1
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Santi A, Kay EJ, Neilson LJ, McGarry L, Lilla S, Mullin M, Paul NR, Fercoq F, Koulouras G, Rodriguez Blanco G, Athineos D, Mason S, Hughes M, Thomson G, Kieffer Y, Nixon C, Blyth K, Mechta-Grigoriou F, Carlin LM, Zanivan S. Cancer-associated fibroblasts produce matrix-bound vesicles that influence endothelial cell function. Sci Signal 2024; 17:eade0580. [PMID: 38470957 DOI: 10.1126/scisignal.ade0580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 02/26/2024] [Indexed: 03/14/2024]
Abstract
Intercellular communication between different cell types in solid tumors contributes to tumor growth and metastatic dissemination. The secretome of cancer-associated fibroblasts (CAFs) plays major roles in these processes. Using human mammary CAFs, we showed that CAFs with a myofibroblast phenotype released extracellular vesicles that transferred proteins to endothelial cells (ECs) that affected their interaction with immune cells. Mass spectrometry-based proteomics identified proteins transferred from CAFs to ECs, which included plasma membrane receptors. Using THY1 as an example of a transferred plasma membrane-bound protein, we showed that CAF-derived proteins increased the adhesion of a monocyte cell line to ECs. CAFs produced high amounts of matrix-bound EVs, which were the primary vehicles of protein transfer. Hence, our work paves the way for future studies that investigate how CAF-derived matrix-bound EVs influence tumor pathology by regulating the function of neighboring cancer, stromal, and immune cells.
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Affiliation(s)
- Alice Santi
- Cancer Research UK Scotland Institute, Glasgow G61 1BD, UK
- Department of Experimental and Clinical Biomedical Sciences, Università degli Studi di Firenze, viale Morgagni 50, 50134 Firenze, Italy
| | - Emily J Kay
- Cancer Research UK Scotland Institute, Glasgow G61 1BD, UK
| | - Lisa J Neilson
- Cancer Research UK Scotland Institute, Glasgow G61 1BD, UK
| | - Lynn McGarry
- Cancer Research UK Scotland Institute, Glasgow G61 1BD, UK
| | - Sergio Lilla
- Cancer Research UK Scotland Institute, Glasgow G61 1BD, UK
| | - Margaret Mullin
- College of Medical, Veterinary, and Life Sciences, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8QQ, UK
| | - Nikki R Paul
- Cancer Research UK Scotland Institute, Glasgow G61 1BD, UK
| | | | - Grigorios Koulouras
- Cancer Research UK Scotland Institute, Glasgow G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | | | | | - Susan Mason
- Cancer Research UK Scotland Institute, Glasgow G61 1BD, UK
| | - Mark Hughes
- Cancer Research UK Scotland Institute, Glasgow G61 1BD, UK
| | - Gemma Thomson
- Cancer Research UK Scotland Institute, Glasgow G61 1BD, UK
| | - Yann Kieffer
- Equipe Labellisée Ligue Nationale Contre le Cancer, Institut Curie, PSL Research University, 26, rue d'Ulm, 75005 Paris, France
- INSERM, U830, 75005 Paris, France
| | - Colin Nixon
- Cancer Research UK Scotland Institute, Glasgow G61 1BD, UK
| | - Karen Blyth
- Cancer Research UK Scotland Institute, Glasgow G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - Fatima Mechta-Grigoriou
- Equipe Labellisée Ligue Nationale Contre le Cancer, Institut Curie, PSL Research University, 26, rue d'Ulm, 75005 Paris, France
- INSERM, U830, 75005 Paris, France
| | - Leo M Carlin
- Cancer Research UK Scotland Institute, Glasgow G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - Sara Zanivan
- Cancer Research UK Scotland Institute, Glasgow G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, UK
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2
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Nevárez-Ramírez AJ, Guzmán-Ortiz AL, Cortes-Reynosa P, Perez-Salazar E, Jaimes-Ortega GA, Valle-Rios R, Marín-Hernández Á, Rodríguez-Zavala JS, Ruiz-May E, Castrejón-Flores JL, Quezada H. Shotgun Proteomics of Co-Cultured Leukemic and Bone Marrow Stromal Cells from Different Species as a Preliminary Approach to Detect Intercellular Protein Transfer. Proteomes 2023; 11:proteomes11020015. [PMID: 37092456 PMCID: PMC10123657 DOI: 10.3390/proteomes11020015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/25/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023] Open
Abstract
Cellular interactions within the bone marrow microenvironment modulate the properties of subsets of leukemic cells leading to the development of drug-resistant phenotypes. The intercellular transfer of proteins and organelles contributes to this process but the set of transferred proteins and their effects in the receiving cells remain unclear. This study aimed to detect the intercellular protein transfer from mouse bone marrow stromal cells (OP9 cell line) to human T-lymphoblasts (CCRF-CEM cell line) using nanoLC-MS/MS-based shotgun proteomics in a 3D co-culture system. After 24 h of co-culture, 1513 and 67 proteins from human and mouse origin, respectively, were identified in CCRF-CEM cells. The presence of mouse proteins in the human cell line, detected by analyzing the differences in amino acid sequences of orthologous peptides, was interpreted as the result of intercellular transfer. The transferred proteins might have contributed to the observed resistance to vincristine, methotrexate, and hydrogen peroxide in the co-cultured leukemic cells. Our results suggest that shotgun proteomic analyses of co-cultured cells from different species could be a simple option to get a preliminary survey of the proteins exchanged among interacting cells.
