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Beutgen VM, Shinkevich V, Pörschke J, Meena C, Steitz AM, Pogge von Strandmann E, Graumann J, Gómez-Serrano M. Secretome analysis using Affinity Proteomics and Immunoassays: a focus on Tumor Biology. Mol Cell Proteomics 2024:100830. [PMID: 39147028 DOI: 10.1016/j.mcpro.2024.100830] [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: 02/29/2024] [Revised: 07/20/2024] [Accepted: 08/12/2024] [Indexed: 08/17/2024] Open
Abstract
The study of the cellular secretome using proteomic techniques continues to capture the attention of the research community across a broad range of topics in biomedical research. Due to their untargeted nature, independence from the model system employed, historically superior depth of analysis, as well as comparative affordability, mass spectrometry-based approaches traditionally dominate such analyses. More recently, however, affinity-based proteomic assays have massively gained in analytical depth, which together with their high sensitivity, dynamic range coverage as well as high throughput capabilities render them exquisitely suited to secretome analysis. In this review, we revisit the analytical challenges implied by secretomics and provide an overview of affinity-based proteomic platforms currently available for such analyses, using the study of the tumor secretome as an example for basic and translational research.
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Affiliation(s)
- Vanessa M Beutgen
- Institute of Translational Proteomics, Biochemical/Pharmacological Centre, Philipps University, Marburg, Germany; Core Facility Translational Proteomics, Biochemical/Pharmacological Centre, Philipps University, Marburg, Germany
| | - Veronika Shinkevich
- Institute of Pharmacology, Biochemical/Pharmacological Centre, Philipps University, Marburg, Germany
| | - Johanna Pörschke
- Institute for Tumor Immunology, Center for Tumor Biology and Immunology, Philipps University, Marburg, Germany
| | - Celina Meena
- Institute for Tumor Immunology, Center for Tumor Biology and Immunology, Philipps University, Marburg, Germany
| | - Anna M Steitz
- Translational Oncology Group, Center for Tumor Biology and Immunology, Philipps University, Marburg, Germany
| | - Elke Pogge von Strandmann
- Institute for Tumor Immunology, Center for Tumor Biology and Immunology, Philipps University, Marburg, Germany
| | - Johannes Graumann
- Institute of Translational Proteomics, Biochemical/Pharmacological Centre, Philipps University, Marburg, Germany; Core Facility Translational Proteomics, Biochemical/Pharmacological Centre, Philipps University, Marburg, Germany.
| | - María Gómez-Serrano
- Institute for Tumor Immunology, Center for Tumor Biology and Immunology, Philipps University, Marburg, Germany.
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Temperini ME, Di Giacinto F, Romanò S, Di Santo R, Augello A, Polito R, Baldassarre L, Giliberti V, Papi M, Basile U, Niccolini B, Krasnowska EK, Serafino A, De Spirito M, Di Gaspare A, Ortolani M, Ciasca G. Antenna-enhanced mid-infrared detection of extracellular vesicles derived from human cancer cell cultures. J Nanobiotechnology 2022; 20:530. [PMID: 36514065 PMCID: PMC9746222 DOI: 10.1186/s12951-022-01693-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 10/30/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Extracellular Vesicles (EVs) are sub-micrometer lipid-bound particles released by most cell types. They are considered a promising source of cancer biomarkers for liquid biopsy and personalized medicine due to their specific molecular cargo, which provides biochemical information on the state of parent cells. Despite this potential, EVs translation process in the diagnostic practice is still at its birth, and the development of novel medical devices for their detection and characterization is highly required. RESULTS In this study, we demonstrate mid-infrared plasmonic nanoantenna arrays designed to detect, in the liquid and dry phase, the specific vibrational absorption signal of EVs simultaneously with the unspecific refractive index sensing signal. For this purpose, EVs are immobilized on the gold nanoantenna surface by immunocapture, allowing us to select specific EV sub-populations and get rid of contaminants. A wet sample-handling technique relying on hydrophobicity contrast enables effortless reflectance measurements with a Fourier-transform infrared (FTIR) spectro-microscope in the wavelength range between 10 and 3 µm. In a proof-of-principle experiment carried out on EVs released from human colorectal adenocarcinoma (CRC) cells, the protein absorption bands (amide-I and amide-II between 5.9 and 6.4 µm) increase sharply within minutes when the EV solution is introduced in the fluidic chamber, indicating sensitivity to the EV proteins. A refractive index sensing curve is simultaneously provided by our sensor in the form of the redshift of a sharp spectral edge at wavelengths around 5 µm, where no vibrational absorption of organic molecules takes place: this permits to extract of the dynamics of EV capture by antibodies from the overall molecular layer deposition dynamics, which is typically measured by commercial surface plasmon resonance sensors. Additionally, the described metasurface is exploited to compare the spectral response of EVs derived from cancer cells with increasing invasiveness and metastatic potential, suggesting that the average secondary structure content in EVs can be correlated with cell malignancy. CONCLUSIONS Thanks to the high protein sensitivity and the possibility to work with small sample volumes-two key features for ultrasensitive detection of extracellular vesicles- our lab-on-chip can positively impact the development of novel laboratory medicine methods for the molecular characterization of EVs.
