarkers for the detection, prognosis and therapeutics of a myriad of diseases. In this review, we describe recent advances related to the regulatory mechanisms of exosome biogenesis, release and molecular composition, as well as their role in health and disease, and their potential use as disease biomarkers and therapeutic targets. In addition, the advantages and disadvantages of their main isolation methods, characterization and cargo analysis, as well as the experimental methods used for exosome-mediated drug delivery, are discussed. Finally, we present potential perspectives for the use of exosomes in future clinical practice.
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Affiliation(s)
- Maria I. Mosquera-Heredia
- Department of Medicine, Universidad del Norte, Barranquilla 081007, Colombia; (L.C.M.); (O.M.V.); (C.S.-R.)
| | - Luis C. Morales
- Department of Medicine, Universidad del Norte, Barranquilla 081007, Colombia; (L.C.M.); (O.M.V.); (C.S.-R.)
| | - Oscar M. Vidal
- Department of Medicine, Universidad del Norte, Barranquilla 081007, Colombia; (L.C.M.); (O.M.V.); (C.S.-R.)
| | - Ernesto Barceló
- Instituto Colombiano de Neuropedagogía, Barranquilla 080020, Colombia;
| | - Carlos Silvera-Redondo
- Department of Medicine, Universidad del Norte, Barranquilla 081007, Colombia; (L.C.M.); (O.M.V.); (C.S.-R.)
| | - Jorge I. Vélez
- Department of Industrial Engineering, Universidad del Norte, Barranquilla 081007, Colombia;
| | - Pilar Garavito-Galofre
- Department of Medicine, Universidad del Norte, Barranquilla 081007, Colombia; (L.C.M.); (O.M.V.); (C.S.-R.)
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7
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Reale A, Carmichael I, Xu R, Mithraprabhu S, Khong T, Chen M, Fang H, Savvidou I, Ramachandran M, Bingham N, Simpson RJ, Greening DW, Spencer A. Human myeloma cell- and plasma-derived extracellular vesicles contribute to functional regulation of stromal cells. Proteomics 2021; 21:e2000119. [PMID: 33580572 DOI: 10.1002/pmic.202000119] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 02/04/2021] [Accepted: 02/08/2021] [Indexed: 02/06/2023]
Abstract
Circulating small extracellular vesicles (sEV) represent promising non-invasive biomarkers that may aid in the diagnosis and risk-stratification of multiple myeloma (MM), an incurable blood cancer. Here, we comprehensively isolated and characterized sEV from human MM cell lines (HMCL) and patient-derived plasma (psEV) by specific EV-marker enrichment and morphology. Importantly, we demonstrate that HMCL-sEV are readily internalised by stromal cells to functionally modulate proliferation. psEV were isolated using various commercial approaches and pre-analytical conditions (collection tube types, storage conditions) assessed for sEV yield and marker enrichment. Functionally, MM-psEV was shown to regulate stromal cell proliferation and migration. In turn, pre-educated stromal cells favour HMCL adhesion. psEV isolated from patients with both pre-malignant plasma cell disorders (monoclonal gammopathy of undetermined significance [MGUS]; smouldering MM [SMM]) and MM have a similar ability to promote cell migration and adhesion, suggesting a role for both malignant and pre-malignant sEV in disease progression. Proteomic profiling of MM-psEV (305 proteins) revealed enrichment of oncogenic factors implicated in cell migration and adhesion, in comparison to non-disease psEV. This study describes a protocol to generate morphologically-intact and biologically functional sEV capable of mediating the regulation of stromal cells, and a model for the characterization of tumour-stromal cross-talk by sEV in MM.
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Affiliation(s)
- Antonia Reale
- Myeloma Research Group, Australian Centre for Blood Diseases, Monash University/Alfred Health, Melbourne, Victoria, Australia.,Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Irena Carmichael
- Monash Micro Imaging-AMREP, Monash University, Melbourne, Victoria, Australia
| | - Rong Xu
- Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Nanobiotechnology Laboratory, Australian Centre for Blood Diseases, Monash University/Alfred Health, Melbourne, Victoria, Australia.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Sridurga Mithraprabhu
- Myeloma Research Group, Australian Centre for Blood Diseases, Monash University/Alfred Health, Melbourne, Victoria, Australia.,Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Tiffany Khong
- Myeloma Research Group, Australian Centre for Blood Diseases, Monash University/Alfred Health, Melbourne, Victoria, Australia.,Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Maoshan Chen
- Myeloma Research Group, Australian Centre for Blood Diseases, Monash University/Alfred Health, Melbourne, Victoria, Australia
| | - Haoyun Fang
- Molecular Proteomics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Ioanna Savvidou
- Myeloma Research Group, Australian Centre for Blood Diseases, Monash University/Alfred Health, Melbourne, Victoria, Australia.,Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Malarmathy Ramachandran
- Myeloma Research Group, Australian Centre for Blood Diseases, Monash University/Alfred Health, Melbourne, Victoria, Australia.,Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Nicholas Bingham
- Myeloma Research Group, Australian Centre for Blood Diseases, Monash University/Alfred Health, Melbourne, Victoria, Australia.,Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Richard J Simpson
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - David W Greening
- Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia.,Molecular Proteomics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Andrew Spencer
- Myeloma Research Group, Australian Centre for Blood Diseases, Monash University/Alfred Health, Melbourne, Victoria, Australia.,Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Malignant Haematology and Stem Cell Transplantation, The Alfred Hospital, and Department of Clinical Haematology, Monash University, Melbourne, Victoria, Australia
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