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Affiliation(s)
- Abraham Josué Nevárez-Ramírez
- Laboratorio de Investigación en Inmunología y Proteómica, Hospital Infantil de México Federico Gómez, Dr. Márquez 162, Doctores, Mexico City 06720, Mexico
- Unidad Profesional Interdisciplinaria de Biotecnología, Instituto Politécnico Nacional, Av. Acueducto s/n, Barrio La Laguna, Mexico City 07340, Mexico
| | - Ana Laura Guzmán-Ortiz
- Laboratorio de Investigación en Inmunología y Proteómica, Hospital Infantil de México Federico Gómez, Dr. Márquez 162, Doctores, Mexico City 06720, Mexico
| | - Pedro Cortes-Reynosa
- Departamento de Biología Celular, CINVESTAV-IPN, Av Instituto Politécnico Nacional 2508, San Pedro Zacatenco, Mexico City 07360, Mexico
| | - Eduardo Perez-Salazar
- Departamento de Biología Celular, CINVESTAV-IPN, Av Instituto Politécnico Nacional 2508, San Pedro Zacatenco, Mexico City 07360, Mexico
| | - Gustavo Alberto Jaimes-Ortega
- Laboratorio de Investigación en Inmunología y Proteómica, Hospital Infantil de México Federico Gómez, Dr. Márquez 162, Doctores, Mexico City 06720, Mexico
- División de Investigación, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Circuito interior, Av. Universidad 3000, Ciudad Universitaria, Coyoacán, Mexico City 04510, Mexico
| | - Ricardo Valle-Rios
- Laboratorio de Investigación en Inmunología y Proteómica, Hospital Infantil de México Federico Gómez, Dr. Márquez 162, Doctores, Mexico City 06720, Mexico
- División de Investigación, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Circuito interior, Av. Universidad 3000, Ciudad Universitaria, Coyoacán, Mexico City 04510, Mexico
| | - Álvaro Marín-Hernández
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Juan Badiano 1, Belisario Domínguez—Sección XVI, Mexico City 14080, Mexico
| | - José S. Rodríguez-Zavala
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Juan Badiano 1, Belisario Domínguez—Sección XVI, Mexico City 14080, Mexico
| | - Eliel Ruiz-May
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Carretera Antigua a Coatepec 351, El Haya, Xalapa 91073, Mexico
| | - José Luis Castrejón-Flores
- Unidad Profesional Interdisciplinaria de Biotecnología, Instituto Politécnico Nacional, Av. Acueducto s/n, Barrio La Laguna, Mexico City 07340, Mexico
| | - Héctor Quezada
- Laboratorio de Investigación en Inmunología y Proteómica, Hospital Infantil de México Federico Gómez, Dr. Márquez 162, Doctores, Mexico City 06720, Mexico
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3
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Chen X, Rechavi O. Plant and animal small RNA communications between cells and organisms. Nat Rev Mol Cell Biol 2022; 23:185-203. [PMID: 34707241 PMCID: PMC9208737 DOI: 10.1038/s41580-021-00425-y] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2021] [Indexed: 01/09/2023]
Abstract
Since the discovery of eukaryotic small RNAs as the main effectors of RNA interference in the late 1990s, diverse types of endogenous small RNAs have been characterized, most notably microRNAs, small interfering RNAs (siRNAs) and PIWI-interacting RNAs (piRNAs). These small RNAs associate with Argonaute proteins and, through sequence-specific gene regulation, affect almost every major biological process. Intriguing features of small RNAs, such as their mechanisms of amplification, rapid evolution and non-cell-autonomous function, bestow upon them the capacity to function as agents of intercellular communications in development, reproduction and immunity, and even in transgenerational inheritance. Although there are many types of extracellular small RNAs, and despite decades of research, the capacity of these molecules to transmit signals between cells and between organisms is still highly controversial. In this Review, we discuss evidence from different plants and animals that small RNAs can act in a non-cell-autonomous manner and even exchange information between species. We also discuss mechanistic insights into small RNA communications, such as the nature of the mobile agents, small RNA signal amplification during transit, signal perception and small RNA activity at the destination.
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Affiliation(s)
- Xuemei Chen
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA.
| | - Oded Rechavi
- Department of Neurobiology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel. .,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.
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4
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Swietlik JJ, Sinha A, Meissner F. Dissecting intercellular signaling with mass spectrometry-based proteomics. Curr Opin Cell Biol 2020; 63:20-30. [PMID: 31927463 DOI: 10.1016/j.ceb.2019.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/27/2019] [Accepted: 12/02/2019] [Indexed: 02/07/2023]
Abstract
Physiological functions depend on a coordinated interplay of numerous different cell types. Proteins serve as major signaling molecules between cells; however, their comprehensive investigation in physiologically relevant settings has remained challenging. Mass spectrometry (MS)-based shotgun proteomics is emerging as a powerful technology for the systematic analysis of protein-mediated intercellular signaling and regulated post-translational modifications. Here, we discuss recent advancements in cell biological, chemical, and biochemical MS-based approaches for the profiling of cellular messengers released by sending cells, receptors expressed on the cell surface, and their interactions. We highlight methods tailored toward the mapping of dynamic signal transduction mechanisms at cellular interfaces and approaches to dissect communication cell specifically in heterocellular systems. Thereby, MS-based proteomics contributes a unique systems biology perspective for the identification of intercellular signaling pathways deregulated in disease.
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Affiliation(s)
- Jonathan J Swietlik
- Experimental Systems Immunology Laboratory, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Ankit Sinha
- Experimental Systems Immunology Laboratory, Max-Planck Institute of Biochemistry, Martinsried, Germany; Institute of Translational Cancer Research and Experimental Cancer Therapy, Klinikum Rechts der Isar, TU München, Munich, Germany
| | - Felix Meissner
- Experimental Systems Immunology Laboratory, Max-Planck Institute of Biochemistry, Martinsried, Germany.