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Affiliation(s)
- Maria Eleonora Temperini
- grid.7841.aDepartment of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, 00185 Rome, Italy ,grid.25786.3e0000 0004 1764 2907Center for Life Neuro and Nano Sciences IIT@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Flavio Di Giacinto
- grid.414603.4Fondazione Policlinico Universitario “A. Gemelli”, IRCCS, Rome, Italy ,grid.8142.f0000 0001 0941 3192Dipartimento di Neuroscienze, Sezione di Fisica, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Sabrina Romanò
- grid.414603.4Fondazione Policlinico Universitario “A. Gemelli”, IRCCS, Rome, Italy ,grid.8142.f0000 0001 0941 3192Dipartimento di Neuroscienze, Sezione di Fisica, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Riccardo Di Santo
- grid.414603.4Fondazione Policlinico Universitario “A. Gemelli”, IRCCS, Rome, Italy
| | - Alberto Augello
- grid.414603.4Fondazione Policlinico Universitario “A. Gemelli”, IRCCS, Rome, Italy
| | - Raffaella Polito
- grid.7841.aDepartment of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, 00185 Rome, Italy
| | - Leonetta Baldassarre
- grid.7841.aDepartment of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, 00185 Rome, Italy
| | - Valeria Giliberti
- grid.25786.3e0000 0004 1764 2907Center for Life Neuro and Nano Sciences IIT@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Massimiliano Papi
- grid.414603.4Fondazione Policlinico Universitario “A. Gemelli”, IRCCS, Rome, Italy ,grid.8142.f0000 0001 0941 3192Dipartimento di Neuroscienze, Sezione di Fisica, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Umberto Basile
- grid.414603.4Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy
| | - Benedetta Niccolini
- grid.8142.f0000 0001 0941 3192Dipartimento di Neuroscienze, Sezione di Fisica, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Ewa K. Krasnowska
- grid.5326.20000 0001 1940 4177Institute of Translational Pharmacology, National Research Council of Italy, Rome, Italy
| | - Annalucia Serafino
- grid.5326.20000 0001 1940 4177Institute of Translational Pharmacology, National Research Council of Italy, Rome, Italy
| | - Marco De Spirito
- grid.414603.4Fondazione Policlinico Universitario “A. Gemelli”, IRCCS, Rome, Italy ,grid.8142.f0000 0001 0941 3192Dipartimento di Neuroscienze, Sezione di Fisica, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Alessandra Di Gaspare
- grid.414603.4Fondazione Policlinico Universitario “A. Gemelli”, IRCCS, Rome, Italy ,grid.509494.5NEST, CNR-Istituto Nanoscienze and Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Michele Ortolani
- grid.7841.aDepartment of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, 00185 Rome, Italy ,grid.25786.3e0000 0004 1764 2907Center for Life Neuro and Nano Sciences IIT@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Gabriele Ciasca
- grid.414603.4Fondazione Policlinico Universitario “A. Gemelli”, IRCCS, Rome, Italy ,grid.8142.f0000 0001 0941 3192Dipartimento di Neuroscienze, Sezione di Fisica, Università Cattolica del Sacro Cuore, Rome, Italy
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Morshed A, Karawdeniya BI, Bandara Y, Kim MJ, Dutta P. Mechanical characterization of vesicles and cells: A review. Electrophoresis 2020; 41:449-470. [PMID: 31967658 PMCID: PMC7567447 DOI: 10.1002/elps.201900362] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 12/05/2019] [Accepted: 12/08/2019] [Indexed: 12/30/2022]
Abstract
Vesicles perform many essential functions in all living organisms. They respond like a transducer to mechanical stress in converting the applied force into mechanical and biological responses. At the same time, both biochemical and biophysical signals influence the vesicular response in bearing mechanical loads. In recent years, liposomes, artificial lipid vesicles, have gained substantial attention from the pharmaceutical industry as a prospective drug carrier which can also serve as an artificial cell-mimetic system. The ability of these vesicles to enter through pores of even smaller size makes them ideal candidates for therapeutic agents to reach the infected sites effectively. Engineering of vesicles with desired mechanical properties that can encapsulate drugs and release as required is the prime challenge in this field. This requirement has led to the modifications of the composition of the bilayer membrane by adding cholesterol, sphingomyelin, etc. In this article, we review the manufacturing and characterization techniques of various artificial/synthetic vesicles. We particularly focus on the electric field-driven characterization techniques to determine different properties of vesicle and its membranes, such as bending rigidity, viscosity, capacitance, conductance, etc., which are indicators of their content and mobility. Similarities and differences between artificial vesicles, natural vesicles, and cells are highlighted throughout the manuscript since most of these artificial vesicles are intended for cell mimetic functions.