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5
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Schira-Heinen J, Grube L, Waldera-Lupa DM, Baberg F, Langini M, Etemad-Parishanzadeh O, Poschmann G, Stühler K. Pitfalls and opportunities in the characterization of unconventionally secreted proteins by secretome analysis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:140237. [DOI: 10.1016/j.bbapap.2019.06.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 06/04/2019] [Accepted: 06/06/2019] [Indexed: 02/07/2023]
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6
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Martín-Antonio B, Suñe G, Najjar A, Perez-Amill L, Antoñana-Vildosola A, Castella M, León S, Velasco-de Andrés M, Lozano F, Lozano E, Bueno C, Estanyol JM, Muñoz-Pinedo C, Robinson SN, Urbano-Ispizua A. Extracellular NK histones promote immune cell anti-tumor activity by inducing cell clusters through binding to CD138 receptor. J Immunother Cancer 2019; 7:259. [PMID: 31619273 PMCID: PMC6794915 DOI: 10.1186/s40425-019-0739-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 09/12/2019] [Indexed: 12/25/2022] Open
Abstract
Background Natural killer (NK) cells are important anti-tumor cells of our innate immune system. Their anti-cancer activity is mediated through interaction of a wide array of activating and inhibitory receptors with their ligands on tumor cells. After activation, NK cells also secrete a variety of pro-inflammatory molecules that contribute to the final immune response by modulating other innate and adaptive immune cells. In this regard, external proteins from NK cell secretome and the mechanisms by which they mediate these responses are poorly defined. Methods TRANS-stable-isotope labeling of amino acids in cell culture (TRANS-SILAC) combined with proteomic was undertaken to identify early materials transferred between cord blood-derived NK cells (CB-NK) and multiple myeloma (MM) cells. Further in vitro and in vivo studies with knock-down of histones and CD138, overexpression of histones and addition of exogenous histones were undertaken to confirm TRANS-SILAC results and to determine functional roles of this material transferred. Results We describe a novel mechanism by which histones are actively released by NK cells early after contact with MM cells. We show that extracellular histones bind to the heparan sulfate proteoglycan CD138 on the surface of MM cells to promote the creation of immune-tumor cell clusters bringing immune and MM cells into close proximity, and thus facilitating not only NK but also T lymphocyte anti-MM activity. Conclusion This study demonstrates a novel immunoregulatory role of NK cells against MM cells mediated by histones, and an additional role of NK cells modulating T lymphocytes activity that will open up new avenues to design future immunotherapy clinical strategies.
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Affiliation(s)
- B Martín-Antonio
- Department of Hematology, Hospital Clinic, IDIBAPS, Carrer Rosselló 149-153, 08036, Barcelona, Spain. .,Josep Carreras Leukaemia Research Institute, Carrer Rosselló 149-153, 08036, Barcelona, Spain.
| | - G Suñe
- Department of Hematology, Hospital Clinic, IDIBAPS, Carrer Rosselló 149-153, 08036, Barcelona, Spain.,Josep Carreras Leukaemia Research Institute, Carrer Rosselló 149-153, 08036, Barcelona, Spain
| | - A Najjar
- Department of Pediatrics - Research, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - L Perez-Amill
- Department of Hematology, Hospital Clinic, IDIBAPS, Carrer Rosselló 149-153, 08036, Barcelona, Spain
| | - A Antoñana-Vildosola
- Department of Hematology, Hospital Clinic, IDIBAPS, Carrer Rosselló 149-153, 08036, Barcelona, Spain
| | - M Castella
- Department of Hematology, Hospital Clinic, IDIBAPS, Carrer Rosselló 149-153, 08036, Barcelona, Spain
| | - S León
- Department of Hematology, Hospital Clinic, IDIBAPS, Carrer Rosselló 149-153, 08036, Barcelona, Spain
| | - M Velasco-de Andrés
- Immunoreceptors of the Innate and Adaptive System Group, IDIBAPS, Barcelona, Spain
| | - F Lozano
- Immunoreceptors of the Innate and Adaptive System Group, IDIBAPS, Barcelona, Spain.,Department of Immunology, Hospital Clinic of Barcelona, Barcelona, Spain.,Department of Biomedical Sciences, School of Medicine, University of Barcelona, Barcelona, Spain
| | - E Lozano
- Department of Hematology, Hospital Clinic, IDIBAPS, Carrer Rosselló 149-153, 08036, Barcelona, Spain
| | - C Bueno
- Josep Carreras Leukemia Research Institute and Cell Therapy Program of the School of Medicine, University of Barcelona, Barcelona, Spain
| | - J M Estanyol
- Proteomic department, University of Barcelona, Barcelona, Spain
| | - C Muñoz-Pinedo
- Cell Death Regulation Group, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - S N Robinson
- Department of Stem Cell Transplantation & Cellular Therapy, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - A Urbano-Ispizua
- Department of Hematology, Hospital Clinic, IDIBAPS, Carrer Rosselló 149-153, 08036, Barcelona, Spain.,Josep Carreras Leukaemia Research Institute, Carrer Rosselló 149-153, 08036, Barcelona, Spain.,Department of Hematology, University of Barcelona, Barcelona, Spain
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7
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Du S, Wang D, Lee JS, Peng B, Ge J, Yao SQ. Cell type-selective imaging and profiling of newly synthesized proteomes by using puromycin analogues. Chem Commun (Camb) 2018; 53:8443-8446. [PMID: 28702584 DOI: 10.1039/c7cc04536k] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We have developed a versatile antibody-assisted strategy for the imaging and profiling of newly synthesized proteomes in a cell-specific manner. This strategy remained highly selective even in heterogeneous co-cultured cells, thus enabling labeling and enrichment of nascent proteomes from targeted cells without the need for physical separation.
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Affiliation(s)
- Shubo Du
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore.
| | - Danyang Wang
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore.
| | - Jun-Seok Lee
- Molecular Recognition Research Center & Department of Biological Chemistry, KIST-School Korea Institute of Science & Technology, South Korea
| | - Bo Peng
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore.
| | - Jingyan Ge
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, China.
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore.
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8
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Santi A, Kugeratski FG, Zanivan S. Cancer Associated Fibroblasts: The Architects of Stroma Remodeling. Proteomics 2018; 18:e1700167. [PMID: 29280568 PMCID: PMC5900985 DOI: 10.1002/pmic.201700167] [Citation(s) in RCA: 143] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 12/15/2017] [Indexed: 12/24/2022]
Abstract
Fibroblasts have exceptional phenotypic plasticity and capability to secrete vast amount of soluble factors, extracellular matrix components and extracellular vesicles. While in physiological conditions this makes fibroblasts master regulators of tissue homeostasis and healing of injured tissues, in solid tumors cancer associated fibroblasts (CAFs) co-evolve with the disease, and alter the biochemical and physical structure of the tumor microenvironment, as well as the behavior of the surrounding stromal and cancer cells. Thus CAFs are fundamental regulators of tumor progression and influence response to therapeutic treatments. Increasing efforts are devoted to better understand the biology of CAFs to bring insights to develop complementary strategies to target this cell type in cancer. Here we highlight components of the tumor microenvironment that play key roles in cancer progression and invasion, and provide an extensive overview of past and emerging understanding of CAF biology as well as the contribution that MS-based proteomics has made to this field.
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Affiliation(s)
- Alice Santi
- Cancer Research UK Beatson InstituteGlasgowUK
| | | | - Sara Zanivan
- Cancer Research UK Beatson InstituteGlasgowUK
- Institute of Cancer SciencesUniversity of GlasgowGlasgowUK
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9
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Rainy N, Zayoud M, Kloog Y, Rechavi O, Goldstein I. Viral oncomiR spreading between B and T cells is employed by Kaposi's sarcoma herpesvirus to induce non-cell-autonomous target gene regulation. Oncotarget 2018; 7:41870-41884. [PMID: 27248822 PMCID: PMC5173102 DOI: 10.18632/oncotarget.9627] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 05/08/2016] [Indexed: 12/30/2022] Open
Abstract
The two human lymphotrophic γ-herpesviruses, Kaposi's sarcoma herpesvirus (KSHV) and Epstein-Barr virus (EBV), are a recognized cause of human cancer, encoding multiple miRs that are major players in carcinogenesis. Previously, we discovered that EBV-encoded miRs transfer between infected B and T lymphocytes. To further explore the biological significance of the spreading of γ-herpesvirus-encoded miRs on carcinogenesis, we focused on KSHV-miR-K12-11 (miR-K12-11) that is unique in having an identical seed sequence with the oncomiR hsa-miR-155, implicated in B cell lymphomas development. Here, we show for the first time that miR-K12-11 transfers in vitro from KSHV-infected BCBL-1 and BC-1 lymphoma lines to T cells. The transferred miR-K12-11 is active in the adopting T cells and binds its canonical target, the 3'-UTR of BACH1. Importantly, we show that the transfer of miR-K12-11 from BCBL-1 to Jurkat cells correlates with inhibition of the innate type-I interferons response to viral dsRNAs downstream of IKKε, a validated miR-K12-11 target. Finally, we show that miR-K12-11 spreading is not reduced by blocking the classical ceramide-dependent exosome secretion pathway. In summary, we report for the first time that intercellular viral oncomiR spreading is an additional mechanism employed by KSHV to inhibit host anti-viral immunity and consequently promote oncogenesis.
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Affiliation(s)
- Nir Rainy
- Sheba Cancer Research Center, Chaim Sheba Academic Medical Center, Tel Hashomer, Ramat Gan 5262100, Israel.,Sackler School of Medicine, Tel-Aviv University, Tel-Aviv 6997801, Israel.,Department of Neurobiology, The George S. Wise Faculty of Life Sciences & Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Morad Zayoud
- Sheba Cancer Research Center, Chaim Sheba Academic Medical Center, Tel Hashomer, Ramat Gan 5262100, Israel.,Sackler School of Medicine, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Yoel Kloog
- Department of Neurobiology, The George S. Wise Faculty of Life Sciences & Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Oded Rechavi
- Department of Neurobiology, The George S. Wise Faculty of Life Sciences & Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Itamar Goldstein
- Sheba Cancer Research Center, Chaim Sheba Academic Medical Center, Tel Hashomer, Ramat Gan 5262100, Israel.,Sackler School of Medicine, Tel-Aviv University, Tel-Aviv 6997801, Israel
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10
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Ramberger E, Dittmar G. Tissue Specific Labeling in Proteomics. Proteomes 2017; 5:proteomes5030017. [PMID: 28718811 PMCID: PMC5620534 DOI: 10.3390/proteomes5030017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 07/13/2017] [Accepted: 07/14/2017] [Indexed: 01/08/2023] Open
Abstract
Mass spectrometry-based proteomics is a powerful tool for identifying and quantifying proteins in biological samples. While it is routinely used for the characterization of simple cell line systems, the analysis of the cell specific proteome in multicellular organisms and tissues poses a significant challenge. Isolating a subset of cells from tissues requires mechanical and biochemical separation or sorting, a process which can alter cellular signaling, and thus, the composition of the proteome. Recently, several approaches for cell selective labeling of proteins, that include bioorthogonal amino acids, biotinylating enzymes, and genetic tools, have been developed. These tools facilitate the selective labeling of proteins, their interactome, or of specific cell types within a tissue or an organism, while avoiding the difficult and contamination-prone biochemical separation of cells from the tissue. In this review, we give an overview of existing techniques and their application in cell culture models and whole animals.
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Affiliation(s)
- Evelyn Ramberger
- Mass-Spectrometry Core Unit, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany.
- Berlin School of Integrative Oncology (BSIO), Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany.
| | - Gunnar Dittmar
- Proteome and Genome Research Laboratory, Luxembourg Institute of Health, 1272 Strassen, Luxembourg.
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11
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Tape CJ, Jørgensen C. Cell-Specific Labeling for Analyzing Bidirectional Signaling by Mass Spectrometry. Methods Mol Biol 2017; 1636:219-234. [PMID: 28730482 DOI: 10.1007/978-1-4939-7154-1_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2024]
Abstract
Cell-specific proteome labeling enables global proteome-wide analysis of cell signaling in heterotypic co-cultures. Such approaches have provided unique insight in contact-initiated receptor tyrosine kinase signaling, transfer of proteomic material between heterotypic cells, and interactions between normal and oncogenic cells. Here we describe current methods for cell-specific labeling of heterotypic cells with isotopic labeled amino acids (e.g., SILAC and CTAP). We outline the advantages and disadvantages of individual approaches, describe typical experimental scenarios, and discuss where each experimental approach is optimally applied.
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Affiliation(s)
- Christopher J Tape
- The Institute of Cancer Research, London, SW3 6JB, UK
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Claus Jørgensen
- Systems Oncology, CRUK Manchester Institute, The University of Manchester, Wilmslow Road, Manchester, M20 4QL, UK.