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Affiliation(s)
- Adnan Morshed
- School of Mechanical and Materials Engineering, Washington State University, Pullman, WA 99164-2920
| | - Buddini Iroshika Karawdeniya
- Department of Mechanical Engineering, Lyle School of Engineering, Southern Methodist University, Dallas, Texas, USA
| | - Y.M.NuwanD.Y. Bandara
- Department of Mechanical Engineering, Lyle School of Engineering, Southern Methodist University, Dallas, Texas, USA
| | - Min Jun Kim
- Department of Mechanical Engineering, Lyle School of Engineering, Southern Methodist University, Dallas, Texas, USA
| | - Prashanta Dutta
- School of Mechanical and Materials Engineering, Washington State University, Pullman, WA 99164-2920
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Chin RI, Chen K, Usmani A, Chua C, Harris PK, Binkley MS, Azad TD, Dudley JC, Chaudhuri AA. Detection of Solid Tumor Molecular Residual Disease (MRD) Using Circulating Tumor DNA (ctDNA). Mol Diagn Ther 2019; 23:311-331. [PMID: 30941670 PMCID: PMC6561896 DOI: 10.1007/s40291-019-00390-5] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Circulating tumor DNA (ctDNA) is a component of cell-free DNA that is shed by malignant tumors into the bloodstream and other bodily fluids. Levels of ctDNA are typically low, particularly in patients with localized disease, requiring highly sophisticated methods for detection and quantification. Multiple liquid biopsy methods have been developed for ctDNA analysis in solid tumor malignancies and are now enabling detection and assessment of earlier stages of disease, post-treatment molecular residual disease (MRD), resistance to targeted systemic therapy, and tumor mutational burden. Understanding ctDNA biology, mechanisms of release, and clearance and size characteristics, in conjunction with the application of molecular barcoding and targeted error correction, have increased the sensitivity and specificity of ctDNA detection techniques. Combinatorial approaches including integration of ctDNA data with circulating protein biomarkers may further improve assay sensitivity and broaden the scope of ctDNA applications. Circulating viral DNA may be utilized to monitor disease in some virally induced malignancies. In spite of increasingly accurate methods of ctDNA detection, results need to be interpreted with caution given that somatic mosaicisms such as clonal hematopoiesis of indeterminate potential (CHIP) may give rise to genetic variants in the bloodstream unrelated to solid tumors, and the limited concordance observed between different commercial platforms. Overall, highly precise ctDNA detection and quantification methods have the potential to transform clinical practice via non-invasive monitoring of solid tumor malignancies, residual disease detection at earlier timepoints than standard clinical and/or imaging surveillance, and treatment personalization based on real-time assessment of the tumor genomic landscape.
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Affiliation(s)
- Re-I Chin
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Kevin Chen
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Abul Usmani
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Chanelle Chua
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Peter K Harris
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Michael S Binkley
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Tej D Azad
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jonathan C Dudley
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Aadel A Chaudhuri
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Computer Science and Engineering, Washington University, St. Louis, MO, USA.
- Alvin J. Siteman Cancer Center, Barnes-Jewish Hospital and Washington University School of Medicine, St. Louis, MO, USA.