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12
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Tape CJ. Systems Biology Analysis of Heterocellular Signaling. Trends Biotechnol 2016; 34:627-637. [DOI: 10.1016/j.tibtech.2016.02.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 02/26/2016] [Accepted: 02/29/2016] [Indexed: 10/22/2022]
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13
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Culibrk L, Croft CA, Tebbutt SJ. Systems Biology Approaches for Host-Fungal Interactions: An Expanding Multi-Omics Frontier. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2016; 20:127-38. [PMID: 26885725 PMCID: PMC4799697 DOI: 10.1089/omi.2015.0185] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Opportunistic fungal infections are an increasing threat for global health, and for immunocompromised patients in particular. These infections are characterized by interaction between fungal pathogen and host cells. The exact mechanisms and the attendant variability in host and fungal pathogen interaction remain to be fully elucidated. The field of systems biology aims to characterize a biological system, and utilize this knowledge to predict the system's response to stimuli such as fungal exposures. A multi-omics approach, for example, combining data from genomics, proteomics, metabolomics, would allow a more comprehensive and pan-optic "two systems" biology of both the host and the fungal pathogen. In this review and literature analysis, we present highly specialized and nascent methods for analysis of multiple -omes of biological systems, in addition to emerging single-molecule visualization techniques that may assist in determining biological relevance of multi-omics data. We provide an overview of computational methods for modeling of gene regulatory networks, including some that have been applied towards the study of an interacting host and pathogen. In sum, comprehensive characterizations of host-fungal pathogen systems are now possible, and utilization of these cutting-edge multi-omics strategies may yield advances in better understanding of both host biology and fungal pathogens at a systems scale.
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Affiliation(s)
- Luka Culibrk
- Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Carys A. Croft
- Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Scott J. Tebbutt
- Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
- Department of Medicine, Division of Respiratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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14
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Wang Z, Han QQ, Zhou MT, Chen X, Guo L. Protein turnover analysis in Salmonella Typhimurium during infection by dynamic SILAC, Topograph, and quantitative proteomics. J Basic Microbiol 2016; 56:801-11. [PMID: 26773230 DOI: 10.1002/jobm.201500315] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 12/18/2015] [Indexed: 12/17/2022]
Abstract
Protein turnover affects protein abundance and phenotypes. Comprehensive investigation of protein turnover dynamics has the potential to provide substantial information about gene expression. Here we report a large-scale protein turnover study in Salmonella Typhimurium during infection by quantitative proteomics. Murine macrophage-like RAW 264.7 cells were infected with SILAC labeled Salmonella. Bacterial cells were extracted after 0, 30, 60, 120, and 240 min. Mass spectrometry analyses yielded information about Salmonella protein turnover dynamics and a software program named Topograph was used for the calculation of protein half lives. The half lives of 311 proteins from intracellular Salmonella were obtained. For bacteria cultured in control medium (DMEM), the half lives for 870 proteins were obtained. The calculated median of protein half lives was 69.13 and 99.30 min for the infection group and the DMEM group, respectively, indicating an elevated protein turnover at the initial stage of infection. Gene ontology analyses revealed that a number of protein functional groups were significantly regulated by infection, including proteins involved in ribosome, periplasmic space, cellular amino acid metabolic process, ion binding, and catalytic activity. The half lives of proteins involved in purine metabolism pathway were found to be significantly shortened during infection.
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Affiliation(s)
- Zhe Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Qiang-Qiang Han
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Mao-Tian Zhou
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xi Chen
- Wuhan Institute of Biotechnology, Wuhan, China
| | - Lin Guo
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
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15
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Ramilowski JA, Goldberg T, Harshbarger J, Kloppman E, Lizio M, Satagopam VP, Itoh M, Kawaji H, Carninci P, Rost B, Forrest ARR. A draft network of ligand-receptor-mediated multicellular signalling in human. Nat Commun 2015; 6:7866. [PMID: 26198319 PMCID: PMC4525178 DOI: 10.1038/ncomms8866] [Citation(s) in RCA: 522] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 06/19/2015] [Indexed: 02/07/2023] Open
Abstract
Cell-to-cell communication across multiple cell types and tissues strictly governs proper functioning of metazoans and extensively relies on interactions between secreted ligands and cell-surface receptors. Herein, we present the first large-scale map of cell-to-cell communication between 144 human primary cell types. We reveal that most cells express tens to hundreds of ligands and receptors to create a highly connected signalling network through multiple ligand-receptor paths. We also observe extensive autocrine signalling with approximately two-thirds of partners possibly interacting on the same cell type. We find that plasma membrane and secreted proteins have the highest cell-type specificity, they are evolutionarily younger than intracellular proteins, and that most receptors had evolved before their ligands. We provide an online tool to interactively query and visualize our networks and demonstrate how this tool can reveal novel cell-to-cell interactions with the prediction that mast cells signal to monoblastic lineages via the CSF1-CSF1R interacting pair.
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Affiliation(s)
- Jordan A. Ramilowski
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045 Japan
| | - Tatyana Goldberg
- Department for Bioinformatics and Computational Biology-I12, Technische Universität München (TUM), Boltzmannstrasse 3, 85748 Garching, Germany
- TUM Graduate School, Center of Doctoral Studies in Informatics and its Applications (CeDoSIA), Boltzmannstrasse 11, 85748 Garching, Germany
| | - Jayson Harshbarger
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045 Japan
| | - Edda Kloppman
- Department for Bioinformatics and Computational Biology-I12, Technische Universität München (TUM), Boltzmannstrasse 3, 85748 Garching, Germany
| | - Marina Lizio
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045 Japan
| | - Venkata P. Satagopam
- Luxembourg Centre for Systems Biomedicine, Campus Belval, 7 Avenue des Hauts Fourneaux, L-4362 Belval, Luxembourg
| | - Masayoshi Itoh
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045 Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Hideya Kawaji
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045 Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Piero Carninci
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045 Japan
| | - Burkhard Rost
- Department for Bioinformatics and Computational Biology-I12, Technische Universität München (TUM), Boltzmannstrasse 3, 85748 Garching, Germany
- TUM Graduate School, Center of Doctoral Studies in Informatics and its Applications (CeDoSIA), Boltzmannstrasse 11, 85748 Garching, Germany
| | - Alistair R. R. Forrest
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045 Japan
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, PO Box 7214, 6 Verdun Street, Nedlands, Perth, Western Australia 6008, Australia
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16
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Biran A, Perelmutter M, Gal H, Burton DGA, Ovadya Y, Vadai E, Geiger T, Krizhanovsky V. Senescent cells communicate via intercellular protein transfer. Genes Dev 2015; 29:791-802. [PMID: 25854920 PMCID: PMC4403256 DOI: 10.1101/gad.259341.115] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 03/19/2015] [Indexed: 01/07/2023]
Abstract
Biran et al. show that senescent cells directly transfer proteins to neighboring cells and that this process facilitates immune surveillance of senescent cells by NK cells. The transfer is strictly dependent on cell–cell contact and CDC42-regulated actin polymerization and is mediated at least partially by cytoplasmic bridges. These findings reveal a novel mode of intercellular communication by which senescent cells regulate their immune surveillance and might impact tumorigenesis and tissue aging. Mammalian cells mostly rely on extracellular molecules to transfer signals to other cells. However, in stress conditions, more robust mechanisms might be necessary to facilitate cell–cell communications. Cellular senescence, a stress response associated with permanent exit from the cell cycle and the development of an immunogenic phenotype, limits both tumorigenesis and tissue damage. Paradoxically, the long-term presence of senescent cells can promote tissue damage and aging within their microenvironment. Soluble factors secreted from senescent cells mediate some of these cell-nonautonomous effects. However, it is unknown whether senescent cells impact neighboring cells by other mechanisms. Here we show that senescent cells directly transfer proteins to neighboring cells and that this process facilitates immune surveillance of senescent cells by natural killer (NK) cells. We found that transfer of proteins to NK and T cells is increased in the murine preneoplastic pancreas, a site where senescent cells are present in vivo. Proteomic analysis and functional studies of the transferred proteins revealed that the transfer is strictly dependent on cell–cell contact and CDC42-regulated actin polymerization and is mediated at least partially by cytoplasmic bridges. These findings reveal a novel mode of intercellular communication by which senescent cells regulate their immune surveillance and might impact tumorigenesis and tissue aging.
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Affiliation(s)
- Anat Biran
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Meirav Perelmutter
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Hilah Gal
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Dominick G A Burton
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yossi Ovadya
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ezra Vadai
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tamar Geiger
- Sackler School of Medicine, Tel Aviv University, Tel-Aviv 69978, Israel
| | - Valery Krizhanovsky
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot 76100, Israel;
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17
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Abstract
Stable isotope labeling with amino acids in cell culture (SILAC) has risen as a powerful quantification technique in mass spectrometry (MS)-based proteomics in classical and modified forms. Previously, SILAC was limited to cultured cells because of the requirement of active protein synthesis; however, in recent years, it was expanded to model organisms and tissue samples. Specifically, the super-SILAC technique uses a mixture of SILAC-labeled cells as a spike-in standard for accurate quantification of unlabeled samples, thereby enabling quantification of human tissue samples. Here, we highlight the recent developments in super-SILAC and its application to the study of clinical samples, secretomes, post-translational modifications and organelle proteomes. Finally, we propose super-SILAC as a robust and accurate method that can be commercialized and applied to basic and clinical research.
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Affiliation(s)
- Anjana Shenoy
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
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18
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Tape CJ, Norrie IC, Worboys JD, Lim L, Lauffenburger DA, Jørgensen C. Cell-specific labeling enzymes for analysis of cell-cell communication in continuous co-culture. Mol Cell Proteomics 2014; 13:1866-76. [PMID: 24820872 DOI: 10.1074/mcp.o113.037119] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We report the orthologous screening, engineering, and optimization of amino acid conversion enzymes for cell-specific proteomic labeling. Intracellular endoplasmic-reticulum-anchored Mycobacterium tuberculosis diaminopimelate decarboxylase (DDC(M.tub-KDEL)) confers cell-specific meso-2,6-diaminopimelate-dependent proliferation to multiple eukaryotic cell types. Optimized lysine racemase (Lyr(M37-KDEL)) supports D-lysine specific proliferation and efficient cell-specific isotopic labeling. When ectopically expressed in discrete cell types, these enzymes confer 90% cell-specific isotopic labeling efficiency after 10 days of co-culture. Moreover, DDC(M.tub-KDEL) and Lyr(M37-KDEL) facilitate equally high cell-specific labeling fidelity without daily media exchange. Consequently, the reported novel enzyme pairing can be used to study cell-specific signaling in uninterrupted, continuous co-cultures. Demonstrating the importance of increased labeling stability for addressing novel biological questions, we compare the cell-specific phosphoproteome of fibroblasts in direct co-culture with epithelial tumor cells in both interrupted (daily media exchange) and continuous (no media exchange) co-cultures. This analysis identified multiple cell-specific phosphorylation sites specifically regulated in the continuous co-culture. Given their applicability to multiple cell types, continuous co-culture labeling fidelity, and suitability for long-term cell-cell phospho-signaling experiments, we propose DDC(M.tub-KDEL) and Lyr(M37-KDEL) as excellent enzymes for cell-specific labeling with amino acid precursors.
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Affiliation(s)
- Christopher J Tape
- From the ‡Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK; §Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Ida C Norrie
- From the ‡Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Jonathan D Worboys
- From the ‡Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Lindsay Lim
- From the ‡Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Douglas A Lauffenburger
- §Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Claus Jørgensen
- From the ‡Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK;
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19
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Identification of secreted bacterial proteins by noncanonical amino acid tagging. Proc Natl Acad Sci U S A 2013; 111:433-8. [PMID: 24347637 DOI: 10.1073/pnas.1301740111] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pathogenic microbes have evolved complex secretion systems to deliver virulence factors into host cells. Identification of these factors is critical for understanding the infection process. We report a powerful and versatile approach to the selective labeling and identification of secreted pathogen proteins. Selective labeling of microbial proteins is accomplished via translational incorporation of azidonorleucine (Anl), a methionine surrogate that requires a mutant form of the methionyl-tRNA synthetase for activation. Secreted pathogen proteins containing Anl can be tagged by azide-alkyne cycloaddition and enriched by affinity purification. Application of the method to analysis of the type III secretion system of the human pathogen Yersinia enterocolitica enabled efficient identification of secreted proteins, identification of distinct secretion profiles for intracellular and extracellular bacteria, and determination of the order of substrate injection into host cells. This approach should be widely useful for the identification of virulence factors in microbial pathogens and the development of potential new targets for antimicrobial therapy.