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Rossi M, Taddei AR, Fasciani I, Maggio R, Giorgi F. The cell biology of the thyroid-disrupting mechanism of dichlorodiphenyltrichloroethane (DDT). J Endocrinol Invest 2018. [PMID: 28639207 DOI: 10.1007/s40618-017-0716-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
OBJECTIVE Dichlorodiphenyltrichloroethane (DDT) is an organochlorine known for its pesticide properties and for its negative effects on human health. It was banned in most countries for its toxicity to the endocrine system, but due to its persistence at clinically relevant concentrations in both soil and animal tissues, DDT is still linked to several health and social problems. METHODS We have previously shown that DDT exposure is causally related to the extracellular release of vesicular organelles such as microvesicles and/or exosomes by using immunocytochemistry with gold-tagged antibodies and various fluorescent membrane markers. RESULTS It is now well recognized that microvesicles and/or exosomes organelles are implicated in cell-to-cell communication, and that they are fundamental elements for transferring proteins, RNA, DNA, lipids and transcriptional factors among cells. In this short review, we discussed the role of extracellular vesicle formation in the thyroid-disrupting mechanism of DDT. In particular, we described how DDT, by dislodging the thyrotropin hormone (TSH) receptor from the raft containing compartments of the cells, prevents its activation and internalization. CONCLUSION Based on our earlier finding and on the large body of evidence here reviewed, we propose that DDT-induced formation of extracellular vesicles containing the TSH receptor could be directly involved in the development of autoimmune responses against the TSH receptor and that, therefore, their release could lead to the development of the Graves' disease.
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Affiliation(s)
- M Rossi
- Molecular Signaling Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | - A R Taddei
- Section of Electron Microscopy, Great Equipment Center, University of Tuscia, Viterbo, Italy
| | - I Fasciani
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - R Maggio
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy.
| | - F Giorgi
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
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Qasaimeh MA, Wu YC, Bose S, Menachery A, Talluri S, Gonzalez G, Fulciniti M, Karp JM, Prabhala RH, Karnik R. Isolation of Circulating Plasma Cells in Multiple Myeloma Using CD138 Antibody-Based Capture in a Microfluidic Device. Sci Rep 2017; 7:45681. [PMID: 28374831 PMCID: PMC5379479 DOI: 10.1038/srep45681] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 03/02/2017] [Indexed: 12/15/2022] Open
Abstract
The necessity for bone marrow aspiration and the lack of highly sensitive assays to detect residual disease present challenges for effective management of multiple myeloma (MM), a plasma cell cancer. We show that a microfluidic cell capture based on CD138 antigen, which is highly expressed on plasma cells, permits quantitation of rare circulating plasma cells (CPCs) in blood and subsequent fluorescence-based assays. The microfluidic device is based on a herringbone channel design, and exhibits an estimated cell capture efficiency of ~40–70%, permitting detection of <10 CPCs/mL using 1-mL sample volumes, which is difficult using existing techniques. In bone marrow samples, the microfluidic-based plasma cell counts exhibited excellent correlation with flow cytometry analysis. In peripheral blood samples, the device detected a baseline of 2–5 CD138+ cells/mL in healthy donor blood, with significantly higher numbers in blood samples of MM patients in remission (20–24 CD138+ cells/mL), and yet higher numbers in MM patients exhibiting disease (45–184 CD138+ cells/mL). Analysis of CPCs isolated using the device was consistent with serum immunoglobulin assays that are commonly used in MM diagnostics. These results indicate the potential of CD138-based microfluidic CPC capture as a useful ‘liquid biopsy’ that may complement or partially replace bone marrow aspiration.
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Affiliation(s)
- Mohammad A Qasaimeh
- Division of Engineering, New York University Abu Dhabi, Abu Dhabi, UAE.,Mechanical and Aerospace Engineering Department, New York University, Brooklyn, NY 11201, USA.,Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yichao C Wu
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Suman Bose
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Anoop Menachery
- Division of Engineering, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Srikanth Talluri
- VA Boston Healthcare System, Boston, MA, USA.,Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - Jeffrey M Karp
- Division of BioEngineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Harvard Stem Cell Institute, Harvard-MIT Division of Health Sciences and Technology, 65 Landsdowne St., Cambridge, MA 02139, USA
| | - Rao H Prabhala
- VA Boston Healthcare System, Boston, MA, USA.,Dana-Farber Cancer Institute, Boston, MA, USA.,Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Rohit Karnik
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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