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20
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Goldstein I, Rainy N, Rechavi O, Kloog Y. Intercellular transfer of Ras: implications for immunity. Cell Cycle 2013; 13:7-8. [PMID: 24231770 PMCID: PMC3925737 DOI: 10.4161/cc.27020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Itamar Goldstein
- Sheba Cancer Research Center; Chaim Sheba Medical Center; Tel Hashomer, Ramat Gan, Israel; Sackler Faculty of Medicine; Tel Aviv University; Tel Aviv, Israel
| | - Nir Rainy
- Department of Neurobiology; The George S. Wise Faculty of Life Sciences; Tel Aviv University; Tel-Aviv, Israel
| | - Oded Rechavi
- Department of Neurobiology; The George S. Wise Faculty of Life Sciences; Tel Aviv University; Tel-Aviv, Israel
| | - Yoel Kloog
- Department of Neurobiology; The George S. Wise Faculty of Life Sciences; Tel Aviv University; Tel-Aviv, Israel
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21
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Tian R. Exploring intercellular signaling by proteomic approaches. Proteomics 2013; 14:498-512. [DOI: 10.1002/pmic.201300259] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Revised: 08/15/2013] [Accepted: 08/28/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Ruijun Tian
- Lunenfeld-Tanenbaum Research Institute; Mount Sinai Hospital; Toronto ON Canada
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22
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Yuet KP, Tirrell DA. Chemical tools for temporally and spatially resolved mass spectrometry-based proteomics. Ann Biomed Eng 2013; 42:299-311. [PMID: 23943069 DOI: 10.1007/s10439-013-0878-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 07/24/2013] [Indexed: 11/29/2022]
Abstract
Accurate measurements of the abundances, synthesis rates and degradation rates of cellular proteins are critical for understanding how cells and organisms respond to changes in their environments. Over the past two decades, there has been increasing interest in the use of mass spectrometry for proteomic analysis. In many systems, however, protein diversity as well as cell and tissue heterogeneity limit the usefulness of mass spectrometry-based proteomics. As a result, researchers have had difficulty in systematically identifying proteins expressed within specified time intervals, or low abundance proteins expressed in specific tissues or in a few cells in complex microbial systems. In this review, we present recently-developed tools and strategies that probe these two subsets of the proteome: proteins synthesized during well-defined time intervals--temporally resolved proteomics--and proteins expressed in predetermined cell types, cells or cellular compartments--spatially resolved proteomics--with a focus on chemical and biological mass spectrometry-based methodologies.
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Affiliation(s)
- Kai P Yuet
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
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23
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Rainy N, Chetrit D, Rouger V, Vernitsky H, Rechavi O, Marguet D, Goldstein I, Ehrlich M, Kloog Y. H-Ras transfers from B to T cells via tunneling nanotubes. Cell Death Dis 2013; 4:e726. [PMID: 23868059 PMCID: PMC3730418 DOI: 10.1038/cddis.2013.245] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 06/05/2013] [Accepted: 06/06/2013] [Indexed: 11/08/2022]
Abstract
Lymphocytes form cell-cell connections by various mechanisms, including intercellular networks through actin-supported long-range plasma membrane (PM) extensions, termed tunneling nanotubes (TNTs). In this study, we tested in vitro whether TNTs form between human antigen-presenting B cells and T cells following cell contact and whether they enable the transfer of PM-associated proteins, such as green fluorescent protein (GFP)-tagged H-Ras (GFP-H-Ras). To address this question, we employed advanced techniques, including cell trapping by optical tweezers and live-cell imaging by 4D spinning-disk confocal microscopy. First, we showed that TNTs can form after optically trapped conjugated B and T cells are being pulled apart. Next, we determined by measuring fluorescence recovery after photobleaching that GFP-H-Ras diffuses freely in the membrane of TNTs that form spontaneously between B and T cells during coculturing. Importantly, by 4D time-lapse imaging, we showed that GFP-H-Ras-enriched PM patches accumulate at the junction between TNTs and the T-cell body and subsequently transfer to the T-cell surface. Furthermore, the PM patches adopted by T cells were enriched for another B-cell-derived transmembrane receptor, CD86. As predicted, the capacity of GFP-H-Ras to transfer between B and T cells, during coculturing, was dependent on its normal post-transcriptional lipidation and consequent PM anchorage. In summary, our data indicate that TNTs connecting B and T cells provide a hitherto undescribed route for the transfer of PM patches containing, for example, H-Ras from B to T cells.
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Affiliation(s)
- N Rainy
- Department of Neurobiology, The George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - D Chetrit
- Department of Cell Research and Immunology, The George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - V Rouger
- Centre d'Immunologie de Marseille-Luminy (CIML), Aix-Marseille University, UM2, Marseille, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1104, Marseille, France
- Centre National de la Recherche Scientifique (CNRS), UMR7280, Marseille, France
| | - H Vernitsky
- Sheba Cancer Research Center, Chaim Sheba Medical Center, Tel Hashomer 52621, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - O Rechavi
- Department of Neurobiology, The George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - D Marguet
- Centre d'Immunologie de Marseille-Luminy (CIML), Aix-Marseille University, UM2, Marseille, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1104, Marseille, France
- Centre National de la Recherche Scientifique (CNRS), UMR7280, Marseille, France
| | - I Goldstein
- Sheba Cancer Research Center, Chaim Sheba Medical Center, Tel Hashomer 52621, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - M Ehrlich
- Department of Cell Research and Immunology, The George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Y Kloog
- Department of Neurobiology, The George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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24
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Gauthier NP, Soufi B, Walkowicz WE, Pedicord VA, Mavrakis KJ, Macek B, Gin DY, Sander C, Miller ML. Cell-selective labeling using amino acid precursors for proteomic studies of multicellular environments. Nat Methods 2013; 10:768-73. [PMID: 23817070 PMCID: PMC4002004 DOI: 10.1038/nmeth.2529] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 05/08/2013] [Indexed: 11/23/2022]
Abstract
To address limitations of current high-throughput methods for studying cell-cell communication and determining the cell-of-origin of proteins in multicellular environments, we have developed a technique that selectively and continuously labels the proteome of individual cell types in co-culture. Through transgenic expression of exogenous amino acid biosynthesis enzymes, vertebrate cells overcome their dependence on essential amino acids and can be selectively labeled through metabolic incorporation of amino acids produced from heavy isotope-labeled precursors. We have named this method Type specific labeling with Amino acid Precursors (CTAP). Testing CTAP in several human and mouse cell lines, we were able to differentially label the proteome of distinct cell populations in co-culture and determine the relative expression of proteins by quantitative mass spectrometry. In addition, CTAP successfully identified the cell-of-origin of extracellular proteins in co-culture, highlighting its potential use in biomarker discovery for linking secreted factors to their cellular source.
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Affiliation(s)
- Nicholas P Gauthier
- Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York, USA.
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25
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Vernitsky H, Rechavi O, Rainy N, Besser MJ, Nagar M, Schachter J, Lerenthal Y, Ehrlich M, Kloog Y, Goldstein I. Ras Oncoproteins Transfer from Melanoma Cells to T Cells and Modulate Their Effector Functions. THE JOURNAL OF IMMUNOLOGY 2012; 189:4361-70. [DOI: 10.4049/jimmunol.1200019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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26
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Key issues in the acquisition and analysis of qualitative and quantitative mass spectrometry data for peptide-centric proteomic experiments. Amino Acids 2012; 43:1075-85. [PMID: 22821266 DOI: 10.1007/s00726-012-1287-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Accepted: 04/03/2012] [Indexed: 01/05/2023]
Abstract
Proteomic technologies have matured to a level enabling accurate and reproducible quantitation of peptides and proteins from complex biological matrices. Analysis of samples as diverse as assembled protein complexes, whole cell lysates or sub-cellular proteomes from cell cultures, and direct analysis of animal and human tissues and fluids demonstrate the incredible versatility of the fundamental nature of the technique that forms the basis of most proteomic applications today (mass spectrometry). Determining the mass of biomolecules and their fragments or related products with high accuracy can convey a highly specific assay for detection and identification. Importantly, ion currents representative of these specifically identified analytes can be accurately quantified with the correct application of smart isobaric tagging chemistries, heavy and light isotopically derivatised samples or standards, or by careful application of workflows to compare unlabelled samples in so-called 'label-free' and targeted selected reaction monitoring experiments. In terms of exploring biology, a myriad of protein changes and modifications are being increasingly probed and quantified, including diverse chemical changes from relatively decisive modifications such as protein splicing and truncation, to more transient dynamic modifications such as phosphorylation, acetylation and ubiquitination. Proteomic workflows can be complex beasts and several key considerations to ensure effective applications have been outlined in the recent literature. The past year has witnessed the publication of several excellent reviews that thoroughly describe the fundamental principles underlying the state of the art. This review further elaborates on specific critical issues introduced by these publications and raises other important unaddressed considerations and new developments that directly impact on the effectiveness of proteomic technologies, in particular for, but not necessarily exclusive to peptide-centric experiments. These factors are discussed both in terms of qualitative analyses, including dynamic range and sampling issues, and developments to improve the translation of peptide fragmentation data into peptide and protein identities, as well as quantitative analyses, including data normalisation and the utility of ontology or functional annotation, the effects of modified peptides, and considered experimental design to facilitate the use of robust statistical methods.
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27
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Analysing signalling networks by mass spectrometry. Amino Acids 2012; 43:1061-74. [PMID: 22821269 DOI: 10.1007/s00726-012-1293-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Accepted: 04/03/2012] [Indexed: 12/31/2022]
Abstract
Sequence analysis of the human genome and the association of genetic aberrations with diseases have provided a rough framework whereby the impact of individual genotypes can be assessed. To fully understand the effect of individual and co-occurring genetic aberrations, as well as their individual and collected contribution to the development of diseases, it is critical to analyse the matching proteome and to determine how the organisation, expression level and function of protein networks are affected. Sensitive mass spectrometric platforms in combination with innovative workflows allow qualitative and quantitative analyses of the cellular as well as the extracellular proteome. Importantly, in addition to specifically identifying the content of the proteome, several aspects of the proteomic organisation can be analysed including protein complexes, protein modifications, enzymatic activities and subcellular/organelle localisation. Together, these measurements will provide novel insight into the biological effect of disease-causing mutations ultimately coupling genotype and phenotype.
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28
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Piechura H, Oeljeklaus S, Warscheid B. SILAC for the study of mammalian cell lines and yeast protein complexes. Methods Mol Biol 2012; 893:201-221. [PMID: 22665303 DOI: 10.1007/978-1-61779-885-6_14] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Through crucial advancements in quantitative mass spectrometry (MS), proteomics has evolved from taking mere "snapshots" of proteomes to thoroughly studying dynamic changes in entire proteomes and characterizing intricate protein-protein interaction or signaling networks. Thus, quantitative MS-based proteomics offers the unique potential to place proteins into their functional context and, moreover, to improve our understanding of the molecular processes involved in the development, survival, or pathology of cells and organisms. Among the vast variety of techniques developed for the accurate quantification of proteins via MS, stable isotope labeling by amino acids in cell culture (SILAC) arguably represents the most elegant method. In this chapter, we provide a detailed protocol for the establishment of SILAC for mammalian cell culture systems. In addition, to exemplify the high versatility of SILAC for addressing different biological questions, we describe the successful "pairing" of SILAC with conventional affinity purification (AP)-MS approaches allowing for accurately characterizing protein complexes.
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Affiliation(s)
- Heike Piechura
- Faculty of Biology and BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
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Affiliation(s)
- Xudong Yao
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, USA.
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